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Corrales-Martínez J, Jaramillo K, Tadesse DA, Satán C, Villavicencio FX, Sánchez-Gavilanes L, Rivadeneira-Cueva B, Balcázar JL, Calero-Cáceres W. Genomic characterization of a WHO critical priority isolate Enterobacter kobei ST2070 harboring OXA-10, KPC-2, and CTX-M-12 recovered from a water irrigation channel in Ecuador. Heliyon 2024; 10:e26379. [PMID: 38449644 PMCID: PMC10915343 DOI: 10.1016/j.heliyon.2024.e26379] [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: 12/08/2023] [Revised: 02/06/2024] [Accepted: 02/12/2024] [Indexed: 03/08/2024] Open
Abstract
The discharge of untreated or partially treated wastewater can have detrimental impacts on the quality of water bodies, posing a significant threat to public health and the environment. In Ecuador, previous research indicates a high prevalence of antimicrobial resistant (AMR) bacteria in surface waters affected by human activities, including irrigation channels. In this study, we analyzed sediment samples collected from an irrigation channel utilized for agricultural purposes in northern Ecuador, using microbiological techniques and whole-genome sequencing (WGS). Our investigation revealed the first documented occurrence of E. kobei in Ecuador and the initial report of environmental E. kobei ST2070. Furthermore, we identified the coexistence of OXA-10-type class D β-lactamase and KPC-2-type class A β-lactamase in the E. kobei isolate (UTA41), representing the first report of such a phenomenon in this species. Additionally, we detected various antibiotic resistance genes in the E. kobei UTA41 isolate, including blaCTX-M-12, fosA, aac(6')-lb, sul2, msr(E), and mph(A), as well as virulence genes such as bacterial efflux pump and siderophore biosynthesis genes. We also identified two intact prophage regions (Entero_186 and Klebsi_phiKO2) in the isolate. Our study presents the first evidence of E. kobei isolate containing two carbapenemase-encoding genes in environmental samples from Latin America. This finding indicates the potential spread of critical-priority bacteria in water samples originating from anthropogenic sources, such as urban wastewater discharges and livestock facilities.
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Affiliation(s)
- Joselyn Corrales-Martínez
- UTA-RAM-One Health, Department of Food and Biotechnology Science and Engineering, Universidad Técnica de Ambato, Ambato, Ecuador
| | - Katherine Jaramillo
- Centro de Referencia Nacional de Resistencia a los Antimicrobianos RAM, Instituto Nacional de Investigación en Salud Pública “Dr. Leopoldo Izquieta Pérez” INSPI, Quito, Ecuador
- Facultad de Ciencias de la Salud, Universidad Técnica de Ambato, Ambato, Ecuador
| | - Daniel A. Tadesse
- U.S. Food &Drug Administration, Center for Veterinary Medicine, Office of Applied Science Laurel, MD 20708, USA
| | - Carolina Satán
- Centro de Referencia Nacional de Resistencia a los Antimicrobianos RAM, Instituto Nacional de Investigación en Salud Pública “Dr. Leopoldo Izquieta Pérez” INSPI, Quito, Ecuador
| | - Fernando X. Villavicencio
- Centro de Referencia Nacional de Resistencia a los Antimicrobianos RAM, Instituto Nacional de Investigación en Salud Pública “Dr. Leopoldo Izquieta Pérez” INSPI, Quito, Ecuador
- Veterinary Medicine, Eugenio Espejo Faculty of Health Sciences, Universidad UTE, Quito, Ecuador
| | - Lissette Sánchez-Gavilanes
- UTA-RAM-One Health, Department of Food and Biotechnology Science and Engineering, Universidad Técnica de Ambato, Ambato, Ecuador
| | - Brenda Rivadeneira-Cueva
- UTA-RAM-One Health, Department of Food and Biotechnology Science and Engineering, Universidad Técnica de Ambato, Ambato, Ecuador
| | - José Luis Balcázar
- Catalan Institute for Water Research (ICRA), 17003 Girona, Spain
- University of Girona, 17004 Girona, Spain
| | - William Calero-Cáceres
- UTA-RAM-One Health, Department of Food and Biotechnology Science and Engineering, Universidad Técnica de Ambato, Ambato, Ecuador
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Piccirilli A, Di Marcantonio S, Costantino V, Simonetti O, Busetti M, Luzzati R, Principe L, Di Domenico M, Rinaldi A, Cammà C, Perilli M. Identification of IncA Plasmid, Harboring blaVIM-1 Gene, in S. enterica Goldcoast ST358 and C. freundii ST62 Isolated in a Hospitalized Patient. Antibiotics (Basel) 2023; 12:1659. [PMID: 38136693 PMCID: PMC10741216 DOI: 10.3390/antibiotics12121659] [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: 10/12/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 12/24/2023] Open
Abstract
In the present study, we analyzed the genome of two S. enterica strains TS1 and TS2 from stool and blood cultures, respectively, and one strain of C. freundii TS3, isolated from a single hospitalized patient with acute myeloid leukemia. The S. enterica Goldcoast ST358 (O:8 (C2-C3) serogroup), sequenced by the MiSeq Illumina system, showed the presence of β-lactamase genes (blaVIM-1, blaSHV-12 and blaOXA-10), aadA1, ant(2″)-Ia, aac(6')-Iaa, aac(6')-Ib3, aac(6')-Ib-cr, qnrVC6, parC(T57S), and several incompatibility plasmids. A wide variety of insertion sequences (ISs) and transposon elements were identified. In C. freundii TS3, these were the blaVIM-1, blaCMY-150, and blaSHV-12, aadA1, aac(6')-Ib3, aac(6')-Ib-cr, mph(A), sul1, dfrA14, ARR-2, qnrVC6, and qnrB38. IncA plasmid isolated from E.coli/K12 transconjugant and C. freundii exhibited a sequence identity >99.9%. The transfer of IncA plasmid was evaluated by conjugation experiments.
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Affiliation(s)
- Alessandra Piccirilli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (S.D.M.); (M.P.)
| | - Sascia Di Marcantonio
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (S.D.M.); (M.P.)
| | - Venera Costantino
- Microbiology Unit, Trieste University Hospital (ASUGI), 34125 Trieste, Italy; (V.C.); (M.B.)
| | - Omar Simonetti
- Infectious Diseases Unit, Trieste University Hospital (ASUGI), 34125 Trieste, Italy; (O.S.); (R.L.)
| | - Marina Busetti
- Microbiology Unit, Trieste University Hospital (ASUGI), 34125 Trieste, Italy; (V.C.); (M.B.)
| | - Roberto Luzzati
- Infectious Diseases Unit, Trieste University Hospital (ASUGI), 34125 Trieste, Italy; (O.S.); (R.L.)
| | - Luigi Principe
- Clinical Pathology and Microbiology Unit, “S. Giovanni di Dio” Hospital, 88900 Crotone, Italy;
| | - Marco Di Domenico
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Campo Boario, 64100 Teramo, Italy; (M.D.D.); (A.R.); (C.C.)
| | - Antonio Rinaldi
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Campo Boario, 64100 Teramo, Italy; (M.D.D.); (A.R.); (C.C.)
| | - Cesare Cammà
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise, Campo Boario, 64100 Teramo, Italy; (M.D.D.); (A.R.); (C.C.)
| | - Mariagrazia Perilli
- Department of Biotechnological and Applied Clinical Sciences, University of L’Aquila, 67100 L’Aquila, Italy; (S.D.M.); (M.P.)
