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Guo K, Zhao Z, Yang Y, Jiang X, Xu H, Tao F, Xu Y, Liu W. Emergence of an Extensive Drug Resistant Citrobacter portucalensis Clinical Strain Harboring bla SFO-1, bla KPC-2, and bla NDM-1. Infect Drug Resist 2024; 17:2273-2283. [PMID: 38854780 PMCID: PMC11162216 DOI: 10.2147/idr.s461118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/30/2024] [Indexed: 06/11/2024] Open
Abstract
Background To explore the plasmid characteristics and transfer mechanisms of an extensive drug resistant (XDR) clinical isolate, Citrobacter portucalensis L2724hy, co-producing bla SFO-1, bla NDM-1, and bla KPC-2. Methods Species confirmation of L2724hy was achieved through 16S rRNA sequencing and Average Nucleotide Identity (ANI) analysis. Antimicrobial susceptibility testing (AST) employed the agar dilution and micro broth dilution methods. Identification of resistance genes was carried out by PCR and whole-genome sequencing (WGS). Essential resistance gene locations were verified by S1 nuclease pulsed-field gel electrophoresis (S1-PFGE) and southern hybridization experiments. Subsequent WGS data analysis delved into drug resistance genes and plasmids. Results The confirmation of the strain L2724hy as an extensive drug-resistant Citrobacter portucalensis, resistant to almost all antibiotics tested except polymyxin B and tigecycline, was achieved through 16S rRNA sequencing, ANI analysis and AST results. WGS and subsequent analysis revealed L2724hy carrying bla SFO-1, bla NDM-1, and bla KPC-2 on plasmids of various sizes. The uncommon ESBL gene bla SFO-1 coexists with the fosA3 gene on an IncFII plasmid, featuring the genetic environment IS26-fosA3-IS26-ampR-bla SFO-1-IS26. The bla NDM-1 was found on an IncX3 plasmid, coexisting with bla SHV-12, displaying the sequence IS5-IS3000-IS3000-Tn2-bla NDM-1-ble-trpF-dsbD-cutA-gros-groL, lacking ISAa125. The bla KPC-2 is located on an unclassified plasmid, exhibiting the sequence Tn2-tnpR-ISKpn27-bla KPC-2-ISKpn6-korC. Conjugation assays confirmed the transferability of both bla NDM-1 and bla KPC-2. Conclusion We discovered the coexistence of bla SFO-1, bla NDM-1, and bla KPC-2 in C. portucalensis for the first time, delving into plasmid characteristics and transfer mechanisms. Our finding highlights the importance of vigilant monitoring of drug-resistance genes and insertion elements in uncommon strains.
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Affiliation(s)
- Kexin Guo
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, People’s Republic of China
| | - Zanzan Zhao
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, People’s Republic of China
| | - Yu Yang
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, People’s Republic of China
| | - Xiawei Jiang
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, People’s Republic of China
| | - Hao Xu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Fangfang Tao
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, People’s Republic of China
| | - Ye Xu
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, People’s Republic of China
| | - Wenhong Liu
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, People’s Republic of China
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Monte DFM, Gonzalez-Escalona N, Cao G, Pedrosa GTDS, Saraiva MMS, Balkey M, Jin Q, Brown E, Allard M, Macarisin D, Magnani M. Genomic analysis of a cAmpC (CMY-41)-producing Citrobacter freundii ST64 isolated from patient. Lett Appl Microbiol 2024; 77:ovae010. [PMID: 38327245 DOI: 10.1093/lambio/ovae010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/24/2024] [Accepted: 02/06/2024] [Indexed: 02/09/2024]
Abstract
Antibiotic resistance in Citrobacter freundii is a public health concern. This study evaluated the closed genome of a C. freundii isolated from the stool of a hospitalized patient initially related to a Salmonella outbreak. Confirmation of the isolate was determined by whole-genome sequencing. Nanopore sequencing was performed using a MinION with a Flongle flow cell. Assembly using SPAdes and Unicycler yielded a closed genome annotated by National Center for Biotechnology Information Prokaryotic Genome Annotation Pipeline. Genomic analyses employed MLST 2.0, ResFinder4.1, PlasmidFinder2.1, and VFanalyzer. Phylogenetic comparison utilized the Center for Food Safety and Applied Nutrition (CFSAN)-single nucleotide polymorphism pipeline and Genetic Algorithm for Rapid Likelihood Inference. Antimicrobial susceptibility was tested by broth microdilution following Clinical and Laboratory Standards Institute criteria. Multi-locus sequence type in silico analysis assigned the C. freundii as sequence type 64 and the blaCMY-41 gene was detected in resistome investigation. The susceptibility to antibiotics, determined using Sensititre® plates, revealed resistance to aztreonam, colistin, cefoxitin, amoxicillin/clavulanic acid, sulfisoxazole, ampicillin, and streptomycin. The genetic relatedness of the C. freundii CFSAN077772 with publicly available C. freundii genomes revealed a close relationship to a C. freundii SRR1186659, isolated in 2009 from human stool in Tanzania. In addition, C. freundii CFSAN077772 is nested in the same cluster with C. freundii clinical strains isolated in Denmark, Mexico, Myanmar, and Canada, suggesting a successful intercontinental spread.
