1
|
Pérez-Viso B, Martins-Oliveira I, Gomes R, Silva-Dias A, Peixe L, Novais Â, Pina-Vaz C, Cantón R. Performance of Flow Cytometry-Based Rapid Assay in Detection of Carbapenemase-Producing Enterobacterales. Int J Mol Sci 2024; 25:7888. [PMID: 39063130 PMCID: PMC11276710 DOI: 10.3390/ijms25147888] [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: 06/12/2024] [Revised: 07/12/2024] [Accepted: 07/16/2024] [Indexed: 07/28/2024] Open
Abstract
Carbapenemase-producing Enterobacterales are increasingly being recognized in nosocomial infections. The performance of a flow cytometry-based rapid assay for their detection and differentiation was evaluated. This is a disruptive phenotypic technology, phenotypic and growth-independent, that searches for the lesions produced by drugs acting on cells after a short incubation time. Overall, 180 Gram-negative bacteria were studied, and results were compared with those obtained molecularly by PCR and phenotypically by 'KPC, MBL and OXA-48 Confirm Kit'. This phenotypic method was used as reference for comparison purposes. Susceptibility to carbapenems (imipenem, meropenem, and ertapenem) was determined by standard broth microdilution. Overall, 112 isolates (62.2%) were carbapenemase producers, 41 KPCs, 36 MβLs, and 31 OXA-48, and 4 strains were KPC + MβL co-producers. Sixty-eight isolates were carbapenemase-negative. The percentage of agreement, sensitivity, and specificity were calculated according to ISO 20776-2:2021. The FASTinov assay showed 97.7% agreement with the reference method for carbapenemase detection. Discrepant flow cytometry results were obtained in four isolates compared with both reference and PCR results. The sensitivity and specificity of this new technology were 95.3% and 98.5%, respectively, for KPCs, 97.6% and 99.3% for MβLs, and 96.9% and 98% for OXA-48 detection. In conclusion, we describe a rapid flow cytometry assay with high accuracy for carbapenemase detection and the differentiation of various carbapenemases, which should impact clinical microbiology laboratories and patient management.
Collapse
Affiliation(s)
- Blanca Pérez-Viso
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain;
| | - Inês Martins-Oliveira
- FASTinov, S.A., 4200-135 Porto, Portugal; (I.M.-O.); (R.G.); (A.S.-D.)
- Division of Microbiology, Department of Pathology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
| | - Rosário Gomes
- FASTinov, S.A., 4200-135 Porto, Portugal; (I.M.-O.); (R.G.); (A.S.-D.)
| | - Ana Silva-Dias
- FASTinov, S.A., 4200-135 Porto, Portugal; (I.M.-O.); (R.G.); (A.S.-D.)
- CINTESIS–Center for Health Technology and Services Research, Faculty of Medicine, 4200-450 Porto, Portugal
| | - Luísa Peixe
- UCIBIO-Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (L.P.); (Â.N.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Ângela Novais
- UCIBIO-Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal; (L.P.); (Â.N.)
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Cidália Pina-Vaz
- FASTinov, S.A., 4200-135 Porto, Portugal; (I.M.-O.); (R.G.); (A.S.-D.)
