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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.
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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.
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Garba Z, Kaboré B, Bonkoungou IJO, Natama MH, Rouamba T, Haukka K, Kirveskari JP, Tinto H, Sangaré L, Barro N, Kantele A. Phenotypic Detection of Carbapenemase and AmpC-β-Lactamase Production among Extended Spectrum β-Lactamase (ESBL)-Producing Escherichia coli and Klebsiella spp. Isolated from Clinical Specimens. Antibiotics (Basel) 2023; 13:31. [PMID: 38247589 PMCID: PMC10812623 DOI: 10.3390/antibiotics13010031] [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: 11/09/2023] [Revised: 12/18/2023] [Accepted: 12/21/2023] [Indexed: 01/23/2024] Open
Abstract
Introduction: Data on antimicrobial resistance (AMR) are sparse across numerous African countries, as microbiological analyses are not routinely conducted and surveillance data are not collected. Accordingly, clinical samples are not routinely tested for carbapenem-resistant bacteria and, therefore, the general understanding of their prevalence in the region remains limited. Methods: Between January 2020 and June 2022, we collected extended spectrum β-lactamase (ESBL)-producing Enterobacterales (ESBL-PE) isolates from five hospitals in Burkina Faso. After an initial culture on ESBL-selective media, the species were identified using API20E and isolates were tested against 13 antimicrobial agents using the disc diffusion method on Mueller-Hinton (MH) agar. ESBL production was confirmed via a double-disc synergy test. Production of carbapenemases and AmpC-β-lactamases and phenotypic co-resistance were determined. Results: Among the 473 ESBL-PE, 356 were ESBL-E. coli (ESBL-Ec) and 117 were Klebsiella spp. (ESBL-K). Of these isolates, 5.3% were carbapenemase and 5.3% were AmpC-β-lactamase-positive. Three types of carbapenemases were identified: 19 NDM, 3 OXA-48-like and 1 VIM. Two isolates produced both NDM and OXA-48-like carbapenemases. Carbapenemase producers were detected at all levels of healthcare. Co-resistance rates were up to 85% for aminoglycosides, 90% for sulfonamides, 95% for fluoroquinolones and 25% for chloramphenicol. Fosfomycin resistance was 6% for ESBL-Ec and 49% for ESBL-K (49%). Conclusions: Some of the ESBL-Ec and ESBL-K co-produced carbapenemases and/or AmpC-β-lactamases at all healthcare levels and in various sample types with high co-resistance rates to non-betalactams. Carbapenem resistance is no longer rare, calling for testing in routine diagnostics, a comprehensive resistance surveillance system and infection control within healthcare.
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Affiliation(s)
- Zakaria Garba
- Department of Biochemistry and Microbiology, Université Joseph KI-ZERBO, Ouagadougou 03 BP 7021, Burkina Faso; (I.J.O.B.); (N.B.)
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Ouagadougou 11 BP 218, Burkina Faso; (B.K.); (M.H.N.); (T.R.); (H.T.)
| | - Bérenger Kaboré
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Ouagadougou 11 BP 218, Burkina Faso; (B.K.); (M.H.N.); (T.R.); (H.T.)
| | - Isidore J. O. Bonkoungou
- Department of Biochemistry and Microbiology, Université Joseph KI-ZERBO, Ouagadougou 03 BP 7021, Burkina Faso; (I.J.O.B.); (N.B.)
| | - Magloire H. Natama
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Ouagadougou 11 BP 218, Burkina Faso; (B.K.); (M.H.N.); (T.R.); (H.T.)
| | - Toussaint Rouamba
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Ouagadougou 11 BP 218, Burkina Faso; (B.K.); (M.H.N.); (T.R.); (H.T.)
| | - Kaisa Haukka
- Department of Microbiology, University of Helsinki, 00014 Helsinki, Finland;
- Human Microbiome Research Program, Medical Faculty, University of Helsinki, 00014 Helsinki, Finland
| | - Juha P. Kirveskari
- Helsinki Innovation Services Ltd., University of Helsinki, 00014 Helsinki, Finland;
| | - Halidou Tinto
- Clinical Research Unit of Nanoro, Institut de Recherche en Sciences de la Santé, Ouagadougou 11 BP 218, Burkina Faso; (B.K.); (M.H.N.); (T.R.); (H.T.)
| | - Lassana Sangaré
- Department of Health Sciences, Université Joseph KI-ZERBO, Ouagadougou 03 BP 7021, Burkina Faso;
| | - Nicolas Barro
- Department of Biochemistry and Microbiology, Université Joseph KI-ZERBO, Ouagadougou 03 BP 7021, Burkina Faso; (I.J.O.B.); (N.B.)
| | - Anu Kantele
- Human Microbiome Research Program, Medical Faculty, University of Helsinki, 00014 Helsinki, Finland
- Meilahti Infectious Diseases and Vaccine Research Center MeiVac, Helsinki University Hospital, 00029 Helsinki, Finland
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