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Silva JTP, Santos FF, Valiatti TB, Valêncio A, Ribeiro ÁCDS, Oliveira LFV, Cay R, Pignatari ACC, Gales AC. Unraveling the genomic characteristics of a Klebsiella quasipneumoniae clinical isolate carrying bla NDM-1. J Glob Antimicrob Resist 2024:S2213-7165(24)00110-3. [PMID: 38852850 DOI: 10.1016/j.jgar.2024.05.022] [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: 10/05/2023] [Revised: 05/23/2024] [Accepted: 05/29/2024] [Indexed: 06/11/2024] Open
Abstract
OBJECTIVE Despite the increasing reports of blaNDM in Enterobacterales in Brazil, comprehensive whole genome sequencing (WGS) data remains scarce. To address this knowledge gap, our study focuses on the characterization of the genome of an NDM-1-producing Klebsiella quasipneumoniae subsp. quasipneumoniae (KQPN) clinical strain isolated in Brazil. METHODS The antimicrobial susceptibility profile of the A-73.113 strain was performed by agar dilution or broth microdilution following the BrCAST/EUCAST recommendations. WGS was performed using the Illumina® NextSeq platform and the generated reads were assembled using the SPAdes software. The sequences obtained were submitted to the bioinformatics pipelines to determine the sequence type, resistome, plasmidome, and virulome. RESULTS The A-73.113 strain was identified as KQPN and was susceptible to polymyxins (MICs, ≤0.25 µg/mL), tigecycline (MIC, 0.5 µg/mL), ciprofloxacin (MIC, 0.5 µg/mL), and levofloxacin (MIC, 1 µg/mL). WGS analysis revealed the presence of genes conferring resistance to β-lactams (blaNDM-1, blaCTX-M-15, blaOXA-9, blaOKP-A-5, blaTEM-1), aminoglycosides [aph(3')-VI, aadA1, aac(6')-Ib], and fluoroquinolones (oqxAB, qnrS1, aac(6')-Ib-cr]. Additionally, it was verified the presence of the plasmid replicons Col(pHAD28), IncFIA(HI1), IncFIB(K) (pCAV1099-114), IncFIB(pQil), and IncFII(K), as well as virulence-encoding genes: fimABCDEFGHIK (type 1 fimbria), pilW (type IV pili), iutA (aerobactin), entABCDEFS/fepABCDG/fes (Ent siderophores), iroE (salmochelin), and allABCDRS (allantoin utilization). Furthermore, we found that A-73.113 strain belongs to ST1040. CONCLUSION Here we report the genomic characteristics of an NDM-1-producing KQPN ST1040 strain isolated from blood culture in Brazil. These data will enhance our comprehension of how this species contributes to the acquisition and dissemination of blaNDM-1 in Brazilian nosocomial settings.
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Affiliation(s)
- Juliana Thalita P Silva
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil
| | - Fernanda F Santos
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil.
| | - Tiago B Valiatti
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil
| | - André Valêncio
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil
| | - Ághata Cardoso da Silva Ribeiro
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil
| | | | - Rodrigo Cay
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil; Universidade Federal de São Paulo (UNIFESP), Laboratório de Bacteriologia e Imunologia (LIB), Setor de Biologia Molecular, Microbiologia e Imunologia, Departamento de Ciências Biológicas (DCB), Instituto de Ciências Ambientais, Químicas e Farmacêuticas (ICAQF), Diadema SP, Brazil
| | - Antônio Carlos C Pignatari
- Universidade Federal de São Paulo (UNIFESP), Laboratório Especial de Microbiologia Clínica (LEMC), Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil
| | - Ana Cristina Gales
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil; Universidade Federal de São Paulo (UNIFESP), Laboratório Especial de Microbiologia Clínica (LEMC), Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil.
