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Kulkarni SM, Jacob JJ, Aravind V, Praveen T, Gunasekaran K, Lal Y B, Walia K, Veeraraghavan B. Evolutionary transition of hypervirulent Klebsiella pneumoniae to multidrug-resistant hypervirulent Klebsiella pneumoniae: Indian experience. Indian J Med Microbiol 2024; 50:100619. [PMID: 38848891 DOI: 10.1016/j.ijmmb.2024.100619] [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] [Received: 03/14/2024] [Revised: 05/10/2024] [Accepted: 05/25/2024] [Indexed: 06/09/2024]
Abstract
An emerging pathotype of Klebsiella pneumoniae, initially identified in Southeast Asian countries, has now spread to multiple countries, including India. These convergent strains, carrying both resistance and virulence determinants, are classified as multidrug-resistant Hypervirulent Klebsiella pneumoniae (MDR-HvKp). Since the initial reports, there has been a concerning surge in infections caused by this pathotype globally. In this context, we aim to shed light on the evolutionary changes that have taken place in this relatively novel pathotype. Understanding these changes is crucial for devising diagnosis and targeted intervention strategies to mitigate the spread of MDR-HvKp infections.
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Affiliation(s)
| | - Jobin John Jacob
- Department of Clinical Microbiology, Christian Medical College, Vellore, India.
| | - V Aravind
- Department of Clinical Microbiology, Christian Medical College, Vellore, India.
| | - T Praveen
- Department of Clinical Microbiology, Christian Medical College, Vellore, India.
| | - Karthik Gunasekaran
- Department of Clinical Microbiology, Christian Medical College, Vellore, India.
| | - Binesh Lal Y
- Department of Clinical Microbiology, Christian Medical College, Vellore, India.
| | - Kamini Walia
- Division of Epidemiology and Communicable Diseases, Indian Council of Medical Research, New Delhi, India.
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2
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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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3
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Bhatia M, Shamanna V, Nagaraj G, Gupta P, Omar BJ, Diksha, Rohilla R, Ravikumar KL. Assessment of in vitro colistin susceptibility of carbapenem-resistant clinical Gram-negative bacterial isolates using four commercially available systems & Whole-genome sequencing: A diagnostic accuracy study. Diagn Microbiol Infect Dis 2024; 108:116155. [PMID: 38219381 DOI: 10.1016/j.diagmicrobio.2023.116155] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 10/11/2023] [Accepted: 11/30/2023] [Indexed: 01/16/2024]
Abstract
AIM To analyze the diagnostic utility of commercially available platforms and Whole-genome sequencing (WGS) for accurate determination of colistin susceptibility test results. MATERIAL & METHODS An exploratory diagnostic accuracy study was conducted in which sixty carbapenem-resistant Gram-negative bacteria were subjected to identification and AST using MALDI-TOF MS & MicroScan walkaway 96 Plus. Additional AST was performed using the BD Phoenix system and Mikrolatest colistin kit. The test isolates were subjected to Vitek-2 and WGS at CRL, Bengaluru. RESULTS There was no statistically significant agreement between the colistin susceptibility results obtained by WGS, with those of commercial phenotypic platforms. The MicroScan 96 Plus had the highest sensitivity (31 %) & NPV (77 %), and the BD Phoenix system had the highest specificity (97 %) and PPV (50 %), respectively, for determining colistin resistance. CONCLUSION The utility of WGS as a tool in AMR surveillance and validation of phenotypic AST methods should be explored further.
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Affiliation(s)
- Mohit Bhatia
- Department of Microbiology, Vardhman Mahavir Medical College & Safdarjung Hospital, New Delhi, 110029, India.
| | - Varun Shamanna
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, Karnataka 560070, India; Department of Biotechnology, NMAM Institute of Technology, Nitte, Udupi, Karnataka 574110, India
| | - Geetha Nagaraj
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, Karnataka 560070, India
| | - Pratima Gupta
- Department of Microbiology, All India Institute of Medical Sciences Deoghar, Jharkhand 814152, India
| | - Balram Ji Omar
- Department of Microbiology, All India Institute of Medical Sciences Rishikesh, Uttarakhand 249203, India
| | - Diksha
- Department of Microbiology, All India Institute of Medical Sciences Rishikesh, Uttarakhand 249203, India
| | - Ranjana Rohilla
- Department of Microbiology, Sri Guru Ram Rai Institute of Medical & Health Science, Dehradun, Uttarakhand 248001, India
| | - K L Ravikumar
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, Karnataka 560070, India
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4
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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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5
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Vinchhi R, Yelpure C, Balachandran M, Matange N. Pervasive gene deregulation underlies adaptation and maladaptation in trimethoprim-resistant E. coli. mBio 2023; 14:e0211923. [PMID: 38032208 PMCID: PMC10746255 DOI: 10.1128/mbio.02119-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 10/17/2023] [Indexed: 12/01/2023] Open
Abstract
IMPORTANCE Bacteria employ a number of mechanisms to adapt to antibiotics. Mutations in transcriptional regulators alter the expression levels of genes that can change the susceptibility of bacteria to antibiotics. Two-component signaling proteins are a major class of signaling molecule used by bacteria to regulate transcription. In previous work, we found that mutations in MgrB, a feedback regulator of the PhoQP two-component system, conferred trimethoprim tolerance to Escherichia coli. Here, we elucidate how mutations in MgrB have a domino-like effect on the gene regulatory network of E. coli. As a result, pervasive perturbation of gene regulation ensues. Depending on the environmental context, this pervasive deregulation is either adaptive or maladaptive. Our study sheds light on how deregulation of gene expression can be beneficial for bacteria when challenged with antibiotics, and why regulators like MgrB may have evolved in the first place.
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Affiliation(s)
- Rhea Vinchhi
- Department of Biology, Indian Institute of Science Education and Research, Pashan, Pune, India
| | - Chetna Yelpure
- Department of Biology, Indian Institute of Science Education and Research, Pashan, Pune, India
| | - Manasvi Balachandran
- Department of Biology, Indian Institute of Science Education and Research, Pashan, Pune, India
| | - Nishad Matange
- Department of Biology, Indian Institute of Science Education and Research, Pashan, Pune, India
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6
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Biswas U, Das S, Barik M, Mallick A. Situation Report on mcr-Carrying Colistin-Resistant Clones of Enterobacterales: A Global Update Through Human-Animal-Environment Interfaces. Curr Microbiol 2023; 81:12. [PMID: 37989899 DOI: 10.1007/s00284-023-03521-8] [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: 07/10/2023] [Accepted: 10/10/2023] [Indexed: 11/23/2023]
Abstract
In the twenty-first century, antibiotic resistance (ABR) is one of the acute medical emergencies around the globe, overwhelming human-animal-environmental interfaces. Hit-or-mis use of antibiotics exacerbates the crisis of ABR, dispersing transferable resistance traits and challenging treatment regimens based on life-saving drugs such as colistin. Colistin is the highest priority critically important antimicrobials for human medicine, but its long use as a growth promoter in animal husbandry reduces clinical efficacy. Since 2015, the emergence and spread of mobile colistin resistance (mcr)-carrying colistin-resistant clones of Enterobacterales have been markedly sustained in both humans and animals, especially in developing countries. Hospital and community transmissions of mcr clones pose a high risk for infection prevention and outbreaks at the national and international levels. Several public health and limited one health studies have highlighted the genomic insights of mcr clones, clarifying the chromosomal sequence types (STs) and plasmid incompatibility (Inc) types. But this information is segregated into humans and animals, and rarely are environmental sectors complicating the understanding of possibly intercontinental and sectoral transmission of these clones. India is the hotspot for superbugs, including mcr-carrying colistin-resistant isolates that threaten cross-border transmission. The current review provided an up-to-date worldwide scenario of mcr-carrying STs and plasmid Inc types among the Gram-negative bacilli of Enterobacterales across human-animal-environmental interfaces and correlated with the available information from India.
