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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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Kundu R, Murugadoss K, Manoharan M, Mandal J. Burden of biocide resistance among multidrug-resistant bacteria isolated from various clinical specimens in a tertiary care hospital. Indian J Med Microbiol 2023; 46:100478. [PMID: 37769586 DOI: 10.1016/j.ijmmb.2023.100478] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 08/31/2023] [Accepted: 09/11/2023] [Indexed: 10/03/2023]
Abstract
BACKGROUND Most studies on biocide resistance and its genetic determinants arise from environmental or food-borne microbial isolates and only a few from clinically relevant isolates. OBJECTIVES This study determines the proportion of biocide resistance against five commonly used biocides and detects biocide resistance genes among MDR bacterial isolates using PCR. METHODS Consecutive MDR isolates (n = 180) were included (30 each of Escherichia coli, Klebsiella pneumoniae, Pseudomonas aeruginosa, Acinetobacter baumannii, Staphylococcus aureus, and Enterococcus species) from clinical specimens of various inpatient units at JIPMER. The isolates were challenged at 0.5,1 and 2 Macfarland (McF) inoculum with discrete dilutions of disinfectants. The minimum bactericidal concentrations (MBCs) for 70% Ethanol, 1.5% Cresol, 2% Glutaraldehyde, 1% Cetrimide, and 1% Chlorhexidine were determined for the isolates using ATCC reference strains as controls. PCR was performed targeting qac A/B, G; smr; and nfx B genes. RESULTS For all biocides, MDR isolates had MBCs less than the maximum MBCs of ATCC strains. For MDR K. pneumoniae, A. baumannii, and P. aeruginosa, the highest MBCs of chlorhexidine and cetrimide were ≥75 and ≥ 150 μg/ml respectively at 0.5 McF inoculum; whereas these organisms grew at higher inoculum (2McF) even at commercially recommended biocidal concentration (1%) corresponding to 750 and 1500 μg/ml of chlorhexidine and cetrimide respectively. Meanwhile, the highest MBCs of MDR E. coli were 75 and 150 μg/ml for chlorhexidine and cetrimide respectively. Interestingly, the Gram-positive cocci survived the action of up to 35% ethanol. The nfxB and qacG genes were detected in 87% and 6.67% of MDR P. aeruginosa isolates respectively with no biocide resistance genes detected among the other organisms. CONCLUSIONS Biocide dilutions challenged with higher inoculum indicated a narrow margin of effectiveness for certain biocides. Although a significant proportion of clinical MDR isolates of P. aeruginosa harbored biocide resistance genes, this finding had no phenotypic correlation.
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Affiliation(s)
- Ramit Kundu
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Institute and Research (JIPMER), Dhanvantri Nagar, Gorimedu, Pondicherry-605006, India.
| | - Kamali Murugadoss
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Institute and Research (JIPMER), Dhanvantri Nagar, Gorimedu, Pondicherry-605006, India.
| | - Meerabai Manoharan
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Institute and Research (JIPMER), Dhanvantri Nagar, Gorimedu, Pondicherry-605006, India.
| | - Jharna Mandal
- Department of Microbiology, Jawaharlal Institute of Postgraduate Medical Institute and Research (JIPMER), Dhanvantri Nagar, Gorimedu, Pondicherry-605006, India.
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3
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Zheng Z, Liu L, Ye L, Xu Y, Chen S. Genomic insight into the distribution and genetic environment of bla IMP-4 in clinical carbapenem-resistant Klebsiella pneumoniae strains in China. Microbiol Res 2023; 275:127468. [PMID: 37541025 DOI: 10.1016/j.micres.2023.127468] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 07/28/2023] [Accepted: 07/28/2023] [Indexed: 08/06/2023]
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a major threat to public health due to its resistance to almost all antibiotics. It is associated with substantial morbidity and mortality and poses a significant challenge to healthcare systems around the globe. Based on our previous nationwide survey of carbapenem-resistant Enterobacteriaceae (CRE) in China, seven blaIMP-4-carrying CRKP isolates were identified, all exhibiting MDR and epidemiologically linked to four different regions in China. WGS analysis revealed that the seven blaIMP-4 genes were all located on plasmids, of which five blaIMP-4 genes were located on the IncHI5 plasmids and the other two belonged to the IncN and IncFIIK plasmids, respectively. Except for the IncHI5 plasmid, conjugation assays revealed that the IncN and IncFIIK plasmids could be transferred to the recipient strain Escherichia coli J53. This study revealed significant genetic variation and identified numerous resistance factors among blaIMP-4-carrying CRKP strains in China, suggesting that blaIMP-4-carrying CRKP strains evolved via multiple phylogenetic routes and highlighting a need for expanded surveillance and establishment of control measures to prevent dissemination of CRKP strains, and facilitate development of more effective antibiotic stewardship policies and infection control programs.
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Affiliation(s)
- Zhiwei Zheng
- The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, PR China
| | - Lizhang Liu
- Department of Pathogen Biology & Microbiology, Zhejiang University School of Medicine, Hangzhou, PR China
| | - Lianwei Ye
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Yating Xu
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Sheng Chen
- Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong; City University of Hong Kong Chengdu Research Institute, Chengdu, PR China.
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Wang L, Chen H, Liu W, Yang L, Xu Z, Chen D. Resistome and Genome Analysis of an Extensively Drug-Resistant Klebsiella michiganensis KMIB106: Characterization of a Novel KPC Plasmid pB106-1 and a Novel Cointegrate Plasmid pB106-IMP Harboring blaIMP-4 and blaSHV-12. Antibiotics (Basel) 2023; 12:1463. [PMID: 37760759 PMCID: PMC10525660 DOI: 10.3390/antibiotics12091463] [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: 07/14/2023] [Revised: 09/07/2023] [Accepted: 09/13/2023] [Indexed: 09/29/2023] Open
Abstract
Klebsiella michiganensis is a recently emerging human pathogen causing nosocomial infections. This study aimed to characterize the complete genome sequence of a clinical Klebsiella michiganensis strain KMIB106 which exhibited extensive drug-resistance. The whole genome of the strain was sequenced using PacBio RS III systems and Illumina Nextseq 500. Annotation, transposable elements and resistance gene identification were analyzed by RAST, prokka and Plasmid Finder, respectively. According to the results, KMIB106 was resistant to multiple antimicrobials, including carbapenems, but it remained susceptible to aztreonam. The genome of KMIB106 consisted of a single chromosome and three predicted plasmids. Importantly, a novel KPC plasmid pB106-1 was found to carry the array of resistance genes in a highly different order in its variable regions, including mphA, msrE, mphE, ARR-3, addA16, sul1, dfrA27, tetD and fosA3. Plasmid pB106-2 is a typical IncFII plasmid with no resistant gene. Plasmid pB106-IMP consists of the IncN and IncX3 backbones, and two resistance genes, blaIMP-4 and blaSHV-12, were identified. Our study for the first time reported an extensively drug-resistant Klebsiella michiganensis strain recovered from a child with a respiratory infection in Southern China, which carries three mega plasmids, with pB106-1 firstly identified to carry an array of resistance genes in a distinctive order, and pB106-IMP identified as a novel IncN-IncX3 cointegrate plasmid harboring two resistance genes blaIMP-4 and blaSHV-12.
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Affiliation(s)
- Linjing Wang
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Haijun Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Wanting Liu
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
| | - Ling Yang
- Department of Laboratory Medicine, The First Affiliated Hospital of Guangzhou Medical University, Guangzhou 510120, China
| | - Zhenbo Xu
- School of Food Science and Engineering, Research Institute for Food Nutrition and Human Health, Guangdong Province Key Laboratory for Green Processing of Natural Products and Product Safety, Engineering Research Center of Starch and Vegetable Protein Processing Ministry of Education, South China University of Technology, Guangzhou 510640, China
- Department of Laboratory Medicine, The Second Affiliated Hospital of Shantou University Medical College, Shantou 515141, China
| | - Dingqiang Chen
- Microbiome Medicine Center, Department of Laboratory Medicine, Zhujiang Hospital, Southern Medical University, Guangzhou 510280, China
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Vázquez-López R, Hernández-Martínez T, Larios-Fernández SI, Piña-Leyva C, Lara-Lozano M, Guerrero-González T, Martínez-Bautista J, Gómez-Conde E, González-Barrios JA. Characterization of Beta-Lactam Resistome of Escherichia coli Causing Nosocomial Infections. Antibiotics (Basel) 2023; 12:1355. [PMID: 37760652 PMCID: PMC10525731 DOI: 10.3390/antibiotics12091355] [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: 07/14/2023] [Revised: 08/03/2023] [Accepted: 08/05/2023] [Indexed: 09/29/2023] Open
Abstract
Nosocomial infections caused by Escherichia coli pose significant therapeutic challenges due to the high expression of genes encoding antimicrobial drug resistance. In this study, we investigated the conformation of the beta-lactam resistome responsible for the specific pattern of resistance against beta-lactam antibiotics. A total of 218 Escherichia coli strains were isolated from in-hospital patients diagnosed with nosocomial infections, obtained from various sources such as urine (n = 49, 22.48%), vaginal discharge (n = 46, 21.10%), catheter tips (n = 14, 6.42%), blood (n = 13, 5.96%), feces (n = 12, 5.50%), sputum (n = 11, 5.05%), biopsies (n = 8, 3.67%), cerebrospinal fluid (n = 2, 0.92%) and other unspecified discharges (n = 63, 28.90%). To characterize the beta-lactam resistome, all strains were subjected to antibiotic dilution tests and grown in beta-lactam antibiotics supplemented with Luria culture medium. Subsequently, multiplex PCR and next-generation sequencing were conducted. The results show a multi-drug-resistance phenotype, particularly against beta-lactam drugs. The primary determinant of this resistance was the expression of the blaTEM gene family, with 209 positive strains (95.87%) expressing it as a single gene (n = 47, 21.6%) or in combination with other genes. Common combinations included blaTEM + blaCTX (n = 42, 19.3%), blaTEM + blaCTX + blaSHV (n = 13, 6%) and blaTEM + blaCTX + blaBIL (n = 12, 5.5%), among others. The beta-lactam resistome of nosocomial Escherichia coli strains isolated from inpatients at the "October first" Regional Hospital of ISSSTE was predominantly composed of members of the blaTEM gene family, expressed in various configurations along with different members of other beta-lactamase gene families.