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Affiliation(s)
- Daniel F M Monte
- Department of Animal Science, College for Agricultural Sciences, Federal University of Paraiba (CCA/UFPB), Areia, PB 58397000, Brazil
| | - Narjol Gonzalez-Escalona
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration,, College Park, MD 20740, USA
| | - Guojie Cao
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration,, College Park, MD 20740, USA
| | - Geany Targino de Souza Pedrosa
- Laboratory of Microbial Processes in Foods, Department of Food Engineering, Federal University of Paraíba, João Pessoa, PB 58059900, Brazil
| | - Mauro M S Saraiva
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, SP 14884-900, Brazil
| | - Maria Balkey
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration,, College Park, MD 20740, USA
| | - Qing Jin
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration,, College Park, MD 20740, USA
| | - Eric Brown
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration,, College Park, MD 20740, USA
| | - Marc Allard
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration,, College Park, MD 20740, USA
| | - Dumitru Macarisin
- Division of Microbiology, Office of Regulatory Science, Center for Food Safety and Applied Nutrition, US Food and Drug Administration,, College Park, MD 20740, USA
| | - Marciane Magnani
- Laboratory of Microbial Processes in Foods, Department of Food Engineering, Federal University of Paraíba, João Pessoa, PB 58059900, Brazil
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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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Ahmed T, Islam MS, Nuruzzaman M, Sadekuzzaman M, Kabir SML, Rahman MT, Khan MSR. Draft genome sequence of multidrug-resistant Citrobacter portucalensis BAU_133-2 strain isolated from a domestic duck ( Anas platyrhynchos domesticus) in Bangladesh. Microbiol Resour Announc 2023; 12:e0058723. [PMID: 37909718 PMCID: PMC10720505 DOI: 10.1128/mra.00587-23] [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: 07/03/2023] [Accepted: 10/02/2023] [Indexed: 11/03/2023] Open
Abstract
We announce the genome sequence of the Citrobacter portucalensis BAU_133-2 strain isolated from a domestic duck. Our assembled genome contained a length of 4.8 Mb, 110.0× genome coverage, 51.91% of an average GC content, 1 plasmid, 1 CRISPR array, 8 prophages, 27 antibiotic resistance genes, and 75 virulence factor genes.
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Affiliation(s)
- Tarana Ahmed
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
- Department of Livestock Services, Ministry of Fisheries & Livestock, Government of the Peoples Republic of Bangladesh, Krishi Khamar Sarak, Farmgate, Dhaka, Bangladesh
| | - Md. Saiful Islam
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
- Department of Animal Sciences, University of California—Davis, Davis, California, USA
| | | | - Mohammad Sadekuzzaman
- Department of Livestock Services, Central Disease Investigation Laboratory (CDIL), Ministry of Fisheries & Livestock, Government of the Peoples Republic of Bangladesh, Krishi Khamar Sarak, Farmgate, Dhaka, Bangladesh
| | - S. M. Lutful Kabir
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md. Tanvir Rahman
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
| | - Md. Shahidur Rahman Khan
- Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, Bangladesh
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Chenhaka LH, Van Wyk DAB, Mienie C, Bezuidenhout CC, Lekota KE. The phylogenomic landscape of extended-spectrum β-lactamase producing Citrobacter species isolated from surface water. BMC Genomics 2023; 24:755. [PMID: 38062371 PMCID: PMC10704729 DOI: 10.1186/s12864-023-09867-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Accepted: 12/02/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Citrobacter species are Gram-negative opportunistic pathogens commonly reported in nosocomial-acquired infections. This study characterised four Citrobacter species that were isolated from surface water in the North West Province, South Africa. RESULTS Phenotypic antimicrobial susceptibility profiles of the isolates demonstrated their ability to produce the extended-spectrum β-lactamase (ESBL). Whole genomes were sequenced to profile antibiotic resistance and virulence genes, as well as mobile genetic elements. In silico taxonomic identification was conducted by using multi-locus sequence typing and average nucleotide identity. A pangenome was used to determine the phylogenomic landscape of the Citrobacter species by using 109 publicly available genomes. The strains S21 and S23 were identified as C. braakii, while strains S24 and S25 were C. murliniae and C. portucalensis, respectively. Comparative genomics and sequenced genomes of the ESBL-producing isolates consisted of n = 91; 83% Citrobacter species in which bla-CMY-101 (n = 19; 32,2%) and bla-CMY-59 (n = 12; 38,7%) were prevalent in C. braakii, and C. portucalensis strains, respectively. Macrolide (acrAB-TolC, and mdtG) and aminoglycoside (acrD) efflux pumps genes were identified in the four sequenced Citrobacter spp. isolates. The quinolone resistance gene, qnrB13, was exclusive to the C. portucalensis S25 strain. In silico analysis detected plasmid replicon types IncHI1A, IncP, and Col(VCM04) in C. murliniae S24 and C. portucalensis S25, respectively. These potentially facilitate the T4SS secretion system in Citrobacter species. In this study, the C. braakii genomes could be distinguished from C. murliniae and C. portucalensis on the basis of gene encoding for cell surface localisation of the CPS (vexC) and identification of genes involved in capsule polymer synthesis (tviB and tviE). A cluster for the salmochelin siderophore system (iro-BCDEN) was found in C. murliniae S24. This is important when it comes to the pathogenicity pathway that confers an advantage in colonisation. CONCLUSIONS The emerging and genomic landscapes of these ESBL-producing Citrobacter species are of significant concern due to their dissemination potential in freshwater systems. The presence of these ESBL and multidrug-resistant (MDR) pathogens in aquatic environments is of One Health importance, since they potentially impact the clinical domain, that is, in terms of human health and the agricultural domain, that is, in terms of animal health and food production as well as the environmental domain.