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Affiliation(s)
- Urmy Biswas
- Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Surojit Das
- Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India.
| | - Mili Barik
- Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India
| | - Abhi Mallick
- Biomedical Laboratory Science and Management, Vidyasagar University, Midnapore, West Bengal, 721102, India
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7
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Shen C, Lv T, Huang G, Zhang X, Zheng L, Chen Y. Genomic Insights Into Molecular Characteristics and Phylogenetic Linkage Between the Cases of Carbapenem-Resistant Klebsiella pneumoniae From a Non-tertiary Hospital in China: A Cohort Study. Jundishapur J Microbiol 2023. [DOI: 10.5812/jjm-133210] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/30/2023] Open
Abstract
Background: Carbapenem-resistant Klebsiella pneumoniae (CRKP) strains have been listed as one of the major clinical concerns. Objectives: We investigated CPKP isolates from non-tertiary hospitals to find disseminated clones and analyze extensive phenotypic and genetic diversity in this study. Methods: In this cohort study, a total of 49 CRKP isolates from 3 hospitals in the same region were collected in 2021. The prevalence and antimicrobial susceptibility patterns were analyzed. Clinical data were retrieved from electronic medical record systems. The molecular types, antimicrobial resistance (AMR) profiles, plasmid replicons, and virulence factors were analyzed. The maximum-likelihood phylogenetic tree and transmission networks were constructed using single-nucleotide polymorphisms (SNPs). Results: The median age of patients (N = 49) was 66.0 years, and 85.7% were male. The most common CRKP infection was nosocomial pneumonia (75.5%), followed by bacteremia (10.2%). More than 53% of isolates were resistant to ceftazidime-avibactam (CAZ/AVI). Forty-five isolates were successfully sequenced; the predominant carbapenem-resistant gene was blaKPC-2 (93.3%). The 30-day mortality in our cohort was 24.5%. The most dominant sequence type (ST) was ST11 (60.0%), followed by ST15 (13.3%). Whole genome sequencing (WGS) analysis exhibited dissemination of ST11 strain clones, ST420, and ST15 clones, both within and outside the given hospital. Conclusions: In this surveillance study, several dissemination chains of CRKP were discovered in the hospital and the region, as ST11 was the main epidemic clone. Our findings suggest that effective infection control practices and antimicrobial stewardship are needed in non-tertiary hospitals in China.
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8
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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: 10] [Impact Index Per Article: 5.0] [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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9
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Global Prevalence of Colistin Resistance in Klebsiella pneumoniae from Bloodstream Infection: A Systematic Review and Meta-Analysis. Pathogens 2022; 11:pathogens11101092. [PMID: 36297149 PMCID: PMC9607870 DOI: 10.3390/pathogens11101092] [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: 08/27/2022] [Revised: 09/19/2022] [Accepted: 09/20/2022] [Indexed: 11/18/2022] Open
Abstract
Background: Among gram-negative bacteria, Klebsiella pneumoniae is one of the most common causes of healthcare-related infection. Bloodstream infections (BSIs) caused by Klebsiella pneumoniae are notorious for being difficult to treat due to resistance to commonly used antimicrobials. Klebsiella pneumoniae isolates from bloodstream infections are becoming increasingly resistant to carbapenems. In the fight against carbapenem-resistant Klebsiella pneumoniae, colistin [polymyxin E] is the antimicrobial of choice and is thus widely used. Objective: This study aimed to determine the global prevalence of colistin resistance amongst Klebsiella pneumoniae isolates from bloodstream infections. Methods: PubMed, Medline, Scopus, and the Cochrane Library were searched for published articles without restricting the search period. Studies meeting the predefined inclusion and exclusion criteria were included, and quality was assessed using Joanna Briggs Institute Checklist. We used a statistical random effect model to analyze data with substantial heterogeneity (I2 > 50%) in the meta-analysis. Results: A total of 10 studies out of 2873 search results that met the inclusion criteria were included in the final synthesis for this study. A pooled prevalence of colistin resistance was 3.1%, 95% CI (1.5−4.7%). The highest colistin resistance pooled prevalence was recorded in isolates studied in 2020 and beyond 12.90% (4/31), while Klebsiella pneumoniae isolates studied in 2015 and before and in 2016−2019 showed a pooled colistin resistance rate of 2.89% (48/1661) and 2.95% (28/948), respectively. The highest colistin resistance was found in Klebsiella pneumoniae isolates from Thailand (19.2%), while the least pooled resistance was in Klebsiella pneumoniae from South Korea (0.8%). The pooled prevalence of the multidrug-resistant (MDR) of Klebsiella pneumoniae from bloodstream infection ranged from 80.1%, 95% CI (65.0−95.2%), and the resistance prevalence of other antibiotics by Klebsiella pneumoniae from bloodstream infections were as follows; ciprofloxacin (45.3%), ertapenem (44.4%), meropenem (36.1%), imipenem (35.2%), gentamicin (33.3%), amikacin (25.4%) and tigecycline (5.1%). Klebsiella pneumoniae recovered from the intensive care unit (ICU) showed higher colistin resistance, 11.5% (9/781%), while non-ICU patients showed 3.03% (80/2604) pooled colistin resistance. Conclusion: This study showed low colistin resistance in Klebsiella pneumoniae isolates from global bloodstream infections. However, significant colistin resistance was observed in isolates collected from 2020 and beyond. Significant colistin resistance was also observed in Klebsiella pneumoniae isolates in bloodstream infections from the intensive care unit (ICU) compared to those from non-ICUs. As a result, there is a need to institute colistin administration stewardship in the ICU in clinical settings.
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10
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Isler B, Özer B, Çınar G, Aslan AT, Vatansever C, Falconer C, Dolapçı İ, Şimşek F, Tülek N, Demirkaya H, Menekşe Ş, Akalin H, Balkan İİ, Aydın M, Tigen ET, Demir SK, Kapmaz M, Keske Ş, Doğan Ö, Arabacı Ç, Yağcı S, Hazırolan G, Bakır VO, Gönen M, Chatfield MD, Forde B, Saltoğlu N, Azap A, Azap Ö, Akova M, Paterson DL, Can F, Ergönül Ö. Characteristics and outcomes of carbapenemase harbouring carbapenem-resistant Klebsiella spp. bloodstream infections: a multicentre prospective cohort study in an OXA-48 endemic setting. Eur J Clin Microbiol Infect Dis 2022; 41:841-847. [PMID: 35301623 DOI: 10.1007/s10096-022-04425-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2021] [Accepted: 02/15/2022] [Indexed: 11/03/2022]
Abstract
A prospective, multicentre observational cohort study of carbapenem-resistant Klebsiella spp. (CRK) bloodstream infections was conducted in Turkey from June 2018 to June 2019. One hundred eighty-seven patients were recruited. Single OXA-48-like carbapenemases predominated (75%), followed by OXA-48-like/NDM coproducers (16%). OXA-232 constituted 31% of all OXA-48-like carbapenemases and was mainly carried on ST2096. Thirty-day mortality was 44% overall and 51% for ST2096. In the multivariate cox regression analysis, SOFA score and immunosuppression were significant predictors of 30-day mortality and ST2096 had a non-significant effect. All OXA-48-like producers remained susceptible to ceftazidime-avibactam.
