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Ibáñez-Prada ED, Bustos IG, Gamboa-Silva E, Josa DF, Mendez L, Fuentes YV, Serrano-Mayorga CC, Baron O, Ruiz-Cuartas A, Silva E, Judd LM, Harshegyi T, Africano HF, Urrego-Reyes J, Beltran CC, Medina S, Leal R, Stewardson AJ, Wyres KL, Hawkey J, Reyes LF. Molecular characterization and descriptive analysis of carbapenemase-producing Gram-negative rod infections in Bogota, Colombia. Microbiol Spectr 2024; 12:e0171423. [PMID: 38629835 DOI: 10.1128/spectrum.01714-23] [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: 04/28/2023] [Accepted: 03/13/2024] [Indexed: 06/06/2024] Open
Abstract
In this study, the genetic differences and clinical impact of the carbapenemase-encoding genes among the community and healthcare-acquired infections were assessed. This retrospective, multicenter cohort study was conducted in Colombia and included patients infected with carbapenem-resistant Gram-negative rods between 2017 and 2021. Carbapenem resistance was identified by Vitek, and carbapenemase-encoding genes were identified by whole-genome sequencing (WGS) to classify the alleles and sequence types (STs). Descriptive statistics were used to determine the association of any pathogen or gene with clinical outcomes. A total of 248 patients were included, of which only 0.8% (2/248) had community-acquired infections. Regarding the identified bacteria, the most prevalent pathogens were Pseudomonas aeruginosa and Klebsiella pneumoniae. In the WGS analysis, 228 isolates passed all the quality criteria and were analyzed. The principal carbapenemase-encoding gene was blaKPC, specifically blaKPC-2 [38.6% (88/228)] and blaKPC-3 [36.4% (83/228)]. These were frequently detected in co-concurrence with blaVIM-2 and blaNDM-1 in healthcare-acquired infections. Notably, the only identified allele among community-acquired infections was blaKPC-3 [50.0% (1/2)]. In reference to the STs, 78 were identified, of which Pseudomonas aeruginosa ST111 was mainly related to blaKPC-3. Klebsiella pneumoniae ST512, ST258, ST14, and ST1082 were exclusively associated with blaKPC-3. Finally, no particular carbapenemase-encoding gene was associated with worse clinical outcomes. The most identified genes in carbapenemase-producing Gram-negative rods were blaKPC-2 and blaKPC-3, both related to gene co-occurrence and diverse STs in the healthcare environment. Patients had several systemic complications and poor clinical outcomes that were not associated with a particular gene.IMPORTANCEAntimicrobial resistance is a pandemic and a worldwide public health problem, especially carbapenem resistance in low- and middle-income countries. Limited data regarding the molecular characteristics and clinical outcomes of patients infected with these bacteria are available. Thus, our study described the carbapenemase-encoding genes among community- and healthcare-acquired infections. Notably, the co-occurrence of carbapenemase-encoding genes was frequently identified. We also found 78 distinct sequence types, of which two were novel Pseudomonas aeruginosa, which could represent challenges in treating these infections. Our study shows that in low and middle-income countries, such as Colombia, the burden of carbapenem resistance in Gram-negative rods is a concern for public health, and regardless of the allele, these infections are associated with poor clinical outcomes. Thus, studies assessing local epidemiology, prevention strategies (including trials), and underpinning genetic mechanisms are urgently needed, especially in low and middle-income countries.