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Affiliation(s)
- Lee-Hendra Chenhaka
- Unit for Environment Science and Management, Microbiology, North-West University, Potchefstroom campus, Private Bag X6001, Potchefstroom, 2520, South Africa
| | - Deidré A B Van Wyk
- Unit for Environment Science and Management, Microbiology, North-West University, Mahikeng campus, Private Bag X2046, Mahikeng, 2745, South Africa.
| | - Charlotte Mienie
- Unit for Environment Science and Management, Microbiology, North-West University, Potchefstroom campus, Private Bag X6001, Potchefstroom, 2520, South Africa
| | - Cornelius C Bezuidenhout
- Unit for Environment Science and Management, Microbiology, North-West University, Potchefstroom campus, Private Bag X6001, Potchefstroom, 2520, South Africa
| | - Kgaugelo E Lekota
- Unit for Environment Science and Management, Microbiology, North-West University, Potchefstroom campus, Private Bag X6001, Potchefstroom, 2520, South Africa
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Duman M, Altun S, Saticioglu IB, Romalde JL. A review of bacterial disease outbreaks in rainbow trout (Oncorhynchus mykiss) reported from 2010 to 2022. JOURNAL OF FISH DISEASES 2023. [PMID: 37965781 DOI: 10.1111/jfd.13886] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 10/26/2023] [Accepted: 10/30/2023] [Indexed: 11/16/2023]
Abstract
Outbreaks of bacterial infections in aquaculture have emerged as significant threats to the sustainable production of rainbow trout (Oncorhynchus mykiss) worldwide. Understanding the dynamics of these outbreaks and the bacteria involved is crucial for implementing effective management strategies. This comprehensive review presents an update on outbreaks of bacteria isolated from rainbow trout reported between 2010 and 2022. A systematic literature survey was conducted to identify relevant studies reporting bacterial outbreaks in rainbow trout during the specified time frame. More than 150 published studies in PubMed, Web of Science, Scopus, Google Scholar and relevant databases met the inclusion criteria, encompassing diverse geographical regions and aquaculture systems. The main bacterial pathogens implicated in the outbreaks belong to both gram-negative, namely Chryseobacterium, Citrobacter, Deefgea Flavobacterium, Janthinobacterium, Plesiomonas, Pseudomonas, Shewanella, and gram-positive genera, including Lactococcus and Weissella, and comprise 36 new emerging species that are presented by means of pathogenicity and disturbance worldwide. We highlight the main characteristics of species to shed light on potential challenges in treatment strategies. Moreover, we investigate the role of various risk factors in the outbreaks, such as environmental conditions, fish density, water quality, and stressors that potentially cause outbreaks of these species. Insights into the temporal and spatial patterns of bacterial outbreaks in rainbow trout aquaculture are provided. Furthermore, the implications of these findings for developing sustainable and targeted disease prevention and control measures are discussed. The presented study serves as a comprehensive update on the state of bacterial outbreaks in rainbow trout aquaculture, emphasizing the importance of continued surveillance and research to sustain the health and productivity of this economically valuable species.
