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Khoshbayan A, Narimisa N, Elahi Z, Bostanghadiri N, Razavi S, Shariati A. Global prevalence of mutation in the mgrB gene among clinical isolates of colistin-resistant Klebsiella pneumoniae: a systematic review and meta-analysis. Front Microbiol 2024; 15:1386478. [PMID: 38912352 PMCID: PMC11190090 DOI: 10.3389/fmicb.2024.1386478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 05/22/2024] [Indexed: 06/25/2024] Open
Abstract
Background Colistin is used as a last resort for managing infections caused by multidrug-resistant bacteria. However, the high emergence of colistin-resistant strains has restricted the clinical use of this antibiotic in the clinical setting. In the present study, we evaluated the global prevalence of the mutation in the mgrB gene, one of the most important mechanisms of colistin resistance in Klebsiella pneumoniae. Methods Several databases, including Scopus, Medline (via PubMed), and Web of Science, were searched (until August 2023) to identify those studies that address the mgrB mutation in clinical isolates of K. pneumoniae. Using Stata software, the pooled prevalence of mgrB mutation and subgroup analyses for the year of publication, country, continent, mgrB mutation types, and detection methods of mgrB mutation were analyzed. Results Out of the 115 studies included in the analysis, the prevalence of mgrB mutations in colistin-resistant K. pneumoniae isolates was estimated at 65% of isolates, and mgrB variations with insertional inactivation had the highest prevalence among the five investigated mutations with 69%. The year subgroup analysis indicated an increase in mutated mgrB from 46% in 2014 to 61% in 2022. Europe had the highest prevalence of mutated mgrB at 73%, while Africa had the lowest at 54%. Conclusion Mutations in the mgrB gene are reported as one of the most common mechanisms of colistin resistance in K. pneumoniae, and the results of the present study showed that 65% of the reported colistin-resistant K. pneumoniae had a mutation in this gene.
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Affiliation(s)
- Amin Khoshbayan
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Negar Narimisa
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Zahra Elahi
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
- Vice Chancellery of Education and Research, Torbat Heydariyeh University of Medical Sciences, Torbat Heydariyeh, Iran
| | - Narjess Bostanghadiri
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Shabnam Razavi
- Microbial Biotechnology Research Center, Iran University of Medical Sciences, Tehran, Iran
- Department of Microbiology, School of Medicine, Iran University of Medical Sciences, Tehran, Iran
| | - Aref Shariati
- Molecular and Medicine research center, Khomein University of Medical Sciences, Khomein, Iran
- Infectious Diseases Research Center (IDRC), Arak University of Medical Sciences, Arak, Iran
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Umair M, Walsh TR, Mohsin M. A systematic review and meta-analysis of carbapenem resistance and its possible treatment options with focus on clinical Enterobacteriaceae: Thirty years of development in Pakistan. Heliyon 2024; 10:e28052. [PMID: 38596009 PMCID: PMC11001782 DOI: 10.1016/j.heliyon.2024.e28052] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 03/08/2024] [Accepted: 03/11/2024] [Indexed: 04/11/2024] Open
Abstract
Background Carbapenem resistance is epidemic worldwide, these last resort antimicrobials are listed in the WHO 'watch group' with higher resistance potential. During the years 2017-18 Pakistan Antimicrobial Resistance Surveillance System reported an increase in carbapenem resistance. However, a comprehensive information on prevalence and molecular epidemiology of carbapenem resistance in Pakistan is not available. This systematic review and meta-analysis is aimed to report the current carbapenem resistance situation in Pakistan and its treatment options. Methods In this systematic review and meta-analysis, we investigated the pooled prevalence (PPr) of carbapenem resistance in Enterobacteriaceae and non-Enterobacteriaceae by organizing available data, from Web of Science and PubMed by April 2, 2020, in various groups and subgroups including species, years, provinces, extended spectrum β-lactamase production, clinical presentation, carbapenemase and metallo-β-lactamase production, and New Delhi metallo-β-lactamase (NDM) prevalence. Literature review was updated for the studies publisehd by December 07, 2023. Moreover, we descriptively reviewed the molecular epidemiology of carbapenem resistance in Enterobacteriaceae and non-Enterobacteriaceae in Pakistan. Lastly, we statistically explored different treatment options available for carbapenem resistant infections. We used R package 'metafor' for performing meta-analysis and influence diagnostics and determining treatment options. Results From two academic databases Web of Science and PubMed we identified 343 studies. Eighty-eight studies were selected for the systematic review and meta-analysis. Seventy-four studies were selected for phenotypic analysis, 36 for genotypic analysis, and 31 for available treatment options. PPr-ID of 12% [0.12 (0.07, 0.16)] was observed for phenotypic carbapenem resistance in Enterobacteriaceae with more prevalence recorded in Klebsiella pneumoniae 24% [0.24 (0.05, 0.44)] followed by 9% [0.09 (-0.03, 0.20)] in Escherichia coli. During the last two decades we observed a striking increase in carbapenem resistance PPr i.e., from 0% [0.00 (-0.02, 0.03)] to 36% [0.36 (0.17, 0.56)]. blaNDM with PPr 15% [0.15 (0.06, 0.23)] in naive isolates was found to be the fundamental genetic determinant for carbapenem resistance in Enterobacteriaceae in Pakistan. Polymyxin B, colistin, tigecycline, and fosfomycin were identified as the suggested treatment options available for multidrug resistant infections not responding to carbapenems. Various studies reported carbapenem resistance from human, animal, and environment sources. Conclusion In conclusion, we found that NDM-1 producing carbapenem resistant Enterobacteriaceae are increasing in Pakistan. Meta-analysis showed that metallo-β-lactamases producing E. coli ST405 and K. pneumoniae sequence type11 are the major resistant clones. Number of reported studies in various subgroups and inconsistency in following CLSI guidelines are the potential limitations of this meta-analysis. A National antimicrobial resistance (AMR) surveillance strategy based on One Health is urgently needed to check any future AMR crisis in Pakistan.
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Affiliation(s)
- Muhammad Umair
- Institute of Microbiology, University of Agriculture, Faisalabad, 38000, Pakistan
- INEOS Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Timothy R. Walsh
- INEOS Oxford Institute for Antimicrobial Research, Department of Biology, University of Oxford, Oxford, OX1 3SZ, UK
| | - Mashkoor Mohsin
- Institute of Microbiology, University of Agriculture, Faisalabad, 38000, Pakistan
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Kaza P, Xavier BB, Mahindroo J, Singh N, Baker S, Nguyen TNT, Mavuduru RS, Mohan B, Taneja N. Extensively Drug-Resistant Klebsiella pneumoniae Associated with Complicated Urinary Tract Infection in Northern India. Jpn J Infect Dis 2024; 77:7-15. [PMID: 37648492 DOI: 10.7883/yoken.jjid.2023.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Klebsiella pneumoniae (Kp), which is associated with hospital-acquired infections, is extensively drug-resistant (XDR), making treatment difficult. Understanding the genetic epidemiology of XDR-Kp can help determine its potential to be hypervirulent (hv) through the presence of siderophores. We characterized the genomes of 18 colistin-resistant XDR-Kp isolated from 14 patients with complicated tract infection at an Indian healthcare facility. The 18 organisms comprised the following sequence types (STs): ST14 (n = 9), ST147 (n = 5), ST231 (n = 2), ST2096 (n = 1), and ST25 (n = 1). Many patients in each ward were infected with the same ST, suggesting a common source of infection. Some patients had recurrent infections with multiple STs circulating in the ward, providing evidence of hospital transmission. β-lactamase genes (blaCTX-M-1, blaSHV, and blaampH) were present in all isolates. blaNDM-1 was present in 15 isolates, blaOXA-1 in 16 isolates, blaTEM-1D in 13 isolates, and blaOXA-48 in 3 isolates. Disruption of mgrB by various insertion sequences was responsible for colistin resistance in 6 isolates. The most common K-type among isolates was K2 (n = 10). One XDR convergent hvKp ST2096 mutation (iuc+ybt+blaOXA-1+blaOXA-48) was associated with prolonged hospitalization. Convergent XDR-hvKp has outbreak potential, warranting effective antimicrobial stewardship and infection control.
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Affiliation(s)
- Parinitha Kaza
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, India
| | - Basil Britto Xavier
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Belgium
| | - Jaspreet Mahindroo
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, India
| | - Nisha Singh
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, India
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), Department of Medicine, University of Cambridge, UK
| | - To Nguyen Thi Nguyen
- The Hospital for Tropical Diseases, Wellcome Trust Major Overseas Programme, Oxford University Clinical Research Unit, Vietnam
| | | | - Balvinder Mohan
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, India
| | - Neelam Taneja
- Department of Medical Microbiology, Postgraduate Institute of Medical Education and Research, India
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Aghamohammad S, Khazani Asforooshani M, Malek Mohammadi Y, Sholeh M, Badmasti F. Decoding the genetic structure of conjugative plasmids in international clones of Klebsiella pneumoniae: A deep dive into blaKPC, blaNDM, blaOXA-48, and blaGES genes. PLoS One 2023; 18:e0292288. [PMID: 37971980 PMCID: PMC10653425 DOI: 10.1371/journal.pone.0292288] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2023] [Accepted: 09/17/2023] [Indexed: 11/19/2023] Open
Abstract
Carbapanem-resistant Klebsiella pneumoniae is a globally healthcare crisis. The distribution of plasmids carrying carbapenemase genes among K. pneumoniae poses a serious threat in clinical settings. Here, we characterized the genetic structure of plasmids harboring major carbapenemases (e.g. blaKPC, blaNDM, blaOXA-48-like, and blaGES) from K. pneumoniae using bioinformatics tools. The plasmids carrying at least one major carbapenemase gene were retrieved from the GenBank database. The DNA length, Inc type, and conjugal apparatus of these plasmids were detected. Additionally, allele types, co-existence, co-occurrence of carbapenemase genes, gene repetition, and sequence types of isolates, were characterized. There were 2254 plasmids harboring carbapenemase genes in the database. This study revealed that blaKPC-2, blaNDM-1, blaOXA-48, and blaGES-5 were the most prevalent allele types. Out of 1140 (50%) plasmids were potentially conjugative. IncFII, IncR, IncX3, and IncL replicon types were predominant. The co-existence analysis revealed that the most prevalent of other resistance genes were blaTEM-1 (related to blaKPC), blaOXA-232 (related to blaOXA-48), bleMBL (related to blaNDM), and aac (6')-Ib4 (related to blaGES). The co-occurrence of carbapenemases was detected in 42 plasmids while 15 plasmids contained carbapenemase gene repetitions. Sequence alignments highlighted that plasmids carrying blaKPC and blaOXA-48-like were more homogeneous whereas the plasmids carrying blaNDM were divergent. It seems that K. pneumoniae utilizes diversity of genetic flexibility and recombination for resistance against carbapenems. The genetic structure of the plasmids showed that class I and III, Tn3 family, Tn5403 family derivatives, and Tn7-like elements were strongly associated with carbapenemases. The mobilizable plasmids carrying carbapenemases play an important role in the spread of these genes. In addition, gene repetition maybe is related to carbapenem heteroresistance. According to MST (minimum spanning tree) results, the majority of plasmids belonged to sequence type (ST) 11, ST14, and ST12. These international clones have a high capacity to acquire the carbapenemase-containing plasmids.
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Affiliation(s)
| | - Mahshid Khazani Asforooshani
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
- Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | | | - Mohammad Sholeh
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Farzad Badmasti
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
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Crawford MA, Lascols C, Lomonaco S, Timme RE, Fisher DJ, Anderson K, Hodge DR, Morse SA, Pillai SP, Sharma SK, Khan E, Allard MW, Hughes MA. Enterobacterales draft genome sequences: 15 historical (1998-2004) and 30 contemporary (2015-2016) clinical isolates from Pakistan. Microbiol Resour Announc 2023; 12:e0016323. [PMID: 37504519 PMCID: PMC10508161 DOI: 10.1128/mra.00163-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2023] [Accepted: 06/14/2023] [Indexed: 07/29/2023] Open
Abstract
The continued emergence and spread of antimicrobial resistance among pathogenic bacteria are ever-growing threats to health and economy. Here, we report the draft genomes for 45 Enterobacterales clinical isolates, including historical and contemporary drug-resistant organisms, obtained in Pakistan between 1998 and 2016: 5 Serratia, 3 Salmonella, 3 Enterobacter, and 34 Klebsiella.
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Affiliation(s)
- Matthew A. Crawford
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Christine Lascols
- National Center for Emerging and Zoonotic Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- IHRC, Inc., Atlanta, Georgia, USA
| | - Sara Lomonaco
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Ruth E. Timme
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Debra J. Fisher
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
| | - Kevin Anderson
- Science and Technology Directorate, US Department of Homeland Security, Washington, DC, USA
| | - David R. Hodge
- Science and Technology Directorate, US Department of Homeland Security, Washington, DC, USA
| | | | - Segaran P. Pillai
- Office of the Commissioner, US Food and Drug Administration, Silver Spring, Maryland, USA
| | - Shashi K. Sharma
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Erum Khan
- Department of Pathology and Microbiology, Aga Khan University, Karachi, Pakistan
| | - Marc W. Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration, College Park, Maryland, USA
| | - Molly A. Hughes
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, Virginia, USA
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6
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Lascols C, Cherney B, Conley AB, Rishishwar L, Crawford MA, Morse SA, Fisher DJ, Anderson K, Hodge DR, Pillai SP, Hughes MA, Khan E, Sue D. Investigation of multidrug-resistant plasmids from carbapenemase-producing Klebsiella pneumoniae clinical isolates from Pakistan. Front Microbiol 2023; 14:1192097. [PMID: 37455731 PMCID: PMC10340517 DOI: 10.3389/fmicb.2023.1192097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2023] [Accepted: 06/05/2023] [Indexed: 07/18/2023] Open
Abstract
Objectives The study aim was to investigate multidrug-resistant (MDR) plasmids from a collection of 10 carbapenemase-producing Klebsiella pneumoniae clinical isolates identified within the same healthcare institution in Pakistan. Full characterization of the MDR plasmids including structure, typing characteristics, and AMR content as well as determination of their plasmid-based antimicrobial susceptibility profiles were carried out. Methods Plasmids were isolated from 10 clinical isolates of Klebsiella pneumoniae, and from a corresponding set of Escherichia coli transconjugants, then sequenced using Nanopore/Illumina technology to generate plasmid hybrid assemblies. Full characterization of MDR plasmids, including determination of next generation sequencing (NGS)-based AMR profiles, plasmid incompatibility groups, and types, was carried out. The structure of MDR plasmids was analyzed using the Galileo AMR platform. For E. coli transconjugants, the NGS-based AMR profiles were compared to NGS-predicted AMR phenotypes and conventional broth microdilution (BMD) antimicrobial susceptibility testing (AST) results. Results All carbapenemase-producing K. pneumoniae isolates (carrying either blaNDM-1, or/and blaOXA-48) carried multiple AMR plasmids encoding 34 antimicrobial resistance genes (ARGs) conferring resistance to antimicrobials from 6 different classes. The plasmid incompatibility groups and types identified were: IncC (types 1 and 3), IncFIA (type 26) IncFIB, IncFII (types K1, K2, K7, and K9), IncHI1B, and IncL. None of the blaNDM-1 and blaESBL-plasmids identified in this study were previously described. Most blaNDM-1-plasmids shared identical AMR regions suggesting potential genetic material/plasmid exchange between K. pneumoniae isolates of this collection. The majority of NGS-based AMR profiles from the E. coli transconjugants correlated well with both NGS-based predicted and conventional AST results. Conclusion This study highlights the complexity and diversity of the plasmid-based genetic background of carbapenemase-producing clinical isolates from Pakistan. This study emphasizes the need for characterization of MDR plasmids to determine their complete molecular background and monitor AMR through plasmid transmission between multi-resistant bacterial pathogens.