- Division of Microbiology, Department of Pathology, Faculty of Medicine, University of Porto, 4200-319 Porto, Portugal
- CINTESIS–Center for Health Technology and Services Research, Faculty of Medicine, 4200-450 Porto, Portugal
| | - Rafael Cantón
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal and Instituto Ramón y Cajal de Investigación Sanitaria (IRYCIS), 28034 Madrid, Spain;
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, 28029 Madrid, Spain
| |
Collapse
|
2
|
Liu H, Xiang Y, Xiong M, Xiao X, Zhou J, Tian H, Chen Q, Li Y. Prevalence of ST1049-KL5 carbapenem-resistant Klebsiella pneumoniae with a bla KPC-2 and bla NDM-1 co-carrying hypertransmissible IncM1 plasmid. Commun Biol 2024; 7:695. [PMID: 38844513 PMCID: PMC11156905 DOI: 10.1038/s42003-024-06398-w] [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: 11/17/2023] [Accepted: 05/29/2024] [Indexed: 06/09/2024] Open
Abstract
Infection caused by KPC and NDM carbapenemases co-producing Klebsiella pneumoniae (KPC_NDM_CRKP) poses serious public health concerns. Here, we elucidate the prevalence of a hypertransmissible lncM1 plasmid, pKPC_NDM, co-carrying blaKPC-2 and blaNDM-1 genes in sequence type 1049 K_locus 5 (ST1049-KL5) KPC_NDM_CRKP isolates. Genetic and clonal relatedness analyses using pulsed-field gel electrophoresis, single nucleotide polymorphism analysis and core genome multilocus sequence typing suggested clonal dissemination of ST1049-KL5 KPC_NDM_CRKP strains in our hospital. Whole genome sequencing identified an identical 76,517 bp- blaKPC-2 and blaNDM-1 genes co-carrying IncM1 plasmid pKPC_NDM and a pLVPK-like hypervirulent plasmid in all ST1049-KL5 KPC_NDM_CRKP isolates. pKPC_NDM shared 100% identity with a previously sequenced plasmid CRKP35_unnamed4, demonstrating high transferability in conjugation assay, with conjugation frequencies reaching 10-4 and 10-5 in Escherichia coli and K. pneumoniae recipients, respectively. It also maintained favorable stability and flexible compatibility, with retention rates exceeding 80% after 10 days of continuous passage, and could be compatible with pre-existing blaKPC- or blaNDM-carrying plasmids in recipient strains. This study summarizes the characteristics of KPC_NDM_CRKP outbreaks and highlights the importance of ongoing surveillance and infection control strategies to address the challenges posed by ST1049 K. pneumoniae strains.
Collapse
Affiliation(s)
- Hongmao Liu
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yating Xiang
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Mengyuan Xiong
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Xiao Xiao
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Junying Zhou
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Hongpan Tian
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Qingsong Chen
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China
| | - Yirong Li
- Department of Laboratory Medicine, Zhongnan Hospital of Wuhan University, Wuhan, China.
- Hubei Engineering Center for Infectious Disease Prevention, Control and Treatment, Wuhan, China.
- Wuhan Research Center for Infectious Diseases and Tumors of the Chinese Academy of Medical Sciences, Wuhan, Hubei, China.
| |
Collapse
|
3
|
Sellera FP, Lincopan N, Fuentes-Castillo D, Stehling EG, Furlan JPR. Rapid evolution of pan-β-lactam resistance in Enterobacterales co-producing KPC and NDM: insights from global genomic analysis after the COVID-19 pandemic. THE LANCET. MICROBE 2024; 5:e412-e413. [PMID: 38367635 DOI: 10.1016/s2666-5247(24)00018-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2023] [Revised: 01/12/2024] [Accepted: 01/12/2024] [Indexed: 02/19/2024]
Affiliation(s)
- Fábio Parra Sellera
- Department of Internal Medicine, School of Veterinary Medicine and Animal Science, University of São Paulo, São Paulo, Brazil; School of Veterinary Medicine, Metropolitan University of Santos, Santos, Brazil
| | - Nilton Lincopan
- Department of Microbiology, Instituto de Ciências Biomédicas, University of São Paulo, São Paulo, Brazil; Department of Clinical Analysis, Faculty of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Danny Fuentes-Castillo
- Departamento de Patología y Medicina Preventiva, Facultad de Ciencias Veterinarias, Universidad de Concepción, Chillán, Chile
| | - Eliana Guedes Stehling
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, S/N, Monte Alegre, Ribeirão Preto 14040-903, Brazil
| | - João Pedro Rueda Furlan
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, S/N, Monte Alegre, Ribeirão Preto 14040-903, Brazil.