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Affiliation(s)
- Rosalino Vázquez-López
- Departamento de Microbiología, Centro de Investigación en Ciencias de la Salud (CICSA), Facultad de Ciencias de la Salud Universidad Anáhuac México Norte, Huixquilucan 52786, Mexico;
| | - Tanya Hernández-Martínez
- Laboratorio de Medicina Genómica, Hospital Regional “Primero de Octubre”, ISSSTE, Av. Instituto Politécnico Nacional 1669, Lindavista, Gustavo A. Madero, Ciudad de México 07300, Mexico; (T.H.-M.); (S.I.L.-F.); (C.P.-L.); (M.L.-L.); (T.G.-G.)
| | - Selene Ivonne Larios-Fernández
- Laboratorio de Medicina Genómica, Hospital Regional “Primero de Octubre”, ISSSTE, Av. Instituto Politécnico Nacional 1669, Lindavista, Gustavo A. Madero, Ciudad de México 07300, Mexico; (T.H.-M.); (S.I.L.-F.); (C.P.-L.); (M.L.-L.); (T.G.-G.)
| | - Celia Piña-Leyva
- Laboratorio de Medicina Genómica, Hospital Regional “Primero de Octubre”, ISSSTE, Av. Instituto Politécnico Nacional 1669, Lindavista, Gustavo A. Madero, Ciudad de México 07300, Mexico; (T.H.-M.); (S.I.L.-F.); (C.P.-L.); (M.L.-L.); (T.G.-G.)
| | - Manuel Lara-Lozano
- Laboratorio de Medicina Genómica, Hospital Regional “Primero de Octubre”, ISSSTE, Av. Instituto Politécnico Nacional 1669, Lindavista, Gustavo A. Madero, Ciudad de México 07300, Mexico; (T.H.-M.); (S.I.L.-F.); (C.P.-L.); (M.L.-L.); (T.G.-G.)
| | - Tayde Guerrero-González
- Laboratorio de Medicina Genómica, Hospital Regional “Primero de Octubre”, ISSSTE, Av. Instituto Politécnico Nacional 1669, Lindavista, Gustavo A. Madero, Ciudad de México 07300, Mexico; (T.H.-M.); (S.I.L.-F.); (C.P.-L.); (M.L.-L.); (T.G.-G.)
| | - Javier Martínez-Bautista
- Laboratorio de Microbiología, Hospital Regional “Primero de Octubre”, ISSSTE, Av. Instituto Politécnico Nacional 1669, Lindavista, Gustavo A. Madero, Ciudad de México 07300, Mexico;
| | - Eduardo Gómez-Conde
- Departamento de Inmunobiología, Facultad de Medicina, Benemérita Universidad Autónoma de Puebla (BUAP), Puebla 72420, Mexico;
| | - Juan Antonio González-Barrios
- Laboratorio de Medicina Genómica, Hospital Regional “Primero de Octubre”, ISSSTE, Av. Instituto Politécnico Nacional 1669, Lindavista, Gustavo A. Madero, Ciudad de México 07300, Mexico; (T.H.-M.); (S.I.L.-F.); (C.P.-L.); (M.L.-L.); (T.G.-G.)
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6
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Macesic N, Hawkey J, Vezina B, Wisniewski JA, Cottingham H, Blakeway LV, Harshegyi T, Pragastis K, Badoordeen GZ, Dennison A, Spelman DW, Jenney AWJ, Peleg AY. Genomic dissection of endemic carbapenem resistance reveals metallo-beta-lactamase dissemination through clonal, plasmid and integron transfer. Nat Commun 2023; 14:4764. [PMID: 37553339 PMCID: PMC10409761 DOI: 10.1038/s41467-023-39915-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Accepted: 07/03/2023] [Indexed: 08/10/2023] Open
Abstract
Infections caused by metallo-beta-lactamase-producing organisms (MBLs) are a global health threat. Our understanding of transmission dynamics and how MBLs establish endemicity remains limited. We analysed two decades of blaIMP-4 evolution in a hospital using sequence data from 270 clinical and environmental isolates (including 169 completed genomes) and identified the blaIMP-4 gene across 7 Gram-negative genera, 68 bacterial strains and 7 distinct plasmid types. We showed how an initial multi-species outbreak of conserved IncC plasmids (95 genomes across 37 strains) allowed endemicity to be established through the ability of blaIMP-4 to disseminate in successful strain-genetic setting pairs we termed propagators, in particular Serratia marcescens and Enterobacter hormaechei. From this reservoir, blaIMP-4 persisted through diversification of genetic settings that resulted from transfer of blaIMP-4 plasmids between bacterial hosts and of the integron carrying blaIMP-4 between plasmids. Our findings provide a framework for understanding endemicity and spread of MBLs and may have broader applicability to other carbapenemase-producing organisms.
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Affiliation(s)
- Nenad Macesic
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
- Centre to Impact AMR, Monash University, Clayton, Australia
| | - Jane Hawkey
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
| | - Ben Vezina
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
| | - Jessica A Wisniewski
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
| | - Hugh Cottingham
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
| | - Luke V Blakeway
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
| | - Taylor Harshegyi
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
| | - Katherine Pragastis
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
| | - Gnei Zweena Badoordeen
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
| | | | - Denis W Spelman
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
- Microbiology Unit, Alfred Hospital, Melbourne, Australia
| | - Adam W J Jenney
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia
- Microbiology Unit, Alfred Hospital, Melbourne, Australia
| | - Anton Y Peleg
- Department of Infectious Diseases, The Alfred Hospital and Central Clinical School, Monash University, Melbourne, Australia.
- Centre to Impact AMR, Monash University, Clayton, Australia.
- Infection Program, Monash Biomedicine Discovery Institute, Monash University, Clayton, Australia.
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Ertapenem Supplemented Selective Media as a New Strategy to Distinguish β-Lactam-Resistant Enterobacterales: Application to Clinical and Wastewater Samples. Antibiotics (Basel) 2023; 12:antibiotics12020392. [PMID: 36830303 PMCID: PMC9952050 DOI: 10.3390/antibiotics12020392] [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: 01/05/2023] [Revised: 02/03/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
The increase in carbapenem-resistant Enterobacterales (CRE) is mostly driven by the spread of carbapenemase-producing (CP) strains. In New Caledonia, the majority of carbapenemases found are IMP-type carbapenemases that are difficult to detect on routine selective media. In this study, a culture-based method with ertapenem selection is proposed to distinguish non-CRE, non-CP-CRE, and CP-CRE from samples with very high bacterial loads. Firstly, assays were carried out with phenotypically well-characterized β-lactam-resistant Enterobacterales isolates. Then, this approach was applied to clinical and environmental samples. Presumptive CP-CRE isolates were finally identified, and the presence of a carbapenemase was assessed. In a collection of 27 phenotypically well-characterized β-lactam-resistant Enterobacterales, an ertapenem concentration of 0.5 µg·mL-1 allowed distinguishing CRE from non-CRE. A concentration of 4 µg·mL-1 allowed distinguishing CP-CRE from non-CP-CRE after nine hours of incubation. These methods allowed isolating 18 CP-CRE from hospital effluents, including the first detection of a KPC in New Caledonia. All these elements show that this cost-effective strategy to distinguish β-lactam-resistant Enterobacterales provides fast and reliable results. This could be applied in the Pacific islands or other resource-limited settings, where limited data are available.