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Affiliation(s)
- Christine Lascols
- National Center for Emerging and Zoonotic Infectious DiseasesCenters for Disease Control and Prevention, Atlanta, GA, United States
| | - Blake Cherney
- National Center for Emerging and Zoonotic Infectious DiseasesCenters for Disease Control and Prevention, Atlanta, GA, United States
| | | | | | - Matthew A. Crawford
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA, United States
| | | | - Debra J. Fisher
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Kevin Anderson
- Science and Technology Directorate, U.S. Department of Homeland Security, Washington, DC, United States
| | - David R. Hodge
- Science and Technology Directorate, U.S. Department of Homeland Security, Washington, DC, United States
| | - Segaran P. Pillai
- Office of the Commissioner, U.S. Food and Drug Administration, Silver Spring, MD, United States
| | - Molly A. Hughes
- Division of Infectious Diseases and International Health, Department of Medicine, University of Virginia, Charlottesville, VA, United States
| | - Erum Khan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - David Sue
- National Center for Emerging and Zoonotic Infectious DiseasesCenters for Disease Control and Prevention, Atlanta, GA, United States
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Karim MR, Zakaria Z, Hassan L, Mohd Faiz N, Ahmad NI. Antimicrobial Resistance Profiles and Co-Existence of Multiple Antimicrobial Resistance Genes in mcr-Harbouring Colistin-Resistant Enterobacteriaceae Isolates Recovered from Poultry and Poultry Meats in Malaysia. Antibiotics (Basel) 2023; 12:1060. [PMID: 37370378 DOI: 10.3390/antibiotics12061060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Revised: 05/18/2023] [Accepted: 05/31/2023] [Indexed: 06/29/2023] Open
Abstract
The co-existence of the colistin resistance (mcr) gene with multiple drug-resistance genes has raised concerns about the possibility of the development of pan-drug-resistant bacteria that will complicate treatment. This study aimed to investigate the antibiotic resistance profiles and co-existence of antibiotic resistance genes among the colistin-resistant Enterobacteriaceae isolates recovered from poultry and poultry meats. The antibiotic susceptibility to various classes of antibiotics was performed using the Kirby-Bauer disk diffusion method and selected antimicrobial resistance genes were detected using PCR in a total of 54 colistin-resistant Enterobacteriaceae isolates including Escherichia coli (E. coli) (n = 32), Salmonella spp. (n = 16) and Klebsiella pneumoniae (K. pneumoniae) (n = 6) isolates. Most of the isolates had multi-drug resistance (MDR), with antibiotic resistance against up to seven classes of antibiotics. All mcr-harbouring, colistin-resistant Enterobacteriaceae isolates showed this MDR (100%) phenotype. The mcr-1 harbouring E. coli isolates were co-harbouring multiple antibiotic resistance genes. The seven most commonly identified resistance genes (blaTEM, tetA, floR, aac-3-IV, aadA1, fosA, aac(6_)-lb) were detected in an mcr-1-harbouring E. coli isolate recovered from a cloacal swab. The mcr-5 harbouring Salmonella spp. isolate recovered from poultry meats was positive for blaTEM, tetA, floR, aac-3-IV, fosA and aac(6_)-lb genes. In conclusion, the colistin-resistant Enterobacteriaceae with mcr genes co-existing multiple clinically important antimicrobial resistance genes in poultry and poultry meats may cause potential future threats to infection treatment choices in humans and animals.
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Affiliation(s)
- Md Rezaul Karim
- Department of Veterinary Pathology & Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
- Bangladesh Livestock Research Institute, Savar, Dhaka 1341, Bangladesh
| | - Zunita Zakaria
- Department of Veterinary Pathology & Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
- Institute of Bioscience, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
| | - Latiffah Hassan
- Department of Veterinary Laboratory Diagnostics, Faculty of Veterinary Medicine, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
| | - Nik Mohd Faiz
- Department of Veterinary Clinical Studies, Faculty of Veterinary Medicine, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
| | - Nur Indah Ahmad
- Department of Veterinary Pathology & Microbiology, Faculty of Veterinary Medicine, Universiti Putra Malaysia (UPM), Serdang 43400, Selangor, Malaysia
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Sharma J, Sharma D, Singh A, Sunita K. Colistin Resistance and Management of Drug Resistant Infections. THE CANADIAN JOURNAL OF INFECTIOUS DISEASES & MEDICAL MICROBIOLOGY = JOURNAL CANADIEN DES MALADIES INFECTIEUSES ET DE LA MICROBIOLOGIE MEDICALE 2022; 2022:4315030. [PMID: 36536900 PMCID: PMC9759378 DOI: 10.1155/2022/4315030] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/21/2022] [Accepted: 12/01/2022] [Indexed: 09/19/2023]
Abstract
Colistin resistance is a globalized sensible issue because it has been considered a drug of the last-line resort to treat drug-resistant bacterial infections. The product of the mobilized colistin resistance (mcr) gene and its variants are the significant causes of colistin resistance, which is emerging due to the frequent colistin use in veterinary, and these genes circulate among the bacterial community. Apart from mcr genes, some other intrinsic genes and proteins are also involved in colistin resistance. Researchers focus on the most advanced genomics (whole genome sequencing), proteomics, and bioinformatics approaches to explore the question of colistin resistance. To combat colistin resistance, researchers developed various strategies such as the development of newer drugs, the repurposing of existing drugs, combinatorial treatment by colistin with other drugs, a nano-based approach, photodynamic therapy, a CRISPRi-based strategy, and a phage-based strategy. In this timeline review, we have discussed the development of colistin resistance and its management in developing countries.
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Affiliation(s)
- Juhi Sharma
- School of Life Science, Jaipur National University, Jaipur, India
| | - Divakar Sharma
- Department of Microbiology, Maulana Azad Medical College, Delhi, India
- Department of Microbiology, Lady Hardinge Medical College, Delhi, India
| | - Amit Singh
- Department of Gastroenterology and Human Nutrition, All India Institute of Medical Sciences, Delhi, India
- Department of Microbiology, Central University of Punjab, Bathinda, India
| | - Kumari Sunita
- Department of Botany, Deen Dayal Upadhyay Gorakhpur University, Gorakhpur, Uttar Pradesh, India
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Prevalence of Mutated Colistin-Resistant Klebsiella pneumoniae: A Systematic Review and Meta-Analysis. Trop Med Infect Dis 2022; 7:tropicalmed7120414. [PMID: 36548669 PMCID: PMC9782491 DOI: 10.3390/tropicalmed7120414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Revised: 11/21/2022] [Accepted: 11/28/2022] [Indexed: 12/04/2022] Open
Abstract
The emergence of genetic mutations in chromosomal genes and the transmissible plasmid-mediated colistin resistance gene may have helped in the spread of colistin resistance among various Klebsiella pneumoniae (K. pneumoniae) isolates and other different bacteria. In this study, the prevalence of mutated colistin-resistant K. pneumoniae isolates was studied globally using a systematic review and meta-analysis approach. A systematic search was conducted in databases including PubMed, ScienceDirect, Scopus and Google Scholar. The pooled prevalence of mutated colistin resistance in K. pneumoniae isolates was analyzed using Comprehensive Meta-Analysis Software (CMA). A total of 50 articles were included in this study. The pooled prevalence of mutated colistin resistance in K. pneumoniae was estimated at 75.4% (95% CI = 67.2−82.1) at high heterogeneity (I2 = 81.742%, p-value < 0.001). Meanwhile, the results of the subgroup analysis demonstrated the highest prevalence in Saudi Arabia with 97.9% (95% CI = 74.1−99.9%) and Egypt, with 4.5% (95% CI = 0.6−26.1%), had the lowest. The majority of mutations could be observed in the mgrB gene (88%), pmrB gene (54%) and phoQ gene (44%). The current study showed a high prevalence of the mutation of colistin resistance genes in K. pneumoniae. Therefore, it is recommended that regular monitoring be performed to control the spread of colistin resistance.
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Characterization of Carbapenemase-Producing Klebsiella pneumoniae Isolates from Two Romanian Hospitals Co-Presenting Resistance and Heteroresistance to Colistin. Antibiotics (Basel) 2022; 11:antibiotics11091171. [PMID: 36139950 PMCID: PMC9495256 DOI: 10.3390/antibiotics11091171] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2022] [Revised: 08/12/2022] [Accepted: 08/29/2022] [Indexed: 11/16/2022] Open
Abstract
Klebsiella pneumoniae is a notorious human pathogen involved in healthcare-associated infections. The worldwide expansion of infections induced by colistin-resistant and carbapenemase-producing Enterobacterales (CPE) isolates has been increasingly reported. This study aims to analyze the phenotypic and molecular profiles of 10 colistin-resistant (CR) isolates and 2 pairs of colistin-heteroresistant (ChR) (parental and the corresponding resistant mutants) isolates of K. pneumoniae CPE sourced from two hospitals. The phenotypes of strains in the selected collection had been previously characterized. Antimicrobial susceptibility testing was performed using a Vitek 2 Compact system (BioMérieux SA, Marcy l’Etoile, France), the disc diffusion method, and broth microdilution (BMD) for colistin. Whole-genome sequencing (WGS) did not uncover evidence of any mobile colistin resistance (mcr) genes, although the mgrB gene of seven isolates appeared to be disrupted by insertion sequences (ISKpn25 or ISKpn26). Possible deleterious missense mutations were found in phoP (L4F), phoQ (Q426L, L26Q, L224Q, Q317K), pmrB (R256G, P95L, T157P, V352E), and crrB (P151S) genes. The identified isolates belonged to the following clonal lineages: ST101 (n = 6), ST147 (n = 5), ST258 (n = 2), and ST307 (n = 1). All strains harbored IncF plasmids. OXA-48 producers carried IncL and IncR plasmids, while one blaNDM-1 genome was found to harbor IncC plasmids. Ceftazidime–avibactam remains a therapeutic option for KPC-2 and OXA-48 producers. Resistance to meropenem–vaborbactam has emerged in some blakPC-2-carrying isolates. Our study demonstrates that the results of WGS can provide essential evidence for the surveillance of antimicrobial resistance.
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Chukamnerd A, Pomwised R, Jeenkeawpiam K, Sakunrang C, Chusri S, Surachat K. Genomic insights into bla NDM-carrying carbapenem-resistant Klebsiella pneumoniae clinical isolates from a university hospital in Thailand. Microbiol Res 2022; 263:127136. [PMID: 35870342 DOI: 10.1016/j.micres.2022.127136] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Revised: 05/04/2022] [Accepted: 07/13/2022] [Indexed: 11/18/2022]
Abstract
The emergence of carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates is a serious threat to global health. Here, we elucidate the genetic features of blaNDM-carrying CRKP clinical isolates from a university hospital in Thailand. The entire genomes of 19 CRKP isolates were extracted and then sequenced using the MGISEQ200 platform. Using various bioinformatics tools, we analyzed the antimicrobial resistance (AMR), virulence factors, gene transfer, bacterial defense mechanisms, and genomic diversity of the CRKP isolates. The sequence type (ST) 16 was found in most of the isolates, along with carriages of the blaNDM-1, blaOXA-232, and blaCTX-M-15 genes. The IncFIB(pQil), Col440II, and ColKP3 plasmids were identified with high frequency. The CRKP isolates harbored genes encoding for virulence factors such as adherence, biofilm formation, immune evasion, and iron uptake. The CRISPR-Cas region in the CRKP9 isolate consisted of 28 distinct spacer sequences. The genomes of the CRKP isolates presented restriction-modification (R-M) sites (M.Kpn34618Dcm and M.Kpn928I) and integrated bacteriophage genomes (Klebsiella phage ST16-OXA48phi5.4 and Enterobacteria phage mEp390). Bottromycin and sactipeptides were also identified. The isolates could be separated into three clades according to STs and pairwise single nucleotide polymorphism (SNP) distance. Pairwise average nucleotide identity (ANI) values revealed intra-species. These findings support the importance of whole-genome sequencing (WGS) to the rapid and accurate genomic analysis of clinical isolates of CRKP.
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Affiliation(s)
- Arnon Chukamnerd
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand.
| | - Rattanaruji Pomwised
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.
| | - Kongpop Jeenkeawpiam
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.
| | - Chanida Sakunrang
- Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.
| | - Sarunyou Chusri
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand; Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand.
| | - Komwit Surachat
- Department of Biomedical Sciences and Biomedical Engineering, Faculty of Medicine, Prince of Songkla University, Songkhla, Thailand; Molecular Evolution and Computational Biology Research Unit, Faculty of Science, Prince of Songkla University, Songkhla, Thailand.