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Puljko A, Barišić I, Dekić Rozman S, Križanović S, Babić I, Jelić M, Maravić A, Udiković-Kolić N. Molecular epidemiology and mechanisms of carbapenem and colistin resistance in Klebsiella and other Enterobacterales from treated wastewater in Croatia. ENVIRONMENT INTERNATIONAL 2024; 185:108554. [PMID: 38479059 DOI: 10.1016/j.envint.2024.108554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 01/30/2024] [Accepted: 03/02/2024] [Indexed: 03/26/2024]
Abstract
Among the most problematic bacteria with clinical relevance are the carbapenem-resistant Enterobacterales (CRE), as there are very limited options for their treatment. Treated wastewater can be a route for the release of these bacteria into the environment and the population. The aim of this study was to isolate CRE from treated wastewater from the Zagreb wastewater treatment plant and to determine their phenotypic and genomic characteristics. A total of 200 suspected CRE were isolated, 148 of which were confirmed as Enterobacterales by MALDI-TOF MS. The predominant species was Klebsiella spp. (n = 47), followed by Citrobacter spp. (n = 40) and Enterobacter cloacae complex (cplx.) (n = 35). All 148 isolates were carbapenemase producers with a multidrug-resistant phenotype. Using multi-locus sequence typing and whole-genome sequencing (WGS), 18 different sequence types were identified among these isolates, 14 of which were associated with human-associated clones. The virulence gene analysis of the sequenced Klebsiella isolates (n = 7) revealed their potential pathogenicity. PCR and WGS showed that the most frequent carbapenemase genes in K. pneumoniae were blaOXA-48 and blaNDM-1, which frequently occurred together, while blaKPC-2 together with blaNDM-1 was mainly detected in K. oxytoca, E. cloacae cplx. and Citrobacter spp. Colistin resistance was observed in 40% of Klebsiella and 57% of Enterobacter isolates. Underlying mechanisms identified by WGS include known and potentially novel intrinsic mechanisms (point mutations in the pmrA/B, phoP/Q, mgrB and crrB genes) and acquired mechanisms (mcr-4.3 gene). The mcr-4.3 gene was identified for the first time in K. pneumoniae and is probably located on the conjugative IncHI1B plasmid. In addition, WGS analysis of 13 isolates revealed various virulence genes and resistance genes to other clinically relevant antibiotics as well as different plasmids possibly associated with carbapenemase genes. Our study demonstrates the important role that treated municipal wastewater plays in harboring and spreading enterobacterial pathogens that are resistant to last-resort antibiotics.
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Affiliation(s)
- Ana Puljko
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Ivan Barišić
- Molecular Diagnostics, Austrian Institute of Technology, Giefinggasse 4, 1210 Vienna, Austria
| | - Svjetlana Dekić Rozman
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Stela Križanović
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Ivana Babić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia
| | - Marko Jelić
- Department of Clinical Microbiology, University Hospital for Infectious Diseases, Mirogojska 8, 10 000 Zagreb, Croatia
| | - Ana Maravić
- Department of Biology, Faculty of Science, University of Split, Ruđera Boškovića 33, 21 000 Split, Croatia
| | - Nikolina Udiković-Kolić
- Division for Marine and Environmental Research, Ruđer Bošković Institute, Bijenička 54, P.O. Box 180, 10 002 Zagreb, Croatia.
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Huo M, Xu X, Mi K, Ma W, Zhou Q, Lin X, Cheng G, Huang L. Co-selection mechanism for bacterial resistance to major chemical pollutants in the environment. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 912:169223. [PMID: 38101638 DOI: 10.1016/j.scitotenv.2023.169223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 11/30/2023] [Accepted: 12/07/2023] [Indexed: 12/17/2023]
Abstract
Bacterial resistance is an emerging global public health problem, posing a significant threat to animal and human health. Chemical pollutants present in the environment exert selective pressure on bacteria, which acquire resistance through co-resistance, cross-resistance, co-regulation, and biofilm resistance. Resistance genes are horizontally transmitted in the environment through four mechanisms including conjugation transfer, bacterial transformation, bacteriophage transduction, and membrane vesicle transport, and even enter human bodies through the food chain, endangering human health. Although the co-selection effects of bacterial resistance to chemical pollutants has attracted widespread attention, the co-screening mechanism and co-transmission mechanisms remain unclear. Therefore, this article summarises the current research status of the co-selection effects and mechanism of environmental pollutants resistance, emphasising the necessity of studying the co-selection mechanism of bacteria against major chemical pollutants, and lays a solid theoretical foundation for conducting risk assessment of bacterial resistance.
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Affiliation(s)
- Meixia Huo
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Xiangyue Xu
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Kun Mi
- National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agriculture University, Wuhan 430070, China; MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Wenjin Ma
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Qin Zhou
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Xudong Lin
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Guyue Cheng
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agriculture University, Wuhan 430070, China; MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China
| | - Lingli Huang
- National Laboratory for Veterinary Drug Safety Evaluation, Huazhong Agriculture University, Wuhan 430070, China; MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Hubei 430070, China; National Reference Laboratory of Veterinary Drug Residues (HZAU), Huazhong Agriculture University, Wuhan 430070, China; MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, Hubei 430070, China; College of Veterinary Medicine, Huazhong Agriculture University, Wuhan 430070, China.