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Affiliation(s)
- Burcu Isler
- Centre for Clinical Research, University of Queensland, Brisbane, Australia
| | - Berna Özer
- Clinical Microbiology, School of Medicine, Koç University, Istanbul, Turkey
| | - Güle Çınar
- Infectious Diseases and Clinical Microbiology, Ankara University School of Medicine, Ankara, Turkey
| | - Abdullah Tarık Aslan
- Infectious Diseases and Clinical Microbiology, Hacettepe University School of Medicine, Ankara, Turkey
| | - Cansel Vatansever
- Clinical Microbiology, School of Medicine, Koç University, Istanbul, Turkey
| | - Caitlin Falconer
- Centre for Clinical Research, University of Queensland, Brisbane, Australia
| | - İştar Dolapçı
- Clinical Microbiology, Ankara University School of Medicine, Ankara, Turkey
| | - Funda Şimşek
- Infectious Diseases and Clinical Microbiology, University of Health Sciences, Ministry of Health Prof Dr Cemil Taşçıoğlu City Hospital, Istanbul, Turkey
| | - Necla Tülek
- Infectious Diseases and Clinical Microbiology, Faculty of Medicine, Atilim University, Ankara, Turkey
| | - Hamiyet Demirkaya
- Infectious Diseases and Clinical Microbiology, Başkent University, Ankara Hospital, Ankara, Turkey
| | - Şirin Menekşe
- Infectious Diseases, Koşuyolu Kartal Heart Training and Research Hospital, Istanbul, Turkey
| | - Halis Akalin
- Infectious Diseases and Clinical Microbiology, Uludağ University School of Medicine, Bursa, Turkey
| | - İlker İnanç Balkan
- Infectious Diseases and Clinical Microbiology, School of Medicine, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - Mehtap Aydın
- Infectious Diseases and Clinical Microbiology, Ümraniye Training and Research Hospital, University of Health Sciences, Istanbul, Turkey
| | - Elif Tükenmez Tigen
- Infectious Diseases and Clinical Microbiology, Marmara University, Pendik Training and Research Hospital, Istanbul, Turkey
| | - Safiye Koçulu Demir
- Infectious Diseases and Clinical Microbiology, Demiroglu Bilim University, Istanbul, Turkey
| | - Mahir Kapmaz
- Infectious Diseases and Clinical Microbiology, Koç University Hospital, Istanbul, Turkey
| | - Şiran Keske
- Infectious Diseases, School of Medicine, Koç University, Rumelifeneri, 34450, Sarıyer, Istanbul, Turkey.,Koç University İş Bank Centre for Infectious Diseases (KUISCID), Istanbul, Turkey
| | - Özlem Doğan
- Clinical Microbiology, School of Medicine, Koç University, Istanbul, Turkey
| | - Çiğdem Arabacı
- Clinical Microbiology, University of Health Sciences, Ministry of Health Prof Dr Cemil Taşçıoğlu City Hospital, Istanbul, Turkey
| | - Serap Yağcı
- Clinical Microbiology, Ankara Training and Research Hospital, Ankara, Turkey
| | - Gülşen Hazırolan
- Clinical Microbiology, Hacettepe University School of Medicine, Ankara, Turkey
| | - Veli Oğuzalp Bakır
- Graduate School of Sciences and Engineering, Koç University, Istanbul, Turkey
| | - Mehmet Gönen
- Industrial Engineering, College of Engineering, Koç University, Istanbul, Turkey.,Infectious Diseases, School of Medicine, Koç University, Rumelifeneri, 34450, Sarıyer, Istanbul, Turkey
| | - Mark D Chatfield
- Centre for Clinical Research, University of Queensland, Brisbane, Australia
| | - Brian Forde
- Centre for Clinical Research, University of Queensland, Brisbane, Australia
| | - Neşe Saltoğlu
- Infectious Diseases and Clinical Microbiology, School of Medicine, Istanbul University-Cerrahpaşa, Istanbul, Turkey
| | - Alpay Azap
- Infectious Diseases and Clinical Microbiology, Ankara University School of Medicine, Ankara, Turkey
| | - Özlem Azap
- Infectious Diseases and Clinical Microbiology, Başkent University, Ankara Hospital, Ankara, Turkey
| | - Murat Akova
- Infectious Diseases and Clinical Microbiology, Hacettepe University School of Medicine, Ankara, Turkey
| | - David L Paterson
- Centre for Clinical Research, University of Queensland, Brisbane, Australia
| | - Füsun Can
- Clinical Microbiology, School of Medicine, Koç University, Istanbul, Turkey.,Koç University İş Bank Centre for Infectious Diseases (KUISCID), Istanbul, Turkey
| | - Önder Ergönül
- Infectious Diseases, School of Medicine, Koç University, Rumelifeneri, 34450, Sarıyer, Istanbul, Turkey. .,Koç University İş Bank Centre for Infectious Diseases (KUISCID), Istanbul, Turkey.
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11
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Salvia T, Dolma KG, Dhakal OP, Khandelwal B, Singh LS. Phenotypic Detection of ESBL, AmpC, MBL, and Their Co-occurrence among MDR Enterobacteriaceae Isolates in a Tertiary Care Hospital in Sikkim, India. J Lab Physicians 2022; 14:329-335. [PMID: 36119416 PMCID: PMC9473942 DOI: 10.1055/s-0042-1744239] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Abstract
Background Emergence of extended-spectrum beta-lactamases (ESBLs), AmpC β-lactamases, and metallo-β lactamases (MBL), and their co-existence among members of Enterobacteriaceae pose newer diagnostic and therapeutic challenges. The present study examines the ESBL, AmpC, and MBL production by various phenotypic methods and their co-occurrence among the multidrug-resistant (MDR) Enterobacteriaceae clinical isolates.
Materials and Methods Four hundred non-repetitive Enterobacteriaceae clinical isolates were collected from the Central Referral Hospital, Sikkim. The isolates were used for identification and their antibiotic susceptibility tests were performed according to the Clinical and Laboratory Standard Institute (CLSI) guidelines. ESBL was detected by double-disc synergy test (DDST) and phenotypic confirmatory disc-diffusion test (PCDDT), AmpC detection by AmpC E-test, and boronic acid disc diffusion (BD) test. MBL was detected using the imipenem–imipenem/EDTA disc and carba-NP tests.
Results Around 76% were considered MDR. ESBL was seen in 58% and 50.4% based on DDST and phenotypic confirmation disc-diffusion test (PCDDT), respectively. AmpC was detected in 11.8% and 13.1% using a commercial E-test and boronic acid test, respectively. MBL were identified in 12.8% and 14.8% based on MBL imipenem-EDTA and carba-NP tests, respectively. Co-occurrence of ESBL and AmpC, ESBL and MBL, AmpC and MBL was seen in 5.2%, 11.5%, 1.3%, respectively, whereas a combination of these three β-lactamases was observed in only 0.3% of 304 MDR isolates.
Conclusion The findings highlight a high prevalence of β-lactamases and their co-production among the Enterobacteriaceae, mainly in Klebsiella pneumoniae and Escherichia coli isolates. The study further highlights the necessity to identify the MDR β-lactamases stains for effective therapy in severe as well as mild bacterial infections, thereby enabling to reduce the risk of MDR in hospital and community settings.