| |
Collapse
|
4
|
Rosa RDS, Furlan JPR, Santos LDRD, Ramos MS, Savazzi EA, Stehling EG. Genetic diversity of KPC-2-producing Klebsiella pneumoniae complex from aquatic ecosystems. World J Microbiol Biotechnol 2024; 40:177. [PMID: 38656467 DOI: 10.1007/s11274-024-03994-0] [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: 03/14/2024] [Accepted: 04/19/2024] [Indexed: 04/26/2024]
Abstract
During the COVID-19 pandemic, the occurrence of carbapenem-resistant Klebsiella pneumoniae increased in human clinical settings worldwide. Impacted by this increase, international high-risk clones harboring carbapenemase-encoding genes have been circulating in different sources, including the environment. The blaKPC gene is the most commonly disseminated carbapenemase-encoding gene worldwide, whose transmission is carried out by different mobile genetic elements. In this study, blaKPC-2-positive Klebsiella pneumoniae complex strains were isolated from different anthropogenically affected aquatic ecosystems and characterized using phenotypic, molecular, and genomic methods. K. pneumoniae complex strains exhibited multidrug-resistant and extensively drug-resistant profiles, spotlighting the resistance to carbapenems, ceftazidime-avibactam, colistin, and tigecycline, which are recognized as last-line antimicrobial treatment options. Molecular analysis showed the presence of several antimicrobial resistance, virulence, and metal tolerance genes. In-depth analysis showed that the blaKPC-2 gene was associated with three different Tn4401 isoforms (i.e., Tn4401a, Tn4401b, and Tn4401i) and NTEKPC elements. Different plasmid replicons were detected and a conjugative IncN-pST15 plasmid harboring the blaKPC-2 gene associated with Tn4401i was highlighted. K. pneumoniae complex strains belonging to international high-risk (e.g., ST11 and ST340) and unusual clones (e.g., ST323, ST526, and ST4216) previously linked to clinical settings. In this context, some clones were reported for the first time in the environmental sector. Therefore, these findings evidence the occurrence of carbapenemase-producing K. pneumoniae complex strains in aquatic ecosystems and contribute to the monitoring of carbapenem resistance worldwide.
Collapse
Affiliation(s)
- Rafael da Silva Rosa
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, S/N, Monte Alegre, Ribeirão Preto, 14040-903, Brazil
| | - João Pedro Rueda Furlan
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, S/N, Monte Alegre, Ribeirão Preto, 14040-903, Brazil
| | - Lucas David Rodrigues Dos Santos
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, S/N, Monte Alegre, Ribeirão Preto, 14040-903, Brazil
| | - Micaela Santana Ramos
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, S/N, Monte Alegre, Ribeirão Preto, 14040-903, Brazil
| | | | - Eliana Guedes Stehling
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. do Café, S/N, Monte Alegre, Ribeirão Preto, 14040-903, Brazil.
| |
Collapse
|
5
|
Furlan JPR, da Silva Rosa R, Ramos MS, Dos Santos LDR, Savazzi EA, Stehling EG. Emergence of carbapenem-resistant Klebsiella pneumoniae species complex from agrifood systems: detection of ST6326 co-producing KPC-2 and NDM-1. JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE 2024. [PMID: 38651793 DOI: 10.1002/jsfa.13555] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2024] [Revised: 04/18/2024] [Accepted: 04/19/2024] [Indexed: 04/25/2024]
Abstract
BACKGROUND Klebsiella pneumoniae species complex (KpSC) is an important disseminator of carbapenemase-encoding genes, mainly blaKPC-2 and blaNDM-1, from hospitals to the environment. Consequently, carbapenem-resistant strains can be spread through the agrifood system, raising concerns about food safety. This study therefore aimed to isolate carbapenem-resistant KpSC strains from the agricultural and environmental sectors and characterize them using phenotypic, molecular, and genomic analyses. RESULTS Klebsiella pneumoniae and Klebsiella quasipneumoniae strains isolated from soils used for lemon, guava, and fig cultivation, and from surface waters, displayed an extensive drug-resistance profile and carried blaKPC-2, blaNDM-1, or both. In addition to carbapenemase-encoding genes, KpSC strains harbor a broad resistome (antimicrobial resistance and metal tolerance) and present putative hypervirulence. Soil-derived K. pneumoniae strains were assigned as high-risk clones (ST11 and ST307) and harbored the blaKPC-2 gene associated with Tn4401b and Tn3-like elements on IncN-pST15 and IncX5 plasmids. In surface waters, the coexistence of blaKPC-2 and blaNDM-1 genes was identified in K. pneumoniae ST6326, a new carbapenem-resistant regional Brazilian clone. In this case, blaKPC-2 with Tn4401a isoform and blaNDM-1 associated with a Tn125-like transposon were located on different plasmids. Klebsiella quasipneumoniae ST526 also presented the blaNDM-1 gene associated with a Tn3000 transposon on an IncX3 plasmid. CONCLUSION These findings provide a warning regarding the transmission of carbapenemase-positive KpSC across the agricultural and environmental sectors, raising critical food safety and environmental issues. © 2024 Society of Chemical Industry.