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Guibert F, Espinoza K, Taboada-Blanco C, Alonso CA, Oporto R, Castillo AK, Rojo-Bezares B, López M, Sáenz Y, Pons MJ, Ruiz J. Traditional marketed meats as a reservoir of multidrug-resistant Escherichia coli. Int Microbiol 2023:10.1007/s10123-023-00445-y. [PMID: 37995017 DOI: 10.1007/s10123-023-00445-y] [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: 08/19/2023] [Revised: 10/25/2023] [Accepted: 11/01/2023] [Indexed: 11/24/2023]
Abstract
This study aimed to analyze Escherichia coli from marketed meat samples in Peru. Sixty-six E. coli isolates were recovered from 21 meat samples (14 chicken, 7 beef), and antimicrobial resistance levels and the presence of mechanisms of antibiotic resistance, as well as clonal relationships and phylogeny of colistin-resistant isolates, were established. High levels of antimicrobial resistance were detected, with 93.9% of isolates being multi-drug resistant (MDR) and 76.2% of samples possessing colistin-resistant E. coli; of these, 6 samples from 6 chicken samples presenting mcr-1-producer E. coli. Colistin-resistant isolates were classified into 22 clonal groups, while phylogroup A (15 isolates) was the most common. Extended-spectrum β-lactamase- and pAmpC-producing E. coli were found in 18 and 8 samples respectively, with blaCTX-M-55 (28 isolates; 16 samples) and blaCIT (8 isolates; 7 samples) being the most common of each type. Additionally, blaCTX-M-15, blaCTX-M-65, blaSHV-27, blaOXA-5/10-like, blaDHA, blaEBC and narrow-spectrum blaTEM were detected. In addition, 5 blaCTX-M remained unidentified, and no sought ESBL-encoding gene was detected in other 6 ESBL-producer isolates. The tetA, tetE and tetX genes were found in tigecycline-resistant isolates. This study highlights the presence of MDR E. coli in Peruvian food-chain. The high relevance of CTX-M-55, the dissemination through the food-chain of pAmpC, as well as the high frequency of unrelated colistin-resistant isolates is reported.
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Affiliation(s)
- Fernando Guibert
- Grupo de Investigación en Dinámicas y Epidemiología de la Resistencia a Antimicrobianos - "One Health", Universidad Científica del Sur, Antigua Panamericana Sur Km 19, Villa El Salvador, 15067, Lima, Peru
| | - Kathya Espinoza
- Grupo de Investigación en Dinámicas y Epidemiología de la Resistencia a Antimicrobianos - "One Health", Universidad Científica del Sur, Antigua Panamericana Sur Km 19, Villa El Salvador, 15067, Lima, Peru
| | - Clara Taboada-Blanco
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja, Logroño, Spain
| | - Carla A Alonso
- Servicio de Análisis Clínicos, Laboratorio de Microbiología, Hospital San Pedro, Logroño, Spain
| | - Rosario Oporto
- Grupo de Investigación en Dinámicas y Epidemiología de la Resistencia a Antimicrobianos - "One Health", Universidad Científica del Sur, Antigua Panamericana Sur Km 19, Villa El Salvador, 15067, Lima, Peru
| | - Angie K Castillo
- Grupo de Investigación en Dinámicas y Epidemiología de la Resistencia a Antimicrobianos - "One Health", Universidad Científica del Sur, Antigua Panamericana Sur Km 19, Villa El Salvador, 15067, Lima, Peru
| | - Beatriz Rojo-Bezares
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja, Logroño, Spain
| | - María López
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja, Logroño, Spain
| | - Yolanda Sáenz
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja, Logroño, Spain
| | - Maria J Pons
- Grupo de Investigación en Dinámicas y Epidemiología de la Resistencia a Antimicrobianos - "One Health", Universidad Científica del Sur, Antigua Panamericana Sur Km 19, Villa El Salvador, 15067, Lima, Peru.
| | - Joaquim Ruiz
- Grupo de Investigación en Dinámicas y Epidemiología de la Resistencia a Antimicrobianos - "One Health", Universidad Científica del Sur, Antigua Panamericana Sur Km 19, Villa El Salvador, 15067, Lima, Peru.
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Alonso-García I, Vázquez-Ucha JC, Martínez-Guitián M, Lasarte-Monterrubio C, Rodríguez-Pallares S, Camacho-Zamora P, Rumbo-Feal S, Aja-Macaya P, González-Pinto L, Outeda-García M, Maceiras R, Guijarro-Sánchez P, Muíño-Andrade MJ, Fernández-González A, Oviaño M, González-Bello C, Arca-Suárez J, Beceiro A, Bou G. Interplay between OXA-10 β-Lactamase Production and Low Outer-Membrane Permeability in Carbapenem Resistance in Enterobacterales. Antibiotics (Basel) 2023; 12:999. [PMID: 37370318 DOI: 10.3390/antibiotics12060999] [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: 03/10/2023] [Revised: 04/20/2023] [Accepted: 05/30/2023] [Indexed: 06/29/2023] Open
Abstract
The OXA-10 class D β-lactamase has been reported to contribute to carbapenem resistance in non-fermenting Gram-negative bacilli; however, its contribution to carbapenem resistance in Enterobacterales is unknown. In this work, minimum inhibitory concentrations (MICs), whole genome sequencing (WGS), cloning experiments, kinetic assays, molecular modelling studies, and biochemical assays for carbapenemase detection were performed to determine the impact of OXA-10 production on carbapenem resistance in two XDR clinical isolates of Escherichia coli with the carbapenem resistance phenotype (ertapenem resistance). WGS identified the two clinical isolates as belonging to ST57 in close genomic proximity to each other. Additionally, the presence of the blaOXA-10 gene was identified in both isolates, as well as relevant mutations in the genes coding for the OmpC and OmpF porins. Cloning of blaOXA-10 in an E. coli HB4 (OmpC and OmpF-deficient) demonstrated the important contribution of OXA-10 to increased carbapenem MICs when associated with porin deficiency. Kinetic analysis showed that OXA-10 has low carbapenem-hydrolysing activity, but molecular models revealed interactions of this β-lactamase with the carbapenems. OXA-10 was not detected with biochemical tests used in clinical laboratories. In conclusion, the β-lactamase OXA-10 limits the activity of carbapenems in Enterobacterales when combined with low permeability and should be monitored in the future.