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Affiliation(s)
- Elsa D Ibáñez-Prada
- Unisabana Center for Translational Science, School of Medicine, Universidad de la Sabana, Chía, Colombia
- Critical Care Department, Clínica Universidad de La Sabana, Chía, Colombia
| | - Ingrid G Bustos
- Unisabana Center for Translational Science, School of Medicine, Universidad de la Sabana, Chía, Colombia
- Critical Care Department, Clínica Universidad de La Sabana, Chía, Colombia
| | - Enrique Gamboa-Silva
- Unisabana Center for Translational Science, School of Medicine, Universidad de la Sabana, Chía, Colombia
| | - Diego F Josa
- Unisabana Center for Translational Science, School of Medicine, Universidad de la Sabana, Chía, Colombia
- Microbiology Department, Fundación Clínica Shaio, Bogota, Colombia
| | - Lina Mendez
- Critical Care Department, Clínica Universidad de La Sabana, Chía, Colombia
| | - Yuli V Fuentes
- Unisabana Center for Translational Science, School of Medicine, Universidad de la Sabana, Chía, Colombia
| | | | - Oscar Baron
- Unisabana Center for Translational Science, School of Medicine, Universidad de la Sabana, Chía, Colombia
| | - Alejandra Ruiz-Cuartas
- Unisabana Center for Translational Science, School of Medicine, Universidad de la Sabana, Chía, Colombia
| | - Edwin Silva
- Unisabana Center for Translational Science, School of Medicine, Universidad de la Sabana, Chía, Colombia
- Microbiology Department, Fundación Clínica Shaio, Bogota, Colombia
| | - Louise M Judd
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Taylor Harshegyi
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Hector F Africano
- Critical Care Department, Clínica Universidad de La Sabana, Chía, Colombia
| | | | | | - Sebastian Medina
- Global Medical Scientific Affairs, MSD Colombia, Bogota, Colombia
| | - Rafael Leal
- Microbiology Department, Fundación Clínica Shaio, Bogota, Colombia
| | - Andrew J Stewardson
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Kelly L Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Jane Hawkey
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
| | - Luis Felipe Reyes
- Unisabana Center for Translational Science, School of Medicine, Universidad de la Sabana, Chía, Colombia
- Critical Care Department, Clínica Universidad de La Sabana, Chía, Colombia
- Pandemic Sciences Institute, University of Oxford, Oxford, United Kingdom
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Vega AD, DeRonde K, Jimenez A, Piazza M, Vu C, Martinez O, Rojas LJ, Marshall S, Yasmin M, Bonomo RA, Abbo LM. Difficult-to-treat (DTR) Pseudomonas aeruginosa harboring Verona-Integron metallo-β-lactamase ( blaVIM): infection management and molecular analysis. Antimicrob Agents Chemother 2024; 68:e0147423. [PMID: 38602418 PMCID: PMC11064525 DOI: 10.1128/aac.01474-23] [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: 11/08/2023] [Accepted: 03/11/2024] [Indexed: 04/12/2024] Open
Abstract
Pseudomonas aeruginosa harboring Verona Integron-encoded metallo-β-lactamase enzymes (VIM-CRPA) have been associated with infection outbreaks in several parts of the world. In the US, however, VIM-CRPA remain rare. Starting in December 2018, we identified a cluster of cases in our institution. Herein, we present our epidemiological investigation and strategies to control/manage these challenging infections. This study was conducted in a large academic healthcare system in Miami, FL, between December 2018 and January 2022. Patients were prospectively identified via rapid molecular diagnostics when cultures revealed carbapenem-resistant P. aeruginosa. Alerts were received in real time by the antimicrobial stewardship program and infection prevention teams. Upon alert recognition, a series of interventions were performed as a coordinated effort. A retrospective chart review was conducted to collect patient demographics, antimicrobial therapy, and clinical outcomes. Thirty-nine VIM-CRPA isolates led to infection in 21 patients. The majority were male (76.2%); the median age was 52 years. The majority were mechanically ventilated (n = 15/21; 71.4%); 47.6% (n = 10/21) received renal replacement therapy at the time of index culture. Respiratory (n = 20/39; 51.3%) or bloodstream (n = 13/39; 33.3%) were the most common sources. Most infections (n = 23/37; 62.2%) were treated with an aztreonam-avibactam regimen. Six patients (28.6%) expired within 30 days of index VIM-CRPA infection. Fourteen isolates were selected for whole genome sequencing. Most of them belonged to ST111 (12/14), and they all carried blaVIM-2 chromosomally. This report describes the clinical experience treating serious VIM-CRPA infections with either aztreonam-ceftazidime/avibactam or cefiderocol in combination with other agents. The importance of implementing infection prevention strategies to curb VIM-CRPA outbreaks is also demonstrated.