Collapse
Affiliation(s)
- João Pedro Rueda Furlan
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Rafael da Silva Rosa
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Micaela Santana Ramos
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Lucas David Rodrigues Dos Santos
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | | | - Eliana Guedes Stehling
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| |
Collapse
|
6
|
Posteraro B, De Maio F, Motro Y, Menchinelli G, De Lorenzis D, Marano RBM, Aljanazreh B, Errico FM, Massaria G, Spanu T, Posteraro P, Moran-Gilad J, Sanguinetti M. In-depth characterization of multidrug-resistant NDM-1 and KPC-3 co-producing Klebsiella pneumoniae bloodstream isolates from Italian hospital patients. Microbiol Spectr 2024; 12:e0330523. [PMID: 38411998 PMCID: PMC10986569 DOI: 10.1128/spectrum.03305-23] [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: 09/07/2023] [Accepted: 02/04/2024] [Indexed: 02/28/2024] Open
Abstract
Bloodstream infection (BSI) caused by carbapenem-resistant Klebsiella pneumoniae (KP) poses significant challenges, particularly when the infecting isolate carries multiple antimicrobial resistance (AMR) genes/determinants. This study, employing short- and long-read whole-genome sequencing, characterizes six New Delhi metallo-β-lactamase (NDM) 1 and KP carbapenemase (KPC) 3 co-producing KP isolates, the largest cohort investigated in Europe to date. Five [sequence type (ST) 512] and one (ST11) isolates were recovered from patients who developed BSI from February to August 2022 or February 2023 at two different hospitals in Rome, Italy. Phylogenetic analysis revealed two distinct clusters among ST512 isolates and a separate cluster for the ST11 isolate. Beyond blaNDM-1 and blaKPC-3, various AMR genes, indicative of a multidrug resistance phenotype, including colistin resistance, were found. Each cluster-representative ST512 isolate harbored a blaNDM-1 plasmid (IncC) and a blaKPC-3 plasmid [IncFIB(pQil)/IncFII(K)], while the ST11 isolate harbored a blaNDM-1 plasmid [IncFII(pKPX1)] and a blaKPC-3 plasmid [IncFIB(K)/IncFII(K)]. The blaNDM-1 plasmids carried genes conferring resistance to clinically relevant antimicrobial agents, and the aminoglycoside resistance gene aac(6')-Ib was found on different plasmids. Colistin resistance-associated mgrB/pmrB gene mutations were present in all isolates, and the yersiniabactin-encoding ybt gene was unique to the ST11 isolate. In conclusion, our findings provide insights into the genomic context of blaNDM-1/blaKPC-3 carbapenemase-producing KP isolates.IMPORTANCEThis study underscores the critical role of genomic surveillance as a proactive measure to restrict the spread of carbapenemase-producing KP isolates, especially when key antimicrobial resistance genes, such as blaNDM-1/blaKPC-3, are plasmid borne. In-depth characterization of these isolates may help identify plasmid similarities contributing to their intra-hospital/inter-hospital adaptation and transmission. Despite the lack of data on patient movements, it is possible that carbapenem-resistant isolates were selected to co-produce KP carbapenemase and New Delhi metallo-β-lactamase via plasmid acquisition. Studies employing long-read whole-genome sequencing should be encouraged to address the emergence of KP clones with converging phenotypes of virulence and resistance to last-resort antimicrobial agents.