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Affiliation(s)
- Thounaojam Salvia
- Department of Microbiology, Sikkim Manipal Institute of Medical Sciences, Sikkim Manipal University, Tadong, Gangtok, Sikkim, India
| | - Karma G. Dolma
- Department of Microbiology, Sikkim Manipal Institute of Medical Sciences, Sikkim Manipal University, Tadong, Gangtok, Sikkim, India
| | - Om Prakash Dhakal
- Department of Medicine, Sikkim Manipal Institute of Medical Sciences, Sikkim Manipal University, Tadong, Gangtok, Sikkim, India
| | - Bidita Khandelwal
- Department of Medicine, Sikkim Manipal Institute of Medical Sciences, Sikkim Manipal University, Tadong, Gangtok, Sikkim, India
| | - Laishram Shantikumar Singh
- Department of Microbiology, Assam Down Town University, Guwahati 781026, Assam, India
- Microbial Resource Division, Institute of Bioresources and Sustainable Development (IBSD) Sikkim Centre, DBT, Tadong, Gangtok, Sikkim, India
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Designing Anti-Microbial Peptides Against Major β-Lactamase Enzymes in Clinically Important Gram-Negative Bacterial Pathogens: An In-Silico Study. Probiotics Antimicrob Proteins 2022; 14:263-276. [PMID: 35188617 DOI: 10.1007/s12602-022-09929-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/11/2022] [Indexed: 12/29/2022]
Abstract
Anti-microbial resistance (AMR) creating healthcare concerns worldwide requires ardent exploration of therapeutic alternatives. Although anti-microbial peptides (AMP) are popular for broad-spectrum activity, recent evidence of increasing resistance to membrane-acting AMPs by ESKAPE pathogens has compelled us to design novel AMPs as therapeutic candidates. A library of 60 AMPs comprising natural AMPs and their mutants was constructed through in-silico methods. After physico-chemical property evaluations, each peptide in the library was subjected to flexible molecular docking against four major β-lactamases in Gram-negative ESKAPE pathogens. Among the potent AMP mutants, a Lactoferricin B-Mutant (M4) possessed uniformly high affinity with SHV1, OXA48, NDM1, and AmpC having energies -842.0Kcal/mol, -774.8Kcal/mol, -1103.3Kcal/mol, and -858.8Kcal/mol respectively. Coarse-grained clustering and flexibility analysis further accounted for the residue-level stable configurations of the protein-peptide complexes with high affinity. Highest affinity of Lactoferricin B_M4 was found with NDM1 due to H-bonds, salt-bridges, and hydrophobic interactions with the metallo-β-lactamase domain including crucial active-site residue Asp124. Molecular dynamics simulation further confirmed the stability of Lactoferricin B_M4-NDM1 complex having low residue-level root-mean square deviations (RMSD), atomic-level fluctuations, and radius of gyration (Rg). The study encourages experimental validations and similar methods to identify potential AMPs against drug-resistant pathogens.
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Fordham SME, Mantzouratou A, Sheridan E. Prevalence of insertion sequence elements in plasmids relating to mgrB gene disruption causing colistin resistance in Klebsiella pneumoniae. Microbiologyopen 2022; 11:e1262. [PMID: 35212479 PMCID: PMC8796155 DOI: 10.1002/mbo3.1262] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2021] [Accepted: 01/04/2022] [Indexed: 12/05/2022] Open
Abstract
Colistin is a last resort antibiotic for the treatment of carbapenemase producing Klebsiella pneumoniae. The disruption of the mgrB gene by insertion sequences (ISs) is a mechanism mediating colistin resistance. Plasmids encode mobilizable IS elements which integrate into the mgrB gene in K. pneumoniae causing gene inactivation and colistin resistance. The species prevalence of mgrB-gene disrupting insertion elements ISL3 (ISKpn25), IS5 (ISKpn26), ISKpn14, and IS903B present on plasmids were assessed. IS containing plasmids were also scanned for antimicrobial resistance genes, including carbapenem resistant genes. Plasmids encoding ISs are abundant in K. pneumoniae. IS903B was found in 28 unique Inc groups, while ISKpn25 was largely carried by IncFIB(pQil) plasmids. ISKpn26 and ISKpn14 were most often found associated with IncFII(pHN7A8) plasmids. Of the 34 unique countries which contained any of the IS elements, ISKpn25 was identified from 26. ISKpn26, ISKpn14, and IS903B ISs were identified from 89.3%, 44.9%, and 23.9% plasmid samples from China. Plasmids carrying ISKpn25, ISKpn14, and ISKpn26 IS have a 4.6-, 6.0-, and 6.6-fold higher carbapenemase gene count, respectively, relative to IS903B-carrying plasmids. IS903B bearing plasmids have a 20-, 5-, and 5-fold higher environmental source isolation count relative to ISKpn25, ISKpn14, and ISKpn26 bearing plasmids. ISKpn25 present on IncFIB(pQil) sourced from clinical settings is established across multiple countries, while ISKpn26, ISKpn14, and IS903B appear most often in China. Carbapenemase presence in tandem with IS elements may help promote an extensively drug resistant profile in K. pneumoniae limiting already narrow treatment options.
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Affiliation(s)
| | - Anna Mantzouratou
- Department of Life & Environmental SciencesBournemouth UniversityPooleUK
| | - Elizabeth Sheridan
- Department of Medical MicrobiologyUniversity Hospitals Dorset NHS Foundation Trust, Poole HospitalPooleUK
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14
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Bhatia M, Shamanna V, Nagaraj G, Sravani D, Gupta P, Omar BJ, Chakraborty D, Ravikumar KL. Molecular characterisation of carbapenem-resistant Klebsiella pneumoniae clinical isolates: preliminary experience from a tertiary care teaching hospital in the Himalayas. Trans R Soc Trop Med Hyg 2022; 116:655-662. [PMID: 35029688 PMCID: PMC9259183 DOI: 10.1093/trstmh/trab189] [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: 09/18/2021] [Revised: 11/13/2021] [Accepted: 12/21/2021] [Indexed: 01/16/2023] Open
Abstract
BACKGROUND There is a lack of whole-genome sequencing (WGS) data on multidrug-resistant (MDR) bacteria from the Uttarakhand region of India. The aim of this study was to generate WGS data of carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates recovered from patients in Uttarakhand's tertiary care centre. METHODS A cross-sectional study included 29 MDR K. pneumoniae test isolates obtained from various clinical samples submitted to the bacteriology laboratory for culture and sensitivity testing from July 2018 to August 2019. After preliminary identification and antibiotic susceptibility testing, these isolates were subjected to WGS. RESULTS A total of 27 of 29 isolates were CRKP. ST14 was the most common sequence type (n=8 [29.6%]). Carbapenem resistance was mainly encoded by OXA-48-like genes (21/27 [77.8%]). All isolates had a varied arsenal of resistance genes to different antibiotic classes. KL2 (9/27 [33.3%]) and KL51 (8/27 [29.6%]) were dominant K loci types. O1 and O2 together accounted for 88.9% (n=27) of CRKP isolates. Genes encoding yersiniabactin (ybt) and aerobactin (iuc) were identified in 88.9% (24/27) and 29.6% (8/27) of isolates. The predominant plasmid replicons present were ColKP3 (55.5%), IncFII(K) (51.8%) and IncFIB(pQil) (44.4%). CONCLUSIONS This study emphasises the need for continued genomic surveillance of MDR bacteria that could be instrumental in developing treatment guidelines based on integrating phenotypic and molecular methods.