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Affiliation(s)
- Ana D. Vega
- Department of Pharmacy, Jackson Health System, Miami, Florida, USA
| | - Kailynn DeRonde
- Department of Pharmacy, Jackson Health System, Miami, Florida, USA
| | - Adriana Jimenez
- Department of Pharmacy, Jackson Health System, Miami, Florida, USA
- Department of Epidemiology, Florida International University, Miami, Florida, USA
| | - Michael Piazza
- Department of Medicine, Virtua Medical Group, Medford, New Jersey, USA
| | - Christine Vu
- Department of Pharmacy, Jackson Health System, Miami, Florida, USA
| | - Octavio Martinez
- Department of Pharmacy, Jackson Health System, Miami, Florida, USA
- Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Laura J. Rojas
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - Steven Marshall
- Department of Medicine, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Mohamad Yasmin
- Department of Medicine, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Robert A. Bonomo
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
- Department of Medicine, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Departments of Proteomics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Lilian M. Abbo
- Department of Pharmacy, Jackson Health System, Miami, Florida, USA
- Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida, USA
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Urbanowicz P, Izdebski R, Biedrzycka M, Gniadkowski M. VIM-type metallo-β-lactamase (MBL)-encoding genomic islands in Pseudomonas spp. in Poland: predominance of clc-like integrative and conjugative elements (ICEs). J Antimicrob Chemother 2024; 79:1030-1037. [PMID: 38488311 DOI: 10.1093/jac/dkae068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2023] [Accepted: 02/23/2024] [Indexed: 05/03/2024] Open
Abstract
OBJECTIVES To characterize VIM-type metallo-β-lactamase (MBL)-encoding genomic islands (GIs) in Pseudomonas aeruginosa and P. putida group isolates from Polish hospitals from 2001-2015/16. METHODS Twelve P. aeruginosa and 20 P. putida group isolates producing VIM-like MBLs were selected from a large collection of these based on epidemiological and typing data. The organisms represented all major epidemic genotypes of these species spread in Poland with chromosomally located blaVIM gene-carrying integrons. The previously determined short-read sequences were complemented by long-read sequencing in this study. The comparative structural analysis of the GIs used a variety of bioinformatic tools. RESULTS Thirty different GIs with blaVIM integrons were identified in the 32 isolates, of which 24 GIs from 26 isolates were integrative and conjugative elements (ICEs) of the clc family. These in turn were dominated by 21 variants of the GI2/ICE6441 subfamily with a total of 19 VIM integrons, each inserted in the same position within the ICE's Tn21-like transposon Tn4380. The three other ICEs formed a novel ICE6705 subfamily, lacking Tn4380 and having different VIM integrons located in another site of the elements. The remaining six non-ICE GIs represented miscellaneous structures. The presence of various integrons in the same ICE sublineage, and of the same integron in different GIs, indicated circulation and recombination of the integron-carrying genetic platforms across Pseudomonas species/genotypes. CONCLUSIONS Despite the general diversity of the blaVIM-carrying GIs in Pseudomonas spp. in Poland, a clear predominance of broadly spread and rapidly evolving clc-type ICEs was documented, confirming their significant role in antimicrobial resistance epidemiology.
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Affiliation(s)
- P Urbanowicz
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, Warsaw 00-725, Poland
| | - R Izdebski
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, Warsaw 00-725, Poland
| | - M Biedrzycka
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, Warsaw 00-725, Poland
| | - M Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, Warsaw 00-725, Poland
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Biedrzycka M, Urbanowicz P, Żabicka D, Hryniewicz W, Gniadkowski M, Izdebski R. Country-wide expansion of a VIM-1 carbapenemase-producing Klebsiella oxytoca ST145 lineage in Poland, 2009-2019. Eur J Clin Microbiol Infect Dis 2023; 42:1449-1457. [PMID: 37857919 PMCID: PMC10651708 DOI: 10.1007/s10096-023-04682-x] [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: 10/10/2023] [Indexed: 10/21/2023]
Abstract
PURPOSE To elucidate the role of the Klebsiella oxytoca species complex (KoSC) in epidemiology of VIM-type MBL-producing Enterobacterales in Poland. METHODS The study comprised all 106 VIM-positive KoSC isolates collected by the Polish National Reference Centre for Susceptibility Testing during 2009-2019 from 60 institutions in 35 towns. All isolates were sequenced by Illumina MiSeq, followed by MinION sequencing of selected organisms. Genomes were subjected to bioinformatic analysis, addressing taxonomy, clonality, phylogeny and structural characterisation of key resistance determinants within their chromosomal and plasmidic loci. RESULTS Among five species identified, K. oxytoca was predominant (n = 92), followed by Klebsiella michiganensis (n = 11). MLST distinguished 18 STs, with the most prevalent Klebsiella oxytoca ST145 (n = 83). The clone segregated a lineage with the In237-like integron [blaVIM-1-aacA4 genes; n = 78], recorded in 28 cities almost all over the country. The integron was located in a ~ 49-50 kb chromosomal mosaic region with multiple other resistance genes, linked to a ~ 51 kb phage-like element. The organism might have originated from Greece, and its evolution in Poland included several events of chromosomal ~ 54-258 kb deletions, comprising the natural β-lactamase blaOXY gene. A group of other isolates of various species and clones (n = 12) carried the integron In916 on self-transmissible IncA-type plasmids, effectively spreading in Italy, France and Poland. CONCLUSION KoSC has been one of the major VIM producers in Poland, owing largely to clonal expansion of the specific K. oxytoca-In237-like lineage. Its apparently enhanced epidemic potential may create a danger on international scale.