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Affiliation(s)
- Muhammed Duman
- Department of Aquatic Animal Disease, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, Turkey
| | - Soner Altun
- Department of Aquatic Animal Disease, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, Turkey
| | - Izzet Burcin Saticioglu
- Department of Aquatic Animal Disease, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, Turkey
| | - Jesús L Romalde
- Cross-disciplinary Research Center in Environmental Technologies (CRETUS), Department of Microbiology and Parasitology, CIBUS-Faculty of Biology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
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Ozsefil IC, Miraloglu IH, Ozbayram EG, Uzun O, Ince B, Ince O. Is a floodplain forest a valuable source for lignin-degrading anaerobic microbial communities: A metagenomic approach. CHEMOSPHERE 2023; 339:139675. [PMID: 37517669 DOI: 10.1016/j.chemosphere.2023.139675] [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: 01/23/2023] [Revised: 07/19/2023] [Accepted: 07/27/2023] [Indexed: 08/01/2023]
Abstract
Lignin is one of the most substantial obstacles in the evaluation of lignocellulosic compounds. Although there are numerous approaches for the enhancement of lignin digestion in the literature, there has yet to be an optimized system to date. In this study, samples taken from Igneada floodplain forests were enriched anaerobically at 25 °C and 37 °C, with alkali lignin as the sole carbon source. The activity of the anaerobic lignin-degrading microbial consortium was detected more efficiently at 37 °C, where biogas production exceeded 3.5 mLgas/mLmedium. It was observed that the microbial community initially dominated by Proteobacteria (around 60%) changed completely after enrichment and was led by members of the Firmicutes phylum (up to 90%). The dominant species (Sporomusa termitida, Desulfitobacterium hafniense, Citrobacter freundii, Citrobacter portucalensis, Alkalibacter rhizosphaerae, and Gudongella oleilytica) occupying more than 50% in the final enrichment culture were only around 2% in the raw samples. Therefore, this study, one of the few in which enriched environmental samples were sequenced using MinION, demonstrated that longoses are exceptional reservoirs for lignin-digesting anaerobic microorganisms.
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Affiliation(s)
- Ibrahim Cem Ozsefil
- Bogazici University, Institute of Environmental Sciences, Bebek, 34342, Istanbul, Turkey.
| | | | - E Gozde Ozbayram
- Istanbul University, Faculty of Aquatic Sciences, Department of Marine and Freshwater Resources Management, Fatih, 34134, Istanbul, Turkey
| | - Omer Uzun
- Bogazici University, Institute of Environmental Sciences, Bebek, 34342, Istanbul, Turkey
| | - Bahar Ince
- Bogazici University, Institute of Environmental Sciences, Bebek, 34342, Istanbul, Turkey
| | - Orhan Ince
- Department of Environmental Engineering, Faculty of Civil Engineering, Istanbul Technical University, Maslak, 34396, Istanbul, Turkey
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Furlan JPR, Ribeiro TG, Novais Â, Cabral H, Peixe L, Stehling EG. Citrobacter meridianamericanus sp. nov., isolated from a soil sample. Int J Syst Evol Microbiol 2023; 73. [PMID: 36943338 DOI: 10.1099/ijsem.0.005720] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/23/2023] Open
Abstract
A Gram-stain-negative strain, designated BR102T, isolated from a soil sample in Brazil was characterized by a polyphasic approach. Comparative 16S rRNA gene sequences indicated that strain BR102T belonged to the genus Citrobacter. The recN- and whole-genome-based phylogeny, and multilocus sequence analysis based on concatenated partial fusA, leuS, pyrG and rpoB sequences strongly supported a clade encompassing strain BR102T and a strain from public database that was distinct from currently recognized species of the genus Citrobacter. Average nucleotide identity and digital DNA-DNA hybridization values between strain BR102T and the closest relative Citrobacter freundii ATCC 8090T were 91.8 and 48.8 %, respectively. The ability to metabolize different compounds further discriminated strain BR102T from other closely related species of the genus Citrobacter. The novel variants bla CMY-179 and qnrB97, which encoded a CMY-2-like β-lactamase and a QnrB-type protein, respectively, were identified in strain BR102T. BR102T was resistant to ampicillin, amoxicillin/clavulanate and cefoxitin. The DNA G+C content of strain BR102T is 51.3 mol%. Based on these results, strain BR102T represents a novel species of the genus Citrobacter, for which the name Citrobacter meridianamericanus sp. nov. is proposed. The type strain is BR102T (=MUM 22.55T=IMI 507229T).