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Pot M, Reynaud Y, Couvin D, Dereeper A, Ferdinand S, Bastian S, Foucan T, Pommier JD, Valette M, Talarmin A, Guyomard-Rabenirina S, Breurec S. Emergence of a Novel Lineage and Wide Spread of a blaCTX-M-15/IncHI2/ST1 Plasmid among Nosocomial Enterobacter in Guadeloupe. Antibiotics (Basel) 2022; 11:1443. [PMID: 36290101 PMCID: PMC9598596 DOI: 10.3390/antibiotics11101443] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 10/10/2022] [Accepted: 10/17/2022] [Indexed: 04/04/2024] Open
Abstract
Between April 2018 and August 2019, a total of 135 strains of Enterobacter cloacae complex (ECC) were randomly collected at the University Hospital Center of Guadeloupe to investigate the structure and diversity of the local bacterial population. These nosocomial isolates were initially identified genetically by the hsp60 typing method, which revealed the clinical relevance of E. xiangfangensis (n = 69). Overall, 57/94 of the third cephalosporin-resistant strains were characterized as extended-spectrum-β-lactamase (ESBL) producers, and their whole-genome was sequenced using Illumina technology to determine the clonal relatedness and diffusion of resistance genes. We found limited genetic diversity among sequence types (STs). ST114 (n = 13), ST1503 (n = 9), ST53 (n = 5) and ST113 (n = 4), which belong to three different Enterobacter species, were the most prevalent among the 57 ESBL producers. The blaCTXM-15 gene was the most prevalent ESBL determinant (56/57) and was in most cases associated with IncHI2/ST1 plasmid replicon carriage (36/57). To fully characterize this predominant blaCTXM-15/IncHI2/ST1 plasmid, four isolates from different lineages were also sequenced using Oxford Nanopore sequencing technology to generate long-reads. Hybrid sequence analyses confirmed the circulation of a well-conserved plasmid among ECC members. In addition, the novel ST1503 and its associated species (ECC taxon 4) were analyzed, in view of its high prevalence in nosocomial infections. These genetic observations confirmed the overall incidence of nosocomial ESBL Enterobacteriaceae infections acquired in this hospital during the study period, which was clearly higher in Guadeloupe (1.59/1000 hospitalization days) than in mainland France (0.52/1,000 hospitalization days). This project revealed issues and future challenges for the management and surveillance of nosocomial and multidrug-resistant Enterobacter in the Caribbean.
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Affiliation(s)
- Matthieu Pot
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97139 Les Abymes, France
| | - Yann Reynaud
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97139 Les Abymes, France
| | - David Couvin
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97139 Les Abymes, France
| | - Alexis Dereeper
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97139 Les Abymes, France
| | - Séverine Ferdinand
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97139 Les Abymes, France
| | - Sylvaine Bastian
- Laboratory of Clinical Microbiology, University Hospital Center of Guadeloupe, 97159 Pointe-à-Pitre, France
| | - Tania Foucan
- Operational Hygiene Team, University Hospital Center of Guadeloupe, 97159 Pointe-à-Pitre, France
| | - Jean-David Pommier
- Division of Intensive Care, University Hospital Center of Guadeloupe, 97159 Pointe-à-Pitre, France
| | - Marc Valette
- Division of Intensive Care, University Hospital Center of Guadeloupe, 97159 Pointe-à-Pitre, France
| | - Antoine Talarmin
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97139 Les Abymes, France
| | | | - Sébastien Breurec
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, 97139 Les Abymes, France
- Faculty of Medicine Hyacinthe Bastaraud, University of the Antilles, 97157 Pointe-à-Pitre, France
- INSERM, Center for Clinical Investigation 1424, 97139 Les Abymes, France
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Manageiro V, Salgueiro V, Rosado T, Bandarra NM, Ferreira E, Smith T, Dias E, Caniça M. Genomic Analysis of a mcr-9.1-Harbouring IncHI2-ST1 Plasmid from Enterobacter ludwigii Isolated in Fish Farming. Antibiotics (Basel) 2022; 11:antibiotics11091232. [PMID: 36140011 PMCID: PMC9495039 DOI: 10.3390/antibiotics11091232] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 11/23/2022] Open
Abstract
This study analyzed the resistome, virulome and mobilome of an MCR-9-producing Enterobacter sp. identified in a muscle sample of seabream (Sparus aurata), collected in a land tank from multitrophic fish farming production. Average Nucleotide Identity analysis identified INSAq77 at the species level as an Enterobacter ludwigii INSAq77 strain that was resistant to chloramphenicol, florfenicol and fosfomycin and was susceptible to all other antibiotics tested. In silico antimicrobial resistance analyses revealed genes conferring in silico resistance to β-lactams (blaACT-88), chloramphenicol (catA4-type), fosfomycin (fosA2-type) and colistin (mcr-9.1), as well as several efflux pumps (e.g., oqxAB-type and mar operon). Further bioinformatics analysis revealed five plasmid replicon types, including the IncHI2/HI2A, which are linked to the worldwide dissemination of the mcr-9 gene in different antibiotic resistance reservoirs. The conserved nickel/copper operon rcnR-rcnA-pcoE-ISSgsp1-pcoS-IS903-mcr-9-wbuC was present, which may play a key role in copper tolerance under anaerobic growth and nickel homeostasis. These results highlight that antibiotic resistance in aquaculture are spreading through food, the environment and humans, which places this research in a One Health context. In fact, colistin is used as a last resort for the treatment of serious infections in clinical settings, thus mcr genes may represent a serious threat to human health.
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Affiliation(s)
- Vera Manageiro
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal
- Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, University of Porto, 4051-401 Porto, Portugal
- AL4AnimalS, Associate Laboratory for Animal and Veterinary Sciences, 1300-477 Lisboa, Portugal
| | - Vanessa Salgueiro
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal
- Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, University of Porto, 4051-401 Porto, Portugal
- AL4AnimalS, Associate Laboratory for Animal and Veterinary Sciences, 1300-477 Lisboa, Portugal
| | - Tânia Rosado
- Laboratory of Biology and Ecotoxicology, Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal
| | - Narcisa M. Bandarra
- Division of Aquaculture, Upgrading and Bioprospecting, Portuguese Institute for the Sea and Atmosphere, IPMA, 1749-077 Lisbon, Portugal
- CIIMAR, Interdisciplinary Centre of Marine and Environmental Research, University of Porto, Terminal de Cruzeiros do Porto, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - Eugénia Ferreira
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal
- Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, University of Porto, 4051-401 Porto, Portugal
- AL4AnimalS, Associate Laboratory for Animal and Veterinary Sciences, 1300-477 Lisboa, Portugal
| | - Terry Smith
- Molecular Diagnostics Research Group, School of Biological and Chemical Sciences, National University of Ireland, H91 DK59 Galway, Ireland
- Centre for One Health, Ryan Institute, National University of Ireland, H91 TK33 Galway, Ireland
| | - Elsa Dias
- Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, University of Porto, 4051-401 Porto, Portugal
- AL4AnimalS, Associate Laboratory for Animal and Veterinary Sciences, 1300-477 Lisboa, Portugal
- Laboratory of Biology and Ecotoxicology, Department of Environmental Health, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal
| | - Manuela Caniça
- National Reference Laboratory of Antibiotic Resistances and Healthcare Associated Infections, Department of Infectious Diseases, National Institute of Health Dr. Ricardo Jorge, 1649-016 Lisbon, Portugal
- Centre for the Studies of Animal Science, Institute of Agrarian and Agri-Food Sciences and Technologies, University of Porto, 4051-401 Porto, Portugal
- AL4AnimalS, Associate Laboratory for Animal and Veterinary Sciences, 1300-477 Lisboa, Portugal
- CIISA, Center for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, 1300-477 Lisbon, Portugal
- Correspondence:
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10
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Rios-Miguel AB, Smith GJ, Cremers G, van Alen T, Jetten MS, Op den Camp HJ, Welte CU. Microbial paracetamol degradation involves a high diversity of novel amidase enzyme candidates. WATER RESEARCH X 2022; 16:100152. [PMID: 36042984 PMCID: PMC9420511 DOI: 10.1016/j.wroa.2022.100152] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/13/2022] [Revised: 07/13/2022] [Accepted: 08/03/2022] [Indexed: 06/15/2023]
Abstract
Pharmaceuticals are relatively new to nature and often not completely removed in wastewater treatment plants (WWTPs). Consequently, these micropollutants end up in water bodies all around the world posing a great environmental risk. One exception to this recalcitrant conversion is paracetamol, whose full degradation has been linked to several microorganisms. However, the genes and corresponding proteins involved in microbial paracetamol degradation are still elusive. In order to improve our knowledge of the microbial paracetamol degradation pathway, we inoculated a bioreactor with sludge of a hospital WWTP (Pharmafilter, Delft, NL) and fed it with paracetamol as the sole carbon source. Paracetamol was fully degraded without any lag phase and the enriched microbial community was investigated by metagenomic and metatranscriptomic analyses, which demonstrated that the microbial community was very diverse. Dilution and plating on paracetamol-amended agar plates yielded two Pseudomonas sp. isolates: a fast-growing Pseudomonas sp. that degraded 200 mg/L of paracetamol in approximately 10 h while excreting 4-aminophenol, and a slow-growing Pseudomonas sp. that degraded paracetamol without obvious intermediates in more than 90 days. Each Pseudomonas sp. contained a different highly-expressed amidase (31% identity to each other). These amidase genes were not detected in the bioreactor metagenome suggesting that other as-yet uncharacterized amidases may be responsible for the first biodegradation step of paracetamol. Uncharacterized deaminase genes and genes encoding dioxygenase enzymes involved in the catabolism of aromatic compounds and amino acids were the most likely candidates responsible for the degradation of paracetamol intermediates based on their high expression levels in the bioreactor metagenome and the Pseudomonas spp. genomes. Furthermore, cross-feeding between different community members might have occurred to efficiently degrade paracetamol and its intermediates in the bioreactor. This study increases our knowledge about the ongoing microbial evolution towards biodegradation of pharmaceuticals and points to a large diversity of (amidase) enzymes that are likely involved in paracetamol metabolism in WWTPs.