Collapse
Affiliation(s)
- Brunella Posteraro
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
- Dipartimento di Scienze Mediche e Chirurgiche Addominali ed Endocrino Metaboliche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Flavio De Maio
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Yair Motro
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Giulia Menchinelli
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Desy De Lorenzis
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Roberto B. M. Marano
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Bessan Aljanazreh
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Federica Maria Errico
- GVM - Ospedale San Carlo di Nancy, Laboratorio di Analisi Chimico-Cliniche e Microbiologiche, Rome, Italy
| | | | - Teresa Spanu
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| | - Patrizia Posteraro
- GVM - Ospedale San Carlo di Nancy, Laboratorio di Analisi Chimico-Cliniche e Microbiologiche, Rome, Italy
| | - Jacob Moran-Gilad
- Department of Health Policy and Management, School of Public Health, Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Maurizio Sanguinetti
- Dipartimento di Scienze Biotecnologiche di Base, Cliniche Intensivologiche e Perioperatorie, Università Cattolica del Sacro Cuore, Rome, Italy
- Dipartimento di Scienze di Laboratorio e Infettivologiche, Fondazione Policlinico Universitario A. Gemelli IRCCS, Rome, Italy
| |
Collapse
|
7
|
Cuicapuza D, Loyola S, Velásquez J, Fernández N, Llanos C, Ruiz J, Tsukayama P, Tamariz J. Molecular characterization of carbapenemase-producing Enterobacterales in a tertiary hospital in Lima, Peru. Microbiol Spectr 2024; 12:e0250323. [PMID: 38193666 PMCID: PMC10846045 DOI: 10.1128/spectrum.02503-23] [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: 06/14/2023] [Accepted: 11/26/2023] [Indexed: 01/10/2024] Open
Abstract
Carbapenemase-producing Enterobacterales (CPE) are a growing threat to global health and the economy. Understanding the interactions between resistance and virulence mechanisms of CPE is crucial for managing difficult-to-treat infections and informing outbreak prevention and control programs. Here, we report the characterization of 21 consecutive, unique clinical isolates of CPE collected in 2018 at a tertiary hospital in Lima, Peru. Isolates were characterized by phenotypic antimicrobial susceptibility testing and whole-genome sequencing to identify resistance determinants and virulence factors. Seven Klebsiella pneumoniae isolates were classified as extensively drug-resistant. The remaining Klebsiella, Enterobacter hormaechei, and Escherichia coli isolates were multidrug-resistant. Eighteen strains carried the metallo-β-lactamase NDM-1, two the serine-carbapenemase KPC-2, and one isolate had both carbapenemases. The blaNDM-1 gene was located in the truncated ΔISAba125 element, and the blaKPC-2 gene was in the Tn4401a transposon. ST147 was the most frequent sequence type among K. pneumoniae isolates. Our findings highlight the urgent need to address the emergence of CPE and strengthen control measures and antibiotic stewardship programs in low- and middle-income settings.IMPORTANCEGenomic surveillance of antimicrobial resistance contributes to monitoring the spread of resistance and informs treatment and prevention strategies. We characterized 21 carbapenemase-producing Enterobacterales collected at a Peruvian tertiary hospital in 2018, which exhibited very high levels of resistance and carried numerous resistance genes. We detected the coexistence of carbapenemase-encoding genes (blaNDM-1 and blaKPC-2) in a Klebsiella pneumoniae isolate that also had the PmrB(R256G) mutation associated with colistin resistance. The blaKPC-2 genes were located in Tn4401a transposons, while the blaNDM-1 genes were in the genetic structure Tn125 (ΔISAba125). The presence of high-risk clones among Klebsiella pneumoniae (ST11 and ST147) and Escherichia coli (ST410) isolates is also reported. The study reveals the emergence of highly resistant bacteria in a Peruvian hospital, which could compromise the effectiveness of current treatments and control.