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Hem S, Cummins ML, Wyrsch ER, Drigo B, Hoye BJ, Maute K, Sanderson-Smith M, Gorman J, Bogema DR, Jenkins C, Deutscher AT, Yam J, Hai F, Donner E, Jarocki VM, Djordjevic SP. Genomic analysis of Citrobacter from Australian wastewater and silver gulls reveals novel sequence types carrying critically important antibiotic resistance genes. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 909:168608. [PMID: 37977387 DOI: 10.1016/j.scitotenv.2023.168608] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Revised: 11/08/2023] [Accepted: 11/14/2023] [Indexed: 11/19/2023]
Abstract
Antimicrobial resistance (AMR) is a major public health concern, and environmental bacteria have been recognized as important reservoirs of antimicrobial resistance genes (ARGs). Citrobacter, a common environmental bacterium and opportunistic pathogen in humans and other animals, has been largely understudied in terms of its diversity and AMR potential. Whole-genome (short-read) sequencing on a total of 77 Citrobacter isolates obtained from Australian silver gull (Chroicocephalus novaehollandiae) (n = 17) and influent wastewater samples (n = 60) was performed, revealing a diverse Citrobacter population, with seven different species and 33 sequence types, 17 of which were novel. From silver gull using non-selective media we isolated a broader range of species with little to no mobilised ARG carriage. Wastewater isolates (selected using Carbapenem- Resistant Enterobacterales (CRE) selective media) carried a heavy burden of ARGs (up to 21 ARGs, conferring resistance to nine classes of antibiotics), with several novel multidrug-resistant (MDR) lineages identified, including C. braakii ST1110, which carried ARGs conferring resistance to eight to nine classes of antibiotics, and C. freundii ST1105, which carried two carbapenemase genes, blaIMP-4 in class 1 integron structure, and blaKPC-2. Additionally, we identified an MDR C. portucalensis isolate carrying blaNDM-1, blaSHV-12, and mcr-9. We identified IncC, IncM2, and IncP6 plasmids as the likely vectors for many of the critically important mobilised ARGs. Phylogenetic analyses were performed to assess any epidemiological linkages between isolation sources, demonstrating low relatedness across sources beyond the ST level. However, these analyses did reveal some closer relationships between strains from disparate wastewater sources despite their collection some 13,000 km apart. These findings support the need for future surveillance of Citrobacter populations in wastewater and wildlife populations to monitor for potential opportunistic human pathogens.
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Affiliation(s)
- Sopheak Hem
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, Australia; The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, Australia
| | - Max L Cummins
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, Australia; The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, Australia
| | - Ethan R Wyrsch
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, Australia; The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, Australia
| | - Barbara Drigo
- UniSA STEM, University of South Australia, Adelaide, SA, Australia
| | - Bethany J Hoye
- School of Earth, Atmospheric and Life Sciences, University of Wollongong NSW, Australia; Environmental Futures Research Centre, University of Wollongong NSW, Australia
| | - Kimberly Maute
- School of Earth, Atmospheric and Life Sciences, University of Wollongong NSW, Australia; Environmental Futures Research Centre, University of Wollongong NSW, Australia
| | - Martina Sanderson-Smith
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, NSW, Australia
| | - Jody Gorman
- School of Chemistry and Molecular Bioscience and Molecular Horizons, University of Wollongong, NSW, Australia
| | - Daniel R Bogema
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW, Australia
| | - Cheryl Jenkins
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW, Australia
| | - Ania T Deutscher
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW, Australia
| | - Jerald Yam
- Elizabeth Macarthur Agricultural Institute, NSW Department of Primary Industries, Menangle, NSW, Australia
| | - Faisal Hai
- School of Civil, Mining, Environmental and Architectural Engineering, University of Wollongong, NSW, Australia
| | - Erica Donner
- Cooperative Research Centre for Solving Antimicrobial resistance in Agribusiness, Food, and Environments (CRC SAAFE), Adelaide, South Australia, Australia; Future Industries Institute, University of South Australia, Adelaide, South Australia, Australia
| | - Veronica M Jarocki
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, Australia; The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, Australia.
| | - Steven P Djordjevic
- Australian Institute for Microbiology and Infection, University of Technology Sydney, Ultimo, Australia; The Australian Centre for Genomic Epidemiological Microbiology, University of Technology Sydney, Ultimo, Australia.