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Affiliation(s)
- João Pedro Rueda Furlan
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Teresa Gonçalves Ribeiro
- UCIBIO-Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Ângela Novais
- UCIBIO-Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Hamilton Cabral
- Department of Pharmaceutical Sciences, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
| | - Luísa Peixe
- UCIBIO-Applied Molecular Biosciences Unit, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
- Associate Laboratory i4HB-Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Eliana Guedes Stehling
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, São Paulo, Brazil
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Nobrega D, Peirano G, Matsumura Y, Pitout JDD. Molecular Epidemiology of Global Carbapenemase-Producing Citrobacter spp. (2015-2017). Microbiol Spectr 2023; 11:e0414422. [PMID: 36847542 PMCID: PMC10101073 DOI: 10.1128/spectrum.04144-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 02/09/2023] [Indexed: 03/01/2023] Open
Abstract
The emergence of carbapenem resistance is a significant public health concern. The rate of infections caused by carbapenemase-producing Citrobacter spp., particularly C. freundii, is increasing. Concomitantly, comprehensive global genomic data on carbapenemase-producing Citrobacter spp. are scarce. We used short read whole-genome sequencing to describe the molecular epidemiology and international distribution of eighty-six carbapenemase-producing Citrobacter spp. obtained from two surveillance programs (2015 to 17). The common carbapenemases were KPC-2 (26%), VIM-1 (17%), IMP-4 (14%) and NDM-1 (10%). C. freundii and C. portucalensis were the principal species. C. freundii consisted of multiple clones obtained mainly from Colombia (with KPC-2), the United States (with KPC-2, -3), and Italy (with VIM-1). Two dominant C. freundii clones were identified: ST98 was linked with blaIMP-8 from Taiwan and blaKPC-2 from the United States, and ST22 was linked with blaKPC-2 from Colombia and blaVIM-1 from Italy. C. portucalensis consisted mainly of two clones: ST493 with blaIMP-4 which was limited to Australia, and ST545 with blaVIM-31 which was limited to Turkey. Class I integron (In916) with blaVIM-1 was circulating between multiple sequence types (STs) in Italy, Poland, and Portugal. In73 with blaIMP-8 was circulating between various STs in Taiwan, while In809 with blaIMP-4 was circulating between different STs in Australia. The global carbapenemase-producing Citrobacter spp. population is dominated by diverse STs with different characteristics and varied geographical distribution and thus requires continued monitoring. Ongoing genomic surveillance should use methodologies able to distinguish between C. freundii and C. portucalensis. IMPORTANCE Citrobacter spp. are gaining recognition as important causes of hospital-acquired infections in humans. Among Citrobacter spp., carbapenemase-producing strains are cause of utmost concern to health care services globally due to their ability to resist therapy with virtually any beta-lactam antibiotic. Here, we described the molecular characteristics of a global collection of carbapenemase-producing Citrobacter spp. C. freundii and C. portucalensis were the most common species among Citrobacter spp. with carbapenemases from this survey. Importantly, C. portucalensis was misidentified as C. freundii when using Vitek 2.0/MALDI-TOF MS (matrix-assisted laser desorption/ionization-time of flight mass spectrometry) phenotypic identification, which has important implications for future surveys. Among C. freundii, we identified two dominant clones: ST98 with blaIMP-8 from Taiwan and blaKPC-2 from the United States, and ST22 with blaKPC-2 from Colombia and blaVIM-1 from Italy. As for C. portucalensis, the dominant clones consisted of ST493 with blaIMP-4 from Australia and ST545 with blaVIM-31 from Turkey.
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Affiliation(s)
- Diego Nobrega
- Faculty of Veterinary Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Gisele Peirano
- Alberta Precision Laboratories, Calgary, Alberta, Canada
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | | | - Johann D. D. Pitout
- Alberta Precision Laboratories, Calgary, Alberta, Canada
- Cummings School of Medicine, University of Calgary, Calgary, Alberta, Canada
- University of Pretoria, Pretoria, South Africa
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10
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Zepeda-Velazquez AP, Gómez-De-Anda FR, Aguilar-Mendoza LF, Castrejón-Jiménez NS, Hernández-González JC, Varela-Guerrero JA, de-la-Rosa-Arana JL, Vega-Sánchez V, Reyes-Rodríguez NE. Bullfrogs (Lithobates catesbeianus) as a Potential Source of Foodborne Disease. J Food Prot 2023; 86:100067. [PMID: 36948016 DOI: 10.1016/j.jfp.2023.100067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 02/15/2023] [Accepted: 02/18/2023] [Indexed: 03/24/2023]
Abstract
In Mexico, bullfrogs (Lithobates catesbeianus) are produced as gourmet food. However, bullfrogs can be carriers of pathogens because the frogs' preferred living conditions occur in stagnant water. The present study aimed to identify bacteria that cause foodborne diseases or are associated with human diseases. For molecular identification, based on the sequential analysis by 16S rRNA or rpoD was conducted on all isolates obtained from bullfrog. A total of 91 bacterial isolates were obtained from bullfrogs; 14 genera and 23 species were identified, including Acinetobacter johnsonii 16.5%; Aeromonas media 14.3%; Aeromonas veronii 13.2%; Providencia rettgeri 7.7%; Citrobacter freundii 6.6%; Aeromonas caviae 4.4%; Aeromonas hydrophila and Elizabethkingia ursingii 3.3%; Pseudomonas stutzeri, Raoultella ornithinolytica, and Shewanella putrefaciens 2.2%; Acinetobacter guillouiae, Acinetobacter pseudolwoffii, Citrobacter portucalensis, Citrobacter werkmanii, Edwardsiella anguillarum, Klebsiella michiganensis, Kluyvera intermedia, Kocuria rosea, Myroides odoratimimus, Myroides odoratus, Proteus sp., and Proteus hauseri 1.1%. In this study, 49.4% of the isolates obtained cause foodborne disease, 19.8% are bacteria that play an important role in the spoilage of food, 5.5% of isolates have nosocomial significance, 13.2% of bacteria are considered to be pollutants of the ecosystem, and in the case of A. salmonicida and Edwardsiella anguillarum (12.1%) to have a negative impact on aquaculture. Acinetobacter pseudolwoffii and Citrobacter portucalensis have not been reported to cause disease. Lastly of these isolates, 97.8% (89/91) can cause disease by food consumption or by direct contact for immunocompromised persons. The presence of these bacteria in bullfrogs represents a significant problem for human health. There is evidence that these microorganisms are pathogenic and frogs may also be reservoirs.