Collapse
Affiliation(s)
- Diego Cuicapuza
- Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio de Resistencia Antibiótica e Inmunopatología, Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio de Genómica Microbiana, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
- Emerge (Emerging Diseases and Climate Change Research Unit), Facultad de Salud Pública y Administración, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Steev Loyola
- Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio de Resistencia Antibiótica e Inmunopatología, Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru
- Grupo de Investigación UNIMOL, Facultad de Medicina, Universidad de Cartagena, Cartagena de Indias, Colombia
| | - Jorge Velásquez
- Departamento de Patología Clínica y Banco de Sangre, Hospital Nacional Arzobispo Loayza, Lima, Peru
| | - Nathaly Fernández
- Departamento de Patología Clínica y Banco de Sangre, Hospital Nacional Arzobispo Loayza, Lima, Peru
| | - Carlos Llanos
- Laboratorio de Resistencia Antibiótica e Inmunopatología, Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru
| | - Joaquim Ruiz
- Grupo de Investigación en Dinámicas y Epidemiología de la Resistencia a Antimicrobianos-“One Health”, Universidad Científica de Sur, Lima, Peru
| | - Pablo Tsukayama
- Laboratorio de Genómica Microbiana, Facultad de Ciencias e Ingeniería, Universidad Peruana Cayetano Heredia, Lima, Peru
- Emerge (Emerging Diseases and Climate Change Research Unit), Facultad de Salud Pública y Administración, Universidad Peruana Cayetano Heredia, Lima, Peru
- Instituto de Medicina Tropical Alexander von Humboldt, Universidad Peruana Cayetano Heredia, Lima, Peru
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, United Kingdom
| | - Jesús Tamariz
- Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru
- Laboratorio de Resistencia Antibiótica e Inmunopatología, Facultad de Medicina, Universidad Peruana Cayetano Heredia, Lima, Peru
| |
Collapse
|
8
|
Sun L, Chen Y, Qu T, Shi K, Han X, Wu W, Jiang Y, Yu Y. Characterisation of a Novel Hybrid IncFII pHN7A8:IncR:IncN Plasmid Co-Harboring blaNDM-5 and blaKPC-2 from a Clinical ST11 Carbapenem-Resistant Klebsiella pneumoniae Strain. Infect Drug Resist 2023; 16:7621-7628. [PMID: 38107435 PMCID: PMC10725640 DOI: 10.2147/idr.s435195] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Accepted: 11/16/2023] [Indexed: 12/19/2023] Open
Abstract
Purpose We aimed to characterize a novel blaNDM-5 and blaKPC-2 co-carrying hybrid plasmid from a clinical carbapenem-resistant Klebsiella pneumoniae (CRKP) strain. Methods Antimicrobial susceptibility was determined by the broth microdilution method. Plasmid size and localization were estimated using S1 nuclease pulsed-field gel electrophoresis (S1-PFGE) and Southern blotting. Plasmid transfer ability was evaluated by conjugation experiments. Whole genome sequencing (WGS) was performed using Illumina NovaSeq6000 and Oxford Nanopore MinION platforms. Genomic characteristics were analyzed using bioinformatics methods. Results Strain ZY27320 was a multidrug-resistant (MDR) clinical ST11 K. pneumoniae strain that confers high-level resistance to carbapenems (meropenem, MIC 128 mg/L; imipenem, MIC 64 mg/L) and ceftazidime/avibactam (MIC >128/4 mg/L). Both S1-PFGE-Southern blotting and whole genome sequencing revealed that the carbapenemase genes blaKPC-2 and blaNDM-5 were carried by the same IncFIIpHN7A8:IncR:IncN hybrid plasmid (pKPC2_NDM5). Conjugation experiments indicated that pKPC2_NDM5 was a non-conjugative plasmid. Conclusion This is the first report of a hybrid plasmid carrying both carbapenemase genes blaNDM-5 and blaKPC-2 in a clinical K. pneumoniae ST11 isolate that confers resistance to both ceftazidime/avibactam and carbapenems, thereby presenting a serious threat to treatment in clinical practice.
Collapse
Affiliation(s)
- Lingyan Sun
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Clinical in Vitro Diagnostic Techniques of Zhejiang Province, Hangzhou, People’s Republic of China
- Institute of Laboratory Medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Yan Chen
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Tingting Qu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Infection Control Department, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Keren Shi
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Xinhong Han
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Wenhao Wu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Infection Control Department, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Yan Jiang
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| | - Yunsong Yu
- Department of Infectious Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
- Key Laboratory of Microbial Technology and Bioinformatics of Zhejiang Province, Hangzhou, People’s Republic of China
- Regional Medical Center for National Institute of Respiratory Diseases, Sir Run Run Shaw Hospital, Zhejiang University School of Medicine, Hangzhou, People’s Republic of China
| |
Collapse
|
9
|
Furlan JPR, da Silva Rosa R, Ramos MS, Dos Santos LDR, Savazzi EA, Stehling EG. Genomic features of an extensively drug-resistant and NDM-1-positive Klebsiella pneumoniae ST340 isolated from river water. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2023; 30:114678-114684. [PMID: 37845596 DOI: 10.1007/s11356-023-30374-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 10/06/2023] [Indexed: 10/18/2023]
Abstract
The environmental contamination plays a significant role in the emergence of antimicrobial resistance. In this study, we report a genomic analysis of an extensively drug-resistant and blaNDM-1-producing Klebsiella pneumoniae (EW807) strain recovered from a surface water sample. Strain EW807 belonged to sequence type (ST) 340 and serotype O4:KL15, a high-risk clone of the clonal group 258. This strain carried a broad resistome, including blaNDM-1 and blaCTX-M-15. The core genome multilocus sequence typing phylogenetic analysis revealed that the EW807 strain was most related to strains from Brazil and the USA. An IncX3 plasmid was identified harboring the blaNDM-1 gene, while an IncFIB(K) plasmid was detected carrying the blaCTX-M-15 in addition to multidrug resistance and multimetal tolerance regions. IncX3 and IncFIB(K) plasmids shared high similarity with plasmids from a human in China and a dog in Brazil, respectively. The regions harboring the blaNDM-1 and blaCTX-M-15 genes contained sequences from the Tn3 family. These findings suggest that IncX3 plasmid could play a role in the spread of NDM-1 in a post-pandemic scenario. To the best of our knowledge, this is the first report of blaNDM-1-producing K. pneumoniae ST340 O4:KL15 strain in the environment. Therefore, the presence of high-risk clones of K. pneumoniae carrying carbapenemases in the environment requires strict surveillance.