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Valiatti TB, Bessa-Neto FO, Santos FF, Silva RGB, Veiga R, Cassu-Corsi D, Moura TCF, Lobato ARF, Pignatari ACC, Souza CO, Brasiliense DM, Cayô R, Gales AC. Clonal dissemination of highly virulent Serratia marcescens strains producing KPC-2 in food-producing animals. One Health 2023; 17:100591. [PMID: 37388190 PMCID: PMC10302155 DOI: 10.1016/j.onehlt.2023.100591] [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: 12/22/2022] [Revised: 06/17/2023] [Accepted: 06/20/2023] [Indexed: 07/01/2023] Open
Abstract
Serratia marcescens is a Gram-negative bacterium presenting intrinsic resistance to polymyxins that has emerged as an important human pathogen. Although previous studies reported the occurrence of multidrug-resistance (MDR) S. marcescens isolates in the nosocomial settings, herein, we described isolates of this extensively drug-resistant (XDR) species recovered from stool samples of food-producing animals in the Brazilian Amazon region. Three carbapenem-resistant S. marcescens strains were recovered from stool samples of poultry and cattle. Genetic similarity analysis showed that these strains belonged to the same clone. Whole-genome sequencing of a representative strain (SMA412) revealed a resistome composed of genes encoding resistance to β-lactams [blaKPC-2, blaSRT-2], aminoglycosides [aac(6')-Ib3, aac(6')-Ic, aph(3')-VIa], quinolones [aac(6')-Ib-cr], sulfonamides [sul2], and tetracyclines [tet(41)]. In addition, the analysis of the virulome demonstrated the presence of important genes involved in the pathogenicity of this species (lipBCD, pigP, flhC, flhD, phlA, shlA, and shlB). Our data demonstrate that food-animal production can act as reservoirs for MDR and virulent strains of S. marcescens.
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Affiliation(s)
- Tiago Barcelos Valiatti
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil
| | - Francisco Ozório Bessa-Neto
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil
- Universidade Federal de São Paulo (UNIFESP), Laboratório de Imunologia e Bacteriologia (LIB), Setor de Biologia Molecular, Microbiologia e Imunologia, Departamento de Ciências Biológicas (DCB), Instituto de Ciências Ambientais, Químicas e Farmacêuticas (ICAQF), Diadema, SP, Brazil
| | - Fernanda Fernandes Santos
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil
| | - Ramon Giovanni Brandão Silva
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil
- Universidade Federal de São Paulo (UNIFESP), Laboratório de Imunologia e Bacteriologia (LIB), Setor de Biologia Molecular, Microbiologia e Imunologia, Departamento de Ciências Biológicas (DCB), Instituto de Ciências Ambientais, Químicas e Farmacêuticas (ICAQF), Diadema, SP, Brazil
| | - Ruanita Veiga
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil
| | - Dandara Cassu-Corsi
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil
| | - Tuane Carolina Ferreira Moura
- Seção de Bacteriologia e Micologia, Instituto Evandro Chagas (IEC), Secretaria de Ciência, Tecnologia, Inovação e Insumos Estratégicos em Saúde (SCTIE), Ministério da Saúde, Ananindeua, PA, Brazil
| | - Amalia Raiana Fonseca Lobato
- Seção de Bacteriologia e Micologia, Instituto Evandro Chagas (IEC), Secretaria de Ciência, Tecnologia, Inovação e Insumos Estratégicos em Saúde (SCTIE), Ministério da Saúde, Ananindeua, PA, Brazil
| | - Antonio Carlos Campos Pignatari
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil
- Universidade Federal de São Paulo (UNIFESP), Laboratório Especial de Microbiologia Clínica (LEMC), Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil
| | - Cintya Oliveira Souza
- Seção de Bacteriologia e Micologia, Instituto Evandro Chagas (IEC), Secretaria de Ciência, Tecnologia, Inovação e Insumos Estratégicos em Saúde (SCTIE), Ministério da Saúde, Ananindeua, PA, Brazil
| | - Danielle Murici Brasiliense
- Seção de Bacteriologia e Micologia, Instituto Evandro Chagas (IEC), Secretaria de Ciência, Tecnologia, Inovação e Insumos Estratégicos em Saúde (SCTIE), Ministério da Saúde, Ananindeua, PA, Brazil
| | - Rodrigo Cayô
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil
- Universidade Federal de São Paulo (UNIFESP), Laboratório de Imunologia e Bacteriologia (LIB), Setor de Biologia Molecular, Microbiologia e Imunologia, Departamento de Ciências Biológicas (DCB), Instituto de Ciências Ambientais, Químicas e Farmacêuticas (ICAQF), Diadema, SP, Brazil
| | - Ana Cristina Gales
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil
- Universidade Federal de São Paulo (UNIFESP), Laboratório Especial de Microbiologia Clínica (LEMC), Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo, SP, Brazil