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Affiliation(s)
- Isaac Alonso-García
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Juan Carlos Vázquez-Ucha
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Marta Martínez-Guitián
- NANOBIOFAR, Centre for Research in Molecular Medicine and Chronic Diseases (CiMUS), Universidad de Santiago de Compostela, Campus Vida Avenida Barcelona s/n, 15782 Santiago de Compostela, Spain
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, Universidade da Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Cristina Lasarte-Monterrubio
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Salud Rodríguez-Pallares
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Pablo Camacho-Zamora
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Soraya Rumbo-Feal
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Pablo Aja-Macaya
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Lucía González-Pinto
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Michelle Outeda-García
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Romina Maceiras
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Paula Guijarro-Sánchez
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - María José Muíño-Andrade
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Ana Fernández-González
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
| | - Marina Oviaño
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CiQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Jenaro de la Fuente s/n, 15782 Santiago de Compostela, Spain
| | - Jorge Arca-Suárez
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Alejandro Beceiro
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | - Germán Bou
- Servicio de Microbiología and Instituto de Investigación Biomédica A Coruña (INIBIC), Complexo Hospitalario Universitario A Coruña, As Xubias 84, 15006 A Coruña, Spain
- CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
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Tseng CH, Huang YT, Mao YC, Lai CH, Yeh TK, Ho CM, Liu PY. Insight into the Mechanisms of Carbapenem Resistance in Klebsiella pneumoniae: A Study on IS26 Integrons, Beta-Lactamases, Porin Modifications, and Plasmidome Analysis. Antibiotics (Basel) 2023; 12:antibiotics12040749. [PMID: 37107111 PMCID: PMC10135210 DOI: 10.3390/antibiotics12040749] [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: 02/25/2023] [Revised: 04/03/2023] [Accepted: 04/12/2023] [Indexed: 04/29/2023] Open
Abstract
The emergence of carbapenem-resistant Klebsiella pneumoniae poses a significant threat to public health. In this study, we aimed to investigate the distribution and genetic diversity of plasmids carrying beta-lactamase resistance determinants in a collection of carbapenem-resistant K. pneumoniae blood isolates. Blood isolates of carbapenem-resistant K. pneumoniae bacteremia were collected and identified. Whole-genome sequencing, assembly and analysis were performed for the prediction of antimicrobial resistance determinants. Plasmidome analysis was also performed. Our plasmidome analysis revealed two major plasmid groups, IncFII/IncR and IncC, as key players in the dissemination of carbapenem resistance among carbapenem-resistant K. pneumoniae. Notably, plasmids within the same group exhibited conservation of encapsulated genes, suggesting that these plasmid groups may serve as conservative carriers of carbapenem-resistant determinants. Additionally, we investigated the evolution and expansion of IS26 integrons in carbapenem-resistant K. pneumoniae isolates using long-read sequencing. Our findings revealed the evolution and expansion of IS26 structure, which may have contributed to the development of carbapenem resistance in these strains. Our findings indicate that IncC group plasmids are associated with the endemic occurrence of carbapenem-resistant K. pneumoniae, highlighting the need for targeted interventions to control its spread. Although our study focuses on the endemic presence of carbapenem-resistant K. pneumoniae, it is important to note that carbapenem-resistant K. pneumoniae is indeed a global problem, with cases reported in multiple regions worldwide. Further research is necessary to better understand the factors driving the worldwide dissemination of carbapenem-resistant K. pneumoniae and to develop effective strategies for its prevention and control.
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Affiliation(s)
- Chien-Hao Tseng
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung 40705, Taiwan
| | - Yao-Ting Huang
- Department of Computer Science and Information Engineering, National Chung Cheng University, Chia-Yi 62102, Taiwan
| | - Yan-Chiao Mao
- Division of Clinical Toxicology, Department of Emergency Medicine, Taichung Veterans General Hospital, Taichung 40705, Taiwan
- School of Medicine, National Defense Medical Center, Taipei 11490, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung 402, Taiwan
| | - Chung-Hsu Lai
- Division of Infectious Diseases, Department of Internal Medicine, E-Da Hospital, Kaohsiung 82445, Taiwan
- School of Medicine, College of Medicine, I-Shou University, Kaohsiung 82445, Taiwan
| | - Ting-Kuang Yeh
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung 40705, Taiwan
- Genomic Center for Infectious Diseases, Taichung Veterans General Hospital, Taichung 40705, Taiwan
| | - Chung-Mei Ho
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung 40705, Taiwan
| | - Po-Yu Liu
- Division of Infectious Diseases, Department of Internal Medicine, Taichung Veterans General Hospital, Taichung 40705, Taiwan
- Department of Post-Baccalaureate Medicine, College of Medicine, National Chung Hsing University, Taichung 402, Taiwan
- Genomic Center for Infectious Diseases, Taichung Veterans General Hospital, Taichung 40705, Taiwan
- Rong Hsing Research Center for Translational Medicine, National Chung Hsing University, Taichung 402, Taiwan
- Ph.D. Program in Translational Medicine, National Chung Hsing University, Taichung 402, Taiwan
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6
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Meng L, Liu Z, Liu C, Li C, Shen H, Cao X. The distribution characteristics of global blaOXA-carrying Klebsiella pneumoniae. BMC Infect Dis 2023; 23:182. [PMID: 36991368 PMCID: PMC10053090 DOI: 10.1186/s12879-023-08156-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 03/14/2023] [Indexed: 03/30/2023] Open
Abstract
Abstract
Objective
To analyze the distribution of blaOXA among global Klebsiella pneumoniae and the characteristics of blaOXA-carrying K. pneumoniae.
Materials and Methods
The genomes of global K. pneumoniae were downloaded from NCBI by Aspera software. After quality check, the distribution of blaOXA among the qualified genomes was investigated by annotation with the resistant determinant database. The phylogenetic tree was constructed for the blaOXA variants based on the single nucleotide polymorphism (SNP) to explore the evolutionary relationship between these variants. The MLST (multi-locus sequence type) website and blastn tools were utilized to determine the sequence types (STs) of these blaOXA-carrying strains. and sample resource, isolation country, date and host were extracted by perl program for analyzing the characteristics of these strains.
Results
A total of 12,356 K. pneumoniae genomes were downloaded and 11,429 ones were qualified. Among them, 4386 strains were found to carry 5610 blaOXA variants which belonged to 27 varieties of blaOXAs, blaOXA-1 (n = 2891, 51.5%) and blaOXA-9 (n = 969, 17.3%) were the most prevalent blaOXA variants, followed by blaOXA-48 (n = 800, 14.3%) and blaOXA-232 (n = 480, 8.6%). The phylogenetic tree displayed 8 clades, three of them were composed of carbapenem-hydrolyzing oxacillinase (CHO). Totally, 300 distinct STs were identified among 4386 strains with ST11 (n = 477, 10.9%) being the most predominant one followed by ST258 (n = 410, 9.4%). Homo sapiens (2696/4386, 61.5%) was the main host for blaOXA-carrying K. pneumoniae isolates. The blaOXA-9-carrying K. pneumoniae strains were mostly found in the United States and blaOXA-48-carrying K. pneumoniae strains were mainly distributed in Europe and Asia.
Conclusion
Among the global K. pneumoniae, numerous blaOXA variants were identified with blaOXA-1, blaOXA-9, blaOXA-48 and blaOXA-232 being the most prevalent ones, indicating that blaOXA rapidly evolved under the selective pressure of antimicrobial agents. ST11 and ST258 were the main clones for blaOXA-carrying K. pneumoniae.