Collapse
Affiliation(s)
- João Pedro Rueda Furlan
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. Do Café, S/N, Monte Alegre, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | - Rafael da Silva Rosa
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. Do Café, S/N, Monte Alegre, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | - Micaela Santana Ramos
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. Do Café, S/N, Monte Alegre, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | - Lucas David Rodrigues Dos Santos
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. Do Café, S/N, Monte Alegre, Ribeirão Preto, São Paulo, 14040-903, Brazil
| | | | - Eliana Guedes Stehling
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Av. Do Café, S/N, Monte Alegre, Ribeirão Preto, São Paulo, 14040-903, Brazil.
| |
Collapse
|
10
|
Vásquez-Ponce F, Bispo J, Becerra J, Fontana H, Pariona JGM, Esposito F, Fuga B, Oliveira FA, Brunetti F, Power P, Gutkind G, Schreiber AZ, Lincopan N. Emergence of KPC-113 and KPC-114 variants in ceftazidime-avibactam-resistant Klebsiella pneumoniae belonging to high-risk clones ST11 and ST16 in South America. Microbiol Spectr 2023; 11:e0037423. [PMID: 37671877 PMCID: PMC10580961 DOI: 10.1128/spectrum.00374-23] [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: 01/24/2023] [Accepted: 07/18/2023] [Indexed: 09/07/2023] Open
Abstract
Two novel variants of Klebsiella pneumoniae carbapenemase (KPC) associated with resistance to ceftazidime-avibactam (CZA) and designated as KPC-113 and KPC-114 by NCBI were identified in 2020, in clinical isolates of Klebsiella pneumoniae in Brazil. While K. pneumoniae of ST16 harbored the blaKPC-113 variant on an IncFII-IncFIB plasmid, K. pneumoniae of ST11 carried the blaKPC-114 variant on an IncN plasmid. Both isolates displayed resistance to broad-spectrum cephalosporins, β-lactam inhibitors, and ertapenem and doripenem, whereas K. pneumoniae producing KPC-114 showed susceptibility to imipenem and meropenem. Whole-genome sequencing and in silico analysis revealed that KPC-113 presented a Gly insertion between Ambler positions 264 and 265 (R264_A265insG), whereas KPC-114 displayed two amino acid insertions (Ser-Ser) between Ambler positions 181 and 182 (S181_P182insSS) in KPC-2, responsible for CZA resistance profiles. Our results confirm the emergence of novel KPC variants associated with resistance to CZA in international clones of K. pneumoniae circulating in South America. IMPORTANCE KPC-2 carbapenemases are endemic in Latin America. In this regard, in 2018, ceftazidime-avibactam (CZA) was authorized for clinical use in Brazil due to its significant activity against KPC-2 producers. In recent years, reports of resistance to CZA have increased in this country, limiting its clinical application. In this study, we report the emergence of two novel KPC-2 variants, named KPC-113 and KPC-114, associated with CZA resistance in Klebsiella pneumoniae strains belonging to high-risk clones ST11 and ST16. Our finding suggests that novel mutations in KPC-2 are increasing in South America, which is a critical issue deserving active surveillance.