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Affiliation(s)
- Andrea P Zepeda-Velazquez
- Área Académica de Medicina Veterinaria y Zootecnia, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo, Hidalgo 43600, Mexico.
| | - Fabián-Ricardo Gómez-De-Anda
- Área Académica de Medicina Veterinaria y Zootecnia, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo, Hidalgo 43600, Mexico.
| | - Luis F Aguilar-Mendoza
- Área Académica de Medicina Veterinaria y Zootecnia, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo, Hidalgo 43600, Mexico
| | - Nayeli Shantal Castrejón-Jiménez
- Área Académica de Medicina Veterinaria y Zootecnia, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo, Hidalgo 43600, Mexico.
| | - Juan Carlos Hernández-González
- Área Académica de Medicina Veterinaria y Zootecnia, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo, Hidalgo 43600, Mexico.
| | - Jorge A Varela-Guerrero
- Universidad Autónoma del Estado de México, Centro de Investigación y Estudios Avanzados en Salud Animal (CIESA), Facultad de Medicina Veterinaria y Zootecnia, km 15.5 Carretera Panamericana Toluca-Atlacomulco, Toluca, Estado de México, Mexico.
| | - Jorge-Luis de-la-Rosa-Arana
- Microbiología en Salud Humana, Facultad de Estudios Superiores Cuautitlán, Universidad Nacional Autónoma de México, Avenida 1 de mayo S/N, Campo Uno, Cuautitlán Izcalli, CP 54743 Estado de México, Mexico.
| | - Vicente Vega-Sánchez
- Área Académica de Medicina Veterinaria y Zootecnia, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo, Hidalgo 43600, Mexico.
| | - Nydia E Reyes-Rodríguez
- Área Académica de Medicina Veterinaria y Zootecnia, Instituto de Ciencias Agropecuarias, Universidad Autónoma del Estado de Hidalgo, Tulancingo, Hidalgo 43600, Mexico.
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11
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Yu Y, Xie Z, Yang J, Yang R, Li Y, Zhu Y, Zhao Y, Yang Q, Chen J, Alwathnani HA, Feng R, Rensing C, Herzberg M. Citrobacter portucalensis Sb-2 contains a metalloid resistance determinant transmitted by Citrobacter phage Chris1. JOURNAL OF HAZARDOUS MATERIALS 2023; 443:130184. [PMID: 36270189 DOI: 10.1016/j.jhazmat.2022.130184] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2022] [Revised: 10/05/2022] [Accepted: 10/10/2022] [Indexed: 05/25/2023]
Abstract
Bacterial adaptation to extreme environments is often mediated by horizontal gene transfer (HGT) via genetic mobile elements. Nevertheless, phage-mediated HGT conferring bacterial arsenic resistance determinants has rarely been investigated. In this study, a highly arsenite and antimonite resistant bacterium, Citrobacter portucalensis strain Sb-2, was isolated, and genome analysis showed that several putative arsenite and antimonite resistance determinants were flanked or embedded in prophages. Furthermore, an active bacteriophage carrying one of the ars clusters (arsRDABC arsR-yraQ/arsP) was obtained and sequenced. These genes encoding putative arsenic resistance determinants were induced by arsenic and antimony as demonstrated by RT-qPCR, and one gene arsP/yraQ of the ars cluster was shown to give resistance to MAs(III) and Rox(III), thereby showing function. Here, we were able to directly show that these phage-mediated arsenic and antimony resistances play a significant role in adapting to As- and Sb-contaminated environments. In addition, we demonstrate that this phage is responsible for conferring arsenic and antimony resistances to C. portucalensis strain Sb-2.
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Affiliation(s)
- Yanshuang Yu
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Zhenchen Xie
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Jigang Yang
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Ruixiang Yang
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yuanping Li
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Yongguan Zhu
- State Key Laboratory of Regional and Urban Ecology, Research Center for Eco-Environmental Sciences, Chinese Academy of Sciences, Beijing, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China
| | - Yanlin Zhao
- College of Life Sciences, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China
| | - Qiue Yang
- Fujian Provincial Key Laboratory of Soil Environmental Health and Regulation, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Jichen Chen
- Institute of Soil and Fertilizer, Fujian Academy of Agricultural Sciences, Fuzhou, Fujian 350002, China
| | - Hend A Alwathnani
- Department of Botany and Microbiology, King Saud University, Riyadh, Saudi Arabia
| | - Renwei Feng
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China.
| | - Christopher Rensing
- Institute of Environmental Microbiology, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, Fujian 350002, China; Key Laboratory of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, China.