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Affiliation(s)
- M Biedrzycka
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - P Urbanowicz
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - D Żabicka
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - W Hryniewicz
- Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - M Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland
| | - R Izdebski
- Department of Molecular Microbiology, National Medicines Institute, Chełmska 30/34, 00-725, Warsaw, Poland.
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Fang J, Liu Q, Yang J, Kang X, Mei Y, Liu J, Wang G, Xiang T. Functional Portrait and Genomic Feature of Carbapenem-Resistant Pseudomonas mendocina Harboring blaNDM-1 and blaIMP-1 in China. Foodborne Pathog Dis 2023; 20:502-508. [PMID: 37729068 DOI: 10.1089/fpd.2023.0055] [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: 09/22/2023] Open
Abstract
The purpose of this research was to analyze the functional portraits and genomic features of carbapenem-resistant Pseudomonas mendocina carrying NDM-1 and IMP-1. The resistance mechanism of the strain was verified by in vivo experiments. Genomic data were aligned and analyzed in the NCBI database. Growth curve measurements were used to describe the growth characteristics of the bacteria. The virulence of P. mendocina strain was analyzed by serum killing assay and biofilm formation assay. Plasmid conjugation experiments were performed to verify the transferability of plasmids carrying drug-resistance genes. The P. mendocina strain was highly resistant to carbapenems. In addition, ST typing is unknown and has been submitted to Genebank. The strain carried two carbapenemase genes, including NDM-1 and IMP-1. Among them, blaNDM-1 was located on a 5.62832 Mb chromosome, and blaIMP-1 was located on a 172.851 Kb transferable plasmid, which was a very close relative of pIMP-NY7610 in China. The strain also had a variety of virulence genes, which were expressed in the siderophore, capsule, pilus, alginate, flagella, etc. The study suggests that the functional portrait and genomic features of carbapenem-resistant P. mendocina harboring blaNDM-1 and blaIMP-1 are unique to China. This outcome represents antibiotic resistance exhibited in the genus Pseudomonas by acquiring chromosomes and plasmid genes. The monitoring and supervision of antimicrobial usage must be strengthened since the multi-drug-resistant and moderately virulent P. mendocina will attract much attention in the near future.