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Key Words
- 4-AP, 4-aminophenol
- APAP, N-acetyl-p-aminophenol or paracetamol
- Amidase evolution
- Deaminase
- Dioxygenase
- GAC, granular activated carbon
- HGT, horizontal gene transfer
- HQ, hydroquinone
- HRT, hydraulic retention time
- MAG, metagenome-assembled genome
- MBR, membrane bioreactor
- Metagenomics
- Mobile genetic elements
- Pfast, Pseudomonas sp. isolate growing fast on APAP as sole carbon source
- Pseudomonas
- Pslow, Pseudomonas sp. isolate growing slow on APAP as sole carbon source
- SRT, solid retention time
- TPM, transcripts per million
- WWTP, wastewater treatment plant
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Affiliation(s)
- Ana B. Rios-Miguel
- Department of Microbiology, Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
| | - Garrett J. Smith
- Department of Microbiology, Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
| | - Geert Cremers
- Department of Microbiology, Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
| | - Theo van Alen
- Department of Microbiology, Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
| | - Mike S.M. Jetten
- Department of Microbiology, Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
| | - Huub J.M. Op den Camp
- Department of Microbiology, Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
| | - Cornelia U. Welte
- Department of Microbiology, Radboud University, Radboud Institute for Biological and Environmental Sciences, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
- Soehngen Institute of Anaerobic Microbiology, Radboud University, Heyendaalseweg 135, Nijmegen 6525 AJ, the Netherlands
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11
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Cao Z, Cui L, Liu Q, Liu F, Zhao Y, Guo K, Hu T, Zhang F, Sheng X, Wang X, Peng Z, Dai M. Phenotypic and Genotypic Characterization of Multidrug-Resistant Enterobacter hormaechei Carrying qnrS Gene Isolated from Chicken Feed in China. Microbiol Spectr 2022; 10:e0251821. [PMID: 35467399 PMCID: PMC9241693 DOI: 10.1128/spectrum.02518-21] [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: 12/06/2021] [Accepted: 03/27/2022] [Indexed: 11/20/2022] Open
Abstract
Multidrug resistance (MDR) in Enterobacteriaceae including resistance to quinolones is rising worldwide. The plasmid-mediated quinolone resistance (PMQR) gene qnrS is prevalent in Enterobacteriaceae. However, the qnrS gene is rarely found in Enterobacter hormaechei (E. hormaechei). Here, we reported one multidrug resistant E. hormaechei strain M1 carrying the qnrS1 and blaTEM-1 genes. This study was to analyze the characteristics of MDR E. hormaechei strain M1. The E. hormaechei strain M1 was identified as Enterobacter cloacae complex by biochemical assay and 16S rRNA sequencing. The whole genome was sequenced by the Oxford Nanopore method. Taxonomy of the E. hormaechei was based on multilocus sequence typing (MLST). The qnrS with the other antibiotic resistance genes were coexisted on IncF plasmid (pM1). Besides, the virulence factors associated with pathogenicity were also located on pM1. The qnrS1 gene was located between insertion element IS2A (upstream) and transposition element ISKra4 (downstream). The comparison result of IncF plasmids revealed that they had a common plasmid backbone. Susceptibility experiment revealed that the E. hormaechei M1 showed extensive resistance to the clinical antimicrobials. The conjugation transfer was performed by filter membrane incubation method. The competition and plasmid stability assays suggested the host bacteria carrying qnrS had an energy burden. As far as we know, this is the first report that E. hormaechei carrying qnrS was isolated from chicken feed. The chicken feed and poultry products could serve as a vehicle for these MDR bacteria, which could transfer between animals and humans through the food chain. We need to pay close attention to the epidemiology of E. hormaechei and prevent their further dissemination. IMPORTANCE Enterobacter hormaechei is an opportunistic pathogen. It can cause infections in humans and animals. Plasmid-mediated quinolone resistance (PMQR) gene qnrS can be transferred intergenus, which is leading to increase the quinolone resistance levels in Enterobacteriaceae. Chicken feed could serve as a vehicle for the MDR E. hormaechei. Therefore, antibiotic-resistance genes (ARGs) might be transferred to the intestinal flora after entering the gastrointestinal tract with the feed. Furthermore, antibiotic-resistant bacteria (ARB) were also excreted into environment with feces, posing a huge threat to public health. This requires us to monitor the ARB and antibiotic-resistant plasmids in the feed. Here, we demonstrated the characteristics of one MDR E. hormaechei isolate from chicken feed. The plasmid carrying the qnrS gene is a conjugative plasmid with transferability. The presence of plasmid carrying antibiotic-resistance genes requires the maintenance of antibiotic pressure. In addition, the E. hormaechei M1 belonged to new sequence type (ST). These data show the MDR E. hormaechei M1 is a novel strain that requires our further research.
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Affiliation(s)
- Zhengzheng Cao
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
| | - Luqing Cui
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
| | - Quan Liu
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
| | - Fangjia Liu
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
| | - Yue Zhao
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
| | - Kaixuan Guo
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
| | - Tianyu Hu
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
| | - Fan Zhang
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
| | - Xijing Sheng
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
| | - Xiangru Wang
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Zhong Peng
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
| | - Menghong Dai
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan, China
- MOA Key Laboratory of Food Safety Evaluation/National Reference Laboratory of Veterinary Drug Residue (HZAU), Huazhong Agricultural University, Wuhan, China
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12
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Oka K, Matsumoto A, Tetsuka N, Morioka H, Iguchi M, Ishiguro N, Nagamori T, Takahashi S, Saito N, Tokuda K, Igari H, Fujikura Y, Kato H, Kanai S, Kusama F, Iwasaki H, Furuhashi K, Baba H, Nagao M, Nakanishi M, Kasahara K, Kakeya H, Chikumi H, Ohge H, Azuma M, Tauchi H, Shimono N, Hamada Y, Takajo I, Nakata H, Kawamura H, Fujita J, Yagi T. Clinical characteristics and treatment outcomes of carbapenem-resistant Enterobacterales infections in Japan. J Glob Antimicrob Resist 2022; 29:247-252. [PMID: 35429667 DOI: 10.1016/j.jgar.2022.04.004] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2022] [Revised: 04/05/2022] [Accepted: 04/08/2022] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES The dissemination of difficult-to-treat carbapenem-resistant Enterobacterales (CRE) is of great concern. We clarified the risk factors underlying CRE infection mortality in Japan. METHODS We conducted a retrospective, multicentre, observational cohort study of patients with CRE infections at 28 university hospitals from September 2014 to December 2016, using the Japanese National Surveillance criteria. Clinical information, including patient background, type of infection, antibiotic treatment, and treatment outcome, was collected. The carbapenemase genotype was determined using PCR sequencing. Multivariate analysis was performed to identify the risk factors for 28-day mortality. RESULTS Among the 179 patients enrolled, 65 patients (36.3%) had bloodstream infections, with 37 (20.7%) infections occurring due to carbapenemase-producing Enterobacterales (CPE); all carbapenemases were of IMP-type (IMP-1: 32, IMP-6: 5). Two-thirds of CPE were identified as Enterobacter cloacae complex. Combination therapy was administered only in 46 patients (25.7%), and the 28-day mortality rate was 14.3%. Univariate analysis showed that solid metastatic cancer, Charlson Comorbidity Index ≥3, bloodstream infection, pneumonia, or empyema, central venous catheters, mechanical ventilation, and prior use of quinolones were significant risk factors for mortality. Multivariate analysis revealed that mechanical ventilation (OR: 6.71 [1.42-31.6], P = 0.016), solid metastatic cancers (OR: 5.63 [1.38-23.0], P = 0.016), and bloodstream infections (OR: 3.49 [1.02-12.0], P = 0.046) were independent risk factors for 28-day mortality. CONCLUSION The significant risk factors for 28-day mortality in patients with CRE infections in Japan are mechanical ventilation, solid metastatic cancers, and bloodstream infections.