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Furlan JPR, da Silva Rosa R, Ramos MS, Dos Santos LDR, Lopes R, Savazzi EA, Stehling EG. Genetic plurality of bla KPC-2-harboring plasmids in high-risk clones of Klebsiella pneumoniae of environmental origin. THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 881:163322. [PMID: 37068681 DOI: 10.1016/j.scitotenv.2023.163322] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/27/2023] [Accepted: 04/02/2023] [Indexed: 06/01/2023]
Abstract
International high-risk clones of Klebsiella pneumoniae are important human pathogens that are spreading to the environment. In the COVID-19 pandemic scenario, the frequency of carbapenemase-producing strains increased, which can contribute to the contamination of the environment, impacting the surrounding and associated ecosystems. In this regard, KPC-producing strains were recovered from aquatic ecosystems located in commercial, industrial, or agricultural areas and were submitted to whole-genome characterization. K. pneumoniae and Klebsiella quasipneumoniae subsp. quasipneumoniae strains were assigned to high-risk clones (ST11, ST340, ST307) and the new ST6325. Virulome analysis showed genes related to putative hypervirulence. Strains were resistant to almost all antimicrobials tested, being classified as extensively drug-resistant or multidrug-resistant. In this context, a broad resistome (clinically important antimicrobials and hazardous metal) was detected. Single replicon (IncX5, IncN-pST15, IncU) and multireplicon [IncFII(K1)/IncFIB(pQil), IncFIA(HI1)/IncR] plasmids were identified carrying the blaKPC-2 gene with Tn4401 and non-Tn4401 elements. An unusual association of blaKPC-2 and qnrVC1 and the coexistence of blaKPC-2 and mer operon (mercury tolerance) was found. Comparative analysis revealed that blaKPC-2-bearing plasmids were most similar to plasmids from Enterobacterales of Brazil, China, and the United States, evidencing the long persistence of plasmids at the human-animal-environmental interface. Furthermore, the presence of uncommon plasmids, displaying the interspecies, intraspecies, and clonal transmission, was highlighted. These findings alert for the spread of high-risk clones producing blaKPC-2 in the environmental sector and call attention to rapid dispersion in a post-pandemic world.
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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, Brazil
| | - Rafael da Silva Rosa
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of 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, 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, Brazil
| | - Ralf Lopes
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of 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, Brazil.
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Altayb HN, Hosawi S, Baothman O, Kazmi I, Chaieb K, Abu Zeid IM, Elbadawi HS, Lopes BS, Moglad E. Molecular insights into novel environmental strains of Klebsiella quasipneumoniae harboring different antimicrobial-resistance genes. Front Public Health 2023; 10:1068888. [PMID: 36711372 PMCID: PMC9878601 DOI: 10.3389/fpubh.2022.1068888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/21/2022] [Indexed: 01/14/2023] Open
Abstract
Introduction The emergence of bacterial pathogens in environmental hosts represents a major risk to public health. This study aimed at characterizing seven novel environmental strains of K. quasipneumoniae using a genomic approach which was misidentified by phenotypic methods in a previous batch of 27 species thought to be K. pneumoniae. Methods Whole-genome sequencing was performed using the Illumina platform, and the generated raw reads were de novo assembled. Comparative genomic, resistome, virulome, mobilome, and phylogeny were then investigated using dierent bioinformatics tools. Results Six strains were identified as K. quasipneumoniae subsp similipneumoniae and one as K. quasipneumoniae subsp. quasipneumoniae. All isolates were resistant to ampicillin, cephalexin, and amoxicillin-clavulanic acid and harbored the fosA, bla OKP types, oqxB, and oqxA genes. One isolate additionally harbored a gene cassettes consisting of bla SHV-1, bla OXA-1, aac(6')-Ib-cr, catB genes. The aminoglycoside-modifying enzyme gene aph(3")-Ia was bracketed by two insertion elements. Plasmid analyses showed that IncFIBK was the most prevalent plasmid, circulating in six isolates, while one isolate exhibited seven different plasmids. The isolates have virulence genes responsible for capsule formation, lipopolysaccharide, iron uptake aerobactin (iutA), salmochelins (iroE, iroN), enterobactin siderophore, adherence, and biofilm formation (mrkA, mrkB, mrkC, mrkD, mrkF, and mrkH). Conclusion Our study highlights the ecology and transmission of K. quasipneumoniae (which have the ability to disseminate to other environmental sources including animals) outside the clinical setting and the contribution of water, vegetables, and table surfaces as potential reservoirs of farm-to-fork transmission of disease via local markets in Khartoum, Sudan.