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Affiliation(s)
- Jianhua Fang
- Infectious Disease Department, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Infectious Disease Department, Nanchang University, Nanchang, China
| | - Qiong Liu
- Department of Respiratory and Critial Care Medicine, The First Affiliated Hospital of Nanchang University, Nanchang University, Nanchang, China
- Department of Respiratory and Critial Care Medicine, Nanchang Medical College, Nanchang, China
| | - Jie Yang
- Department of Cerebral Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Xiuhua Kang
- Department of Hospital Infection Control, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Yanfang Mei
- Laboratory Medicine, The First Affiliated Hospital of Nanchang University, Nanchang, China
| | - Jing Liu
- Infectious Disease Department, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Infectious Disease Department, Nanchang University, Nanchang, China
| | - Guoyu Wang
- Infectious Disease Department, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Infectious Disease Department, Nanchang University, Nanchang, China
| | - Tianxin Xiang
- Department of Hospital Infection Control, The First Affiliated Hospital of Nanchang University, Nanchang, China
- Jiangxi Hospital of China-Japan Friendship Hospital, Nanchang, P.R. China
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Izdebski R, Biedrzycka M, Urbanowicz P, Żabicka D, Gniadkowski M. Genome-Based Epidemiologic Analysis of VIM/IMP Carbapenemase-Producing Enterobacter spp., Poland. Emerg Infect Dis 2023; 29:1618-1626. [PMID: 37486192 PMCID: PMC10370858 DOI: 10.3201/eid2908.230199] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/25/2023] Open
Abstract
We sequenced all nonduplicate 934 VIM/IMP carbapenemase-producing Enterobacterales (CPE) reported in Poland during 2006-2019 and found ≈40% of the isolates (n = 375) were Enterobacter spp. During the study period, incidence of those bacteria gradually grew in nearly the entire country. The major factor affecting the increase was clonal spread of several E. hormaechei lineages responsible for multiregional and interregional outbreaks (≈64% of all isolates), representing mainly the pandemic sequence type (ST) 90 or the internationally rare ST89 and ST121 clones. Three main VIM-encoding integron types efficiently disseminated across the clone variants (subclones) with various molecular platforms. Those variants were predominantly Pseudomonas aeruginosa-derived In238-like elements, present with IncHI2+HI2A, IncFII+FIA, IncFIB, or IncN3 plasmids, or chromosomal genomic islands in 30 Enterobacter STs. Another prevalent type, found in 34 STs, were In916-like elements, spreading in Europe recently with a lineage of IncA-like plasmids.
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Kabic J, Fortunato G, Vaz-Moreira I, Kekic D, Jovicevic M, Pesovic J, Ranin L, Opavski N, Manaia CM, Gajic I. Dissemination of Metallo-β-Lactamase-Producing Pseudomonas aeruginosa in Serbian Hospital Settings: Expansion of ST235 and ST654 Clones. Int J Mol Sci 2023; 24:ijms24021519. [PMID: 36675030 PMCID: PMC9863560 DOI: 10.3390/ijms24021519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2022] [Revised: 01/03/2023] [Accepted: 01/09/2023] [Indexed: 01/14/2023] Open
Abstract
This nationwide study aimed to investigate the molecular characteristics of metallo-β-lactamase (MBL)-producing Pseudomonas aeruginosa in Serbia, underlying resistance mechanisms, the genetic context of detected MBL genes, and the clonal relationship between isolates harboring genes-encoding MBL. Overall, 320/5334 isolates collected from 2018 to 2021 were identified as P. aeruginosa. Carbapenem-resistant P. aeruginosa (CRPA) were screened for the presence of blaVIM, blaIMP, and blaNDM, genes whereas MBL-positive isolates were tested for the presence of the blaCTX-M-2, blaPER, blaTEM, blaSHV, blaVEB, and blaGES. Multilocus sequence typing and phylogenomic analysis were performed for P. aeruginosa-producing MBL. The majority of the P. aeruginosa isolates were recovered from the lower respiratory tract (n = 120; 37.5%) and wound specimens (n = 108; 33.75%). CRPA isolates accounted for 43.1% (n = 138) of the tested isolates, 31 out of them being blaNDM-1-positive (22.5%). The colistin resistance rate was 0.3%. MLST analysis revealed the occurrence of ST235 (n = 25) and ST654 (n = 6), mostly confined to Serbia. The distribution of beta-lactamase-encoding genes in these isolates suggested clonal dissemination and possible recombination: ST235/blaNDM-1, ST235/blaNDM-1/blaPER-1, ST654/blaNDM-1, ST654/blaNDM-1/blaPER-1, and ST654/blaNDM-1/blaGES-5. High-risk clones ST235 and ST654 identified for the first time in Serbia, are important vectors of acquired MBL and ESBL and their associated multidrug resistance phenotypes represent a cause for considerable concern.