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Affiliation(s)
- Keisuke Oka
- Department of Infectious Diseases, Nagoya University Hospital, Showa-ku, Nagoya, Aichi, Japan
| | - Akane Matsumoto
- Department of Pediatrics, Kyoto Katsura Hospital, Saikyou-ku, Kyoto, Japan
| | - Nobuyuki Tetsuka
- Department of Infection Control, Gifu University Graduate School of Medicine, Gifu, Japan
| | - Hiroshi Morioka
- Department of Infectious Diseases, Nagoya University Hospital, Showa-ku, Nagoya, Aichi, Japan
| | - Mitsutaka Iguchi
- Department of Infectious Diseases, Nagoya University Hospital, Showa-ku, Nagoya, Aichi, Japan
| | - Nobuhisa Ishiguro
- Division of Infection Control, Hokkaido University Hospital, Sapporo, Hokkaido, Japan
| | - Tsunehisa Nagamori
- Department of Infection Control, Asahikawa Medical University Hospital, Asahikawa, Hokkaido, Japan
| | - Satoshi Takahashi
- Department of Infection Control and Laboratory Medicine, Sapporo Medical University School of Medicine, Sapporo, Hokkaido, Japan
| | - Norihiro Saito
- Department of Clinical Laboratory Medicine, Hirosaki University Graduate School of Medicine, Hirosaki, Aomori, Japan
| | - Koichi Tokuda
- Department of Infection Control and Laboratory Diagnostics, Tohoku University Graduate School of Medicine, Sendai, Miyagi, Japan
| | - Hidetoshi Igari
- Division of Infection Control, Chiba University Hospital, Chiba, Chiba, Japan
| | - Yuji Fujikura
- Division of Infectious Diseases and Respiratory Medicine, Department of Internal Medicine, National Defense Medical College, Tokorozawa, Saitama, Japan
| | - Hideaki Kato
- Infection Prevention and Control Department, Yokohama City University Hospital, Yokohama, Kanagawa, Japan
| | - Shinichiro Kanai
- Department of Infection Control, Shinshu University Hospital, Matsumoto, Nagano, Japan
| | - Fumiko Kusama
- Department of Clinical Laboratory, Niigata University Medical and Dental Hospital, Niigata, Niigata, Japan
| | - Hiromichi Iwasaki
- Department of Infection Control and Prevention, University of Fukui, Fukui, Fukui, Japan
| | - Kazuki Furuhashi
- Department of Laboratory Medicine, Hamamatsu University School of Medicine, Hamamatsu, Shizuoka, Japan
| | - Hisashi Baba
- Centre for Nutrition Support and Infection Control, Gifu University Hospital, Gifu, Gifu, Japan
| | - Miki Nagao
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Kyoto, Japan
| | - Masaki Nakanishi
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Kyoto, Japan
| | - Kei Kasahara
- Centre for Infectious Diseases, Nara Medical University, Kashihara, Nara, Japan
| | - Hiroshi Kakeya
- Department of Infection Control Science, Graduate School of Medicine, Osaka Metropolitan University, Osaka, Osaka, Japan
| | - Hiroki Chikumi
- Centre for Infectious Diseases, Tottori University Hospital, Yonago, Tottori, Japan
| | - Hiroki Ohge
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, Hiroshima, Japan
| | - Momoyo Azuma
- Department of Infection Control, Tokushima University Hospital, Tokushima, Tokushima, Japan
| | - Hisamichi Tauchi
- Division of Infectious Disease, Control and Prevention, Ehime University Hospital, Toon, Ehime, Japan
| | - Nobuyuki Shimono
- Centre for the Study of Global Infection, Kyushu University Hospital, Fukuoka, Fukuoka, Japan
| | - Yohei Hamada
- Department of Infectious Disease and Hospital Epidemiology, Saga University Hospital, Saga, Saga, Japan
| | - Ichiro Takajo
- Center for Infection Control, Miyazaki University Hospital, Miyazaki, Miyazaki, Japan
| | - Hirotomo Nakata
- Department of Infection Control, Kumamoto University Hospital, Kumamoto, Kumamoto, Japan
| | - Hideki Kawamura
- Department of Infection Control, Kagoshima University Hospital, Kagoshima, Kagoshima, Japan
| | - Jiro Fujita
- Department of Infectious, Respiratory, and Digestive Medicine, Graduate School of Medicine, University of the Ryukyus, Nakagami-gun, Okinawa, Japan
| | - Tetsuya Yagi
- Department of Infectious Diseases, Nagoya University Hospital, Showa-ku, Nagoya, Aichi, Japan.
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13
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Cui CY, Li XJ, Chen C, Wu XT, He Q, Jia QL, Zhang XJ, Lin ZY, Li C, Fang LX, Liao XP, Liu YH, Hu B, Sun J. Comprehensive analysis of plasmid-mediated tet(X4)-positive Escherichia coli isolates from clinical settings revealed a high correlation with animals and environments-derived strains. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 806:150687. [PMID: 34597551 DOI: 10.1016/j.scitotenv.2021.150687] [Citation(s) in RCA: 26] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2021] [Revised: 09/23/2021] [Accepted: 09/26/2021] [Indexed: 06/13/2023]
Abstract
The emergence of novel plasmid-mediated high-level tigecycline resistance genes tet(X) in the Enterobacteriaceae has increased public health risk for treating severe bacterial infections. Despite growing reports of tet(X)-positive isolates detected in animal sources, the epidemiological association of animal- and environment-derived isolates with human-derived isolates remains unclear. Here, we performed a comprehensive analysis of tet(X4)-positive Escherichia coli isolates collected in a hospital in Guangdong province, China. A total of 48 tet(X4)-positive E. coli isolates were obtained from 1001 fecal samples. The tet(X4)-positive E. coli isolates were genetically diverse but certain strains that belonged to ST48, ST10, and ST877 etc. also have clonally transmitted. Most of the tet(X4) genes from these patient isolates were located on conjugative plasmids that were successfully transferred (64.6%) and generally coexisted with other antibiotic resistance genes including aadA, floR, blaTEM and qnrS. More importantly, we found the IncX1 type plasmid was a common vector for tet(X4) and was prevalent in these patient-derived strains (31.3%). This plasmid type has been detected in animal-derived strains from different species in different regions demonstrating its strong transmission ability and wide host range. Furthermore, phylogenetic analysis revealed that certain strains of patient and animal origin were closely related indicating that the tet(X4)-positive E. coli isolates were likely to have cross-sectorial clonal transmission between humans, animals, and farm environments. Our research greatly expands the limited epidemiological knowledge of tet(X4)-positive strains in clinical settings and provides definitive evidence for the epidemiological link between human-derived tet(X4)-positive isolates and animal-derived isolates.
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Affiliation(s)
- Chao-Yue Cui
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Xiao-Jie Li
- Department of Laboratory Medicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China
| | - Chong Chen
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China
| | - Xiao-Ting Wu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Qian He
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Qiu-Lin Jia
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Xiao-Jing Zhang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Zhuo-Yu Lin
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Cang Li
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Liang-Xing Fang
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Xiao-Ping Liao
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Ya-Hong Liu
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China
| | - Bo Hu
- Department of Laboratory Medicine, The Third Affiliated Hospital, Sun Yat-sen University, Guangzhou 510630, China.
| | - Jian Sun
- National Risk Assessment Laboratory for Antimicrobial Resistance of Animal Original Bacteria, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China; Guangdong Laboratory for Lingnan Modern Agriculture, South China Agricultural University, Guangzhou 510642, China; Guangdong Key Laboratory for Veterinary Drug Development and Safety Evaluation, College of Veterinary Medicine, South China Agricultural University, Guangzhou 510642, China.
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14
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Huang L, Fu L, Hu X, Liang X, Gong G, Xie C, Zhang F, Wang Y, Zhou Y. Co-occurrence of Klebsiella variicola and Klebsiella pneumoniae Both Carrying bla KPC from a Respiratory Intensive Care Unit Patient. Infect Drug Resist 2021; 14:4503-4510. [PMID: 34744441 PMCID: PMC8565889 DOI: 10.2147/idr.s330977] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 10/08/2021] [Indexed: 12/28/2022] Open
Abstract
Objective The aim of this study was to use whole-genome sequencing to characterize Klebsiella pneumoniae SKp2F and Klebsiella variicola SKv2E, both carrying blaKPC, co-isolated from the same sputum specimen. Methods Antimicrobial susceptibility testing was performed using microbroth dilution. Biofilm formation was determined by crystal violet staining and virulence was measured by a serum killing assay. Whole-genome sequencing of SKp2F and SKv2E was performed using an Illumina sequencer and the genetic characteristics were analyzed by computer. Results SKp2F and SKv2E were sensitive only to tigecycline and polymyxin among the tested antibiotics. The biofilm-forming ability of SKv2E is stronger than that of SKp2F. The grades of serum resistance of SKp2F and SKv2E are 4 and 3. MLST analysis of the 6,115,610 bp and 5,403,687 bp of SKv2E and SKp2F showed associations with ST1615 and ST631, respectively. SKv2E carried 13 resistance genes (blaKPC-2, blaTEM-1A, blaLEN17, aadA16, arr-3, qnrB4, oqxA/B, dfrA27, sul1, tetD, fosA, qacEΔ1) and SKp2F carried 23 (blaKPC-2, blaCTX-M-3, blaTEM-1B, blaCTX-M-65, blaSHV-27, aac(6ʹ)-IIa, rmtB, arr-3, aph(3ʹ)-Ia, aadA16, qnrS1, aac(6ʹ)-Ib-cr, qnrB91, oqxA/B, mph(A), tet(A), fosA, dfrA27, and two copies of qacEΔ1-sul1). Most of them were carried by various mobile genetic elements, such as IncFIB(K)/IncFII(K)/IncFII(Yp), IncFII(K) plasmid, Tn6338, and In469. Both SKv2E and SKp2F carried a large number of virulence factors, including type 1 and 3 fimbriae, capsule, aerobactin (iutA), ent siderophore (entABCDEFS, fepABCDGfes), and salmochelin (iroE/iroEN). SKv2E also carried type IV pili (pilW), fimbrial adherence (steB, stfD), and capsule biosynthesis gene (glf). Conclusion blaKPC-2-carrying K. variicola and K. pneumoniae, which carried multiple resistance genes, virulence factors, and highly similar mobile genetic elements, were identified from the same specimen, indicating that clinical samples may carry multiple bacteria. We should avoid misidentification, and bear in mind that resistance genes carrying mobile genetic elements can be transmitted or integrated between bacteria in the same host.