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12
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Ramaloko WT, Osei Sekyere J. Phylogenomics, Epigenomics, Virulome, and Mobilome of Gram-negative Bacteria Co-resistant to Carbapenems and Polymyxins: A One-Health Systematic Review and Meta-analyses. Environ Microbiol 2022; 24:1518-1542. [PMID: 35129271 DOI: 10.1111/1462-2920.15930] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2020] [Accepted: 01/30/2022] [Indexed: 11/29/2022]
Abstract
Gram-negative bacteria (GNB) continue to develop resistance against important antibiotics including last-resort ones such as carbapenems and polymyxins. An analysis of GNB with co-resistance to carbapenems and polymyxins from a One Health perspective is presented. Data of species name, country, source of isolation, resistance genes (ARGs), plasmid type, clones, and mobile genetic elements (MGEs) were deduced from 129 articles from January 2016 to March 2021. Available genomes and plasmids were obtained from PATRIC and NCBI. Resistomes and methylomes were analysed using BAcWGSTdb and REBASE whilst Kaptive was used to predict capsule typing. Plasmids and other MEGs were identified using MGE Finder and ResFinder. Phylogenetic analyses were done using RAxML and annotated with MEGA 7. A total of 877 isolates, 32 genomes and 44 plasmid sequences were analysed. Most of these isolates were reported in Asian countries and were isolated from clinical, animal, and environmental sources. Colistin resistance was mostly mediated by mgrB inactivation (37%; n = 322) and mcr-1 (36%; n = 312), while OXA-48/181 was the most reported carbapenemase. IncX and IncI were the most common plasmids hosting carbapenemases and mcr genes. The isolates were co-resistant to other antibiotics, with floR (chloramphenicol) and fosA3 (fosfomycin) being common; E. coli ST156 and K. pneumoniae ST258 strains were common globally. Virulence genes and capsular KL-types were also detected. Type I, II, III and IV restriction modification systems were detected, comprising various MTases and restriction enzymes. The escalation of highly resistant isolates drains the economy due to untreatable bacterial infections, which leads to increasing global mortality rates and healthcare costs. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Winnie Thabisa Ramaloko
- Department of Medical Microbiology, School of Medicine, Faculty of Health Sciences, University of Pretoria, South Africa
| | - John Osei Sekyere
- Department of Medical Microbiology, School of Medicine, Faculty of Health Sciences, University of Pretoria, South Africa
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13
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Naha S, Sands K, Mukherjee S, Dutta S, Basu S. OUP accepted manuscript. J Antimicrob Chemother 2022; 77:1586-1591. [PMID: 35323923 DOI: 10.1093/jac/dkac083] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 02/16/2022] [Indexed: 11/13/2022] Open
Affiliation(s)
- Sharmi Naha
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Kirsty Sands
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Suchandra Mukherjee
- Department of Neonatology, Institute of Post-Graduate Medical Education & Research and SSKM Hospital, Kolkata, West Bengal, India
| | - Shanta Dutta
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
| | - Sulagna Basu
- Division of Bacteriology, ICMR-National Institute of Cholera and Enteric Diseases, Kolkata, West Bengal, India
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14
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Gordinskaya NA, Boriskina E, Kryazhev D. Phenotypic and genetic characteristics of antimicrobial resistance of Klebsiella pneumoniae clinical isolates in hospitals of Nizhny Novgorod. CLINICAL MICROBIOLOGY AND ANTIMICROBIAL CHEMOTHERAPY 2022. [DOI: 10.36488/cmac.2022.3.268-272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Objective.
To study in vitro antimicrobial resistance and prevalence of the most clinically important carbapenemases genes in Klebsiella pneumoniae clinical isolates in Nizhny Novgorod.
Materials and Methods.
A total of 238 K. pneumoniae clinical isolates from upper and lower respiratory tracts, abdominal cavity, urogenital tract, and wound discharge were tested in this study. Species identification was done using WalkAway 96 analyzer (Siemens, Germany) with POS Combo Type 20 tablets (Beckman Coulter, USA) and Multiscan FC spectrophotometer (Thermo Scientific, Finland) with Microlatest tablets (PLIVA-Lachema, Czech Republic). Antimicrobial resistance was determined by discdiffusion method and using microbiological analyzer WalkAway 96 (Siemens, Germany). Minimal inhibitory concentrations for colistin were determined using the “MIC Colistin” kit (Erba Mannheim, Czech Republic). Detection of carbapenemases genes (KPC, OXA-48 group, IMP, VIM and NDM) was performed by RT-PCR using CFX-96 machine (Bio-Rad, USA) and commercial kits «MDR KPC/OXA-48-FL» and «MDR MBL-FL» (AmpliSens, Russia).
Results.
More than 90% of K. pneumoniae isolates in Nizhny Novgorod were resistant to III–V generation cephalosporins, 53.8% – to gentamicin, 71.2% – to ciprofloxacin, 81.2% – to co-trimoxazole, 88.1% – to ertapenem, 37.1% – to doripenem, 21.6% – to imipenem, 34.3% – to meropenem, 3.2% – to colistin. Genes of КРС-like carbapenemases were detected in 13.1% of isolates, OХA-48 – in 21.6%. Metallobeta-lactamases were not identified among tested isolates.
Conclusions.
Currently, there are no antimicrobials that active against all K. pneumoniae isolates in Nizhny Novgorod. Carbapenems and polymyxins remain active against more than 50% of isolates.
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Affiliation(s)
- Nataliya A. Gordinskaya
- Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology (Nizhny Novgorod, Russia)
| | - E.V. Boriskina
- Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology (Nizhny Novgorod, Russia)
| | - D.V. Kryazhev
- Academician I.N. Blokhina Nizhny Novgorod Scientific Research Institute of Epidemiology and Microbiology (Nizhny Novgorod, Russia)
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15
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Alfouzan W, Dhar R, Mohsin J, Khamis F, Mokaddas E, Abdullah A, Mustafa AS, Otero A, Wanis P, Matar SH, Khalil S, Alekseeva I, Young K. OUP accepted manuscript. JAC Antimicrob Resist 2022; 4:dlac035. [PMID: 35465239 PMCID: PMC9021015 DOI: 10.1093/jacamr/dlac035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Accepted: 03/07/2022] [Indexed: 11/29/2022] Open
Abstract
Background The treatment options for infections caused by MDR Gram-negative bacteria have been limited, especially for infections caused by bacteria that produce carbapenemases and/or ESBLs. Ceftolozane/tazobactam is a cephalosporin/β-lactamase inhibitor developed to treat Gram-negative bacteria. Methods Ceftolozane/tazobactam and 14 comparators (amikacin, aztreonam, cefepime, cefotaxime, cefoxitin, ceftazidime, ceftriaxone, ciprofloxacin, colistin, ertapenem, imipenem, levofloxacin, meropenem and piperacillin/tazobactam) were evaluated against Pseudomonas aeruginosa and Enterobacterales isolates collected from Kuwait and Oman (n = 606) during 2016–17. In addition, further analysis of resistance mechanisms to ceftolozane/tazobactam was done utilizing WGS. Non-susceptible isolates from ceftolozane/tazobactam surveillance were selected for analysis. Overall, 35 strains underwent WGS. Results Among isolates from Kuwait, susceptibility of P. aeruginosa, Escherichia coli and Klebsiella pneumoniae to ceftolozane/tazobactam was 79.8%, 95.7% and 87.5%, respectively, and from Oman was 92.3%, 93.1% and 88.5%, respectively. No P. aeruginosa with a ceftolozane/tazobactam MIC <32 mg/L encoded β-lactamases besides normal chromosomal enzymes (PDC variants or OXA-50-like) whereas all but one P. aeruginosa isolate with MIC >32 mg/L encoded either MBLs (60%), VEB-1 (19%) or additional OXAs (3.7%). Conclusions Colistin followed by ceftolozane/tazobactam showed the greatest activity against P. aeruginosa. Enterobacterales showed more susceptibility to ceftolozane/tazobactam than to piperacillin/tazobactam, but meropenem and colistin showed better activity.
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Affiliation(s)
- Wadha Alfouzan
- Microbiology Unit, Department of Laboratories, Farwania Hospital, Kuwait City, Kuwait
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
- Corresponding author. E-mail:
| | - Rita Dhar
- Microbiology Unit, Department of Laboratories, Farwania Hospital, Kuwait City, Kuwait
| | | | | | - Eiman Mokaddas
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
- Microbiology Unit, Department of Laboratories, Ibn Sina Hospital, Kuwait City, Kuwait
| | - Abrar Abdullah
- Microbiology Unit, Department of Laboratories, Amiri hospital, Kuwait City, Kuwait
| | - Abu Salim Mustafa
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait City, Kuwait
| | | | - Paulette Wanis
- Merck Sharp & Dohme IDEA Middle East, Dubai Healthcare City, AlFaris building #39, 4th floor, MSD Office, Dubai, UAE
| | - Samar Hussien Matar
- Merck Sharp & Dohme IDEA Middle East, Dubai Healthcare City, AlFaris building #39, 4th floor, MSD Office, Dubai, UAE
| | - Sherif Khalil
- Merck Sharp & Dohme IDEA Middle East, Dubai Healthcare City, AlFaris building #39, 4th floor, MSD Office, Dubai, UAE
| | - Irina Alekseeva
- Merck Sharp & Dohme IDEA Middle East, Dubai Healthcare City, AlFaris building #39, 4th floor, MSD Office, Dubai, UAE
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16
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Masood KI, Umar S, Hasan Z, Farooqi J, Razzak SA, Jabeen N, Rao J, Shakoor S, Hasan R. Lipid A-Ara4N as an alternate pathway for (colistin) resistance in Klebsiella pneumonia isolates in Pakistan. BMC Res Notes 2021; 14:449. [PMID: 34906210 PMCID: PMC8670247 DOI: 10.1186/s13104-021-05867-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/29/2021] [Indexed: 11/23/2022] Open
Abstract
Objectives This study aimed to explore mechanism of colistin resistance amongst Klebsiella pneumoniae isolates through plasmid mediated mcr-1 gene in Pakistan. Carbapenem and Colistin resistant K. pneumoniae isolates (n = 34) stored at − 80 °C as part of the Aga Khan University Clinical Laboratory strain bank were randomly selected and subjected to mcr-1 gene PCR. To investigate mechanisms of resistance, other than plasmid mediated mcr-1 gene, whole genome sequencing was performed on 8 clinical isolates, including 6 with colistin resistance (MIC > 4 μg/ml) and 2 with intermediate resistance to colistin (MIC > 2 μg/ml). Results RT-PCR conducted revealed absence of mcr-1 gene in all isolates tested. Whole genome sequencing results revealed modifications in Lipid A-Ara4N pathway. Modifications in Lipid A-Ara4N pathway were detected in ArnA_ DH/FT, UgdH, ArnC and ArnT genes. Mutation in ArnA_ DH/FT gene were detected in S3, S5, S6 and S7 isolates. UgdH gene modifications were found in all isolates except S3, mutations in ArnC were present in all except S1, S2 and S8 and ArnT were detected in all except S4 and S7. In the absence of known mutations linked with colistin resistance, lipid pathway modifications may possibly explain the phenotype resistance to colistin, but this needs further exploration. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-021-05867-3.
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Affiliation(s)
- Kiran Iqbal Masood
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Seema Umar
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Zahra Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Joveria Farooqi
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Safina Abdul Razzak
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Nazish Jabeen
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Jason Rao
- Health Security Partners, Washington, DC, 20009, USA
| | - Sadia Shakoor
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan
| | - Rumina Hasan
- Department of Pathology and Laboratory Medicine, Aga Khan University, Karachi, Pakistan. .,Department of Infection Biology, Faculty Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, UK.
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17
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Mouftah SF, Pál T, Higgins PG, Ghazawi A, Idaghdour Y, Alqahtani M, Omrani AS, Rizvi TA, Sonnevend Á. Diversity of carbapenem-resistant Klebsiella pneumoniae ST14 and emergence of a subgroup with KL64 capsular locus in the Arabian Peninsula. Eur J Clin Microbiol Infect Dis 2021:10.1007/s10096-021-04384-2. [PMID: 34855011 DOI: 10.1007/s10096-021-04384-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/16/2021] [Indexed: 10/19/2022]
Abstract
To understand the reasons of successful spread of carbapenem-resistant Klebsiella pneumoniae ST14 (CRKP-ST14) in countries of the Arabian Peninsula, the resistome, capsular locus, carbapenemase carrying plasmid types, and core genome of isolates from the region were compared to global isolates. Thirty-nine CRKP-ST14 strains isolated from 13 hospitals in the United Arab Emirates, Bahrain, and Saudi Arabia were selected for whole genome sequencing on Illumina MiSeq platform based on the variety of carbapenemase genes carried and plasmids bearing these genes. Their resistome, capsular locus, and core genome MLST were compared to 173 CRKP-ST14 genomes available in public databases. The selected 39 CRKP-ST14 produced either NDM-1, OXA-48, OXA-162, OXA-232, KPC-2, or co-produced NDM-1 and an OXA-48-like carbapenemase. cgMLST revealed three clusters: 16 isolates from five UAE cities (C1), 11 isolates from three UAE cities and Bahrain (C2), and 5 isolates from Saudi Arabia (C3), respectively, and seven singletons. Resistance gene profile, carbapenemase genes, and their plasmid types were variable in both C1 and C2 clusters. The majority of CRKP-ST14 had KL2, but members of the C2 cluster and two further singletons possessed KL64 capsular locus. Based on cgMLST comparison of regional and global isolates, CRKP-ST14 with KL64 from four continents formed a distinct cluster, suggesting a recent emergence and spread of this variant. Our findings confirmed clonal transmission coupled with likely horizontal gene transfer in carbapenem-resistant Klebsiella pneumoniae ST14. Dissemination of this genetically flexible, highly resistant clone warrants further monitoring.
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Affiliation(s)
- Shaimaa F Mouftah
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- Department of Biomedical Sciences, Zewail City of Science and Technology, Giza, Egypt
| | - Tibor Pál
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary
| | - Paul G Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, Cologne, Germany
| | - Akela Ghazawi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
| | - Youssef Idaghdour
- Pathology and Laboratory Medicine Department, BDF Hospital - Royal Medical Services, Riffa, Kingdom of Bahrain
| | - Manaf Alqahtani
- New York University Abu Dhabi, Abu Dhabi, United Arab Emirates
| | - Ali S Omrani
- King Faisal Specialty Hospital, Riyadh, Saudi Arabia
- Communicable Diseases Center Hamad Medical Corporation, Doha, Qatar
| | - Tahir A Rizvi
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates
- Zayed Bin Sultan Al Nahyan Center for Health Sciences, Al Ain, United Arab Emirates
| | - Ágnes Sonnevend
- Department of Medical Microbiology and Immunology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, United Arab Emirates.