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Affiliation(s)
- Hisham N. Altayb
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia,Center of Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah, Saudi Arabia,*Correspondence: Hisham N. Altayb ✉
| | - Salman Hosawi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Othman Baothman
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Kamel Chaieb
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Isam M. Abu Zeid
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hana S. Elbadawi
- Microbiology and Parasitology Department, Soba University Hospital, University of Khartoum, Khartoum, Sudan
| | - Bruno Silvester Lopes
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom,National Horizons Centre, Teesside University, Darlington, United Kingdom,Bruno Silvester Lopes ✉
| | - Ehssan Moglad
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi Arabia
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8
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Knecht CA, García Allende N, Álvarez VE, Prack McCormick B, Massó MG, Piekar M, Campos J, Fox B, Camicia G, Gambino AS, Leguina ACDV, Donis N, Fernández-Canigia L, Quiroga MP, Centrón D. Novel insights related to the rise of KPC-producing Enterobacter cloacae complex strains within the nosocomial niche. Front Cell Infect Microbiol 2022; 12:951049. [DOI: 10.3389/fcimb.2022.951049] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2022] [Accepted: 09/29/2022] [Indexed: 11/13/2022] Open
Abstract
According to the World Health Organization, carbapenem-resistant Enterobacteriaceae (CRE) belong to the highest priority group for the development of new antibiotics. Argentina-WHONET data showed that Gram-negative resistance frequencies to imipenem have been increasing since 2010 mostly in two CRE bacteria: Klebsiella pneumoniae and Enterobacter cloacae Complex (ECC). This scenario is mirrored in our hospital. It is known that K. pneumoniae and the ECC coexist in the human body, but little is known about the outcome of these species producing KPC, and colonizing or infecting a patient. We aimed to contribute to the understanding of the rise of the ECC in Argentina, taking as a biological model both a patient colonized with two KPC-producing strains (one Enterobacter hormaechei and one K. pneumoniae) and in vitro competition assays with prevalent KPC-producing ECC (KPC-ECC) versus KPC-producing K. pneumoniae (KPC-Kp) high-risk clones from our institution. A KPC-producing E. hormaechei and later a KPC-Kp strain that colonized a patient shared an identical novel conjugative IncM1 plasmid harboring blaKPC-2. In addition, a total of 19 KPC-ECC and 58 KPC-Kp strains isolated from nosocomial infections revealed that high-risk clones KPC-ECC ST66 and ST78 as well as KPC-Kp ST11 and ST258 were prevalent and selected for competition assays. The competition assays with KCP-ECC ST45, ST66, and ST78 versus KPC-Kp ST11, ST18, and ST258 strains analyzed here showed no statistically significant difference. These assays evidenced that high-risk clones of KPC-ECC and KPC-Kp can coexist in the same hospital environment including the same patient, which explains from an ecological point of view that both species can exchange and share plasmids. These findings offer hints to explain the worldwide rise of KPC-ECC strains based on the ability of some pandemic clones to compete and occupy a certain niche. Taken together, the presence of the same new plasmid and the fitness results that showed that both strains can coexist within the same patient suggest that horizontal genetic transfer of blaKPC-2 within the patient cannot be ruled out. These findings highlight the constant interaction that these two species can keep in the hospital environment, which, in turn, can be related to the spread of KPC.