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Affiliation(s)
- Mohit Bhatia
- Corresponding author: Tel: +918750549280; E-mail: ;
| | - Varun Shamanna
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, Karnataka, India 560070
| | - Geetha Nagaraj
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, Karnataka, India 560070
| | - Dharmavaram Sravani
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, Karnataka, India 560070
| | - Pratima Gupta
- Department of Microbiology, All India Institute of Medical Sciences Rishikesh, Uttarakhand, India 249203
| | - Balram Ji Omar
- Department of Microbiology, All India Institute of Medical Sciences Rishikesh, Uttarakhand, India 249203
| | - Deepika Chakraborty
- Department of Microbiology, All India Institute of Medical Sciences Rishikesh, Uttarakhand, India 249203
| | - K L Ravikumar
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, Karnataka, India 560070
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15
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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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Bakthavatchalam YD, Routray A, Mane A, Kamat S, Gupta A, Bari AK, Rohit A, Poojary A, Mukherjee DN, Sethuraman N, Munshi N, Shah S, Balaji V, Gupta Y. nIn vitro activity of ceftazidime – avibactam and its comparators against carbapenem resistant collected across India: Results from ATLAS surveillance 2018-2019. Diagn Microbiol Infect Dis 2022; 103:115652. [DOI: 10.1016/j.diagmicrobio.2022.115652] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2021] [Revised: 01/07/2022] [Accepted: 01/20/2022] [Indexed: 11/15/2022]
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17
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Das A, Sahoo RK, Gaur M, Dey S, Sahoo S, Sahu A, Behera DU, Dixit S, Jain PS, Jain B, Sahu KK, Kumari KS, Subudhi E. Molecular prevalence of resistance determinants, virulence factors and capsular serotypes among colistin resistance carbapenemase producing Klebsiella pneumoniae: a multi-centric retrospective study. 3 Biotech 2022; 12:30. [PMID: 35070620 PMCID: PMC8714614 DOI: 10.1007/s13205-021-03056-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Accepted: 11/05/2021] [Indexed: 01/03/2023] Open
Abstract
The emergence of colistin-carbapenem-resistant Klebsiella pneumoniae (CCR-Kp) in bloodstream infection results in high mortality, and virulence factor contributes further to the difficulty of treatment. A total of 158 carbapenem-resistant K. pneumoniae (CRKP) isolates causing bloodstream infection were collected from three Indian tertiary care hospitals during the 9-month study period, of which 27 isolates exhibited resistance to both colistin and carbapenem antibiotics. In this study, all the strains were characterized for antimicrobial resistance, virulence factors and capsular serotypes that facilitate the development of colistin and carbapenem-resistant K.pneumoniae (CCR-Kp) in bloodstream infection. Fourteen isolates displayed extremely drug resistance (XDR), susceptible only to tigecycline, and the remaining 13 isolates displayed multidrug resistance (MDR). The gene prevalence analysis for CCR-Kp isolates showed the predominance of bla KPC (81.48%) followed by bla NDM (62.96%), bla VIM (37.03%) and bla IMP (18.51%) genes. The distribution of virulence genes was found to be fimH (81.48%), wabG (59.25%), mrkD (55.56%), entB (48.15%), irp1 (33.33%), and rmpA (18.52%). The capsular serotypes K1, K2, K5 and K54 have been identified in 16 isolates. The absence of plasmid-mediated colistin resistance (mcr) genes implies the involvement of other mechanisms. The ERIC and (GTG)5 molecular typing methods detected 18 and 22 distinct clustering patterns among the CCR-Kp isolates, respectively. A strong correlation between ERIC and (GTG)5 genotyping method was established with antimicrobial resistance patterns and virulence determinants at P < 0.05, while no correlation was found with capsular serotyping. Similar virulence and resistance typing among the isolates suggest hospital-acquired infection in a health care setup. These outcomes will advance our awareness of CCR-Kp outbreaks associated with tertiary care hospitals and help forecast their occurrence in the near future. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-03056-4.
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Affiliation(s)
- Aradhana Das
- Centre for Biotechnology, Siksha O Anusandhan (Deemed to be University), Khandagiri, Bhubaneswar, Odisha 751003 India
| | - Rajesh Kumar Sahoo
- Centre for Biotechnology, Siksha O Anusandhan (Deemed to be University), Khandagiri, Bhubaneswar, Odisha 751003 India
| | - Mahendra Gaur
- Centre for Biotechnology, Siksha O Anusandhan (Deemed to be University), Khandagiri, Bhubaneswar, Odisha 751003 India
| | - Suchanda Dey
- Centre for Biotechnology, Siksha O Anusandhan (Deemed to be University), Khandagiri, Bhubaneswar, Odisha 751003 India
| | - Saubhagini Sahoo
- Centre for Biotechnology, Siksha O Anusandhan (Deemed to be University), Khandagiri, Bhubaneswar, Odisha 751003 India
| | - Anshuman Sahu
- Centre for Biotechnology, Siksha O Anusandhan (Deemed to be University), Khandagiri, Bhubaneswar, Odisha 751003 India
| | - Dibyajyoti Uttameswar Behera
- Centre for Biotechnology, Siksha O Anusandhan (Deemed to be University), Khandagiri, Bhubaneswar, Odisha 751003 India
| | - Sangita Dixit
- Centre for Biotechnology, Siksha O Anusandhan (Deemed to be University), Khandagiri, Bhubaneswar, Odisha 751003 India
| | | | - Bhawana Jain
- Vivekananda Polyclinic and Institute of Medical Sciences, Lucknow, Uttar Pradesh 226007 India
| | - Kundan Kumar Sahu
- Institute of Medical Sciences and SUM Hospital, Siksha O Anusandhan (Deemed to be University), Bhubaneswar, Odisha 751003 India
| | - K. Swapna Kumari
- Institute of Dental Science, Siksha O Anusandhan (Deemed to be University), Bhubaneswar, Odisha 751003 India
| | - Enketeswara Subudhi
- Centre for Biotechnology, Siksha O Anusandhan (Deemed to be University), Khandagiri, Bhubaneswar, Odisha 751003 India
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18
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Tartor YH, Abd El-Aziz NK, Gharieb RMA, El Damaty HM, Enany S, Soliman EA, Abdellatif SS, Attia ASA, Bahnass MM, El-Shazly YA, Elbediwi M, Ramadan H. Whole-Genome Sequencing of Gram-Negative Bacteria Isolated From Bovine Mastitis and Raw Milk: The First Emergence of Colistin mcr- 10 and Fosfomycin fosA5 Resistance Genes in Klebsiella pneumoniae in Middle East. Front Microbiol 2021; 12:770813. [PMID: 34956131 PMCID: PMC8692987 DOI: 10.3389/fmicb.2021.770813] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 11/01/2021] [Indexed: 01/10/2023] Open
Abstract
Antimicrobial resistance is a major concern in the dairy industry. This study investigated the prevalence, antimicrobial resistance phenotypes, and genome sequencing of Gram-negative bacteria isolated from clinical (n = 350) and subclinical (n = 95) bovine mastitis, and raw unpasteurized milk (n = 125). Klebsiella pneumoniae, Aeromonas hydrophila, Enterobacter cloacae (100% each), Escherichia coli (87.78%), and Proteus mirabilis (69.7%) were the most prevalent multidrug-resistant (MDR) species. Extensive drug-resistance (XDR) phenotype was found in P. mirabilis (30.30%) and E. coli (3.33%) isolates. Ten isolates (four E. coli, three Klebsiella species and three P. mirabilis) that displayed the highest multiple antibiotic resistance (MAR) indices (0.54–0.83), were exposed to whole-genome sequencing (WGS). Two multilocus sequence types (MLST): ST2165 and ST7624 were identified among the sequenced E. coli isolates. Three E. coli isolates (two from clinical mastitis and one from raw milk) belonging to ST2165 showed similar profile of plasmid replicon types: IncFIA, IncFIB, IncFII, and IncQ1 with an exception to an isolate that contained IncR, whereas E. coli ST7624 showed a different plasmid profile including IncHI2, IncHI2A, IncI1α, and IncFII replicon types. ResFinder findings revealed the presence of plasmid-mediated colistin mcr-10 and fosfomycin fosA5 resistance genes in a K. pneumoniae (K1) isolate from bovine milk. Sequence analysis of the reconstructed mcr-10 plasmid from WGS of K1 isolate, showed that mcr-10 gene was bracketed by xerC and insertion sequence IS26 on an IncFIB plasmid. Phylogenetic analysis revealed that K1 isolate existed in a clade including mcr-10-harboring isolates from human and environment with different STs and countries [United Kingdom (ST788), Australia (ST323), Malawi (ST2144), Myanmar (ST705), and Laos (ST2355)]. This study reports the first emergence of K. pneumoniae co-harboring mcr-10 and fosA5 genes from bovine milk in the Middle East, which constitutes a public health threat and heralds the penetration of the last-resort antibiotics. Hence, prudent use of antibiotics in both humans and animals and antimicrobial surveillance plans are urgently required.