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Affiliation(s)
- Lianjiang Huang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xiamen Medical College, Xiamen, 361021, People's Republic of China
| | - Li Fu
- The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, People's Republic of China
| | - Xiaoyan Hu
- Department of Pathogen Biology, School of Basic Medicine, Public Center of Experimental Technology of Pathogen Biology Technology Platform, Southwest Medical University, Luzhou, 646000, People's Republic of China
| | - Xiaoliang Liang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xiamen Medical College, Xiamen, 361021, People's Republic of China
| | - Guozhong Gong
- Department of Clinical Laboratory, Suining First People's Hospital, Suining, 629000, People's Republic of China
| | - Chunhong Xie
- Department of Clinical Laboratory, The Second Affiliated Hospital of Xiamen Medical College, Xiamen, 361021, People's Republic of China
| | - Feiyang Zhang
- Department of Pathogen Biology, School of Basic Medicine, Public Center of Experimental Technology of Pathogen Biology Technology Platform, Southwest Medical University, Luzhou, 646000, People's Republic of China
| | - Ying Wang
- Department of Pathogen Biology, School of Basic Medicine, Public Center of Experimental Technology of Pathogen Biology Technology Platform, Southwest Medical University, Luzhou, 646000, People's Republic of China
| | - Yingshun Zhou
- Department of Pathogen Biology, School of Basic Medicine, Public Center of Experimental Technology of Pathogen Biology Technology Platform, Southwest Medical University, Luzhou, 646000, People's Republic of China
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15
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Abe R, Oyama F, Akeda Y, Nozaki M, Hatachi T, Okamoto Y, Yoshida H, Hamaguchi S, Tomono K, Matsumoto Y, Motooka D, Iida T, Hamada S. Hospital-wide outbreaks of carbapenem-resistant Enterobacteriaceae horizontally spread through a clonal plasmid harbouring blaIMP-1 in children's hospitals in Japan. J Antimicrob Chemother 2021; 76:3314-3317. [PMID: 34477841 DOI: 10.1093/jac/dkab303] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 07/26/2021] [Indexed: 12/22/2022] Open
Affiliation(s)
- Ryuichiro Abe
- Japan-Thailand Research Collaboration Center on Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Department of Bacterial Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Department of Anaesthesiology and Intensive Care Medicine, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Fumiya Oyama
- Japan-Thailand Research Collaboration Center on Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Yukihiro Akeda
- Japan-Thailand Research Collaboration Center on Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Division of Infection Control and Prevention, Osaka University Hospital, Suita, Japan.,Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, Osaka, Japan.,National Institute of Infectious Diseases, Tokyo, Japan
| | - Masatoshi Nozaki
- Department of Neonatal Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Takeshi Hatachi
- Department of Intensive Care Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Yuya Okamoto
- Department of Laboratory Medicine, Osaka Women's and Children's Hospital, Osaka, Japan
| | - Hisao Yoshida
- Division of Infection Control and Prevention, Osaka University Hospital, Suita, Japan.,Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Shigeto Hamaguchi
- Division of Infection Control and Prevention, Osaka University Hospital, Suita, Japan.,Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Kazunori Tomono
- Division of Infection Control and Prevention, Osaka University Hospital, Suita, Japan.,Department of Infection Control and Prevention, Graduate School of Medicine, Osaka University, Osaka, Japan
| | - Yuki Matsumoto
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Daisuke Motooka
- Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Tetsuya Iida
- Japan-Thailand Research Collaboration Center on Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Department of Bacterial Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan.,Department of Infection Metagenomics, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
| | - Shigeyuki Hamada
- Japan-Thailand Research Collaboration Center on Emerging and Re-emerging Infections, Research Institute for Microbial Diseases, Osaka University, Osaka, Japan
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16
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Lipworth S, Vihta KD, Chau K, Barker L, George S, Kavanagh J, Davies T, Vaughan A, Andersson M, Jeffery K, Oakley S, Morgan M, Hopkins S, Peto TEA, Crook DW, Walker AS, Stoesser N. Ten-year longitudinal molecular epidemiology study of Escherichia coli and Klebsiella species bloodstream infections in Oxfordshire, UK. Genome Med 2021; 13:144. [PMID: 34479643 PMCID: PMC8414751 DOI: 10.1186/s13073-021-00947-2] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 08/03/2021] [Indexed: 11/17/2022] Open
Abstract
Background The incidence of Gram-negative bloodstream infections (BSIs), predominantly caused by Escherichia coli and Klebsiella species, continues to increase; however, the causes of this are unclear and effective interventions are therefore hard to design. Methods In this study, we sequenced 3468 unselected isolates over a decade in Oxfordshire (UK) and linked this data to routinely collected electronic healthcare records and mandatory surveillance reports. We annotated genomes for clinically relevant genes, contrasting the distribution of these within and between species, and compared incidence trends over time using stacked negative binomial regression. Results We demonstrate that the observed increases in E. coli incidence were not driven by the success of one or more sequence types (STs); instead, four STs continue to dominate a stable population structure, with no evidence of adaptation to hospital/community settings. Conversely in Klebsiella spp., most infections are caused by sporadic STs with the exception of a local drug-resistant outbreak strain (ST490). Virulence elements are highly structured by ST in E. coli but not Klebsiella spp. where they occur in a diverse spectrum of STs and equally across healthcare and community settings. Most clinically hypervirulent (i.e. community-onset) Klebsiella BSIs have no known acquired virulence loci. Finally, we demonstrate a diverse but largely genus-restricted mobilome with close associations between antimicrobial resistance (AMR) genes and insertion sequences but not typically specific plasmid replicon types, consistent with the dissemination of AMR genes being highly contingent on smaller mobile genetic elements (MGEs). Conclusions Our large genomic study highlights distinct differences in the molecular epidemiology of E. coli and Klebsiella BSIs and suggests that no single specific pathogen genetic factors (e.g. AMR/virulence genes/sequence type) are likely contributing to the increasing incidence of BSI overall, that association with AMR genes in E. coli is a contributor to the increasing number of E. coli BSIs, and that more attention should be given to AMR gene associations with non-plasmid MGEs to try and understand horizontal gene transfer networks. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00947-2.
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Affiliation(s)
- Samuel Lipworth
- Nuffield Department of Medicine, University of Oxford, Oxford, UK. .,Oxford University Hospitals NHS Foundation Trust, Oxford, UK. .,John Radcliffe Hospital, Oxford, OX3 9DU, UK.
| | | | - Kevin Chau
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Leanne Barker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Sophie George
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - James Kavanagh
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Timothy Davies
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Alison Vaughan
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | - Katie Jeffery
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Sarah Oakley
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Marcus Morgan
- Oxford University Hospitals NHS Foundation Trust, Oxford, UK
| | - Susan Hopkins
- National Infection Service, Public Health England, Colindale, London, UK
| | - Timothy E A Peto
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Oxford University Hospitals NHS Foundation Trust, Oxford, UK.,John Radcliffe Hospital, Oxford, OX3 9DU, UK.,NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK
| | - Derrick W Crook
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Oxford University Hospitals NHS Foundation Trust, Oxford, UK.,NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK.,NIHR Biomedical Research Centre, Oxford, UK
| | - Ann Sarah Walker
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,NIHR Health Protection Research Unit in Healthcare Associated Infections and Antimicrobial Resistance at University of Oxford in partnership with Public Health England, Oxford, UK.,NIHR Biomedical Research Centre, Oxford, UK
| | - Nicole Stoesser
- Nuffield Department of Medicine, University of Oxford, Oxford, UK.,Oxford University Hospitals NHS Foundation Trust, Oxford, UK
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17
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Li Z, Ding Z, Yang J, Liu Y, Jin X, Xie J, Li T, Ding Y, Zeng Z, Liu J. Carbapenem-Resistant Klebsiella pneumoniae in Southwest China: Molecular Characteristics and Risk Factors Caused by KPC and NDM Producers. Infect Drug Resist 2021; 14:3145-3158. [PMID: 34413658 PMCID: PMC8370685 DOI: 10.2147/idr.s324244] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2021] [Accepted: 08/04/2021] [Indexed: 12/19/2022] Open
Abstract
Background Carbapenem-resistant Klebsiella pneumoniae (CRKP) infection has attracted worldwide concern and became a serious challenge for clinical treatment. The aims of this study were to evaluate the molecular characteristics and risk factors for CRKP infection. Methods All the CRKP strains were screened for antimicrobial resistance genes, virulence genes, and integron by polymerase chain reaction (PCR). Plasmid typing was performed by plasmid conjugation assay and PCR-based replicon typing (PBRT). The genetic environments of blaKPC-2 and blaNDM-1 were analyzed by using overlapping PCR and molecular typing was performed by multi-locus sequence typing (MLST). Risk factors for CRKP infection were analyzed by logistic regression model. Results All the 66 CRKP isolates were multidrug-resistant, but all of them were susceptible to tigecycline and polymyxin B. Among the CRKP isolates, 42 blaKPC-2-positive strains were identified carrying IncFII plasmids. Meanwhile, 24 blaNDM-positive strains were found on lncX3 plasmids, including 20 blaNDM-1 isolates and 4 blaNDM-5 isolates. Most of CRKP isolates contained several virulence genes and the class I integron (intl1). The genetic environments of blaKPC-2 and blaNDM-1 revealed that the conserved regions (tnpA-tnpR-ISkpn8-blaKPC-2) and (blaNDM-1-bleMBL-trpF-tat) were associated with the dissemination of KPC-2 and NDM-1. ST11 was the most common type in this work. Hematological disease, tracheal cannula, and use of β-lactams and β-lactamase inhibitor combination were identified as independent risk factors for CRKP infection. Conclusion This study established the resistance pattern, molecular characteristics, clonal relatedness, and risk factors of CRKP infection. The findings of the novel strain that co-harboring blaNDM-5 and blaIMP-4, and the novel ST4495 indicated that the brand-new types have spread in Southwest China, emphasizing the prevent and control the further dissemination of CRKP isolates are highly needed.