| | - Martin Herzberg
- Molecular Microbiology, Institute for Biology/Microbiology, Martin-Luther-University Halle-Wittenberg, Kurt-Mothes-Str. 3, 06120 Halle(Saale), Germany
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György É, Laslo É, Salamon B. Antimicrobial impacts of selected Lamiaceae plants on bacteria isolated from vegetables and their application in edible films. FOOD BIOSCI 2023. [DOI: 10.1016/j.fbio.2022.102280] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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13
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Ju X, Wang S, Yang X, Han W, Cai C, Wu Y, Liu C, Qian J, Zhao X, Qian X, Sun Q, Zhang R, Chen G. Epidemiology and Molecular Characteristics of mcr-9 in Citrobacter spp. from Healthy Individuals and Patients in China. Microbiol Spectr 2022; 10:e0134622. [PMID: 36374095 PMCID: PMC9769852 DOI: 10.1128/spectrum.01346-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2022] [Accepted: 10/22/2022] [Indexed: 11/16/2022] Open
Abstract
With the globally prevailing carbapenemase-producing (CP) Citrobacter spp., polymyxin antibiotics have been reconsidered as one of the last-resort treatment options. Our study was conducted to investigate the prevalence of mcr-9 in Citrobacter species. From October to November 2021, 650 fecal samples and 215 Citrobacter isolates were collected from healthy individuals and infected patients, respectively. Isolates were screened for the presence of the mcr-9 gene by the PCR method. mcr-9-carrying strains were identified by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry. Due to the susceptibility to colistin, Citrobacter spp. isolates were first induced to increase the expression of mcr-9 on China blue agar plates containing colistin and were then subjected to conjugation experiments. Whole-genome sequencing was performed on the Illumina NovaSeq PE150 system. The prevalence of mcr-9 in the Citrobacter genus from healthy guts and infected patients was 0.62% and 1.86%, respectively. In all mcr-9-positive strains, MICs of polymyxin B were observed at ≤2 μg/mL, displaying a nonresistant phenotype. As for conjugation experiments, only one isolate successfully transferred the mcr-9 gene to Escherichia coli C600. Whole-genome sequencing showed that eight mcr-9-positive Citrobacter isolates carried mcr-9 and genes encoding resistance to beta-lactam antibiotics, including blaCMY, blaDHA, blaSHV, blaTEM, and blaCTX-M. We also discovered that mcr-9 could be located on the pKPC-CAV1321 plasmid. Our study investigated the prevalence of mcr-9 in Citrobacter spp. in both healthy individuals and infected patients and described the carriage of mcr-9 on the pKPC-CAV1321 plasmid for the first time. IMPORTANCE The emergence of mcr homologues posed a serious threat to the therapeutic efficiency of polymyxin antibiotics. Citrobacter freundii is generally regarded as an opportunistic pathogen associated with a variety of nosocomial infections. In this study, we investigated the prevalence of mcr-9 in Citrobacter spp. isolates from healthy individuals and infected patients and highlighted the importance of the rational use of antibiotics. In addition, this epidemiological investigation is the first to describe the carriage of mcr-9 on plasmid pKPC-CAV1321 and confirms the horizontal transfer of this plasmid. Our research may shed new light on further studies of mcr-9 dissemination in humans.
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Affiliation(s)
- Xiaoyang Ju
- Clinical Microbiology Laboratory, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Siheng Wang
- Clinical Microbiology Laboratory, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Xuemei Yang
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Hong Kong, China
| | - Weihua Han
- Clinical Microbiology Laboratory, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Chang Cai
- China Australia Joint Laboratory for Animal Health Big Data Analytics, College of Animal Science and Technology, Zhejiang Agricultural and Forestry University, Hangzhou, China
| | - Yuchen Wu
- Clinical Microbiology Laboratory, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Congcong Liu
- Clinical Microbiology Laboratory, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Jiao Qian
- Clinical Laboratory Department, Taizhou Hospital of Zhejiang Province, Wenzhou Medical University, Taizhou, China
| | - Xiaofei Zhao
- The Affiliated Hospital of Hangzhou Normal University, Hangzhou, China
| | - Xiang Qian
- Department of Clinical Laboratory, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang, China
| | - Qiaoling Sun
- Department of Laboratory Medicine, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang, China
| | - Rong Zhang
- Clinical Microbiology Laboratory, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
| | - Gongxiang Chen
- Clinical Microbiology Laboratory, The Second Affiliated Hospital of Zhejiang University School of Medicine, Zhejiang University, Hangzhou, China
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14
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Adsit FG, Randall TA, Locklear J, Kurtz DM. The emergence of the tetrathionate reductase operon in the Escherichia coli/Shigella pan-genome. Microbiologyopen 2022; 11:e1333. [PMID: 36479628 PMCID: PMC9638481 DOI: 10.1002/mbo3.1333] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 10/18/2022] [Accepted: 10/20/2022] [Indexed: 11/09/2022] Open
Abstract
Escherichia coli pathogenic variants (pathovars) are generally characterized by defined virulence traits and are susceptible to the evolution of hybridized identities due to the considerable plasticity of the E. coli genome. We have isolated a strain from a purified diet intended for research animals that further demonstrates the ability of E. coli to acquire novel genetic elements leading potentially to emergent new pathovars. Utilizing next generation sequencing to obtain a whole genome profile, we report an atypical strain of E. coli, EcoFA807-17, possessing a tetrathionate reductase (ttr) operon, which enables the utilization of tetrathionate as an electron acceptor, thus facilitating respiration in anaerobic environments such as the mammalian gut. The ttr operon is a potent virulence factor for several enteric pathogens, most prominently Salmonella enterica. However, the presence of chromosomally integrated tetrathionate reductase genes does not appear to have been previously reported in wild-type E. coli or Shigella. Accordingly, it is possible that the appearance of this virulence factor may signal the evolution of new mechanisms of pathogenicity in E. coli and Shigella and may potentially alter the effectiveness of existing assays using tetrathionate reductase as a unique marker for the detection of Salmonella enterica.