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Affiliation(s)
- Jovana Kabic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Dr Subotica Starijeg 1, 11000 Belgrade, Serbia
| | - Gianuario Fortunato
- CBQF—Centro de Biotecnologia e Química Fina—Laboratório Associado, Universidade Católica Portuguesa, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
| | - Ivone Vaz-Moreira
- CBQF—Centro de Biotecnologia e Química Fina—Laboratório Associado, Universidade Católica Portuguesa, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
| | - Dusan Kekic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Dr Subotica Starijeg 1, 11000 Belgrade, Serbia
| | - Milos Jovicevic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Dr Subotica Starijeg 1, 11000 Belgrade, Serbia
| | - Jovan Pesovic
- Faculty of Biology, University of Belgrade, Studentski trg 16, 11000 Belgrade, Serbia
| | - Lazar Ranin
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Dr Subotica Starijeg 1, 11000 Belgrade, Serbia
| | - Natasa Opavski
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Dr Subotica Starijeg 1, 11000 Belgrade, Serbia
| | - Célia M. Manaia
- CBQF—Centro de Biotecnologia e Química Fina—Laboratório Associado, Universidade Católica Portuguesa, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005 Porto, Portugal
| | - Ina Gajic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Dr Subotica Starijeg 1, 11000 Belgrade, Serbia
- Correspondence: ; Tel.: +381-113643-3373
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Urbanowicz P, Izdebski R, Biedrzycka M, Literacka E, Hryniewicz W, Gniadkowski M. Genomic Epidemiology of MBL-Producing Pseudomonas putida Group Isolates in Poland. Infect Dis Ther 2022; 11:1725-1740. [PMID: 35689153 PMCID: PMC9334476 DOI: 10.1007/s40121-022-00659-z] [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: 04/12/2022] [Accepted: 05/12/2022] [Indexed: 11/28/2022] Open
Abstract
Introduction Pseudomonas putida group are described as low-incidence opportunistic pathogens, but also as a significant reservoir of antimicrobial resistance (AMR) genes, including those of metallo-β-lactamases (MBLs). Our objective was the molecular and genomic characterization of MBL-producing P. putida (MPPP) group isolates from Poland, focusing on population structures, successful genotypes and MBL-encoding integrons. Methods During a country-wide MBL surveillance in Pseudomonas spp., 59 non-duplicate MPPP isolates were collected from 36 hospitals in 23 towns from 2003 to 2016. All of the isolates were subjected to whole-genome sequencing (WGS), followed by species identification, multi-locus sequence typing (MLST), single-nucleotide polymorphism (SNP)-based phylogenetic/clonality analysis, resistome determination, and susceptibility testing. Results The study collection comprised 12 species, of which P. alloputida (n = 19), P. monteilii (n = 15), and P. asiatica (n = 11) prevailed, while the others were P. kurunegalensis, P. putida, P. soli, P. mosselii, P. juntendi, and four potentially new species. MLST classified the isolates into 23 sequence types (STs) of which 21 were new, with three main clones, namely P. alloputida ST69, P.monteilii ST95 and P. asiatica ST15. The isolates produced VIM-like MBLs only, largely VIM-2 (n = 40), encoded by 24 different class 1 integrons (ten new), a number of which occurred also in P. aeruginosa and/or Enterobacterales in Poland. The plasmid pool was dominated by IncP-9, IncP-2, and pMOS94-like types. Multiple isolates were extensively drug-resistant. Conclusions This study, being one of the most comprehensive analyses of MPPP so far, has shown high diversity of the isolates in general, with three apparently international lineages, each internally diversified by MBL-encoding structures. Supplementary Information The online version contains supplementary material available at 10.1007/s40121-022-00659-z.
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Affiliation(s)
- Paweł Urbanowicz
- Department of Molecular Microbiology, National Medicines Institute, ul. Chełmska 30/34, 00-725, Warsaw, Poland.
| | - Radosław Izdebski
- Department of Molecular Microbiology, National Medicines Institute, ul. Chełmska 30/34, 00-725, Warsaw, Poland
| | - Marta Biedrzycka
- Department of Molecular Microbiology, National Medicines Institute, ul. Chełmska 30/34, 00-725, Warsaw, Poland
| | - Elżbieta Literacka
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, 00-725, Warsaw, Poland
| | - Waleria Hryniewicz
- Department of Epidemiology and Clinical Microbiology, The National Reference Centre for Susceptibility Testing, National Medicines Institute, 00-725, Warsaw, Poland
| | - Marek Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, ul. Chełmska 30/34, 00-725, Warsaw, Poland
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