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Pincus NB, Rosas-Lemus M, Gatesy SWM, Bertucci HK, Brunzelle JS, Minasov G, Shuvalova LA, Lebrun-Corbin M, Satchell KJF, Ozer EA, Hauser AR, Bachta KER. Functional and Structural Characterization of OXA-935, a Novel OXA-10-Family β-Lactamase from Pseudomonas aeruginosa. Antimicrob Agents Chemother 2022; 66:e0098522. [PMID: 36129295 PMCID: PMC9578422 DOI: 10.1128/aac.00985-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2022] [Accepted: 08/29/2022] [Indexed: 11/20/2022] Open
Abstract
Resistance to antipseudomonal penicillins and cephalosporins is often driven by the overproduction of the intrinsic β-lactamase AmpC. However, OXA-10-family β-lactamases are a rich source of resistance in Pseudomonas aeruginosa. OXA β-lactamases have a propensity for mutation that leads to extended spectrum cephalosporinase and carbapenemase activity. In this study, we identified isolates from a subclade of the multidrug-resistant (MDR) high risk P. aeruginosa clonal complex CC446 with a resistance to ceftazidime. A genomic analysis revealed that these isolates harbored a plasmid containing a novel allele of blaOXA-10, named blaOXA-935, which was predicted to produce an OXA-10 variant with two amino acid substitutions: an aspartic acid instead of a glycine at position 157 and a serine instead of a phenylalanine at position 153. The G157D mutation, present in OXA-14, is associated with the resistance of P. aeruginosa to ceftazidime. Compared to OXA-14, OXA-935 showed increased catalytic efficiency for ceftazidime. The deletion of blaOXA-935 restored the sensitivity to ceftazidime, and susceptibility profiling of P. aeruginosa laboratory strains expressing blaOXA-935 revealed that OXA-935 conferred ceftazidime resistance. To better understand the impacts of the variant amino acids, we determined the crystal structures of OXA-14 and OXA-935. Compared to OXA-14, the F153S mutation in OXA-935 conferred increased flexibility in the omega (Ω) loop. Amino acid changes that confer extended spectrum cephalosporinase activity to OXA-10-family β-lactamases are concerning, given the rising reliance on novel β-lactam/β-lactamase inhibitor combinations, such as ceftolozane-tazobactam and ceftazidime-avibactam, to treat MDR P. aeruginosa infections.
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Affiliation(s)
- Nathan B. Pincus
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Monica Rosas-Lemus
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Samuel W. M. Gatesy
- Department of Medicine, Division of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Hanna K. Bertucci
- Department of Medicine, Division of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Joseph S. Brunzelle
- Northwestern Synchrotron Research Center, Life Sciences Collaborative Access Team, Northwestern University, Argonne, Illinois, USA
| | - George Minasov
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Ludmilla A. Shuvalova
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Marine Lebrun-Corbin
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Karla J. F. Satchell
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Center for Structural Genomics of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Egon A. Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Center for Pathogen Genomics and Microbial Evolution, Institute for Global Health, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Alan R. Hauser
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Department of Medicine, Division of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
| | - Kelly E. R. Bachta
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
- Department of Medicine, Division of Infectious Diseases, Northwestern University, Feinberg School of Medicine, Chicago, Illinois, USA
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8
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Avci FG, Tastekil I, Jaisi A, Ozbek Sarica P, Sariyar Akbulut B. A review on the mechanistic details of OXA enzymes of ESKAPE pathogens. Pathog Glob Health 2022; 117:219-234. [PMID: 35758005 PMCID: PMC10081068 DOI: 10.1080/20477724.2022.2088496] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022] Open
Abstract
The production of β-lactamases is a prevalent mechanism that poses serious pressure on the control of bacterial resistance. Furthermore, the unavoidable and alarming increase in the transmission of bacteria producing extended-spectrum β-lactamases complicates treatment alternatives with existing drugs and/or approaches. Class D β-lactamases, designated as OXA enzymes, are characterized by their activity specifically towards oxacillins. They are widely distributed among the ESKAPE bugs that are associated with antibiotic resistance and life-threatening hospital infections. The inadequacy of current β-lactamase inhibitors for conventional treatments of 'OXA' mediated infections confirms the necessity of new approaches. Here, the focus is on the mechanistic details of OXA-10, OXA-23, and OXA-48, commonly found in highly virulent and antibiotic-resistant pathogens Acinetobacter baumannii, Klebsiella pneumoniae, Pseudomonas aeruginosa, and Enterobacter spp. to describe their similarities and differences. Furthermore, this review contains a specific emphasis on structural and computational perspectives, which will be valuable to guide efforts in the design/discovery of a common single-molecule drug against ESKAPE pathogens.
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Affiliation(s)
- Fatma Gizem Avci
- Bioengineering Department, Uskudar University, Uskudar, 34662, Turkey
| | - Ilgaz Tastekil
- Bioengineering Department, Marmara University, Kadikoy, 34722, Turkey
| | - Amit Jaisi
- Drug and Cosmetics Excellence Center, School of Pharmacy, Walailak University, 80160, Nakhon Si Thammarat, Thailand
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9
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Ma X, Lv X, Feng S, Liu R, Fu H, Gao F, Xu H. Genetic Characterization of an ST5571 Hypervirulent Klebsiella pneumoniae Strain Co-Producing NDM-1, MCR-1, and OXA-10 Causing Bacteremia. Infect Drug Resist 2022; 15:2293-2299. [PMID: 35517899 PMCID: PMC9064484 DOI: 10.2147/idr.s360715] [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: 02/01/2022] [Accepted: 04/12/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose To investigate the phenotypic and genomic characteristics of the multi-drug resistant and hypervirulent Klebsiella pneumoniae strain recovered from bacteremia. Methods Antimicrobial susceptibility testing (AST) was performed by the microdilution method. Antimicrobial resistance genes, virulence-associated genes, multilocus sequence typing (MLST), and plasmid replicon were characterized by next-generation sequencing (NGS) and nanopore sequencing. S1 nuclease-pulsed field gel electrophoresis (S1-PFGE) and Southern blotting were performed to characterize the plasmid profile. Results The hypervirulent colistin- and carbapenem-resistant K. pneumoniae strain DY2009 was identified as ST5571, co-carrying mcr-1, bla NDM-1, and bla OXA-10. In silico analysis found that it was K2 serotype. AST results revealed that DY2009 was resistant to carbapenems, cephalosporins, ciprofloxacin, chloramphenicol, and colistin but remained susceptible to aztreonam, gentamicin, amikacin, and tigecycline. Through the whole-genome analysis, a variety of virulence determinants were identified, including rmpA. Plasmid analysis confirmed that the mcr-1 and bla NDM-1 gene harbored a ~33 kb IncX4 plasmid and a ~44 kb IncX3 plasmid. In contrast, bla OXA-10 was encoded by chromosome. Conclusion To the best of our knowledge, we first report the clinical hypervirulent K. pneumoniae isolate co-producing MCR-1, NDM-1, and OXA-10 causing bacteremia. We found that mcr-1 and bla NDM-1 genes were located on two self-conjugative epidemic plasmids, contributing to the widespread MCR-1 and NDM-1 in China. The results of this work improve our understanding of the genetic background of colistin- and carbapenem-resistant K. pneumoniae isolate from bacteremia and the resistance mechanisms. Our findings highlight the urgent need for infection control of such strain to prevent it from becoming an extensive-drug resistant clone.