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Affiliation(s)
- Zhaoyinqian Li
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Zixuan Ding
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Jia Yang
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Yao Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Xinrui Jin
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Jingling Xie
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Tingting Li
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Yinhuan Ding
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Zhangrui Zeng
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
| | - Jinbo Liu
- Department of Laboratory Medicine, The Affiliated Hospital of Southwest Medical University, Luzhou, 646000, Sichuan, People's Republic of China
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18
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McKew G, Merlino J, Beukers A, van Hal S, Gottlieb T. Success of ceftazidime-avibactam and aztreonam in combination for a refractory biliary infection with recurrent bacteraemia due to blaIMP-4 carbapenemase-producing Enterobacter hormaechei subsp. oharae. Access Microbiol 2021; 3:000248. [PMID: 34888479 PMCID: PMC8650849 DOI: 10.1099/acmi.0.000248] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2021] [Accepted: 06/11/2021] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Infections due to metallo-beta-lactamase (MBL)-producing organisms are becoming a significant problem, and antibiotic treatment options are limited. Aztreonam inhibits MBLs, and its use in combination with ceftazidime-avibactam (CAZ-AVI-AZT) to inhibit other beta-lactamases shows promise. METHODS A 45-year-old woman suffered from recurrent and sustained MBL (blaIMP-4)+ Enterobacter cloacae complex bacteraemia from an undrainable biliary source, and had failed nine alternative antibiotic regimens over a 5-month period. The 10th episode was successfully treated with CAZ-AVI-AZT, and she has had no further relapses. Three of the isolates underwent whole-genome sequencing (WGS) on the MiSeq platform and were analysed with the Nullarbor pipeline. RESULTS A layered Etest method for synergy between CAZ-AVI and aztreonam demonstrated an MIC of 2 mg l-1 for the combination. Isolates were identified by WGS as Enterobacter hormaechei subsp. oharae . All three of the isolates had blaTEM-4 ESBL, blaOXA-1 and blaACT-25. Two of the carbapenem-resistant isolates contained blaIMP-4. CONCLUSION While aztreonam inhibits MBLs, MBL-positive isolates often express other beta-lactamase enzymes. Avibactam inhibits ESBLs and other beta-lactamases, and its use in this case possibly contributed to therapeutic success due to inhibition of the concomitant blaTEM-4 in the isolates. This case demonstrates that phenotypic antimicrobial susceptibility testing (layered Etests for synergy), backed up by WGS, can produce results that allow tailored antimicrobial therapy in difficult infections. This case adds to the evidence for using CAZ-AVI-AZT in serious MBL infections.
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Affiliation(s)
- Genevieve McKew
- Department of Microbiology and Infectious Diseases, NSW Pathology, Concord Repatriation General Hospital, Concord, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - John Merlino
- Department of Microbiology and Infectious Diseases, NSW Pathology, Concord Repatriation General Hospital, Concord, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
| | - Alicia Beukers
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Department of Microbiology and Infectious Diseases, NSW Pathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Sebastian van Hal
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
- Department of Microbiology and Infectious Diseases, NSW Pathology, Royal Prince Alfred Hospital, Camperdown, NSW, Australia
| | - Thomas Gottlieb
- Department of Microbiology and Infectious Diseases, NSW Pathology, Concord Repatriation General Hospital, Concord, NSW, Australia
- Faculty of Medicine and Health, The University of Sydney, Sydney, NSW, Australia
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19
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Zhao Y, Chen X, Hu X, Shi Y, Zhao X, Xu J, Ding H, Wu R, Huang J, Zhao Z. Characterization of a carbapenem-resistant Citrobacter amalonaticus coharbouring bla IMP-4 and qnrs1 genes. J Med Microbiol 2021; 70. [PMID: 34170219 DOI: 10.1099/jmm.0.001364] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Members of the genus Citrobacter are facultative anaerobic Gram-negative bacilli belonging to the Enterobacterales [Janda J Clin Microbiol 1994; 32(8):1850-1854; Arens Clin Microbiol Infect 1997;3(1):53-57]. Formerly, Citrobacter species were occasionally reported as nosocomial pathogens with low virulence [Pepperell Antimicrob Agents Chemother 2002;46(11):3555-60]. Now, they are consistently reported to cause nosocomial infections of the urinary tract, respiratory tract, bone, peritoneum, endocardium, meninges, intestines, bloodstream and central nervous system. Among Citrobacter species, the most common isolates are C. koseri and C. freundii, while C. amalonaticus has seldom been isolated [Janda J Clin Microbiol 1994; 32(8):1850-1854; Marak Infect Dis (Lond) 2017;49(7):532-9]. Further, Citrobacter spp. are usually susceptible to carbapenems, aminoglycosides, tetracyclines and colistin [Marak Infect Dis (Lond) 2017;49(7):532-9].Hypothesis/Gap Statement. As C. amalonaticus is rare, only one clinical isolate, coharbouring carbapenem resistance gene bla IMP-4 and quinolone resistance gene qnrs1, has been reported.Aim. To characterize a carbapenem-resistant C. amalonaticus strain from PR China coharbouring bla IMP-4 and qnrs1.Methodology. Three hundred and forty nonrepetitive carbapenem-resistant Enterobacterales (CRE) strains were collected during 2011-2018. A carbapenem-resistant C. amalonaticus strain was detected and confirmed using a VITEK mass spectrometry-based microbial identification system and 16S rRNA sequencing. Minimum inhibitory concentrations (MICs) for clinical antimicrobials were obtained by the broth microdilution method. Whole-genome sequencing (WGS) was performed for antibiotic resistance gene analysis, and a phylogenetic tree of C. amalonaticus strains was constructed using the Bacterial Pan Genome Analysis (BPGA) tool. The transferability of the resistance plasmid was verified by conjugal transfer.Results. A rare carbapenem-resistant C. amalonaticus strain (CA71) was recovered from a patient with cerebral obstruction and the sequences of 16S rRNA gene shared more than 99 % similarity with C. amalonaticus CITRO86, FDAARGOS 165. CA71 is resistant to β-lactam, quinolone and aminoglycoside antibiotics, and even imipenem and meropenem (MICs of 2 and 4 mg l-1 respectively), and is only sensitive to polymyxin B and tigecycline. Six antibiotic resistance genes were detected via WGS, including the β-lactam genes bla IMP-4, bla CTX-M-18 and bla Sed1, the quinolone gene qnrs1, and the aminoglycoside genes AAC(3)-VIIIa, AadA24. Interestingly, bla IMP-4 and qnrs1 coexist on an IncN1-type plasmid (pCA71-IMP) and successfully transferred to Escherichia coli J53 via conjugal transfer. Phylogenetic analysis showed that CA71 is most similar to C. amalonaticus strain CJ25 and belongs to the same evolutionary cluster along with seven other strains.Conclusion. To the best of our knowledge, this is the first report of a carbapenem-resistant C. amalonaticus isolate coharbouring bla IMP-4 and qnrs1.