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Affiliation(s)
- Yasmine H Tartor
- Microbiology Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Norhan K Abd El-Aziz
- Microbiology Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Rasha M A Gharieb
- Zoonoses Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Hend M El Damaty
- Animal Medicine Department (Infectious Diseases), Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Shymaa Enany
- Microbiology and Immunology Department, Faculty of Pharmacy, Suez Canal University, Ismailia, Egypt
| | - Enas A Soliman
- Bacteriology, Immunology and Mycology Department, Faculty of Veterinary Medicine, Benha University, Benha, Egypt
| | - Samah S Abdellatif
- Food Control Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Amira S A Attia
- Veterinary Public Health Department, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Mosa M Bahnass
- Animal Medicine Department (Infectious Diseases), Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Yousry A El-Shazly
- Veterinary Hospital, Faculty of Veterinary Medicine, Zagazig University, Zagazig, Egypt
| | - Mohammed Elbediwi
- Animal Health Research Institute, Agriculture Research Center, Cairo, Egypt.,Institute of Veterinary Sciences, Department of Veterinary Medicine, College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Hazem Ramadan
- Hygiene and Zoonoses Department, Faculty of Veterinary Medicine, Mansoura University, Mansoura, Egypt.,Bacterial Epidemiology and Antimicrobial Resistance Research Unit, US National Poultry Research Center, US Department of Agriculture, Agricultural Research Service (USDA-ARS), Athens, GA, United States
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19
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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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20
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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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21
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Argimón S, David S, Underwood A, Abrudan M, Wheeler NE, Kekre M, Abudahab K, Yeats CA, Goater R, Taylor B, Harste H, Muddyman D, Feil EJ, Brisse S, Holt K, Donado-Godoy P, Ravikumar KL, Okeke IN, Carlos C, Aanensen DM. Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch. Clin Infect Dis 2021; 73:S325-S335. [PMID: 34850838 PMCID: PMC8634497 DOI: 10.1093/cid/ciab784] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Klebsiella species, including the notable pathogen K. pneumoniae, are increasingly associated with antimicrobial resistance (AMR). Genome-based surveillance can inform interventions aimed at controlling AMR. However, its widespread implementation requires tools to streamline bioinformatic analyses and public health reporting. METHODS We developed the web application Pathogenwatch, which implements analytics tailored to Klebsiella species for integration and visualization of genomic and epidemiological data. We populated Pathogenwatch with 16 537 public Klebsiella genomes to enable contextualization of user genomes. We demonstrated its features with 1636 genomes from 4 low- and middle-income countries (LMICs) participating in the NIHR Global Health Research Unit (GHRU) on AMR. RESULTS Using Pathogenwatch, we found that GHRU genomes were dominated by a small number of epidemic drug-resistant clones of K. pneumoniae. However, differences in their distribution were observed (eg, ST258/512 dominated in Colombia, ST231 in India, ST307 in Nigeria, ST147 in the Philippines). Phylogenetic analyses including public genomes for contextualization enabled retrospective monitoring of their spread. In particular, we identified hospital outbreaks, detected introductions from abroad, and uncovered clonal expansions associated with resistance and virulence genes. Assessment of loci encoding O-antigens and capsule in K. pneumoniae, which represent possible vaccine candidates, showed that 3 O-types (O1-O3) represented 88.9% of all genomes, whereas capsule types were much more diverse. CONCLUSIONS Pathogenwatch provides a free, accessible platform for real-time analysis of Klebsiella genomes to aid surveillance at local, national, and global levels. We have improved representation of genomes from GHRU participant countries, further facilitating ongoing surveillance.
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Affiliation(s)
- Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Sophia David
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Anthony Underwood
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Monica Abrudan
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Nicole E Wheeler
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Mihir Kekre
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Khalil Abudahab
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Corin A Yeats
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Centre for Genomic Pathogen Surveillance, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Old Road Campus, Oxford, United Kingdom
| | - Richard Goater
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Ben Taylor
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Centre for Genomic Pathogen Surveillance, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Old Road Campus, Oxford, United Kingdom
| | - Harry Harste
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Dawn Muddyman
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Edward J Feil
- Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Sylvain Brisse
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Kathryn Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Pilar Donado-Godoy
- Colombian Integrated Program for Antimicrobial Resistance Surveillance (Coipars), CI Tibaitatá, Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Tibaitatá–Mosquera, Cundinamarca, Colombia
| | - K L Ravikumar
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Iruka N Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Oyo State, Nigeria
| | - Celia Carlos
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Centre for Genomic Pathogen Surveillance, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Old Road Campus, Oxford, United Kingdom
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22
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Singh S, Pathak A, Rahman M, Singh A, Nag S, Sahu C, Prasad KN. Genetic Characterisation of Colistin Resistant Klebsiella pneumoniae Clinical Isolates From North India. Front Cell Infect Microbiol 2021; 11:666030. [PMID: 34235092 PMCID: PMC8256276 DOI: 10.3389/fcimb.2021.666030] [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: 02/09/2021] [Accepted: 05/13/2021] [Indexed: 01/28/2023] Open
Abstract
Background Increasing use of colistin has led to the world-wide emergence of mobile colistin resistant gene (mcr). The present study aimed to identify and characterise mcr and other drug-resistant genes in colistin resistant Klebsiella pneumoniae clinical isolates. Methods Twenty-two colistin resistant K. pneumoniae were analysed for mcr and other drug-resistant genes, efflux pumps, and virulence genes, and for their biofilm forming ability. Pulsed-field gel electrophoresis (PFGE) and multi-locus sequence typing (MLST) were performed for all mcr-1 positive isolates. S1-PFGE and Southern hybridisation were performed for localisation of mcr-1 and blaNDM. Results Nineteen colistin resistant K. pneumoniae harboured mcr-1 and 3 had mgrB disruption. All isolates harboured blaOXA-48-type and ESBL genes; eight strains (five with mcr-1 and three with mgrB disruption) co-harboured blaNDM. Efflux pumps genes AcrAB and mdtK were detected in all 22 and tol-C in 21 isolates. Virulence-related genes entB and irp-1 were detected in all 22, mrkD in 20, and fimH-1 in 18 isolates; 11 isolates were strong biofilm producers. PFGE clustered mcr-1 positive isolates into eight groups based on ≥90% similarity; MLST revealed diverse sequence types, predominant being ST-15 (n = 4) and ST-16 (n = 4). Both mcr-1 and blaNDM were localised on plasmid and chromosome; mcr-1 was present on IncFII type and blaNDM on IncFIB and IncA/C type plasmids. Conclusions Colistin resistance in K. pneumoniae was predominantly mediated by mcr-1. Co-existence of colistin, carbapenem, and other drug-resistant genes along with efflux pumps indicates towards enormous genomic plasticity in K. pneumoniae with ability to emerge as super-spreader of drug-resistance.