- Department of Medical Microbiology and Immunology, Medical School, University of Pécs, Pécs, Hungary.
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18
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Bolourchi N, Shahcheraghi F, Giske CG, Nematzadeh S, Solgi H, Badmasti F. Genome analysis of an OXA-48-producing carbapenem- and colistin-resistant Klebsiella pneumoniae sequence type 11 clone isolated from an inpatient. GENE REPORTS 2021. [DOI: 10.1016/j.genrep.2021.101394] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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19
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Ngbede EO, Adekanmbi F, Poudel A, Kalalah A, Kelly P, Yang Y, Adamu AM, Daniel ST, Adikwu AA, Akwuobu CA, Abba PO, Mamfe LM, Maurice NA, Adah MI, Lockyear O, Butaye P, Wang C. Concurrent Resistance to Carbapenem and Colistin Among Enterobacteriaceae Recovered From Human and Animal Sources in Nigeria Is Associated With Multiple Genetic Mechanisms. Front Microbiol 2021; 12:740348. [PMID: 34690985 PMCID: PMC8528161 DOI: 10.3389/fmicb.2021.740348] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/09/2021] [Indexed: 01/01/2023] Open
Abstract
Resistance to last resort drugs such as carbapenem and colistin is a serious global health threat. This study investigated carbapenem and colistin resistance in 583 non-duplicate Enterobacteriaceae isolates utilizing phenotypic methods and whole genome sequencing (WGS). Of the 583 isolates recovered from humans, animals and the environment in Nigeria, 18.9% (110/583) were resistant to at least one carbapenem (meropenem, ertapenem, and imipenem) and 9.1% (53/583) exhibited concurrent carbapenem-colistin resistance. The minimum inhibitory concentrations of carbapenem and colistin were 2–32 μg/mL and 8 to >64 μg/mL, respectively. No carbapenem resistant isolates produced carbapenemase nor harbored any known carbapenemase producing genes. WGS supported that concurrent carbapenem-colistin resistance was mediated by novel and previously described alterations in chromosomal efflux regulatory genes, particularly mgrB (M1V) ompC (M1_V24del) ompK37 (I70M, I128M) ramR (M1V), and marR (M1V). In addition, alterations/mutations were detected in the etpA, arnT, ccrB, pmrB in colistin resistant bacteria and ompK36 in carbapenem resistant bacteria. The bacterial isolates were distributed into 37 sequence types and characterized by the presence of internationally recognized high-risk clones. The results indicate that humans and animals in Nigeria may serve as reservoirs and vehicles for the global spread of the isolates. Further studies on antimicrobial resistance in African countries are warranted.
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Affiliation(s)
- Emmanuel O Ngbede
- Department of Veterinary Microbiology, College of Veterinary Medicine, Federal University of Agriculture Makurdi, Makurdi, Nigeria
| | - Folasade Adekanmbi
- Department of Pathobiology, Auburn University College of Veterinary Medicine, Auburn, AL, United States
| | - Anil Poudel
- Department of Pathobiology, Auburn University College of Veterinary Medicine, Auburn, AL, United States
| | - Anwar Kalalah
- Department of Pathobiology, Auburn University College of Veterinary Medicine, Auburn, AL, United States
| | - Patrick Kelly
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis
| | - Yi Yang
- Yangzhou University College of Veterinary Medicine, Yangzhou, China
| | - Andrew M Adamu
- Department of Veterinary Public Health and Preventive Medicine, Faculty of Veterinary Medicine, University of Abuja, Abuja, Nigeria
| | - Salem T Daniel
- Department of Microbiology, College of Sciences, Federal University of Agriculture Makurdi, Makurdi, Nigeria
| | - Alex A Adikwu
- Department of Veterinary Public Health and Preventive Medicine, College of Veterinary Medicine, Federal University of Agriculture Makurdi, Makurdi, Nigeria
| | - Chinedu A Akwuobu
- Department of Veterinary Microbiology, College of Veterinary Medicine, Federal University of Agriculture Makurdi, Makurdi, Nigeria
| | - Paul O Abba
- Department of Medical Microbiology and Parasitology, Benue State University Teaching Hospital, Makurdi, Nigeria
| | - Levi M Mamfe
- Department of Veterinary Microbiology, College of Veterinary Medicine, Federal University of Agriculture Makurdi, Makurdi, Nigeria
| | - Nanven A Maurice
- Department of Diagnostics and Extension, National Veterinary Research Institute, Vom, Nigeria
| | - Mohammed I Adah
- Department of Veterinary Medicine, College of Veterinary Medicine, Federal University of Agriculture Makurdi, Makurdi, Nigeria
| | - Olivia Lockyear
- Department of Pathobiology, Auburn University College of Veterinary Medicine, Auburn, AL, United States
| | - Patrick Butaye
- Department of Biomedical Sciences, Ross University School of Veterinary Medicine, Basseterre, Saint Kitts and Nevis.,Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Chengming Wang
- Department of Pathobiology, Auburn University College of Veterinary Medicine, Auburn, AL, United States
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20
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Sakulworakan R, Chokmangmeepisarn P, Dinh-Hung N, Sivaramasamy E, Hirono I, Chuanchuen R, Kayansamruaj P, Rodkhum C. Insight Into Whole Genome of Aeromonas veronii Isolated From Freshwater Fish by Resistome Analysis Reveal Extensively Antibiotic Resistant Traits. Front Microbiol 2021; 12:733668. [PMID: 34603262 PMCID: PMC8484913 DOI: 10.3389/fmicb.2021.733668] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 08/19/2021] [Indexed: 11/23/2022] Open
Abstract
Aeromonas veronii outbreaks in tilapia farming caused relatively high mortalities, and the bacteria was resistant to many kinds of antimicrobials used in Thailand aquaculture. According to the CLSI standard, the determination of antimicrobials efficacy has been limited to phenotypic analyses, and a genomics study is required. This research aimed to analyze the resistome of A. veronii isolated from diseased tilapia in Chainat, Nong Khai, and Uttaradit provinces in Thailand. A total of 12 isolates of A. veronii were identified based on the gyrB sequencing and then, the MIC values to eight antimicrobials (AMP, AML, GEN, ENR, OXO, OTC, SXT, and FFC) were determined. According to the MIC patterns, whole genome sequencing (WGS) of five representatives and resistome analysis were performed, including 15 genomes of A. veronii isolated from freshwater fish available in the NCBI. All tilapia isolates were susceptible to FFC but resistant to AML and AMP while OTC resistance was the most dominant. In addition to the WGS analysis, 4.5 Mbp of A. veronii was characterized. A total of 20 ARGs were detected by resistome analysis and 16 genes were shared among the A. veronii population. In conclusion, A. veronii strains isolated from tilapia exhibited a resistance to several antimicrobials and multidrug resistance (MDR) which was related to the presence of multiple ARGs. Aeromonas veronii shared the ARGs in their population worldwide with a possibility of a plasmid-mediated acquisition due to the presence of resistance islands.
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Affiliation(s)
- Rungnapa Sakulworakan
- The International Graduate Program of Veterinary Science and Technology (VST), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Center of Excellent in Fish Infectious Diseases (CE FID), Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Putita Chokmangmeepisarn
- The International Graduate Program of Veterinary Science and Technology (VST), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand.,Center of Excellent in Fish Infectious Diseases (CE FID), Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Nguyen Dinh-Hung
- The International Graduate Program of Veterinary Science and Technology (VST), Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Elayaraja Sivaramasamy
- Center of Excellent in Fish Infectious Diseases (CE FID), Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Ikuo Hirono
- Tokyo University of Marine Science and Technology, Minato-ku, Japan
| | - Rungthip Chuanchuen
- Department of Veterinary Public Health, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | | | - Channarong Rodkhum
- Center of Excellent in Fish Infectious Diseases (CE FID), Department of Veterinary Microbiology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
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21
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Stefaniuk EM, Kozińska A, Waśko I, Baraniak A, Tyski S. Occurrence of Beta-Lactamases in Colistin-Resistant Enterobacterales Strains in Poland - a Pilot Study. Pol J Microbiol 2021; 70:283-288. [PMID: 34349817 PMCID: PMC8326981 DOI: 10.33073/pjm-2021-021] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/06/2021] [Accepted: 05/10/2021] [Indexed: 11/05/2022] Open
Abstract
Sixty-five colistin-resistant Enterobacterales isolates recovered from different clinical specimens were analyzed. The strains were collected in 12 hospitals all over Poland within a period of nine months. Strains were analyzed for eight genes from the mcr family. The presence of mcr-1 gene was detected in three Escherichia coli strains. The 45/65 isolates were identified as ESBL producers. CTX-M-1-like enzymes were the most common ESBLs (n = 40). One E. coli and seven Klebsiella pneumoniae strains produced carbapenemases, with the NDM being produced by five isolates. Among all the strains tested, four and five were resistant to new drugs meropenem/vaborbactam and ceftazidime/avibactam, respectively.
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Affiliation(s)
- Elżbieta M Stefaniuk
- Department of Antibiotics and Microbiology, National Medicines Institute, Warsaw, Poland
| | - Aleksandra Kozińska
- Department of Medicines Biotechnology and Bioinformatics, National Medicines Institute, Warsaw, Poland
| | - Izabela Waśko
- Department of Medicines Biotechnology and Bioinformatics, National Medicines Institute, Warsaw, Poland
| | - Anna Baraniak
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - Stefan Tyski
- Department of Antibiotics and Microbiology, National Medicines Institute, Warsaw, Poland.,Department of Pharmaceutical Microbiology, Medical University of Warsaw, Warsaw, Poland
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22
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Abdul Rahim N, Zhu Y, Cheah SE, Johnson MD, Yu HH, Sidjabat HE, Butler MS, Cooper MA, Fu J, Paterson DL, Nation RL, Boyce JD, Creek DJ, Bergen PJ, Velkov T, Li J. Synergy of the Polymyxin-Chloramphenicol Combination against New Delhi Metallo-β-Lactamase-Producing Klebsiella pneumoniae Is Predominately Driven by Chloramphenicol. ACS Infect Dis 2021; 7:1584-1595. [PMID: 33834753 DOI: 10.1021/acsinfecdis.0c00661] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Carbapenem-resistant Klebsiella pneumoniae has been classified as an Urgent Threat by the Centers for Disease Control and Prevention (CDC). The combination of two "old" antibiotics, polymyxin and chloramphenicol, displays synergistic killing against New Delhi metallo-β-lactamase (NDM)-producing K. pneumoniae. However, the mechanism(s) underpinning their synergistic killing are not well studied. We employed an in vitro pharmacokinetic/pharmacodynamic model to mimic the pharmacokinetics of the antibiotics in patients and examined bacterial killing against NDM-producing K. pneumoniae using a metabolomic approach. Metabolomic analysis was integrated with an isolate-specific genome-scale metabolic network (GSMN). Our results show that metabolic responses to polymyxin B and/or chloramphenicol against NDM-producing K. pneumoniae involved the inhibition of cell envelope biogenesis, metabolism of arginine and nucleotides, glycolysis, and pentose phosphate pathways. Our metabolomic and GSMN modeling results highlight the novel mechanisms of a synergistic antibiotic combination at the network level and may have a significant potential in developing precision antimicrobial chemotherapy in patients.
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Affiliation(s)
- Nusaibah Abdul Rahim
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Yan Zhu
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Soon-Ee Cheah
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Matthew D. Johnson
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Heidi H. Yu
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Hanna E. Sidjabat
- University of Queensland Centre for Clinical Research, Herston, Queensland 4029, Australia
| | - Mark S. Butler
- Institute for Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Matthew A. Cooper
- Institute for Molecular Biosciences, The University of Queensland, Brisbane, Queensland 4072, Australia
| | - Jing Fu
- Department of Mechanical and Aerospace Engineering, Faculty of Engineering, Monash University, Clayton, Victoria 3800, Australia
| | - David L. Paterson
- University of Queensland Centre for Clinical Research, Herston, Queensland 4029, Australia
- Pathology Queensland, Royal Brisbane and Women’s Hospital Campus, Herston, Queensland 4029, Australia
| | - Roger L. Nation
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - John D. Boyce
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
| | - Darren J. Creek
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
| | - Phillip J. Bergen
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
- Centre for Medicine Use and Safety, Monash University, Parkville, Victoria 3052, Australia
| | - Tony Velkov
- Department of Pharmacology & Therapeutics, Faculty of Medicine, Dentistry and Health Sciences, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Jian Li
- Drug Delivery, Disposition and Dynamics, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, Victoria 3052, Australia
- Biomedicine Discovery Institute, Department of Microbiology, Monash University, Clayton, Victoria 3800, Australia
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23
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Bilal H, Zhang G, Rehman T, Han J, Khan S, Shafiq M, Yang X, Yan Z, Yang X. First Report of blaNDM-1 Bearing IncX3 Plasmid in Clinically Isolated ST11 Klebsiella pneumoniae from Pakistan. Microorganisms 2021; 9:microorganisms9050951. [PMID: 33924918 PMCID: PMC8146611 DOI: 10.3390/microorganisms9050951] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 04/23/2021] [Accepted: 04/23/2021] [Indexed: 02/05/2023] Open
Abstract
The New Delhi Metallo-β-lactamase (NDM) is among the most threatening forms of carbapenemases produced by K. pneumoniae, well-known to cause severe worldwide infections. The molecular epidemiology of blaNDM-1-harboring K. pneumoniae is not well elucidated in Pakistan. Herein, we aim to determine the antibiotics-resistance profile, genes type, molecular type, and plasmid analysis of 125 clinically isolated K. pneumoniae strains from urine samples during July 2018 to January 2019 in Pakistan. A total of 34 (27.2%) K. pneumoniae isolates were carbapenemases producers, and 23 (18.4%) harbored the blaNDM-1 gene. The other carbapenemases encoding genes, i.e., blaIMP-1 (7.2%), blaVIM-1 (3.2%), and blaOXA-48 (2.4%) were also detected. The Multi Locus Sequence Typing (MLST) results revealed that all blaNDM-1-harboring isolates were ST11. The other sequence types detected were ST1, ST37, and ST105. The cluster analysis of Xbal Pulsed Field Gel Electrophoresis (PFGE) revealed variation amongst the clusters of the identical sequence type isolates. The blaNDM-1 gene in all of the isolates was located on a 45-kb IncX3 plasmid, successfully transconjugated. For the first time, blaNDM-1-bearing IncX3 plasmids were identified from Pakistan, and this might be a new primary vehicle for disseminating blaNDM-1 in Enterobacteriaceae as it has a high rate of transferability.