Collapse
Affiliation(s)
- Felipe Vásquez-Ponce
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
| | - Jessica Bispo
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
| | - Johana Becerra
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
| | - Herrison Fontana
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Jesus G. M. Pariona
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Fernanda Esposito
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Bruna Fuga
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Flavio A. Oliveira
- School of Medical Sciences, University of Campinas, Campinas, São Paulo, Brazil
| | - Florencia Brunetti
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriologia y Virología Molecular, Universidad de Buenos Aires, and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Pablo Power
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriologia y Virología Molecular, Universidad de Buenos Aires, and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Gabriel Gutkind
- Facultad de Farmacia y Bioquímica, Instituto de Investigaciones en Bacteriologia y Virología Molecular, Universidad de Buenos Aires, and Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | | | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| |
Collapse
|
11
|
Boralli CMDS, Paganini JA, Meneses RS, Mata CPSMD, Leite EMM, Schürch AC, Paganelli FL, Willems RJL, Camargo ILBC. Characterization of blaKPC-2 and blaNDM-1 Plasmids of a K. pneumoniae ST11 Outbreak Clone. Antibiotics (Basel) 2023; 12:antibiotics12050926. [PMID: 37237829 DOI: 10.3390/antibiotics12050926] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Revised: 05/10/2023] [Accepted: 05/15/2023] [Indexed: 05/28/2023] Open
Abstract
The most common resistance mechanism to carbapenems is the production of carbapenemases. In 2021, the Pan American Health Organization warned of the emergence and increase in new carbapenemase combinations in Enterobacterales in Latin America. In this study, we characterized four Klebsiella pneumoniae isolates harboring blaKPC and blaNDM from an outbreak during the COVID-19 pandemic in a Brazilian hospital. We assessed their plasmids' transference ability, fitness effects, and relative copy number in different hosts. The K. pneumoniae BHKPC93 and BHKPC104 strains were selected for whole genome sequencing (WGS) based on their pulsed-field gel electrophoresis profile. The WGS revealed that both isolates belong to ST11, and 20 resistance genes were identified in each isolate, including blaKPC-2 and blaNDM-1. The blaKPC gene was present on a ~56 Kbp IncN plasmid and the blaNDM-1 gene on a ~102 Kbp IncC plasmid, along with five other resistance genes. Although the blaNDM plasmid contained genes for conjugational transfer, only the blaKPC plasmid conjugated to E. coli J53, without apparent fitness effects. The minimum inhibitory concentrations (MICs) of meropenem/imipenem against BHKPC93 and BHKPC104 were 128/64 and 256/128 mg/L, respectively. Although the meropenem and imipenem MICs against E. coli J53 transconjugants carrying the blaKPC gene were 2 mg/L, this was a substantial increment in the MIC relative to the original J53 strain. The blaKPC plasmid copy number was higher in K. pneumoniae BHKPC93 and BHKPC104 than in E. coli and higher than that of the blaNDM plasmids. In conclusion, two ST11 K. pneumoniae isolates that were part of a hospital outbreak co-harbored blaKPC-2 and blaNDM-1. The blaKPC-harboring IncN plasmid has been circulating in this hospital since at least 2015, and its high copy number might have contributed to the conjugative transfer of this particular plasmid to an E. coli host. The observation that the blaKPC-containing plasmid had a lower copy number in this E. coli strain may explain why this plasmid did not confer phenotypic resistance against meropenem and imipenem.
Collapse
Affiliation(s)
- Camila Maria Dos Santos Boralli
- Laboratory of Molecular Epidemiology and Microbiology, Department of Physics and Interdisciplinary Science, São Carlos Institute of Physics, University of São Paulo, São Carlos 13563-120, Brazil
| | | | - Rodrigo Silva Meneses
- University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | | | | | - Anita C Schürch
- University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Fernanda L Paganelli
- University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Rob J L Willems
- University Medical Center Utrecht, Heidelberglaan 100, 3584 CX Utrecht, The Netherlands
| | - Ilana Lopes Baratella Cunha Camargo
- Laboratory of Molecular Epidemiology and Microbiology, Department of Physics and Interdisciplinary Science, São Carlos Institute of Physics, University of São Paulo, São Carlos 13563-120, Brazil
| |
Collapse
|