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Affiliation(s)
- Yunan Zhao
- The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, Zhejiang, PR China
| | - Xuefeng Chen
- People's Hospital of Liandu City, Lishui, PR China
| | - Xiaolei Hu
- The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, Zhejiang, PR China
| | - Yang Shi
- The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, Zhejiang, PR China
| | - Xinmi Zhao
- The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, Zhejiang, PR China
| | - Jianfen Xu
- The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, Zhejiang, PR China
| | - Hui Ding
- The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, Zhejiang, PR China
| | - Rongzhen Wu
- The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, Zhejiang, PR China
| | - Jiansheng Huang
- The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, Zhejiang, PR China
| | - Zhigang Zhao
- The Fifth Affiliated Hospital of Wenzhou Medical University, Lishui, Zhejiang, PR China
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20
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Epidemic HI2 Plasmids Mobilising the Carbapenemase Gene blaIMP-4 in Australian Clinical Samples Identified in Multiple Sublineages of Escherichia coli ST216 Colonising Silver Gulls. Microorganisms 2021; 9:microorganisms9030567. [PMID: 33801844 PMCID: PMC7999438 DOI: 10.3390/microorganisms9030567] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 03/04/2021] [Accepted: 03/05/2021] [Indexed: 12/28/2022] Open
Abstract
Escherichia coli ST216, including those that carry blaKPC-2, blaFOX-5, blaCTX-M-15 and mcr-1, have been linked to wild and urban-adapted birds and the colonisation of hospital environments causing recalcitrant, carbapenem-resistant human infections. Here we sequenced 22 multiple-drug resistant ST216 isolates from Australian silver gull chicks sampled from Five Islands, of which 21 carried nine or more antibiotic resistance genes including blaIMP-4 (n = 21), blaTEM-1b (n = 21), aac(3)-IId (n = 20), mph(A) (n = 20), catB3 (n = 20), sul1 (n = 20), aph(3”)-Ib (n = 18) and aph(6)-Id (n = 18) on FIB(K) (n = 20), HI2-ST1 (n = 11) and HI2-ST3 (n = 10) plasmids. We show that (i) all HI2 plasmids harbour blaIMP-4 in resistance regions containing In809 flanked by IS26 (HI2-ST1) or IS15DI (HI2-ST3) and diverse metal resistance genes; (ii) HI2-ST1 plasmids are highly related to plasmids reported in diverse Enterobacteriaceae sourced from humans, companion animals and wildlife; (iii) HI2 were a feature of the Australian gull isolates and were not observed in international ST216 isolates. Phylogenetic analyses identified close relationships between ST216 from Australian gull and clinical isolates from overseas. E. coli ST216 from Australian gulls harbour HI2 plasmids encoding resistance to clinically important antibiotics and metals. Our studies underscore the importance of adopting a one health approach to AMR and pathogen surveillance.
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21
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Pong CH, Hall RM. An X1α plasmid from a Salmonella enterica serovar Ohio isolate carrying a novel IS26-bounded tet(C) pseudo-compound transposon. Plasmid 2021; 114:102561. [PMID: 33485833 DOI: 10.1016/j.plasmid.2021.102561] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Revised: 10/19/2020] [Accepted: 10/21/2020] [Indexed: 11/19/2022]
Abstract
The sequence of a conjugative plasmid, pSRC22-2, found in a multiply antibiotic resistant Salmonella enterica serovar Ohio isolate SRC22 originally cultured from swine in 1999, was determined. Plasmid pSRC22-2 has a copy number of approximately 40 and transfers tetracycline resistance at very high frequency. It was typed as IncX1 using the three typing schemes proposed for X-type plasmids, which utilize the replication region, iteron region and taxC conjugation gene and pSRC22-2 belongs to the X1α subgroup. The plasmid backbone, derived by removing mobile elements, is shared with pOLA52, which was the first fully sequenced IncX1 plasmid, and five other X1α plasmids. The pSRC22-2 backbone is interrupted by a complete copy of an IS903 isoform, partial copies of IS1 and IS903 on either side of a 5930 bp IS26-bounded pseudo-compound transposon (PCT), and a novel 256 bp miniature inverted repeat transposable element (MITE). The MITE belongs to the Tn3 family and was named MITESen1. The PCT, which carries a tet(C) tetracycline resistance determinant, is bounded by copies of a novel IS26 variant, IS26-v4, and was designated PTn6184. Comparison of PTn6184 with other tet(C)-carrying PCTs revealed that it can be derived from the largest, PTntet(C), via a two-step process that re-orders the central fragment and involves both an IS26-mediated event and homologous recombination. IS26-v4, which encodes a variant transposase, Tnp26 G184D, has appeared in only 46 entries in the GenBank non-redundant database.
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Affiliation(s)
- Carol H Pong
- School of Life and Environmental Sciences, The University of Sydney, NSW, Australia
| | - Ruth M Hall
- School of Life and Environmental Sciences, The University of Sydney, NSW, Australia.
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Bassetti M, Di Pilato V, Giani T, Vena A, Rossolini GM, Marchese A, Giacobbe DR. Treatment of severe infections due to metallo-β-lactamases-producing Gram-negative bacteria. Future Microbiol 2020; 15:1489-1505. [PMID: 33140656 DOI: 10.2217/fmb-2020-0210] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In the last decades, there was an important paucity of agents for adequately treating infections due to metallo-β-lactamases-producing Gram-negative bacteria (MBL-GNB). Cefiderocol, a novel siderophore cephalosporin showing in vitro activity against MBL-GNB, has been recently marketed, and a combination of aztreonam and ceftazidime/avibactam has shown a possible favorable effect on survival of patients with severe MBL-GNB infections in observational studies. Other agents showing in vitro activity against MBL-GNB are currently in clinical development (e.g., cefepime/taniborbactam, LYS228, cefepime/zidebactam) that could be an important addition to our future armamentarium for severe MBL-GNB infections. Nonetheless, we should not discontinue our efforts to optimize the use of non-β-lactams agents, since they could remain an essential last-resort or alternative option in selected cases.
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Affiliation(s)
- Matteo Bassetti
- Infectious Diseases Unit, Ospedale Policlinico San Martino - IRCCS, Genoa, Italy
- Department of Health Sciences, University of Genoa, Genoa, Italy
| | - Vincenzo Di Pilato
- Department of Surgical Sciences & Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy
| | - Tommaso Giani
- Department of Experimental & Clinical Medicine, University of Florence, Florence, Italy
- Microbiology & Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Antonio Vena
- Infectious Diseases Unit, Ospedale Policlinico San Martino - IRCCS, Genoa, Italy
| | - Gian Maria Rossolini
- Department of Experimental & Clinical Medicine, University of Florence, Florence, Italy
- Microbiology & Virology Unit, Florence Careggi University Hospital, Florence, Italy
| | - Anna Marchese
- Department of Surgical Sciences & Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy
- Microbiology Unit, Ospedale Policlinico San Martino - IRCCS, Genoa, Italy
| | - Daniele R Giacobbe
- Infectious Diseases Unit, Ospedale Policlinico San Martino - IRCCS, Genoa, Italy
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Citrobacter telavivum sp. nov. with chromosomal mcr-9 from hospitalized patients. Eur J Clin Microbiol Infect Dis 2020; 40:123-131. [DOI: 10.1007/s10096-020-04003-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 07/30/2020] [Indexed: 10/23/2022]
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24
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Genomic Epidemiology of Complex, Multispecies, Plasmid-Borne bla KPC Carbapenemase in Enterobacterales in the United Kingdom from 2009 to 2014. Antimicrob Agents Chemother 2020; 64:AAC.02244-19. [PMID: 32094139 DOI: 10.1128/aac.02244-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 02/21/2020] [Indexed: 01/29/2023] Open
Abstract
Carbapenem resistance in Enterobacterales is a public health threat. Klebsiella pneumoniae carbapenemase (encoded by alleles of the bla KPC family) is one of the most common transmissible carbapenem resistance mechanisms worldwide. The dissemination of bla KPC historically has been associated with distinct K. pneumoniae lineages (clonal group 258 [CG258]), a particular plasmid family (pKpQIL), and a composite transposon (Tn4401). In the United Kingdom, bla KPC has represented a large-scale, persistent management challenge for some hospitals, particularly in North West England. The dissemination of bla KPC has evolved to be polyclonal and polyspecies, but the genetic mechanisms underpinning this evolution have not been elucidated in detail; this study used short-read whole-genome sequencing of 604 bla KPC-positive isolates (Illumina) and long-read assembly (PacBio)/polishing (Illumina) of 21 isolates for characterization. We observed the dissemination of bla KPC (predominantly bla KPC-2; 573/604 [95%] isolates) across eight species and more than 100 known sequence types. Although there was some variation at the transposon level (mostly Tn4401a, 584/604 [97%] isolates; predominantly with ATTGA-ATTGA target site duplications, 465/604 [77%] isolates), bla KPC spread appears to have been supported by highly fluid, modular exchange of larger genetic segments among plasmid populations dominated by IncFIB (580/604 isolates), IncFII (545/604 isolates), and IncR (252/604 isolates) replicons. The subset of reconstructed plasmid sequences (21 isolates, 77 plasmids) also highlighted modular exchange among non-bla KPC and bla KPC plasmids and the common presence of multiple replicons within bla KPC plasmid structures (>60%). The substantial genomic plasticity observed has important implications for our understanding of the epidemiology of transmissible carbapenem resistance in Enterobacterales for the implementation of adequate surveillance approaches and for control.
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