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Affiliation(s)
- Sanjay Singh
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Ashutosh Pathak
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Mohibur Rahman
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Avinash Singh
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Soumyabrata Nag
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Chinmoy Sahu
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India
| | - Kashi Nath Prasad
- Department of Microbiology, Sanjay Gandhi Post Graduate Institute of Medical Sciences, Lucknow, India.,Department of Microbiology, Apollomedics Super Speciality Hospital, Lucknow, India
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Nwabor OF, Terbtothakun P, Voravuthikunchai SP, Chusri S. A Bibliometric Meta-Analysis of Colistin Resistance in Klebsiella pneumoniae. Diseases 2021; 9:44. [PMID: 34202931 PMCID: PMC8293170 DOI: 10.3390/diseases9020044] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Revised: 06/15/2021] [Accepted: 06/15/2021] [Indexed: 11/16/2022] Open
Abstract
Colistin is a last resort antibiotic medication for the treatment of infections caused by carbapenem-resistant Klebsiella pneumoniae. In recent years, various mechanisms have been reported to mediate colistin resistance in K. pneumoniae. This study reports a bibliometric analysis of published articles retrieved from the Scopus database relating to colistin resistance in K. pneumoniae. The research trends in colistin resistance and mechanisms of resistance were considered. A total of 1819 research articles published between 1995 and 2019 were retrieved, and the results indicated that 50.19% of the documents were published within 2017-2019. The USA had the highest participation with 340 (14.31%) articles and 14087 (17.61%) citations. Classification based on the WHO global epidemiological regions showed that the European Region contributed 42% of the articles while the American Region contributed 21%. The result further indicated that 45 countries had published at least 10 documents with strong international collaborations amounting to 272 links and a total linkage strength of 735. A total of 2282 keywords were retrieved; however, 57 keywords had ≥15 occurrences with 764 links and a total linkage strength of 2388. Furthermore, mcr-1, colistin resistance, NDM, mgrB, ceftazidime-avibactam, MDR, combination therapy, and carbapenem-resistant Enterobacteriaceae were the trending keywords. Concerning funders, the USA National Institute of Health funded 9.1% of the total research articles, topping the list. The analysis indicated poor research output, collaboration, and funding from Africa and South-East Asia and demands for improvement in international research collaboration.
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Affiliation(s)
- Ozioma Forstinus Nwabor
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; (O.F.N.); (P.T.)
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand;
| | - Pawarisa Terbtothakun
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; (O.F.N.); (P.T.)
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand;
| | - Supayang P. Voravuthikunchai
- Division of Biological Science, Faculty of Science, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand;
| | - Sarunyou Chusri
- Division of Infectious Diseases, Department of Internal Medicine, Faculty of Medicine, Prince of Songkla University, Hat Yai, Songkhla 90112, Thailand; (O.F.N.); (P.T.)
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24
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Shankar C, Jacob JJ, Sugumar SG, Natarajan L, Rodrigues C, Mathur P, Mukherjee DN, Sharma A, Chitnis DS, Bharagava A, Manesh A, Gunasekaran K, Veeraraghavan B. Distinctive Mobile Genetic Elements Observed in the Clonal Expansion of Carbapenem-Resistant Klebsiella pneumoniae in India. Microb Drug Resist 2021; 27:1096-1104. [PMID: 33720791 DOI: 10.1089/mdr.2020.0316] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Background: Klebsiella pneumoniae (Kp), a common multidrug-resistant pathogen, causes a wide spectrum of nosocomial infections with high rates of morbidity and mortality. The emergence of pan drug-resistant international high-risk clones such as ST258, ST14, ST15, ST147, and ST101 is a global concern. This study was performed to investigate the carbapenemases, the plasmid profile, and the clonal relationship among Indian K. pneumoniae. Materials and Methods: A total of 290 K. pneumoniae isolates from seven centers in India were characterized to determine sequence types (STs) and carbapenemases. A subset of isolates was subjected to whole genome sequencing and hybrid genome assembly to obtain the complete genome. Plasmids carrying carbapenemases were characterized to determine the dissemination of carbapenem-resistant (CR) K. pneumoniae. Results: From this study, 75 different STs were observed with ST231 being predominant. About 79% of the analyzed isolates were CR with 59% (n = 136) producing OXA48-like carbapenemases. While ST231 was the predominant clone among the OXA48-like producers; NDM producers and NDM+OXA48-like producers were mostly associated with ST14. Interestingly, 61% (n = 138) of the total CR K. pneumoniae were colistin resistant, belonging to 22 different STs. Plasmid profiling shows that blaOXA48-like was exclusively carried by ColKP3, whereas blaNDM was associated with IncFII-like plasmids. Conclusion: The highly mosaic genome of K. pneumoniae coupled with the diverse ecological niches in India makes it a hotspot for antimicrobial resistance, leading to increased morbidity and mortality. Extensive molecular surveillance of the clonal spread of K. pneumoniae could help in understanding AMR dynamics and thus rework therapeutic management.
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Affiliation(s)
- Chaitra Shankar
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Jobin John Jacob
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Suganya Gopal Sugumar
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Lavanya Natarajan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Camilla Rodrigues
- Department of Laboratory Medicine, All India Institute of Medical Sciences Trauma Centre, New Delhi, India
| | - Purva Mathur
- Microbiology Section, Department of Laboratory Medicine, P.D. Hinduja Hospital and Research Centre, Mumbai, India
| | - Dip Narayan Mukherjee
- Department of Microbiology, Woodlands Multispeciality Hospital, Kolkata, West Bengal, India
| | - Anita Sharma
- Department of Laboratory Medicine, Fortis Hospital, Mohali, Chandigarh, India
| | - D S Chitnis
- Department of Microbiology and Immunology, Choithram Hospital, Indore, Madhya Pradesh, India
| | - Anudita Bharagava
- Department of Microbiology, All India Institute of Medical Sciences, Raipur, India
| | - Abi Manesh
- Department of Infectious Diseases, Christian Medical College, Vellore, Tamil Nadu, India
| | - Karthik Gunasekaran
- Department of Medicine, Christian Medical College, Vellore, Tamil Nadu, India
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
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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: 24] [Impact Index Per Article: 8.0] [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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Fodor A, Abate BA, Deák P, Fodor L, Gyenge E, Klein MG, Koncz Z, Muvevi J, Ötvös L, Székely G, Vozik D, Makrai L. Multidrug Resistance (MDR) and Collateral Sensitivity in Bacteria, with Special Attention to Genetic and Evolutionary Aspects and to the Perspectives of Antimicrobial Peptides-A Review. Pathogens 2020; 9:pathogens9070522. [PMID: 32610480 PMCID: PMC7399985 DOI: 10.3390/pathogens9070522] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2020] [Revised: 06/23/2020] [Accepted: 06/23/2020] [Indexed: 12/18/2022] Open
Abstract
Antibiotic poly-resistance (multidrug-, extreme-, and pan-drug resistance) is controlled by adaptive evolution. Darwinian and Lamarckian interpretations of resistance evolution are discussed. Arguments for, and against, pessimistic forecasts on a fatal “post-antibiotic era” are evaluated. In commensal niches, the appearance of a new antibiotic resistance often reduces fitness, but compensatory mutations may counteract this tendency. The appearance of new antibiotic resistance is frequently accompanied by a collateral sensitivity to other resistances. Organisms with an expanding open pan-genome, such as Acinetobacter baumannii, Pseudomonas aeruginosa, and Klebsiella pneumoniae, can withstand an increased number of resistances by exploiting their evolutionary plasticity and disseminating clonally or poly-clonally. Multidrug-resistant pathogen clones can become predominant under antibiotic stress conditions but, under the influence of negative frequency-dependent selection, are prevented from rising to dominance in a population in a commensal niche. Antimicrobial peptides have a great potential to combat multidrug resistance, since antibiotic-resistant bacteria have shown a high frequency of collateral sensitivity to antimicrobial peptides. In addition, the mobility patterns of antibiotic resistance, and antimicrobial peptide resistance, genes are completely different. The integron trade in commensal niches is fortunately limited by the species-specificity of resistance genes. Hence, we theorize that the suggested post-antibiotic era has not yet come, and indeed might never come.