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Affiliation(s)
- Hazrat Bilal
- Faculty of Health Sciences, Institute of Physical Sciences and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, China; (H.B.); (G.Z.); (J.H.); (S.K.); (X.Y.); (Z.Y.)
| | - Gaojian Zhang
- Faculty of Health Sciences, Institute of Physical Sciences and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, China; (H.B.); (G.Z.); (J.H.); (S.K.); (X.Y.); (Z.Y.)
| | - Tayyab Rehman
- Institute of Basic Medical Sciences, Khyber Medical University, Phase V, Hayatabad, Peshawar 25120, Khyber Pakhtunkhwa, Pakistan;
| | - Jianxion Han
- Faculty of Health Sciences, Institute of Physical Sciences and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, China; (H.B.); (G.Z.); (J.H.); (S.K.); (X.Y.); (Z.Y.)
| | - Sabir Khan
- Faculty of Health Sciences, Institute of Physical Sciences and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, China; (H.B.); (G.Z.); (J.H.); (S.K.); (X.Y.); (Z.Y.)
| | - Muhammad Shafiq
- Department of Cell Biology and Genetics, Shantou University Medical College, Shantou 515041, China;
| | - Xuegang Yang
- Faculty of Health Sciences, Institute of Physical Sciences and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, China; (H.B.); (G.Z.); (J.H.); (S.K.); (X.Y.); (Z.Y.)
| | - Zhongkang Yan
- Faculty of Health Sciences, Institute of Physical Sciences and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, China; (H.B.); (G.Z.); (J.H.); (S.K.); (X.Y.); (Z.Y.)
| | - Xingyuan Yang
- Faculty of Health Sciences, Institute of Physical Sciences and Information Technology, Anhui University, 111 Jiulong Road, Hefei 230601, China; (H.B.); (G.Z.); (J.H.); (S.K.); (X.Y.); (Z.Y.)
- Correspondence:
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24
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Xu J, Zhang N, Luo M, Wang M, Wang L, Li J, Li Z, Zhao H, Li Z, Kan B, Lu X. Rapid Identification of Plasmid Replicon Type and Coexisting Plasmid-Borne Antimicrobial Resistance Genes by S1-Pulsed-Field Gel Electrophoresis-Droplet Digital Polymerase Chain Reaction. Foodborne Pathog Dis 2021; 18:298-305. [PMID: 33661029 DOI: 10.1089/fpd.2020.2865] [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] [Indexed: 11/12/2022] Open
Abstract
Bacterial drug resistance is a significant food safety problem and public health threat. Plasmids carrying drug resistance genes may result in the rapid spread of resistance among different bacteria, hosts, and environments; therefore, antibiotic resistance monitoring and continuing research into the mechanisms of drug resistance are urgently needed. Southern blotting with probes for antibiotic resistance genes and even next-generation sequencing have been used previously to detect plasmid-borne resistance genes, but these approaches are complex and time-consuming. The next-generation sequencing requires strict laboratory conditions and bioinformatics analysis ability. In this study, we developed a simplified and sensitive method to detect plasmid-borne antimicrobial resistance genes and plasmid replicon types. Salmonella strains carrying plasmids of three different replicon types that contained mcr-1 and two ESBL-producing genes were used to verify the new method. The plasmids harbored by the Salmonella strains were separated by S1 nuclease treatment and pulsed-field gel electrophoresis (PFGE), then recovered and used as the templates for droplet digital polymerase chain reaction (ddPCR) to identify target genes. The target genes were present in significantly higher copy numbers on the plasmids than the background noise. These results were consistent with the plasmid sequencing results. This S1-PFGE-ddPCR method was less time-consuming to perform than Southern blot and complete plasmid sequencing. Therefore, this method represents a time-saving alternative for detecting plasmid-borne genes, and is likely to be a valuable tool for detecting coexisting plasmid-borne drug resistance genes.
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Affiliation(s)
- Jialiang Xu
- School of Light Industry, Beijing Technology and Business University, Beijing, China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ning Zhang
- School of Light Industry, Beijing Technology and Business University, Beijing, China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Ming Luo
- Laboratory Medicine, Yulin Center for Disease Control and Prevention, Guangxi, China
| | - Mengyu Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China.,School of Public Health, Nanchang University, Jiangxi, China
| | - Ling Wang
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Jiaqi Li
- School of Light Industry, Beijing Technology and Business University, Beijing, China.,State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhe Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Hongqun Zhao
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Zhenpeng Li
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Biao Kan
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xin Lu
- State Key Laboratory of Infectious Disease Prevention and Control, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
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25
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Azam M, Gaind R, Yadav G, Sharma A, Upmanyu K, Jain M, Singh R. Colistin Resistance Among Multiple Sequence Types of Klebsiella pneumoniae Is Associated With Diverse Resistance Mechanisms: A Report From India. Front Microbiol 2021; 12:609840. [PMID: 33692764 PMCID: PMC7937630 DOI: 10.3389/fmicb.2021.609840] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 01/22/2021] [Indexed: 12/25/2022] Open
Abstract
Background: The resistance to colistin and carbapenems in Klebsiella pneumoniae infections have been associated with increased morbidity and mortality worldwide. A retrospective observational study was conducted to determine the prevalence and molecular events contributing to colistin resistance. Methods: Clinical samples were screened for colistin resistance and underlying mechanisms were studied by PCR-based amplification and sequence analysis of genes of two-component regulatory system (phoPQ and pmrAB), regulatory transmembrane protein-coding mgrB, and mobilized colistin resistance genes (mcr-1-8). Gene expression of pmrC and pmrK was analyzed by qRT-PCR, and the genetic relationship was assessed by MLST. The putative effect of amino-acid substitutions was predicted by a combination of bioinformatics tools. Results: Of 335 Klebsiella spp. screened, 11 (3.2%) were identified as colistin-resistant (MIC range, 8 to >128 μg/ml). K. pneumoniae isolates belonged to clonal complex-11 (CC11) with sequence types (STs): 14, 16, 43, 54, 147 and 395, whereby four isolates conferred three novel STs (3986, 3987 and 3988) profiles. Sequence analysis revealed non-synonymous potentially deleterious mutations in phoP (T151A), phoQ (del87–90, del263–264, L30Q, and A351D), pmrA (G53S), pmrB (D150V, T157P, L237R, G250C, A252G, R315P, and Q331H), and mgrB (C28G) genes. The mgrB gene in three strains was disrupted by insertion sequences encoding IS1-like and IS5/IS1182 family-like transposase genes. All 11 isolates showed an elevation in the transcription level of pmrC gene. Mobilized colistin-resistance (mcr) genes were not detected. All but one of the colistin-resistant isolates was also resistant to carbapenems; β-lactamase genes blaNDM-1-like, blaOXA-48-like, and blaCTX-M-like were detected in eight, five, and nine isolates, respectively. Conclusion: All the studied colistin- and carbapenem-resistant K. pneumoniae isolates were genetically distinct, and various mechanisms of colistin resistance were detected, indicating its spontaneous emergence in this bacterial species.
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Affiliation(s)
- Mudsser Azam
- ICMR-National Institute of Pathology, New Delhi, India
| | - Rajni Gaind
- Department of Microbiology, VMMC and Safdarjung Hospital, New Delhi, India
| | - Gulshan Yadav
- ICMR-National Institute of Pathology, New Delhi, India
| | - Amit Sharma
- Department of Microbiology, VMMC and Safdarjung Hospital, New Delhi, India
| | - Kirti Upmanyu
- ICMR-National Institute of Pathology, New Delhi, India
| | - Manisha Jain
- Department of Microbiology, VMMC and Safdarjung Hospital, New Delhi, India
| | - Ruchi Singh
- ICMR-National Institute of Pathology, New Delhi, India
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26
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de Souza GHDA, dos Santos Radai JA, Mattos Vaz MS, Esther da Silva K, Fraga TL, Barbosa LS, Simionatto S. In vitro and in vivo antibacterial activity assays of carvacrol: A candidate for development of innovative treatments against KPC-producing Klebsiella pneumoniae. PLoS One 2021; 16:e0246003. [PMID: 33617571 PMCID: PMC7899316 DOI: 10.1371/journal.pone.0246003] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 01/12/2021] [Indexed: 12/13/2022] Open
Abstract
Dissemination of carbapenem-resistant Klebsiella pneumoniae poses a threat to the successful treatment of bacterial diseases and increases the need for new antibacterial agents development. The objective of this study was to determine the antimicrobial activity of carvacrol against multidrug-resistant K. pneumoniae. Carbapenemase production was detected by MALDI-TOF. The PCR and sequencing showed that the blaKPC-2,blaOXA-48, blaNDM-1, blaCTX-M-8 genes were present in carbapenem-resistant K. pneumoniae strains. The polymyxin-resistant K. pneumoniae strain exhibited alterations in mgrB gene. The antimicrobial activity of carvacrol was evaluated in vitro using broth microdilution and time-kill methods. For this, carbapenem-resistant K. pneumoniae and polymyxin-resistant strains, were evaluated. The in vitro results showed that carvacrol had antimicrobial activity against all isolates evaluated. The survival curves showed that carvacrol eradicated all of the bacterial cells within 4 h. The antimicrobial effect of carvacrol in vivo was determined using a mouse model of infection with Klebsiella pneumoniae carbapenemase (KPC). The treatment with carvacrol was associated with increased survival, and significantly reduced bacterial load in peritoneal lavage. In addition, groups treated with carvacrol, had a significant reduction in the total numbers of white cell and significantly increased of platelets when compared to the untreated group. In vivo and in vitro studies showed that carvacrol regimens exhibited significant antimicrobial activity against KPC-producing K. pneumoniae, making it an interesting candidate for development of alternative treatments.
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Affiliation(s)
| | - Joyce Alencar dos Santos Radai
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados—UFGD, Dourados, Mato Grosso do Sul, Brazil
| | - Marcia Soares Mattos Vaz
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados—UFGD, Dourados, Mato Grosso do Sul, Brazil
| | - Kesia Esther da Silva
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados—UFGD, Dourados, Mato Grosso do Sul, Brazil
| | - Thiago Leite Fraga
- Centro Universitário da Grande Dourados–UNIGRAN, Dourados, Mato Grosso do Sul, Brazil
| | - Leticia Spanivello Barbosa
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados—UFGD, Dourados, Mato Grosso do Sul, Brazil
| | - Simone Simionatto
- Laboratório de Pesquisa em Ciências da Saúde, Universidade Federal da Grande Dourados—UFGD, Dourados, Mato Grosso do Sul, Brazil
- * E-mail:
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27
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Imtiaz W, Syed Z, Rafaque Z, Andrews SC, Dasti JI. Analysis of Antibiotic Resistance and Virulence Traits (Genetic and Phenotypic) in Klebsiella pneumoniae Clinical Isolates from Pakistan: Identification of Significant Levels of Carbapenem and Colistin Resistance. Infect Drug Resist 2021; 14:227-236. [PMID: 33531820 PMCID: PMC7846821 DOI: 10.2147/idr.s293290] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 01/01/2021] [Indexed: 12/19/2022] Open
Abstract
Background The emergence of carbapenem-resistant and hypervirulent hypermucoviscous Klebsiella pneumoniae strains poses a significant public health challenge. We determined the MDR profiles, antibiotic resistance factors, virulence gene complement, and hypermucoviscous features of 200 clinical K. pneumoniae isolates from two major tertiary care hospitals in Islamabad and Rawalpindi, Pakistan. Methods Susceptibility profiling and phenotypic analysis were performed according to the CLSI guidelines. Genetic determinants of antibiotic resistance and virulence were detected by PCR. Biofilm formation analysis was performed by microtiter plate assay. Results The isolates displayed a high degree of antibiotic resistance: 36% MDR-CRKP; 38% carbapenem resistance; 55% gentamicin resistance; 53% ciprofloxacin resistance; and 59% aztreonam resistance. In particular, the level of resistance against fosfomycin (22%) and colistin (15%) is consistent with previous reports of increased resistance levels. Combined resistance to carbapenem and colistin was 7%. Genetic factors associated with colistin resistance (mcr-1 and mcr-2 genes) were detected in 12 and 9% of the isolates, respectively. Significant differences in resistance to gentamicin and levofloxacin were observed between the 200 isolates. Many of the isolates harbored genes specifying extended-spectrum and/or carbapenem-resistant β-lactamases: bla CTX-M-15 (46%), bla NDM-1 (39%), and bla OXA-48 (24%). The prevalence of the hypermucoviscous phenotype was 22% and 13% of the MDR isolates carried the rmpA gene (regulator for mucoid phenotype). Key virulence factor genes detected include those encoding: porins (ompK35 and ompK36; at 56 and 55% prevalence, respectively); adhesins (fimH, mrkD, and ycfM; at 19, 18, and 22% prevalence, respectively); and the polysaccharide regulator, bss, at 16% prevalence. Conclusion This report highlights carbapenem-resistant K. pneumoniae (CRKP) prevalence, emerging resistance to fosfomycin, and the presence of mcr-1 and mcr-2 in colistin-resistant isolates. Further, the detection of rmpA signifies the prevalence of the hypermucoviscous trait in CRKP clinical isolates from Pakistan.