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Affiliation(s)
- Xiaolong Ma
- Department of Respiratory Medicine, the First Hospital of Jiaxing (Affiliated Hospital of Jiaxing University), Jiaxing, People’s Republic of China
| | - Xiaodong Lv
- Department of Respiratory Medicine, the First Hospital of Jiaxing (Affiliated Hospital of Jiaxing University), Jiaxing, People’s Republic of China
| | - Sihan Feng
- Department of Respiratory Medicine, the First Hospital of Jiaxing (Affiliated Hospital of Jiaxing University), Jiaxing, People’s Republic of China
| | - Ruishan Liu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of China
- Department of Laboratory Medicine, the First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Hao Fu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Feng Gao
- Department of Respiratory Medicine, the First Hospital of Jiaxing (Affiliated Hospital of Jiaxing University), Jiaxing, People’s Republic of China
| | - Hao Xu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of China
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10
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Savin M, Bierbaum G, Mutters NT, Schmithausen RM, Kreyenschmidt J, García-Meniño I, Schmoger S, Käsbohrer A, Hammerl JA. Genetic Characterization of Carbapenem-Resistant Klebsiella spp. from Municipal and Slaughterhouse Wastewater. Antibiotics (Basel) 2022; 11:antibiotics11040435. [PMID: 35453187 PMCID: PMC9027467 DOI: 10.3390/antibiotics11040435] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Revised: 03/16/2022] [Accepted: 03/22/2022] [Indexed: 12/18/2022] Open
Abstract
Currently, human and veterinary medicine are threatened worldwide by an increasing resistance to carbapenems, particularly present in opportunistic Enterobacterales pathogens (e.g., Klebsiella spp.). However, there is a lack of comprehensive and comparable data on their occurrence in wastewater, as well as on the phenotypic and genotypic characteristics for various countries including Germany. Thus, this study aims to characterize carbapenem-resistant Klebsiella spp. isolated from municipal wastewater treatment plants (mWWTPs) and their receiving water bodies, as well as from wastewater and process waters from poultry and pig slaughterhouses. After isolation using selective media and determination of carbapenem (i.e., ertapenem) resistance using broth microdilution to apply epidemiological breakpoints, the selected isolates (n = 30) were subjected to WGS. The vast majority of the isolates (80.0%) originated from the mWWTPs and their receiving water bodies. In addition to ertapenem, Klebsiella spp. isolates exhibited resistance to meropenem (40.0%) and imipenem (16.7%), as well as to piperacillin-tazobactam (50.0%) and ceftolozan-tazobactam (50.0%). A high diversity of antibiotic-resistance genes (n = 68), in particular those encoding β-lactamases, was revealed. However, with the exception of blaGES-5-like, no acquired carbapenemase-resistance genes were detected. Virulence factors such as siderophores (e.g., enterobactin) and fimbriae type 1 were present in almost all isolates. A wide genetic diversity was indicated by assigning 66.7% of the isolates to 12 different sequence types (STs), including clinically relevant ones (e.g., ST16, ST252, ST219, ST268, ST307, ST789, ST873, and ST2459). Our study provides information on the occurrence of carbapenem-resistant, ESBL-producing Klebsiella spp., which is of clinical importance in wastewater and surface water in Germany. These findings indicate their possible dissemination in the environment and the potential risk of colonization and/or infection of humans, livestock and wildlife associated with exposure to contaminated water sources.
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Affiliation(s)
- Mykhailo Savin
- Institute for Hygiene and Public Health, University Hospital Bonn, 53127 Bonn, Germany;
- Institute of Animal Sciences, University of Bonn, 53115 Bonn, Germany;
- Correspondence: (M.S.); (J.A.H.)
| | - Gabriele Bierbaum
- Institute for Medical Microbiology, Immunology and Parasitology, Medical Faculty, University of Bonn, 53115 Bonn, Germany;
| | - Nico T. Mutters
- Institute for Hygiene and Public Health, University Hospital Bonn, 53127 Bonn, Germany;
| | - Ricarda Maria Schmithausen
- Department of Hygiene and Environmental Medicine, University Hospital Essen, University of Duisburg-Essen, 45147 Essen, Germany;
| | - Judith Kreyenschmidt
- Institute of Animal Sciences, University of Bonn, 53115 Bonn, Germany;
- Department of Fresh Produce Logistics, Hochschule Geisenheim University, 65366 Geisenheim, Germany
| | - Isidro García-Meniño
- Department for Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany; (I.G.-M.); (S.S.); (A.K.)
- Laboratorio de Referencia de Escherichia coli (LREC), Departamento de Microbioloxía e Parasitoloxía, Facultade de Veterinaria, Universidade de Santiago de Compostela (USC), 27002 Lugo, Spain
| | - Silvia Schmoger
- Department for Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany; (I.G.-M.); (S.S.); (A.K.)
| | - Annemarie Käsbohrer
- Department for Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany; (I.G.-M.); (S.S.); (A.K.)
- Unit for Veterinary Public Health and Epidemiology, University of Veterinary Medicine, AT-1210 Vienna, Austria
| | - Jens Andre Hammerl
- Department for Biological Safety, German Federal Institute for Risk Assessment, 10589 Berlin, Germany; (I.G.-M.); (S.S.); (A.K.)
- Correspondence: (M.S.); (J.A.H.)
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11
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Sun Y, Han R, Ding L, Yang Y, Guo Y, Wu S, Hu F, Yin D. First Report of bla OXA-677 with Enhanced Meropenem-Hydrolyzing Ability in Pseudomonas aeruginosa in China. Infect Drug Resist 2022; 14:5725-5733. [PMID: 35002263 PMCID: PMC8725689 DOI: 10.2147/idr.s340662] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 12/09/2021] [Indexed: 12/18/2022] Open
Abstract
Purpose OXA-10-type class D β-lactamases have shown their evolutionary potential of enhancing carbapenem resistance. This study aimed to elucidate the role of OXA-10 variants in clinical isolated multidrug resistant (MDR) Pseudomonas aeruginosa and characterize the first appearance of OXA-677 in China. Methods Six blaOXA-10-like-positive strains were screened by PCR from 41 P. aeruginosa strains, which were resistant to both carbapenems and ceftazidime-avibactam, collected across China in 2018. The minimum inhibitory concentrations (MIC) were determined with the broth microdilution method. The resistance-associated genes and genetic environment were investigated by whole-genome sequencing (WGS). The function and mechanism of OXA-677 β-lactamase were identified by molecular cloning and protein structure modeling. Results All the blaOXA-10-like-positive Pseudomonas aeruginosa were MDR strains. They also had outer membrane porin defects and produced β-lactam resistance gene blaPER-1, fluoroquinolone-resistant gene crpP, aminoglycoside-resistance gene aph(3ʹ)-IIb, aph(6)-Id, aacA and aadA, fosfomycin-resistance gene fosA, sulfamethoxazole-resistance gene sul1, and chloramphenicol-resistance gene catB7. All blaOXA-10 variants were located in a Tn1403-related transposon, containing aacA4-12-blaOXA-677-aadA1, aacA4-12-blaOXA-101-aadA5, and blaOXA-246-aacA3-aadA13 gene cassette arrays, respectively. Notably, the blaOXA-677 producer showed a high MIC level of meropenem (MIC>64 mg/L). Compared to blaOXA-10, blaOXA-677 was found a G-to-T transversion at position 350, leading to a phenylalanine-for-valine substitution in position 117, which is closer to leucine155 in the omega loop of the active site. MIC of meropenem for E. coli DH5α with the recombinant plasmid pHSG398 carrying blaOXA-677 was elevated by 8 times. Conclusion We speculate that the OXA-10-like enzymes and the decrease of membrane permeability confer carbapenem resistance, and the V117 substitution in OXA-677 might lead to a higher resistance level of meropenem.