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Affiliation(s)
- András Fodor
- Department of Genetics, University of Szeged, H-6726 Szeged, Hungary;
- Correspondence: or (A.F.); (L.M.); Tel.: +36-(30)-490-9294 (A.F.); +36-(30)-271-2513 (L.M.)
| | - Birhan Addisie Abate
- Ethiopian Biotechnology Institute, Agricultural Biotechnology Directorate, Addis Ababa 5954, Ethiopia;
| | - Péter Deák
- Department of Genetics, University of Szeged, H-6726 Szeged, Hungary;
- Institute of Biochemistry, Biological Research Centre, H-6726 Szeged, Hungary
| | - László Fodor
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, P.O. Box 22, H-1581 Budapest, Hungary;
| | - Ervin Gyenge
- Hungarian Department of Biology and Ecology, Faculty of Biology and Geology, Babeș-Bolyai University, 5-7 Clinicilor St., 400006 Cluj-Napoca, Romania; (E.G.); (G.S.)
- Institute for Research-Development-Innovation in Applied Natural Sciences, Babeș-Bolyai University, 30 Fântânele St., 400294 Cluj-Napoca, Romania
| | - Michael G. Klein
- Department of Entomology, The Ohio State University, 1680 Madison Ave., Wooster, OH 44691, USA;
| | - Zsuzsanna Koncz
- Max-Planck Institut für Pflanzenzüchtungsforschung, Carl-von-Linné-Weg 10, D-50829 Köln, Germany;
| | | | - László Ötvös
- OLPE, LLC, Audubon, PA 19403-1965, USA;
- Institute of Medical Microbiology, Semmelweis University, H-1085 Budapest, Hungary
- Arrevus, Inc., Raleigh, NC 27612, USA
| | - Gyöngyi Székely
- Hungarian Department of Biology and Ecology, Faculty of Biology and Geology, Babeș-Bolyai University, 5-7 Clinicilor St., 400006 Cluj-Napoca, Romania; (E.G.); (G.S.)
- Institute for Research-Development-Innovation in Applied Natural Sciences, Babeș-Bolyai University, 30 Fântânele St., 400294 Cluj-Napoca, Romania
- Centre for Systems Biology, Biodiversity and Bioresources, Babeș-Bolyai University, 5-7 Clinicilor St., 400006 Cluj-Napoca, Romania
| | - Dávid Vozik
- Research Institute on Bioengineering, Membrane Technology and Energetics, Faculty of Engineering, University of Veszprem, H-8200 Veszprém, Hungary; or or
| | - László Makrai
- Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, P.O. Box 22, H-1581 Budapest, Hungary;
- Correspondence: or (A.F.); (L.M.); Tel.: +36-(30)-490-9294 (A.F.); +36-(30)-271-2513 (L.M.)
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27
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Tian X, Huang C, Ye X, Jiang H, Zhang R, Hu X, Xu D. Molecular Epidemiology of and Risk Factors for Extensively Drug-Resistant Klebsiella pneumoniae Infections in Southwestern China: A Retrospective Study. Front Pharmacol 2019; 10:1307. [PMID: 31736765 PMCID: PMC6838015 DOI: 10.3389/fphar.2019.01307] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 10/15/2019] [Indexed: 12/23/2022] Open
Abstract
Background: The increasing prevalence of extensively drug-resistant Klebsiella pneumoniae (XDR-KP) poses a serious threat to clinical anti-infective treatment. This retrospective study assessed the molecular epidemiology of and risk factors for infections with XDR-KP to investigate the mechanism of drug resistance and the epidemiological characteristics. Methods: A retrospective 1:2 case-control study was conducted at Chongqing Renji Affiliated Hospital of the Chinese Academy of Sciences University from January 2015 to December 2017. A total of 69 non-repetitive XDR-KP strains were collected. Patients infected with XDR-KP comprised the case group, and 138 matched patients with non-XDR-KP infection at the same site comprised the control group. The chi-square test and logistic regression were performed to evaluate the related risk factors. Molecular typing was performed by multilocus sequence typing (MLST). Potential resistance genes were detected by polymerase chain reaction (PCR) and sequencing. Predictors of 28-day mortality in patients with XDR-KP infection were also identified in our study. Results: Only tigecycline and polymyxin B showed favorable in vitro drug sensitivity tests. These XDR-KP strains had a high prevalence rate (n = 66, 95.7%) of carbapenemase-related drug resistance genes. Among them, KPC-2 was the most frequently detected gene (n = 52, 75.4%). Particularly, all of the isolates harbored multiple drug resistance genes. Epidemiological analysis showed that fifty-eight XDR-KP isolates were resistant strains with the ST-11 genotype. Multivariate logistic regression analysis showed that ICU admission (OR: 3.28, 95% CI: 1.66–6.49, P < 0.001), tracheal cannula (OR: 3.16, 95% CI: 1.48–6.76, P = 0.003), and carbapenem exposure (OR: 3.16, 95% CI: 1.25–7.98, P = 0.015) were independent risk factors for XDR-KP infection. Solid tumors (OR: 7.22, 95% CI: 1.84–28.34, P = 0.005) and septic shock (OR: 9.46, 95% CI: 2.00–44.72, P = 0.005) were independent risk factors for 28-day mortality from XDR-KP infection. Conclusion: This study showed that XDR-KP isolates were highly resistant and exhibited clonal transmission. ST11 was the predominant epidemic type of XDR-KP producing KPC-2 in Southwestern China. Physicians should be aware of these high-risk patients with notable predictive factors for XDR-KP infection. These findings may provide some recommendation for the diagnosis and treatment of patients infected with XDR-KP strains in Southwestern China.
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Affiliation(s)
- Xiaolang Tian
- Department of Clinical Laboratory, University of Chinese Academy of Sciences Chongqing Renji Hospital, Fifth People's Hospital of Chongqing, Chongqing, China
| | - Changwu Huang
- Department of Clinical Laboratory, University of Chinese Academy of Sciences Chongqing Renji Hospital, Fifth People's Hospital of Chongqing, Chongqing, China
| | - Xiaoli Ye
- Department of Clinical Laboratory, University of Chinese Academy of Sciences Chongqing Renji Hospital, Fifth People's Hospital of Chongqing, Chongqing, China
| | - Hongyan Jiang
- Department of Clinical Laboratory, University of Chinese Academy of Sciences Chongqing Renji Hospital, Fifth People's Hospital of Chongqing, Chongqing, China
| | - Rufang Zhang
- Department of Clinical Laboratory, University of Chinese Academy of Sciences Chongqing Renji Hospital, Fifth People's Hospital of Chongqing, Chongqing, China
| | - Xiaofang Hu
- Department of Clinical Laboratory, University of Chinese Academy of Sciences Chongqing Renji Hospital, Fifth People's Hospital of Chongqing, Chongqing, China
| | - Dongshuang Xu
- Department of Clinical Laboratory, University of Chinese Academy of Sciences Chongqing Renji Hospital, Fifth People's Hospital of Chongqing, Chongqing, China
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