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Affiliation(s)
- Wajiha Imtiaz
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan.,School of Biological Sciences, Whiteknights, University of Reading, Reading RG6 6AJ, UK
| | - Zainab Syed
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
| | - Zara Rafaque
- Department of Microbiology, Hazara University, Mansehra, Pakistan
| | - Simon Colin Andrews
- School of Biological Sciences, Whiteknights, University of Reading, Reading RG6 6AJ, UK
| | - Javid Iqbal Dasti
- Department of Microbiology, Faculty of Biological Sciences, Quaid-i-Azam University, Islamabad 45320, Pakistan
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28
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Kopotsa K, Mbelle NM, Osei Sekyere J. Epigenomics, genomics, resistome, mobilome, virulome and evolutionary phylogenomics of carbapenem-resistant Klebsiella pneumoniae clinical strains. Microb Genom 2020; 6:mgen000474. [PMID: 33170117 PMCID: PMC8116673 DOI: 10.1099/mgen.0.000474] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 10/28/2020] [Indexed: 12/12/2022] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) remains a major clinical pathogen and public health threat with few therapeutic options. The mobilome, resistome, methylome, virulome and phylogeography of CRKP in South Africa and globally were characterized. CRKP collected in 2018 were subjected to antimicrobial susceptibility testing, screening by multiplex PCR, genotyping by repetitive element palindromic (REP)-PCR, plasmid size, number, incompatibility and mobility analyses, and PacBio's SMRT sequencing (n=6). There were 56 multidrug-resistant CRKP, having blaOXA-48-like and blaNDM-1/7 carbapenemases on self-transmissible IncF, A/C, IncL/M and IncX3 plasmids endowed with prophages, traT, resistance islands, and type I and II restriction modification systems (RMS). Plasmids and clades detected in this study were respectively related to globally established/disseminated plasmids clades/clones, evincing transboundary horizontal and vertical dissemination. Reduced susceptibility to colistin occurred in 23 strains. Common clones included ST307, ST607, ST17, ST39 and ST3559. IncFIIk virulent plasmid replicon was present in 56 strains. Whole-genome sequencing of six strains revealed least 41 virulence genes, extensive ompK36 mutations, and four different K- and O-loci types: KL2, KL25, KL27, KL102, O1, O2, O4 and O5. Types I, II and III RMS, conferring m6A (GATC, GATGNNNNNNTTG, CAANNNNNNCATC motifs) and m4C (CCWGG) modifications on chromosomes and plasmids, were found. The nature of plasmid-mediated, clonal and multi-clonal dissemination of blaOXA-48-like and blaNDM-1 mirrors epidemiological trends observed for closely related plasmids and sequence types internationally. Worryingly, the presence of both blaOXA-48 and blaNDM-1 in the same isolates was observed. Plasmid-mediated transmission of RMS, virulome and prophages influence bacterial evolution, epidemiology, pathogenicity and resistance, threatening infection treatment. The influence of RMS on antimicrobial and bacteriophage therapy needs urgent investigation.
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Affiliation(s)
- Katlego Kopotsa
- Department of Medical Microbiology, School of Medicine, Faculty of Health Sciences, University of Pretoria, 0084 Pretoria, South Africa
| | - Nontombi M. Mbelle
- Department of Medical Microbiology, School of Medicine, Faculty of Health Sciences, University of Pretoria, 0084 Pretoria, South Africa
| | - John Osei Sekyere
- Department of Medical Microbiology, School of Medicine, Faculty of Health Sciences, University of Pretoria, 0084 Pretoria, South Africa
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29
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Hadjadj L, Syed MA, Abbasi SA, Rolain JM, Jamil B. Diversity of Carbapenem Resistance Mechanisms in Clinical Gram-Negative Bacteria in Pakistan. Microb Drug Resist 2020; 27:760-767. [PMID: 33211640 DOI: 10.1089/mdr.2019.0387] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
Antibiotic resistance is a health challenge worldwide. Carbapenem resistance in Gram-negative bacteria is a major problem since treatment options are very limited. Tigecycline and colistin are drugs of choice in this case, but resistance to these drugs is also high. The aim of this study was to describe the diversity of resistance mechanisms in carbapenem-resistant clinical Gram-negative bacteria from Pakistan. Carbapenem-hydrolyzing enzyme-encoding genes were detected using PCR and DNA sequencing and clonal types determined by multilocus sequence typing (MLST). Forty-four carbapenem-resistant isolates were collected from the microbiology laboratory of Fauji Foundation Hospital and Al-Syed Hospital, Rawalpindi, Pakistan, including Klebsiella spp., Escherichia coli, Acinetobacter baumannii, Pseudomonas aeruginosa, Enterobacter cloacae, and Achromobacter xylosoxidans. blaNDM-1, blaNDM-4, blaNDM-5, blaNDM-7, blaOXA-48, and blaOXA-181 were detected in Enterobacteriaceae; blaOXA-23, blaOXA-72, and blaNDM-1 in A. baumannii, and blaVIM-6 and blaVIM-11 in P. aeruginosa. MLST analysis revealed several predominant clonal types: ST167 in E. coli, ST147 in Klebsiella pneumoniae, ST2 in Acinetobacter, and ST664 in P. aeruginosa. In Acinetobacter, a new clonal type was observed for the first time. To the best of our knowledge, this is the first study describing the clonality and resistance mechanisms of carbapenem-resistant Gram-negative bacteria in Pakistan.
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Affiliation(s)
- Linda Hadjadj
- Faculté de Médecine et de Pharmacie, Aix Marseille Univ, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Muhammad Ali Syed
- Department of Microbiology, The University of Haripur, Haripur, Pakistan
| | | | - Jean-Marc Rolain
- Faculté de Médecine et de Pharmacie, Aix Marseille Univ, IRD, APHM, MEPHI, IHU Méditerranée Infection, Marseille, France
| | - Bushra Jamil
- Department of Medical Laboratory Sciences, University of Lahore, Islamabad Campus, Islamabad, Pakistan
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Ahmed I, Laiq S, Shaheen N, Wahab K, Farooqi J, Shahid A, Hasan R, Shakoor S. 'Breakpoint broth microdilution plate' for susceptibility testing of Gram negative bacilli against colistin sulfate. Pract Lab Med 2020; 22:e00192. [PMID: 33299918 PMCID: PMC7702188 DOI: 10.1016/j.plabm.2020.e00192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 11/18/2020] [Indexed: 11/17/2022] Open
Abstract
The MIC method applicable to Gram negative bacilli including Acinetobacter spp. is broth microdilution (BMD). Cost and/or availability issues limit the use of commercial MIC panels in resource limited settings. OBJECTIVES To design and implement an in-house breakpoint BMD panel (BBMD) for colistin against Gram negative bacilli. DESIGN BBMD panel was prepared in 96-well plate. MIC concentrations of 1, 2, & 4 μg/mL for test, and 0.25, 0.5, 1, 2 & 4 μg/mL for control strains were selected to accommodate 19 test and 3 quality control strains per plate. Plates were frozen at -80 °C until testing. Validation was performed using strains from a previously published study and compared with freshly prepared MIC panel of 16-0.03 μg/mL. RESULTS Validation showed 100% agreement with the reference method and BBMD was introduced into routine laboratory practice for colistin susceptibility of carbapenem resistant Enterobacterales (CRE), Acinetobacter baumannii complex and Pseudomonas aeruginosa. From 2nd July-16th September 2018, a total of 1294 (mean 16.8 ± 5.5 isolates/day) clinical isolates were tested; 1157/1294 were reported (MIC ≤2 μg/mL) within 24-h, whereas 133 required resistance confirmation by full-range BMD. Resistance was confirmed for all but 24 isolates. These discrepancies were mostly due to contamination with bacterial genera inherently resistant to colistin. CONCLUSION This BBMD plate is a high through-put and practical method that could reliably be utilized in a routine microbiology laboratory for colistin susceptibility testing of CRE, A. bauamanii complex and P. aeruginosa.
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Affiliation(s)
- Imran Ahmed
- Department of Pathology & Laboratory Medicine, Aga Khan University, Pakistan
| | | | | | - Khalid Wahab
- Department of Pathology & Laboratory Medicine, Aga Khan University, Pakistan
| | - Joveria Farooqi
- Department of Pathology & Laboratory Medicine, Aga Khan University, Pakistan
| | - Asima Shahid
- Department of Pathology & Laboratory Medicine, Aga Khan University, Pakistan
| | - Rumina Hasan
- Department of Pathology & Laboratory Medicine, Aga Khan University, Pakistan
| | - Sadia Shakoor
- Department of Pathology & Laboratory Medicine, Aga Khan University, Pakistan
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Gondal AJ, Saleem S, Jahan S, Choudhry N, Yasmin N. Novel Carbapenem-Resistant Klebsiella pneumoniae ST147 Coharboring bla NDM-1, bla OXA-48 and Extended-Spectrum β-Lactamases from Pakistan. Infect Drug Resist 2020; 13:2105-2115. [PMID: 32669863 PMCID: PMC7337428 DOI: 10.2147/idr.s251532] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 05/07/2020] [Indexed: 12/14/2022] Open
Abstract
Purpose The emergence of multidrug-resistant Klebsiella pneumoniae (K. pneumoniae) is associated with the acquisition of multiple carbapenemases. Their clonal spread is a worldwide concern due to their critical role in nosocomial infections. Therefore, the identification of high-risk clones with antibiotic resistance genes is very crucial for controlling its global spread. Materials and Methods A total of 227 K. pneumoniae strains collected during April 2018 to November 2019 were confirmed by PCR. Carbapenemases and extended-spectrum β-lactamases (ESBL) were detected phenotypically. Confirmation of carbapenemases was carried out by PCR and Sanger sequencing. The clonal lineages were assigned to selected isolates by multilocus sequence typing (MLST), and the plasmid analysis was done by PCR-based detection of the plasmid replicon typing. Results Of the total K. pneumoniae, 117 (51.5%) were carbapenem resistant (CRKP) and 140 (61.7%) were identified as ESBL producers. Intermediate to high resistance was detected in the tested β-lactam drugs while polymyxin-B and tigecycline were found to be susceptible. Among CRKP, 91 (77.8%) isolates were detected as carbapenemase producing, while 55 (47%) were positive for blaNDM-1 23.9% (n=28), blaOXA-48 22.2% (n=26) and blaVIM 0.85% (n=1) while 12.7% (n=7) carried both blaNDM-1 and blaOXA-48 genes. The CRKP coharboring blaNDM-1 and blaOXA-48 genes (n=7) were positive for blaCTX-MblaSHV (n=3), blaSHV (n=1) and blaCTX-M (n=3). The novel CRKP with the coexistence of blaNDM-1, blaOXA-48, blaCTX-M and blaSHV genes were associated with the high-risk clone ST147 (n=5) and ST11 (n=2). The assigned replicon types were IncL/M, IncFII, IncA/C and IncH1. Conclusion This is the first report of the coexistence of blaNDM-1, blaOXA-48, blaCTX-M and blaSHV genes on a high-risk lineage ST147 from Pakistan. This study highlights the successful dissemination of carbapenemase resistance genes in the high-risk clones that emphasizes the importance of monitoring and controlling the spread of these diverse clones globally.
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Affiliation(s)
- Aamir Jamal Gondal
- Department of Microbiology, University of Health Sciences, Lahore, Pakistan.,Department of Biomedical Sciences, King Edward Medical University, Lahore, Pakistan
| | - Sidrah Saleem
- Department of Microbiology, University of Health Sciences, Lahore, Pakistan
| | - Shah Jahan
- Department of Immunology, University of Health Sciences, Lahore, Pakistan
| | - Nakhshab Choudhry
- Department of Biochemistry, King Edward Medical University, Lahore, Pakistan
| | - Nighat Yasmin
- Department of Biomedical Sciences, King Edward Medical University, Lahore, Pakistan
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Loconsole D, Accogli M, De Robertis AL, Capozzi L, Bianco A, Morea A, Mallamaci R, Quarto M, Parisi A, Chironna M. Emerging high-risk ST101 and ST307 carbapenem-resistant Klebsiella pneumoniae clones from bloodstream infections in Southern Italy. Ann Clin Microbiol Antimicrob 2020; 19:24. [PMID: 32487201 PMCID: PMC7266126 DOI: 10.1186/s12941-020-00366-y] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 05/25/2020] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Carbapenem-resistant Klebsiella pneumoniae (CR-KP) is an urgent public health issue in Italy. This pattern of resistance is due mainly to dissemination of carbapenemase genes. Molecular characterization of carbapenem-resistant Klebsiella pneumoniae (CR-KP) strains was performed over a three-year period. In-depth analysis was performed on a subset of emerging CR-KP ST101 and ST307 clones. METHODS A prospective study was performed on 691 patients with CR-KP bloodstream infections hospitalized in 19 hospitals located in three large provinces in Southern Italy. Carbapenemase genes were identified via genotyping methods. Multi-locus sequence typing (MLST) and Whole Genome Sequencing (WGS) were carried out on ST101 and ST307 isolates. RESULTS Among the CR-KP isolates, blaKPC was found in 95.6%, blaVIM was found in 3.5%, blaNDM was found in 0.1% and blaOXA-48 was found in 0.1%. The blaKPC-3 variant was identified in all 104 characterized KPC-KP isolates. MLST of 231 representative isolates revealed ST512 in 45.5%, ST101 in 20.3% and ST307 in 18.2% of the isolates. cgMLST of ST307 and ST101 isolates revealed presence of more than one beta-lactam resistance gene. Amino acid substitution in the chromosomal colistin-resistance gene pmrB was found in two ST101 isolates. CONCLUSIONS ST512 is widespread in Southern Italy, but ST101 and ST307 are emerging since they were found in a significant proportion of cases. Aggressive infection control measures and a continuous monitoring of these high-risk clones are necessary to avoid rapid spread of CR-KP, especially in hospital settings.
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Affiliation(s)
- Daniela Loconsole
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Marisa Accogli
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Anna Lisa De Robertis
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Loredana Capozzi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Angelica Bianco
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Anna Morea
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Rosanna Mallamaci
- Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari "Aldo Moro", Bari, Italy
| | - Michele Quarto
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", Bari, Italy
| | - Antonio Parisi
- Istituto Zooprofilattico Sperimentale della Puglia e della Basilicata, Foggia, Italy
| | - Maria Chironna
- Department of Biomedical Sciences and Human Oncology, Hygiene Unit, University of Bari "Aldo Moro", Bari, Italy.