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Affiliation(s)
- Yue Sun
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People's Republic of China.,Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, People's Republic of China
| | - Renru Han
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People's Republic of China.,Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, People's Republic of China
| | - Li Ding
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People's Republic of China.,Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, People's Republic of China
| | - Yang Yang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People's Republic of China.,Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, People's Republic of China
| | - Yan Guo
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People's Republic of China.,Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, People's Republic of China
| | - Shi Wu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People's Republic of China.,Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, People's Republic of China
| | - Fupin Hu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People's Republic of China.,Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, People's Republic of China
| | - Dandan Yin
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, People's Republic of China.,Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, People's Republic of China
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12
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Analysis of Wastewater Reveals the Spread of Diverse Extended-Spectrum β-Lactamase-Producing E. coli Strains in uMgungundlovu District, South Africa. Antibiotics (Basel) 2021; 10:antibiotics10070860. [PMID: 34356780 PMCID: PMC8300763 DOI: 10.3390/antibiotics10070860] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 07/08/2021] [Accepted: 07/09/2021] [Indexed: 11/27/2022] Open
Abstract
Wastewater treatment plants (WWTPs) are major reservoirs of antibiotic-resistant bacteria (ARB), favouring antibiotic resistance genes (ARGs) interchange among bacteria and they can provide valuable information on ARB circulating in a community. This study characterised extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli from the influent and effluent of four WWTPs in uMgungundlovu District, KwaZulu-Natal, South Africa. E. coli was enumerated using the membrane filtration method and confirmed using the API 20E test and real-time polymerase chain reaction. ESBL-producers were phenotypically identified by their susceptibility to the third-generation cephalosporins using the disc diffusion and the double-disc synergy methods against cefotaxime (30 µg) with and without 10 µg clavulanic acid. Genotypic verification was by PCR of the TEM, SHV, and CTX-M genes. The clonality of isolates was assessed by ERIC-PCR. The highest E. coli count ranged between 1.1 × 105 (influent) and 4.3 × 103 CFU/mL (effluent). Eighty pure isolates were randomly selected, ten from the influent and effluent of each of the four WWTP. ESBLs were phenotypically confirmed in 49% (n = 39) of the isolates, of which 77% (n = 30) were genotypically confirmed. Seventy-three percent of the total isolates were multidrug-resistant (MDR). Only two isolates were susceptible to all antibiotics. Overall, resistance to first and second-generation cephalosporins was higher than to third and fourth generation cephalosporins. Also, 15% of the isolates were resistant to carbapenems. The CTX-M-type ESBL (67%; n = 20) was the most common ESBL antibiotic resistance gene (ARG) followed by TEM (57%; n = 17) and SHV-types (27%; n = 8). Also, a substantial number of isolates simultaneously carried all three ESBL genes. ERIC-PCR revealed a high diversity of isolates. The diversity of the isolates observed in the influent samples suggest the potential circulation of different ESBL-producing strains within the studied district, requiring a more comprehensive epidemiological study to prevent the spread of ESBL-producing bacteria within impoverished communities.
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13
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Arca-Suárez J, Lasarte-Monterrubio C, Rodiño-Janeiro BK, Cabot G, Vázquez-Ucha JC, Rodríguez-Iglesias M, Galán-Sánchez F, Beceiro A, González-Bello C, Oliver A, Bou G. Molecular mechanisms driving the in vivo development of OXA-10-mediated resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of XDR Pseudomonas aeruginosa infections. J Antimicrob Chemother 2021; 76:91-100. [PMID: 33083833 DOI: 10.1093/jac/dkaa396] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 08/25/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND The development of resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of Pseudomonas aeruginosa infections is concerning. OBJECTIVES Characterization of the mechanisms leading to the development of OXA-10-mediated resistance to ceftolozane/tazobactam and ceftazidime/avibactam during treatment of XDR P. aeruginosa infections. METHODS Four paired ceftolozane/tazobactam- and ceftazidime/avibactam-susceptible/resistant isolates were evaluated. MICs were determined by broth microdilution. STs, resistance mechanisms and genetic context of β-lactamases were determined by genotypic methods, including WGS. The OXA-10 variants were cloned in PAO1 to assess their impact on resistance. Models for the OXA-10 derivatives were constructed to evaluate the structural impact of the amino acid changes. RESULTS The same XDR ST253 P. aeruginosa clone was detected in all four cases evaluated. All initial isolates showed OprD deficiency, produced an OXA-10 enzyme and were susceptible to ceftazidime, ceftolozane/tazobactam, ceftazidime/avibactam and colistin. During treatment, the isolates developed resistance to all cephalosporins. Comparative genomic analysis revealed that the evolved resistant isolates had acquired mutations in the OXA-10 enzyme: OXA-14 (Gly157Asp), OXA-794 (Trp154Cys), OXA-795 (ΔPhe153-Trp154) and OXA-824 (Asn143Lys). PAO1 transformants producing the evolved OXA-10 derivatives showed enhanced ceftolozane/tazobactam and ceftazidime/avibactam resistance but decreased meropenem MICs in a PAO1 background. Imipenem/relebactam retained activity against all strains. Homology models revealed important changes in regions adjacent to the active site of the OXA-10 enzyme. The blaOXA-10 gene was plasmid borne and acquired due to transposition of Tn6746 in the pHUPM plasmid scaffold. CONCLUSIONS Modification of OXA-10 is a mechanism involved in the in vivo acquisition of resistance to cephalosporin/β-lactamase inhibitor combinations in P. aeruginosa.
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Affiliation(s)
- Jorge Arca-Suárez
- Servicio de Microbiología-Instituto de Investigación Biomédica (INIBIC), Complexo Hospitalario Universitario A Coruña, A Coruña, Spain
| | - Cristina Lasarte-Monterrubio
- Servicio de Microbiología-Instituto de Investigación Biomédica (INIBIC), Complexo Hospitalario Universitario A Coruña, A Coruña, Spain
| | - Bruno-Kotska Rodiño-Janeiro
- Prof. Martin Polz Laboratory, University of Vienna, Department for Microbiology and Ecosystem Science, Division of Microbial Ecology, Vienna, Austria
| | - Gabriel Cabot
- Servicio de Microbiología and Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdiSBA), Palma de Mallorca, Spain
| | - Juan Carlos Vázquez-Ucha
- Servicio de Microbiología-Instituto de Investigación Biomédica (INIBIC), Complexo Hospitalario Universitario A Coruña, A Coruña, Spain
| | - Manuel Rodríguez-Iglesias
- Servicio de Microbiología and Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Hospital Universitario Puerta del Mar; Departamento de Biomedicina, Biotecnología y Salud Pública, Universidad de Cádiz, Cádiz, Spain
| | - Fátima Galán-Sánchez
- Servicio de Microbiología and Instituto de Investigación e Innovación Biomédica de Cádiz (INiBICA), Hospital Universitario Puerta del Mar; Departamento de Biomedicina, Biotecnología y Salud Pública, Universidad de Cádiz, Cádiz, Spain
| | - Alejandro Beceiro
- Servicio de Microbiología-Instituto de Investigación Biomédica (INIBIC), Complexo Hospitalario Universitario A Coruña, A Coruña, Spain
| | - Concepción González-Bello
- Centro Singular de Investigación en Química Biolóxica e Materiais Moleculares (CIQUS), Departamento de Química Orgánica, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Antonio Oliver
- Servicio de Microbiología and Unidad de Investigación, Hospital Universitario Son Espases, Instituto de Investigación Sanitaria Illes Balears (IdiSBA), Palma de Mallorca, Spain
| | - Germán Bou
- Servicio de Microbiología-Instituto de Investigación Biomédica (INIBIC), Complexo Hospitalario Universitario A Coruña, A Coruña, Spain
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Emerging Transcriptional and Genomic Mechanisms Mediating Carbapenem and Polymyxin Resistance in Enterobacteriaceae: a Systematic Review of Current Reports. mSystems 2020; 5:5/6/e00783-20. [PMID: 33323413 PMCID: PMC7771540 DOI: 10.1128/msystems.00783-20] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
The spread of carbapenem- and polymyxin-resistant Enterobacteriaceae poses a significant threat to public health, challenging clinicians worldwide with limited therapeutic options. This review describes the current coding and noncoding genetic and transcriptional mechanisms mediating carbapenem and polymyxin resistance, respectively. The spread of carbapenem- and polymyxin-resistant Enterobacteriaceae poses a significant threat to public health, challenging clinicians worldwide with limited therapeutic options. This review describes the current coding and noncoding genetic and transcriptional mechanisms mediating carbapenem and polymyxin resistance, respectively. A systematic review of all studies published in PubMed database between 2015 to October 2020 was performed. Journal articles evaluating carbapenem and polymyxin resistance mechanisms, respectively, were included. The search identified 171 journal articles for inclusion. Different New Delhi metallo-β-lactamase (NDM) carbapenemase variants had different transcriptional and affinity responses to different carbapenems. Mutations within the Klebsiella pneumoniae carbapenemase (KPC) mobile transposon, Tn4401, affect its promoter activity and expression levels, increasing carbapenem resistance. Insertion of IS26 in ardK increased imipenemase expression 53-fold. ompCF porin downregulation (mediated by envZ and ompR mutations), micCF small RNA hyperexpression, efflux upregulation (mediated by acrA, acrR, araC, marA, soxS, ramA, etc.), and mutations in acrAB-tolC mediated clinical carbapenem resistance when coupled with β-lactamase activity in a species-specific manner but not when acting without β-lactamases. Mutations in pmrAB, phoPQ, crrAB, and mgrB affect phosphorylation of lipid A of the lipopolysaccharide through the pmrHFIJKLM (arnBCDATEF or pbgP) cluster, leading to polymyxin resistance; mgrB inactivation also affected capsule structure. Mobile and induced mcr, efflux hyperexpression and porin downregulation, and Ecr transmembrane protein also conferred polymyxin resistance and heteroresistance. Carbapenem and polymyxin resistance is thus mediated by a diverse range of genetic and transcriptional mechanisms that are easily activated in an inducing environment. The molecular understanding of these emerging mechanisms can aid in developing new therapeutics for multidrug-resistant Enterobacteriaceae isolates.