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9
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Di Conza J, Badaracco ME, Calza Y, Fontana H, Lincopan N, Peña L, Gutkind G. Emergence of Urease-Negative Klebsiella pneumoniae ST340 Carrying an IncP6 Plasmid-Mediated blaKPC-2 Gene. Microb Drug Resist 2022; 28:957-961. [PMID: 35984997 DOI: 10.1089/mdr.2021.0466] [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: 10/15/2022] Open
Abstract
An unusual biotype of KPC-2-producing Klebsiella pneumoniae (KPC-Kpn) isolates was detected in Corrientes, Argentina, which, to their isolation date, had been free of KPC-Kpn outbreaks. Our aim was to describe the clinical epidemiology focused on genomic characterization of atypical urease-negative KPC-Kpn clinical isolates belonging to the high-risk hospital-associated clonal lineage ST340/CC258. Thirteen isolates were recovered, all of them from inpatients with KPC-Kpn infection (August 2015 to January 2016). These isolates displayed identical enterobacterial repetitive intergenic consensus-PCR electropherotype belonging to a single clonal sequence type ST340. Whole genome sequencing was performed on two KPC-Kpn and the resistome analyses revealed the following acquired resistance genes: blaKPC-2, blaCTX-M-15, blaOXA-1, blaSHV-11, aac(3)-IId, aph(3')-Ia, aac(6')-Ib-cr, sul1, dfrA14, catB3, fosA, and arr-3. Mutations in GyrA (S83I) and ParC (S80I) were also identified. Among the virulence determinants, yersiniabactin was detected in both strains, specifically the ybt9 locus located in ICEKp3. Five plasmid incompatibility groups were observed in this clone and an unusual IncP6 plasmid bearing blaKPC-2 gene (named pKpn3KP) was fully characterized. In this study, we present the first draft genome sequences of two clinical isolates of KPC-2/CTX-M-15-producing K. pneumoniae belonging to the high-risk clonal lineage ST340/CC258 associated with nosocomial outbreaks in Argentina.
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Affiliation(s)
- José Di Conza
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Maria E Badaracco
- Instituto Cardiologico de Corrientes "Juana Francisca Cabral," Corrientes, Argentina
| | - Yanina Calza
- Instituto Cardiologico de Corrientes "Juana Francisca Cabral," Corrientes, Argentina
| | - Herrison Fontana
- Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, Sao Paulo, Brazil
| | - Nilton Lincopan
- Department of Microbiology, Instituto de Ciências Biomédicas, Universidade de São Paulo, Sao Paulo, Brazil
| | - Laura Peña
- Instituto Cardiologico de Corrientes "Juana Francisca Cabral," Corrientes, Argentina
| | - Gabriel Gutkind
- Instituto de Investigaciones en Bacteriología y Virología Molecular (IBaViM), Facultad de Farmacia y Bioquímica, Universidad de Buenos Aires, Buenos Aires, Argentina.,Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
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Kvesić M, Šamanić I, Novak A, Fredotović Ž, Dželalija M, Kamenjarin J, Goić Barišić I, Tonkić M, Maravić A. Submarine Outfalls of Treated Wastewater Effluents are Sources of Extensively- and Multidrug-Resistant KPC- and OXA-48-Producing Enterobacteriaceae in Coastal Marine Environment. Front Microbiol 2022; 13:858821. [PMID: 35602062 PMCID: PMC9121779 DOI: 10.3389/fmicb.2022.858821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2022] [Accepted: 04/06/2022] [Indexed: 11/13/2022] Open
Abstract
The rapid and ongoing spread of carbapenemase-producing Enterobacteriaceae has led to a global health threat. However, a limited number of studies have addressed this problem in the marine environment. We investigated their emergence in the coastal waters of the central Adriatic Sea (Croatia), which are recipients of submarine effluents from two wastewater treatment plants. Fifteen KPC-producing Enterobacteriaceae (nine Escherichia coli, four Klebsiella pneumoniae and two Citrobacter freundii) were recovered, and susceptibility testing to 14 antimicrobials from 10 classes showed that four isolates were extensively drug resistant (XDR) and two were resistant to colistin. After ERIC and BOX-PCR typing, eight isolates were selected for whole genome sequencing. The E. coli isolates belonged to serotype O21:H27 and sequence type (ST) 2795, while K. pneumoniae isolates were assigned to STs 37 and 534. Large-scale genome analysis revealed an arsenal of 137 genes conferring resistance to 19 antimicrobial drug classes, 35 genes associated with virulence, and 20 plasmid replicons. The isolates simultaneously carried 43–90 genes encoding for antibiotic resistance, while four isolates co-harbored carbapenemase genes blaKPC-2 and blaOXA-48. The blaOXA-48 was associated with IncL-type plasmids in E. coli and K. pneumoniae. Importantly, the blaKPC-2 in four E. coli isolates was located on ~40 kb IncP6 broad-host-range plasmids which recently emerged as blaKPC-2 vesicles, providing first report of these blaKPC-2-bearing resistance plasmids circulating in E. coli in Europe. This study also represents the first evidence of XDR and potentially virulent strains of KPC-producing E. coli in coastal waters and the co-occurrence of blaKPC-2 and blaOXA-48 carbapenemase genes in this species. The leakage of these strains through submarine effluents into coastal waters is of concern, indicating a reservoir of this infectious threat in the marine environment.