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Molecular Typing, Characterization of Antimicrobial Resistance, Virulence Profiling and Analysis of Whole-Genome Sequence of Clinical Klebsiella pneumoniae Isolates. Antibiotics (Basel) 2020; 9:antibiotics9050261. [PMID: 32429555 PMCID: PMC7277670 DOI: 10.3390/antibiotics9050261] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 05/12/2020] [Accepted: 05/15/2020] [Indexed: 12/14/2022] Open
Abstract
Klebsiella pneumoniae is one of the most important pathogens concerned with multidrug resistance in healthcare-associated infections. The treating of infections caused by this bacterium is complicated due to the emergence and rapid spreading of carbapenem-resistant strains, which are associated with high mortality rates. Recently, several hypervirulent and carbapenemase-producing isolates were reported that make the situation even more complicated. In order to better understand the resistance and virulence mechanisms, and, in turn, to develop effective treatment strategies for the infections caused by multidrug-resistant K. pneumoniae, more comprehensive genomic and phenotypic data are required. Here, we present the first detailed molecular epidemiology report based on second and third generation (long-read) sequencing for the clinical isolates of K. pneumoniae in the Russian Federation. The data include three schemes of molecular typing, phenotypic and genotypic antibiotic resistance determination, as well as the virulence and plasmid profiling for 36 K. pneumoniae isolates. We have revealed 2 new multilocus sequence typing (MLST)-based sequence types, 32 multidrug-resistant (MDR) isolates and 5 colistin-resistant isolates in our samples. Three MDR isolates belonged to a very rare ST377 type. The whole genome sequences and additional data obtained will greatly facilitate further investigations in the field of antimicrobial resistance studies.
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Di Tella D, Tamburro M, Guerrizio G, Fanelli I, Sammarco ML, Ripabelli G. Molecular Epidemiological Insights into Colistin-Resistant and Carbapenemases-Producing Clinical Klebsiella pneumoniae Isolates. Infect Drug Resist 2019; 12:3783-3795. [PMID: 31819559 PMCID: PMC6899070 DOI: 10.2147/idr.s226416] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Accepted: 10/02/2019] [Indexed: 01/09/2023] Open
Abstract
Purpose Carbapenemases-producing Klebsiella pneumoniae are challenging antimicrobial therapy of hospitalised patients, which is further complicated by colistin resistance. This study describes molecular epidemiological insights into colistin-resistant and carbapenemases-producing clinical K. pneumoniae. Patients and methods Cultures collected from 26 hospitalised patients during 2014-2017 in the main hospital in Molise Region, central Italy, were characterized. The minimum inhibitory concentration for 19 antibiotics was determined, including carbapenems and colistin. Prevalence of resistance-associated genes was investigated through PCR, detecting bla KPC, bla GES, bla VIM, bla IMP, bla NDM, bla OXA-48, bla CTX-M, bla TEM, bla SHV, and mcr-1,2,3,4,5,6,7,8. The mgrB gene was also analysed in colistin-resistant strains by PCR and sequencing assays. K. pneumoniae were typed by pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing (MLST). Results Twenty out of 26 K. pneumoniae were phenotypically resistant to carbapenems and 19 were resistant to colistin. All isolates harbored bla KPC, and bla SHV, bla TEM and bla VIM were further the most common resistance-associated genes. In colistin-resistant strains, mcr-1,2,3,4,5,6,7,8 variants were not detected, while mutations and insertion elements in mgrB were observed in 68.4% (n=13) in 31.6% (n=6) isolates, respectively. PFGE revealed 12 clusters and 18 pulsotypes at 85% and 95% cut-off, while the Sequence Types ST512 (n=13, 50%), ST101 (n=10, 38.5%), ST307 (n=2, 7.7%) plus a novel ST were detected using MLST. Conclusion All K. pneumoniae showed a multidrug-resistant phenotype, particularly to carbapenems and colistin. According to national data, bla KPC was the prevailing carbapenemase, followed by bla VIM, while bla TEM and bla SHV were among the most frequent beta-lactamases. Consistent with previous reports in Italy, ST512 was the most common clone, particularly during 2014-15, whilst ST101 became dominant in 2016-17. Colistin resistance was mainly associated with deleterious mutations and transposon in the mgrB gene. Improvements of surveillance, compliance with infection prevention procedures and antimicrobial stewardship are essential to limit the spread of resistant K. pneumoniae.
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Affiliation(s)
- Domiziana Di Tella
- Department of Medicine and Health Sciences "Vincenzo Tiberio", University of Molise, Campobasso, Italy
| | - Manuela Tamburro
- Department of Medicine and Health Sciences "Vincenzo Tiberio", University of Molise, Campobasso, Italy
| | - Giuliana Guerrizio
- Department of Medicine and Health Sciences "Vincenzo Tiberio", University of Molise, Campobasso, Italy
| | - Incoronata Fanelli
- Department of Medicine and Health Sciences "Vincenzo Tiberio", University of Molise, Campobasso, Italy
| | - Michela Lucia Sammarco
- Department of Medicine and Health Sciences "Vincenzo Tiberio", University of Molise, Campobasso, Italy
| | - Giancarlo Ripabelli
- Department of Medicine and Health Sciences "Vincenzo Tiberio", University of Molise, Campobasso, Italy
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Le L, Tran LK, Le-Ha TD, Tran BP, Le-Vo HN, Nguyen YN, Nguyen HL, Hoang-Ngoc KQ, Matsumoto Y, Motooka D, Nakamura S, Jones JW, Iida T, Cao V. Coexistence Of Plasmid-Mediated mcr-1 And bla NDM-4 Genes In A Klebsiella pneumoniae Clinical Strain In Vietnam. Infect Drug Resist 2019; 12:3703-3707. [PMID: 31819552 PMCID: PMC6885539 DOI: 10.2147/idr.s226612] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2019] [Accepted: 10/13/2019] [Indexed: 12/13/2022] Open
Abstract
In this study, we characterized the first clinical Klebsiella pneumoniae strain co- harboring mcr-1 and blaNDM-4 genes in Vietnam, which was recovered from a patient admitted to hospital in 2015. This strain demonstrated nonsusceptible to all tested antibiotics, including last-line antibiotics such as carbapenems (MICs ≥128 μg/mL) and colistin (MIC =32 μg/mL), except tigecycline (MIC =1 μg/mL). Whole-genome analysis using both MinION and MiSeq data revealed that the strain carried 29 resistance genes. Particularly, mcr-1 and blaNDM-4 genes were carried by different self-conjugative plasmids and able to be transferred to a recipient by conjugation. The colistin resistance of this strain was conferred by mcr-1 and additional chromosomal resistance determinants. Eight amino acid substitutions found in PmrA, PmrB, PmrC, PmrI, and PmrJ, all proteins that are involved in lipopolysaccharide modifications, may be associated with chromosomal colistin resistance. The accumulation of multiple antibiotic resistance mechanisms in this clinical isolate raises alarm on potential spread of extensively drug-resistant K. pneumoniae in healthcare settings.
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Affiliation(s)
- Lien Le
- Department of Immunology and Microbiology, Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Linh Khanh Tran
- Department of Immunology and Microbiology, Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Tam-Duong Le-Ha
- Department of Immunology and Microbiology, Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Bich-Phuong Tran
- Department of Immunology and Microbiology, Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Hong-Ngoc Le-Vo
- Department of Immunology and Microbiology, Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Yen-Nhi Nguyen
- Department of Immunology and Microbiology, Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Hanh-Lan Nguyen
- Department of Immunology and Microbiology, Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Khanh-Quynh Hoang-Ngoc
- Department of Immunology and Microbiology, Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City, Vietnam
| | - Yuki Matsumoto
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Daisuke Motooka
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Shota Nakamura
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - James W Jones
- Department of Bacterial and Parasitic Diseases, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Tetsuya Iida
- Genome Information Research Center, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Department of Bacterial Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Van Cao
- Department of Immunology and Microbiology, Pasteur Institute in Ho Chi Minh City, Ho Chi Minh City, Vietnam
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Bardhan T, Chakraborty M, Bhattacharjee B. Bactericidal Activity of Lactic Acid against Clinical, Carbapenem-Hydrolyzing, Multi-Drug-Resistant Klebsiella pneumoniae Planktonic and Biofilm-Forming Cells. Antibiotics (Basel) 2019; 8:antibiotics8040181. [PMID: 31600988 PMCID: PMC6963607 DOI: 10.3390/antibiotics8040181] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2019] [Revised: 10/01/2019] [Accepted: 10/08/2019] [Indexed: 12/15/2022] Open
Abstract
Carbapenem resistant Klebsiella pneumoniae has been highlighted to be a critical pathogen by the World Health Organization. The objectives of this study were to assess the efficacy of lactic acid (LA) against planktonic cells and biofilms formed by carbapenem-hydrolyzing K. pneumoniae isolates obtained from the nares of preterm neonates. Time-kill assays with graded percentages of (v/v) LA in water were initially carried out against planktonic cells of a meropenem (MRP)-resistant K. pneumoniae isolate, JNM11.C4. The efficacy parameters such as optimal incubation time and minimum inhibitory concentration were determined by comparing colony-forming unit counts (log(10) CFU). Scanning electron microscopy was used to visualize cell damage. Likewise, JNM11.C4 biofilms were treated with graded series of (v/v) LA. Six carbapenem-hydrolyzing isolates were next used to validate the results. A reduction of 3.6 ± 0.6 log(10) CFU/mL in JNM11.C4 planktonic cells and >3 ± 0.03log(10) CFU/mL in biofilm-forming cells were observed using 0.225% and 2% LA, respectively, after three hours. Similar decreases in viable cell-counts were observed both in the case of planktonic (˃3.6 ± 0.3log(10) CFU/mL) and biofilm-forming cells (3.8 ± 0.3log(10) CFU/mL) across all the six clinical isolates. These results indicate that LA is an effective antimicrobial against planktonic carbapenem-hydrolyzing K. pneumoniae cells and biofilms.
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Affiliation(s)
- Taniya Bardhan
- National Institute of Biomedical Genomics, Kalyani, West Bengal 741251, India
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Kopotsa K, Osei Sekyere J, Mbelle NM. Plasmid evolution in carbapenemase-producing Enterobacteriaceae: a review. Ann N Y Acad Sci 2019; 1457:61-91. [PMID: 31469443 DOI: 10.1111/nyas.14223] [Citation(s) in RCA: 121] [Impact Index Per Article: 24.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Revised: 07/22/2019] [Accepted: 07/26/2019] [Indexed: 12/17/2022]
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) have been listed by the WHO as high-priority pathogens owing to their high association with mortalities and morbidities. Resistance to multiple β-lactams complicates effective clinical management of CRE infections. Using plasmid typing methods, a wide distribution of plasmid replicon groups has been reported in CREs around the world, including IncF, N, X, A/C, L/M, R, P, H, I, and W. We performed a literature search for English research papers, published between 2013 and 2018, reporting on plasmid-mediated carbapenem resistance. A rise in both carbapenemase types and associated plasmid replicon groups was seen, with China, Canada, and the United States recording a higher increase than other countries. blaKPC was the most prevalent, except in Angola and the Czech Republic, where OXA-181 (n = 50, 88%) and OXA-48-like (n = 24, 44%) carbapenemases were most prevalent, respectively; blaKPC-2/3 accounted for 70% (n = 956) of all reported carbapenemases. IncF plasmids were found to be responsible for disseminating different antibiotic resistance genes worldwide, accounting for almost 40% (n = 254) of plasmid-borne carbapenemases. blaCTX-M , blaTEM , blaSHV , blaOXA-1/9 , qnr, and aac-(6')-lb were mostly detected concurrently with carbapenemases. Most reported plasmids were conjugative but not present in multiple countries or species, suggesting limited interspecies and interboundary transmission of a common plasmid. A major limitation to effective characterization of plasmid evolution was the use of PCR-based instead of whole-plasmid sequencing-based plasmid typing.
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Affiliation(s)
- Katlego Kopotsa
- Department of Medical Microbiology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria, Gauteng, South Africa
| | - John Osei Sekyere
- Department of Medical Microbiology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria, Gauteng, South Africa
| | - Nontombi Marylucy Mbelle
- Department of Medical Microbiology, Faculty of Health Sciences, School of Medicine, University of Pretoria, Pretoria, Gauteng, South Africa.,National Health Laboratory Service, Tshwane Division, Department of Medical Microbiology, University of Pretoria, Pretoria, Gauteng, South Africa
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Li Z, Cao Y, Yi L, Liu JH, Yang Q. Emergent Polymyxin Resistance: End of an Era? Open Forum Infect Dis 2019; 6:5550895. [PMID: 31420655 PMCID: PMC6767968 DOI: 10.1093/ofid/ofz368] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Indexed: 12/03/2022] Open
Abstract
Until recently, the polymyxin antibiotics were used sparingly due to dose limiting toxicities. However, the lack of therapeutic alternatives for infections caused by highly resistant Gram-negative bacteria has led to the increased use of the polymyxins. Unfortunately, the world has witnessed increased rates of polymyxin resistance in the last decade, which is likely in part due to its irrational use in human and veterinary medicine. The spread of polymyxin resistance has been aided by the dissemination of the transferable polymyxin-resistance gene, mcr, in humans and the environment. The mortality of colistin-resistant bacteria (CoRB) infections varies in different reports. However, poor clinical outcome was associated with prior colistin treatment, illness severity, complications, and multidrug resistance. Detection of polymyxin resistance in the clinic is possible through multiple robust and practical tests, including broth microdilution susceptibility testing, chromogenic agar testing, and molecular biology assays. There are multiple risk factors that increase a person’s risk for infection with a polymyxin-resistant bacteria, including age, prior colistin treatment, hospitalization, and ventilator support. For patients that are determined to be infected by polymyxin-resistant bacteria, various antibiotic treatment options currently exist. The rising trend of polymyxin resistance threatens patient care and warrants effective control.