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Aertker KMJ, Chan HTH, Lohans CT, Schofield CJ. Analysis of β-lactone formation by clinically observed carbapenemases informs on a novel antibiotic resistance mechanism. J Biol Chem 2020; 295:16604-16613. [PMID: 32963107 PMCID: PMC7864059 DOI: 10.1074/jbc.ra120.014607] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2020] [Revised: 09/07/2020] [Indexed: 01/18/2023] Open
Abstract
An important mechanism of resistance to β-lactam antibiotics is via their β-lactamase-catalyzed hydrolysis. Recent work has shown that, in addition to the established hydrolysis products, the reaction of the class D nucleophilic serine β-lactamases (SBLs) with carbapenems also produces β-lactones. We report studies on the factors determining β-lactone formation by class D SBLs. We show that variations in hydrophobic residues at the active site of class D SBLs (i.e. Trp105, Val120, and Leu158, using OXA-48 numbering) impact on the relative levels of β-lactones and hydrolysis products formed. Some variants, i.e. the OXA-48 V120L and OXA-23 V128L variants, catalyze increased β-lactone formation compared with the WT enzymes. The results of kinetic and product studies reveal that variations of residues other than those directly involved in catalysis, including those arising from clinically observed mutations, can alter the reaction outcome of class D SBL catalysis. NMR studies show that some class D SBL variants catalyze formation of β-lactones from all clinically relevant carbapenems regardless of the presence or absence of a 1β-methyl substituent. Analysis of reported crystal structures for carbapenem-derived acyl-enzyme complexes reveals preferred conformations for hydrolysis and β-lactone formation. The observation of increased β-lactone formation by class D SBL variants, including the clinically observed carbapenemase OXA-48 V120L, supports the proposal that class D SBL-catalyzed rearrangement of β-lactams to β-lactones is important as a resistance mechanism.
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Affiliation(s)
| | - H T Henry Chan
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom
| | - Christopher T Lohans
- Chemistry Research Laboratory, University of Oxford, Oxford, United Kingdom; Department of Biomedical and Molecular Sciences, Queen's University, Kingston, Ontario, Canada.
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Leiros HKS, Thomassen AM, Samuelsen Ø, Flach CF, Kotsakis SD, Larsson DGJ. Structural insights into the enhanced carbapenemase efficiency of OXA-655 compared to OXA-10. FEBS Open Bio 2020; 10:1821-1832. [PMID: 32683794 PMCID: PMC7459404 DOI: 10.1002/2211-5463.12935] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 06/17/2020] [Accepted: 07/15/2020] [Indexed: 11/17/2022] Open
Abstract
Carbapenemases are the main cause of carbapenem resistance in Gram‐negative bacteria. How β‐lactamases with weak carbapenemase activity, such as the OXA‐10‐type class D β‐lactamases, contribute to anti‐bacterial drug resistance is unclear. OXA‐655 is a T26M and V117L OXA‐10 variant, recently identified from hospital wastewater. Despite exhibiting stronger carbapenemase activity towards ertapenem (ETP) and meropenem (MEM) in Escherichia coli, OXA‐655 exhibits reduced activity towards oxyimino‐substituted β‐lactams like ceftazidime. Here, we have solved crystal structures of OXA‐10 in complex with imipenem (IPM) and ETP, and OXA‐655 in complex with MEM in order to unravel the structure–function relationship and the impact of residue 117 in enzyme catalysis. The new crystal structures show that L117 is situated at a critical position with enhanced Van der Waals interactions to L155 in the omega loop. This restricts the movements of L155 and could explain the reduced ability for OXA‐655 to bind a bulky oxyimino group. The V117L replacement in OXA‐655 makes the active site S67 and the carboxylated K70 more water exposed. This could affect the supply of new deacylation water molecules required for hydrolysis and possibly the carboxylation rate of K70. But most importantly, L117 leaves more space for binding of the hydroxyethyl group in carbapenems. In summary, the crystal structures highlight the importance of residue 117 in OXA‐10 variants for carbapenemase activity. This study also illustrates the impact of a single amino acid substitution on the substrate profile of OXA‐10 and the evolutionary potential of new OXA‐10 variants.