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Affiliation(s)
- Marija Kvesić
- Center of Excellence for Science and Technology, Integration of Mediterranean Region, University of Split, Split, Croatia
- Doctoral Study of Biophysics, Faculty of Science, University of Split, Split, Croatia
| | - Ivica Šamanić
- Department of Biology, Faculty of Science, University of Split, Split, Croatia
| | - Anita Novak
- School of Medicine, University of Split, Split, Croatia
- University Hospital Split, Split, Croatia
| | - Željana Fredotović
- Department of Biology, Faculty of Science, University of Split, Split, Croatia
| | - Mia Dželalija
- Department of Biology, Faculty of Science, University of Split, Split, Croatia
| | - Juraj Kamenjarin
- Department of Biology, Faculty of Science, University of Split, Split, Croatia
| | - Ivana Goić Barišić
- School of Medicine, University of Split, Split, Croatia
- University Hospital Split, Split, Croatia
| | - Marija Tonkić
- School of Medicine, University of Split, Split, Croatia
- University Hospital Split, Split, Croatia
| | - Ana Maravić
- Department of Biology, Faculty of Science, University of Split, Split, Croatia
- *Correspondence: Ana Maravić,
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11
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blaKPC-2-Encoding IncP-6 Plasmids in Citrobacter freundii and Klebsiella variicola Strains from Hospital Sewage in Japan. Appl Environ Microbiol 2022; 88:e0001922. [PMID: 35380451 DOI: 10.1128/aem.00019-22] [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: 11/20/2022] Open
Abstract
Klebsiella pneumoniae carbapenemase (KPC) producers are an emerging threat to global health, and the hospital water environment is considered an important reservoir of these life-threatening bacteria. We characterized plasmids of KPC-2-producing Citrobacter freundii and Klebsiella variicola isolates recovered from hospital sewage in Japan. Antimicrobial susceptibility testing, whole-genome sequencing analysis, bacterial conjugation, and transformation experiments were performed for both KPC-2 producers. The blaKPC-2 gene was located on the Tn3 transposon-related region from an IncP-6 replicon plasmid that could not be transferred via conjugation. Compared to the blaKPC-2-encoding plasmid of the C. freundii isolate, alignment analysis of plasmids with blaKPC-2 showed that the blaKPC-2-encoding plasmid of the K. variicola isolate was a novel IncP-6/IncF-like hybrid plasmid containing a 75,218-bp insertion sequence composed of IncF-like plasmid conjugative transfer proteins. Carbapenem-resistant transformants harboring blaKPC-2 were obtained for both isolates. However, no IncF-like insertion region was found in the K. variicola donor plasmid of the transformant, suggesting that this IncF-like region is not readily functional for plasmid conjugative transfer and is maintained depending on the host cells. The findings on the KPC-2 producers and novel genetic content emphasize the key role of hospital sewage as a potential reservoir of pathogens and its linked dissemination of blaKPC-2 through the hospital water environment. Our results indicate that continuous monitoring for environmental emergence of antimicrobial-resistant bacteria might be needed to control the spread of these infectious bacteria. Moreover, it will help elucidate both the evolution and transmission pathways of these bacteria harboring antimicrobial resistance. IMPORTANCE Antimicrobial resistance is a significant problem for global health, and the hospital environment has been recognized as a reservoir of antimicrobial resistance. Here, we provide insight into the genomic features of blaKPC-2-harboring isolates of Citrobacter freundii and Klebsiella variicola obtained from hospital sewage in Japan. The findings of carbapenem-resistant bacteria containing this novel genetic context emphasize that hospital sewage could act as a potential reservoir of pathogens and cause the subsequent spread of blaKPC-2 via horizontal gene transfer in the hospital water environment. This indicates that serial monitoring for environmental bacteria possessing antimicrobial resistance may help us control the spread of infection and also lead to elucidating the evolution and transmission pathways of these bacteria.
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