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Affiliation(s)
- Zekun Li
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China.,Department of Laboratory Medicine, Xiangya School of Medicine, Central South University, Changsha, China
| | - Yuping Cao
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Lingxian Yi
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Jian-Hua Liu
- College of Veterinary Medicine, South China Agricultural University, Guangzhou, China
| | - Qiwen Yang
- Department of Clinical Laboratory, Peking Union Medical College Hospital, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China.,Beijing Key Laboratory for Mechanisms Research and Precision Diagnosis of Invasive Fungal Diseases, Beijing, China
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Niu H, Zhang W, Wei L, Liu M, Liu H, Zhao C, Zhang P, Liao Q, Liu Y, Yuan Q, Wu S, Kang M, Geng J. Rapid Nanopore Assay for Carbapenem-Resistant Klebsiella pneumoniae. Front Microbiol 2019; 10:1672. [PMID: 31417504 PMCID: PMC6682601 DOI: 10.3389/fmicb.2019.01672] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 07/08/2019] [Indexed: 02/05/2023] Open
Abstract
The prevalence of carbapenem-resistant Klebsiella pneumoniae (CRKP) is rapidly increasing worldwide in recent decades and poses a challenge for today's clinical practice. Rapid detection of CRKP can avoid inappropriate antimicrobial therapy and save lives. Traditional detection methods for CRKP are extremely time-consuming; PCR and other sequencing methods are too expensive and technologically demanding, making it hard to meet the clinical demands. Nanopore assay has been used for screening biomarkers of diseases recently because of its high sensitivity, real-time detection, and low cost. In this study, we distinguished CRKP from carbapenem-sensitive K. pneumoniae (CSKP) by the detection of increasing amount of extracted 16S ribosomal RNA (16S rRNA) from bacterial culture with antibiotics imipenem, indicating the uninhibited growth of CRKP by the imipenem. Specific signals from single channel recording of 16S rRNA bound with probes by MspA nanopore allowed the ultra-sensitive and fast quantitative detection of 16S rRNA. We proved that only 4 h of CRKP culture time was needed for nanopore assay to distinguish the CRKP and CSKP. The time-cost of the assay is only about 5% of disk diffusion method while reaching the similar accuracy. This new method has the potential application in the fast screening of drug resistance in clinical microorganism samples.
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Affiliation(s)
- Haofu Niu
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
- Department of Microbiology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Weili Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Liangwan Wei
- Department of Microbiology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Meng Liu
- Department of Microbiology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Hao Liu
- Department of Microbiology, West China School of Basic Medical Sciences and Forensic Medicine, Sichuan University, Chengdu, China
| | - Changjian Zhao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Peng Zhang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Quanfeng Liao
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Ya Liu
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Qingyue Yuan
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Siying Wu
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Mei Kang
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
| | - Jia Geng
- Department of Laboratory Medicine, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University and Collaborative Innovation Center, Chengdu, China
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Song JE, Jeong H, Lim YS, Ha EJ, Jung IY, Jeong W, Choi H, Jeong SJ, Ku NS, Park ES, Yong D, Lee K, Kim JM, Choi JY. An Outbreak of KPC-Producing Klebsiella pneumoniae Linked with an Index Case of Community-Acquired KPC-Producing Isolate: Epidemiological Investigation and Whole Genome Sequencing Analysis. Microb Drug Resist 2019; 25:1475-1483. [PMID: 31334673 DOI: 10.1089/mdr.2018.0475] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Aims: A hospital outbreak of Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae (KPN) linked with an index case of community-acquired infection occurred in an urban tertiary care hospital in Seoul, South Korea. Therefore, we performed an outbreak investigation and whole genome sequencing (WGS) analysis to trace the outbreak and investigate the molecular characteristics of the isolates. Results: From October 2014 to January 2015, we identified a cluster of three patients in the neurosurgery ward with sputum cultures positive for carbapenem-resistant KPN. An epidemiological investigation, including pulsed-field gel electrophoresis analysis was performed to trace the origins of this outbreak. The index patient's infection was community acquired. Active surveillance cultures using perirectal swabbing from exposed patients, identified one additional patient with KPC-producing KPN colonization. WGS analyses using PacBio RSII instruments were performed for four linked isolates. WGS revealed a genetic linkage of the four isolates belonging to the same sequence type (ST307). All KPN isolates harbored conjugative resistance plasmids, which has blaKPC-2 carbapenemase genes contained within the Tn4401 "a" isoform and other resistance genes. However, WGS showed only three isolates among four KPC-producing KPN were originated from a common origin. Conclusions: This report demonstrates the challenge that KPC-2-producing KPN with the conjugative resistance plasmid may spread not only in hospitals but also in community, and WGS can help to accurately characterize the outbreak.
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Affiliation(s)
- Je Eun Song
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea.,Department of Internal Medicine, Inje University Ilsan Paik Hospital, Goyang, South Korea
| | - Haeyoung Jeong
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Young Sun Lim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea.,AIDS Research Institute, Yonsei University College of Medicine, Seoul, South Korea
| | - Eun Jin Ha
- Infection Control Unit, Yonsei University College of Medicine, Seoul, South Korea
| | - In Young Jung
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Wooyong Jeong
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Heun Choi
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Su Jin Jeong
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Nam Su Ku
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea.,AIDS Research Institute, Yonsei University College of Medicine, Seoul, South Korea
| | - Eun Suk Park
- Infection Control Unit, Yonsei University College of Medicine, Seoul, South Korea
| | - Dongeun Yong
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Kyungwon Lee
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - June Myung Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea.,AIDS Research Institute, Yonsei University College of Medicine, Seoul, South Korea
| | - Jun Yong Choi
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea.,AIDS Research Institute, Yonsei University College of Medicine, Seoul, South Korea
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Kim YJ, Kim S, Kim J, Bae S. Tracking short-term changes in the genetic diversity and antimicrobial resistance of OXA-232-producing Klebsiella pneumoniae ST14 in clinical settings. Clin Microbiol Infect 2019; 26:78-86. [PMID: 31128287 DOI: 10.1016/j.cmi.2019.05.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 04/15/2019] [Accepted: 05/11/2019] [Indexed: 11/17/2022]
Abstract
OBJECTIVES To track stepwise changes in genetic diversity and antimicrobial resistance in rapidly evolving OXA-232-producing Klebsiella pneumoniae ST14, an emerging carbapenem-resistant high-risk clone, in clinical settings. METHODS Twenty-six K. pneumoniae ST14 isolates were collected by the Korean Nationwide Surveillance of Antimicrobial Resistance system over the course of 1 year. Isolates were subjected to whole-genome sequencing and MIC determinations using 33 antibiotics from 14 classes. RESULTS Single-nucleotide polymorphism (SNP) typing identified 72 unique SNP sites spanning the chromosomes of the isolates, dividing them into three clusters (I, II and III). The initial isolate possessed two plasmids with 18 antibiotic-resistance genes, including blaOXA-232, and exhibited resistance to 11 antibiotic classes. Four other plasmids containing 12 different resistance genes, including blaCTX-M-15 and strA/B, were introduced over time, providing additional resistance to aztreonam and streptomycin. Moreover, chromosomal integration of insertion sequence Ecp1-blaCTX-M-15 mediated the inactivation of mgrB responsible for colistin resistance in four isolates from cluster III. To the best of our knowledge, this is the first description of K. pneumoniae ST14 resistant to both carbapenem and colistin in South Korea. Furthermore, although some acquired genes were lost over time, the retention of 12 resistance genes and inactivation of mgrB provided resistance to 13 classes of antibiotics. CONCLUSIONS We describe stepwise changes in OXA-232-producing K. pneumoniae ST14 in vivo over time in terms of antimicrobial resistance. Our findings contribute to our understanding of the evolution of emerging high-risk K. pneumoniae clones and provide reference data for future outbreaks.
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Affiliation(s)
- Y-J Kim
- Division of Antimicrobial Resistance, Center for Infectious Diseases Research, Korea National Institute of Health, Cheongju, Republic of Korea
| | - S Kim
- Division of Antimicrobial Resistance, Center for Infectious Diseases Research, Korea National Institute of Health, Cheongju, Republic of Korea
| | - J Kim
- Division of Antimicrobial Resistance, Center for Infectious Diseases Research, Korea National Institute of Health, Cheongju, Republic of Korea
| | - S Bae
- Division of Antimicrobial Resistance, Center for Infectious Diseases Research, Korea National Institute of Health, Cheongju, Republic of Korea.
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Pishnian Z, Haeili M, Feizi A. Prevalence and molecular determinants of colistin resistance among commensal Enterobacteriaceae isolated from poultry in northwest of Iran. Gut Pathog 2019; 11:2. [PMID: 30728861 PMCID: PMC6354369 DOI: 10.1186/s13099-019-0282-0] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/24/2018] [Accepted: 01/21/2019] [Indexed: 02/07/2023] Open
Abstract
Background The emergence of colistin-resistant Enterobacteriaceae from human and animal sources is a public health concern as this antibiotic is considered to be the last line therapeutic option for infections caused by multidrug-resistant Gram-negative bacteria. Here we aimed to determine the prevalence of colistin resistance, among enterobacteria isolated from poultry and the possible underlying colistin resistance mechanisms. Methods A collection of 944 cloacal samples were obtained from poultry and screened for colistin resistance. To uncover the molecular mechanism behind colistin resistance, the presence of plasmid encoded colistin resistance genes mcr-1, mcr-2, mcr-3 and mcr-4 was examined by PCR. The nucleotide sequences of the mgrB, pmrA, pmrB, phoP, phoQ, crrA and crrB genes were determined. The genetic relatedness of the colistin resistant (ColR) isolates was evaluated by Multilocus sequence typing. Three ColR mutants were generated in vitro by repetitive drug exposure. Results Overall from 931 enteric bacteria isolated from poultry samples obtained from 131 farms, nine ColR bacteria (0.96%) with high level colistin resistance (MICs ≥ 64 mg/L) were detected all being identified as K. pneumoniae. The 9 ColR bacteria originated from different farms and belonged to 7 distinct Sequence types including ST11 (22.2%) and ST726 (22.2%) being the most prevalent STs followed by ST37, ST74, ST485, ST525 and novel sequence type 3380 (11.1% each). mcr-type genes were not detected in any isolate. In 88.8% of the isolates (n = 8), MgrB was inactivated by Insertion of IS elements (IS1-like, IS3-like, IS5-like families, positions + 75, + 113, + 117, + 135) and nonsense mutations at codons 8, 16, 30. All ColR isolates harboured wild type PmrA, PhoP, PhoQ or polymorphic variants of PmrB. Sequence analysis of the CrrB revealed a familiar S195N and 4 novel I27V, T150R, F303S and K325R substitutions. PmrB T93N substitution and mgrB locus deletion were identified in two laboratory induced ColR mutants and one mutant lacked alteration in the studied loci. In one ColR isolate with wild type MgrB an A83V substitution was detected in CrrA. Conclusion It is concluded from our results that colistin resistance in the studied avian K. pneumoniae isolates was mostly linked to alterations identified within the mgrB gene.
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Affiliation(s)
- Zeinab Pishnian
- 1Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Mehri Haeili
- 1Department of Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran
| | - Adel Feizi
- 2Department of Clinical Sciences, Faculty of Veterinary Medicine, Islamic Azad University of Tabriz, Tabriz, Iran
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Antochevis LC, Magagnin CM, Nunes AG, Goulart TM, Martins AS, Cayô R, Gales AC, Barth AL, Zavascki AP. KPC-producing Klebsiella pneumoniae bloodstream isolates from Brazilian hospitals: What (still) remains active? J Glob Antimicrob Resist 2018; 15:173-177. [PMID: 30071353 DOI: 10.1016/j.jgar.2018.07.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Revised: 07/07/2018] [Accepted: 07/18/2018] [Indexed: 01/20/2023] Open
Abstract
OBJECTIVES This study assessed susceptibility to polymyxin B (PMB) and alternative antimicrobials, with focus on aminoglycosides and tigecycline, according to different breakpoints in KPC-producing Klebsiella pneumoniae (KPC-Kp) bloodstream isolates from Brazilian hospitals. METHODS Bloodstream K. pneumoniae isolates non-susceptible to any of the three carbapenems (meropenem, imipenem or ertapenem) from four Brazilian tertiary-care hospitals were selected. Antimicrobial susceptibility was determined and interpreted according to distinct breakpoints. Twenty-nine PMB-resistant KPC-Kp isolates were selected for molecular typing. RESULTS A total of 158 KPC-Kp were analysed. MIC50/90 values for PMB were 0.25/16mg/L; 40 isolates (25.3%) were resistant to PMB. MIC50/90 values for meropenem were 32/≥256mg/L; no isolates were susceptible to meropenem according to CLSI, but 10 isolates were intermediate using EUCAST breakpoints (1, MIC=4mg/L; 9, MIC=8mg/L). MIC50/90 values for tigecycline were 2/8mg/L; 53 (33.5%) and 94 (59.5%) isolates were susceptible according to EUCAST and FDA breakpoints, respectively. MIC50/90 values were 32/≥64mg/L for amikacin and ≥16/≥16mg/L for gentamicin; 48 (30.4%), 28 (17.7%) and 16 (10.1%) were susceptible to amikacin according to CLSI, EUCAST and USCAST, respectively, but susceptibility rates to gentamicin were <7.0%. Eighteen distinct clonal profiles were identified among 29 PMB-resistant isolates by DNA macrorestriction. Most clones belonged to CC11. CONCLUSION Elevated rates of PMB-resistant KPC-Kp bloodstream infections were found in four Brazilian hospitals, mostly of polyclonal origin. Alternative antimicrobials with the highest in vitro activity were tigecycline and amikacin, although susceptibility rates significantly decreased using criteria with stricter breakpoints (e.g. EUCAST, USCAST).
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Affiliation(s)
- Laura C Antochevis
- Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil; Laboratório Weinmann-Grupo Fleury, Porto Alegre, Brazil
| | - Cibele M Magagnin
- Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil; Laboratório Weinmann-Grupo Fleury, Porto Alegre, Brazil
| | - Aline G Nunes
- Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Taíse M Goulart
- Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Amanda S Martins
- Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Rodrigo Cayô
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo, São Paulo, Brazil
| | - Ana C Gales
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo, São Paulo, Brazil
| | - Afonso L Barth
- Laboratório de Pesquisa em Resistência Bacteriana (LABRESIS), Centro de Pesquisa Experimental, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil
| | - Alexandre P Zavascki
- Department of Internal Medicine, Medical School, Universidade Federal do Rio Grande do Sul, Porto Alegre, Brazil; Infectious Diseases Service, Hospital de Clínicas de Porto Alegre, Porto Alegre, Brazil; Infectious Diseases Service, Hospital Moinhos de Vento, Porto Alegre, Brazil.
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