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Affiliation(s)
- Hanna-Kirsti S Leiros
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ane Molden Thomassen
- The Norwegian Structural Biology Centre (NorStruct), Department of Chemistry, Faculty of Science and Technology, UiT The Arctic University of Norway, Tromsø, Norway
| | - Ørjan Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway.,Department of Pharmacy, UiT The Arctic University of Norway, Tromsø, Norway
| | - Carl-Fredrik Flach
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - Stathis D Kotsakis
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
| | - D G Joakim Larsson
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.,Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
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Zhou H, Zhang K, Chen W, Chen J, Zheng J, Liu C, Cheng L, Zhou W, Shen H, Cao X. Epidemiological characteristics of carbapenem-resistant Enterobacteriaceae collected from 17 hospitals in Nanjing district of China. Antimicrob Resist Infect Control 2020; 9:15. [PMID: 31956404 PMCID: PMC6958626 DOI: 10.1186/s13756-019-0674-4] [Citation(s) in RCA: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Accepted: 12/23/2019] [Indexed: 12/19/2022] Open
Abstract
Objective In total, 97 carbapenem-resistant Enterobacteriaceae (CRE) were collected from 17 hospitals located in Nanjing, Southeast China, and analyzed for epidemiological characteristics. Methods Antimicrobial susceptibility was determined; followed by determination of the prevalence of resistance determinants, including extended-spectrum β-lactamase (ESBLs), plasmid-mediated AmpC enzyme (pAmpCs), plasmid-mediated quinolone resistance genes (PMQRs), fosfomycin resistance gene and exogenously acquired 16S rRNA methyltransferase (16S-RMTase) using PCR and DNA sequencing. The sequence types (STs) of CRE were determined by multi-locus sequence typing (MLST). The plasmid profiles were detected by PCR-based replicon typing (PBRT). Results All the CRE strains displayed high MIC50 and MIC90 for nearly all clinical available antibiotics, except for aztreonam/avibactam, minocycline, ceftazidime/avibactam, tigecycline, and colistin. KPC-2 (79.4%) and NDM (19.6%) were the main carbapenemases, CTX-M (76.3%) and SHV (60.8%) were the predominant ESBLs. In addition, oqxAB (70.1%) and qnr (63.9%) were the major PMQRs; rmtB (47.4%) was the main 16S-RMTase; fosA (76.3%) and fosA3 (37.1%) were the fosfomycin resistance gene. PBRT analysis showed presence of IncR (66.0%) and IncFII (64.9%) replicon types in the majority of the isolates, followed by IncFIB (46.4%) and IncX3 (16.5%). The IncFII and IncR replicon-types were found mainly in K. pneumoniae (68.8%), whereas the IncX3 replicons dominated in E. coli isolates (100.0%). The three dominating MLST-types ST11, ST15 and ST268 comprised 68.0% of the 77 K. pneumoniae. Seven distinct STs were identified among 8 E. coli. Conclusions The treatment for infections caused by CRE isolates is challenged by the presence of multiple resistance determinants and plasmid replicons. Our results highlighted the expansion of blaKPC-2 carrying K. pneumoniae ST11, the new emergency of single blaNDM-5 carrying K. oxytoca ST36, as well as blaIMP-4 and blaNDM-1 co-carrying E. cloacae ST418, which alert us on the urgency for antimicrobial resistant surveillance, to prevent dissemination of these highly transmissible and dangerous lineages.
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Affiliation(s)
- Hui Zhou
- 1Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the affiliated Hospital of Nanjing University Medical School, Zhongshan Road 321, Gulou District, Nanjing, Jiangsu People's Republic of China
| | - Kui Zhang
- 1Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the affiliated Hospital of Nanjing University Medical School, Zhongshan Road 321, Gulou District, Nanjing, Jiangsu People's Republic of China
| | - Wei Chen
- 2Clinical Research Center, the second hospital of Nanjing, Nanjing University of Chinese Medicine, Nanjing, 210003 China
| | - Junhao Chen
- 1Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the affiliated Hospital of Nanjing University Medical School, Zhongshan Road 321, Gulou District, Nanjing, Jiangsu People's Republic of China
| | - Jie Zheng
- 1Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the affiliated Hospital of Nanjing University Medical School, Zhongshan Road 321, Gulou District, Nanjing, Jiangsu People's Republic of China
| | - Chang Liu
- 1Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the affiliated Hospital of Nanjing University Medical School, Zhongshan Road 321, Gulou District, Nanjing, Jiangsu People's Republic of China
| | - Li Cheng
- 1Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the affiliated Hospital of Nanjing University Medical School, Zhongshan Road 321, Gulou District, Nanjing, Jiangsu People's Republic of China
| | - Wanqing Zhou
- 1Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the affiliated Hospital of Nanjing University Medical School, Zhongshan Road 321, Gulou District, Nanjing, Jiangsu People's Republic of China
| | - Han Shen
- 1Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the affiliated Hospital of Nanjing University Medical School, Zhongshan Road 321, Gulou District, Nanjing, Jiangsu People's Republic of China
| | - Xiaoli Cao
- 1Department of Laboratory Medicine, Nanjing Drum Tower Hospital, the affiliated Hospital of Nanjing University Medical School, Zhongshan Road 321, Gulou District, Nanjing, Jiangsu People's Republic of China
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Marathe NP, Berglund F, Razavi M, Pal C, Dröge J, Samant S, Kristiansson E, Larsson DGJ. Sewage effluent from an Indian hospital harbors novel carbapenemases and integron-borne antibiotic resistance genes. MICROBIOME 2019; 7:97. [PMID: 31248462 PMCID: PMC6598227 DOI: 10.1186/s40168-019-0710-x] [Citation(s) in RCA: 63] [Impact Index Per Article: 12.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/11/2019] [Accepted: 06/05/2019] [Indexed: 05/17/2023]
Abstract
BACKGROUND Hospital wastewaters contain fecal material from a large number of individuals, of which many are undergoing antibiotic therapy. It is, thus, plausible that hospital wastewaters could provide opportunities to find novel carbapenemases and other resistance genes not yet described in clinical strains. Our aim was therefore to investigate the microbiota and antibiotic resistome of hospital effluent collected from the city of Mumbai, India, with a special focus on identifying novel carbapenemases. RESULTS Shotgun metagenomics revealed a total of 112 different mobile antibiotic resistance gene types, conferring resistance against almost all classes of antibiotics. Beta-lactamase genes, including encoding clinically important carbapenemases, such as NDM, VIM, IMP, KPC, and OXA-48, were abundant. NDM (0.9% relative abundance to 16S rRNA genes) was the most common carbapenemase gene, followed by OXA-58 (0.84% relative abundance to 16S rRNA genes). Among the investigated mobile genetic elements, class 1 integrons (11% relative abundance to 16S rRNA genes) were the most abundant. The genus Acinetobacter accounted for as many as 30% of the total 16S rRNA reads, with A. baumannii accounting for an estimated 2.5%. High throughput sequencing of amplified integron gene cassettes identified a novel functional variant of an IMP-type (proposed IMP-81) carbapenemase gene (eight aa substitutions) along with recently described novel resistance genes like sul4 and blaRSA1. Using a computational hidden Markov model, we detected 27 unique metallo-beta-lactamase (MBL) genes in the shotgun data, of which nine were novel subclass B1 genes, one novel subclass B2, and 10 novel subclass B3 genes. Six of the seven novel MBL genes were functional when expressed in Escherichia coli. CONCLUSION By exploring hospital wastewater from India, our understanding of the diversity of carbapenemases has been extended. The study also demonstrates that the microbiota of hospital wastewater can serve as a reservoir of novel resistance genes, including previously uncharacterized carbapenemases with the potential to spread further.
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Affiliation(s)
- Nachiket P Marathe
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
- Institute of Marine Research (IMR), Bergen, Norway
| | - Fanny Berglund
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| | - Mohammad Razavi
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden
| | - Chandan Pal
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Plant Health and Environment Laboratory (PHEL), Ministry for Primary Industries (MPI), Auckland, New Zealand
| | - Johannes Dröge
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| | - Sharvari Samant
- Mahatma Gandhi Mission medical college, Navi Mumbai, Maharashtra, India
| | - Erik Kristiansson
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden
- Department of Mathematical Sciences, Chalmers University of Technology and University of Gothenburg, Gothenburg, Sweden
| | - D G Joakim Larsson
- Centre for Antibiotic Resistance Research (CARe), University of Gothenburg, Gothenburg, Sweden.
- Department of Infectious Diseases, Institute of Biomedicine, Sahlgrenska Academy, University of Gothenburg, Gothenburg, Sweden.
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