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Affiliation(s)
- Floyd G. Adsit
- Quality Assurance Laboratory (QAL), Comparative Medicine Branch (CMB)National Institute of Environmental Health Sciences (NIEHS)DurhamNorth CarolinaUSA
| | - Thomas A. Randall
- Integrative BioinformaticsNational Institute of Environmental Health Sciences (NIEHS)DurhamNorth CarolinaUSA
| | - Jacqueline Locklear
- Quality Assurance Laboratory (QAL), Comparative Medicine Branch (CMB)National Institute of Environmental Health Sciences (NIEHS)DurhamNorth CarolinaUSA
| | - David M. Kurtz
- Quality Assurance Laboratory (QAL), Comparative Medicine Branch (CMB)National Institute of Environmental Health Sciences (NIEHS)DurhamNorth CarolinaUSA
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15
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Luo X, Yu L, Feng J, Zhang J, Zheng C, Hu D, Dai P, Xu M, Li P, Lin R, Mu K. Emergence of Extensively Drug-Resistant ST170 Citrobacter portucalensis with Plasmids pK218-KPC, pK218-NDM, and pK218-SHV from a Tertiary Hospital, China. Microbiol Spectr 2022; 10:e0251022. [PMID: 36154205 PMCID: PMC9603283 DOI: 10.1128/spectrum.02510-22] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2022] [Accepted: 09/09/2022] [Indexed: 01/04/2023] Open
Abstract
The objective of this study is to characterize the molecular mechanism of a clinical carbapenem-resistant Citrobacter portucalensis strain K218, which coproduces KPC and NDM carbapenemases. K218 was isolated from a patient's blood sample in a Chinese tertiary hospital. Carbapenemases were detected by the immunocolloidal gold technique. The MIC values were determined by VITEK2. Whole-genome sequencing was performed on K218 and sequence data were analyzed using phylogenetics and extensive genomic comparison. This study reveals that K218 contains a single 5.08 Mb chromosome (51.8% GC content) and four plasmids, pK218-KPC (106 Kb), pK218-NDM (111 Kb), pK218-SHV (191 Kb), and pK218-NR (5 Kb). Twenty-nine types of antibiotic resistance genes were carried on K218, including blaKPC-2 harbored on pK218-KPC and blaNDM-1 harbored on pK218-NDM. Detailed comparison of related plasmids of pK218-KPC, pK218-NDM, and pK218-SHV showed that they shared similar conserved backbone regions, respectively. Comprehensive annotation revealed large accessory modules were recombined on the genome of K218. Further analysis speculated that mobile genetic elements bearing abundant resistance genes facilitated the formation of these accessory modules. In conclusion, this study provides an in-depth understanding of the genomic characterization of K218, an extensively drug-resistant C. portucalensis strain coproducing NDM and KPC carbapenemase. To the best of our knowledge, this is the first report of C. portucalensis strain coharboring blaKPC-2 and blaNDM-1 from the clinical setting. IMPORTANCE This is the first report of extensively drug-resistant C. portucalensis harboring both blaKPC-2 and blaNDM-1. This study will not only extend the understanding of the structural dissection of plasmids and chromosomes carried in C. portucalensis, but also expand knowledge of the genetic environment of the blaKPC-2 and blaNDM-1 genes. blaKPC-2 and blaNDM-1 genes have been suggested to facilitate the propagation and persistence of their host bacteria under different antimicrobial selection pressures. Large accessory regions carrying blaKPC-2 and blaNDM-1 genes have become hot spots for transposition and integration, and their structural variation and evolution should receive attention. The multidrug-resistant plasmids pK218-KPC, pK218-NDM, and pK218-SHV with several multidrug resistance regions and the chromosome cK218 with two novel transposons Tn7410 and Tn7411 contribute to the formation of extensively drug-resistant C. portucalensis.
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Affiliation(s)
- Xinhua Luo
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, China
| | - Lianhua Yu
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, China
| | - Jiao Feng
- Institutes of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Jin Zhang
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, China
| | - Cheng Zheng
- Department of Critical Care Medicine, Taizhou Municipal Hospital, Taizhou, China
| | - Dakang Hu
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, China
| | - Piaopiao Dai
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, China
| | - Mengqiao Xu
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, China
| | - Piaopiao Li
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital, Taizhou, China
| | - Ronghai Lin
- Department of Critical Care Medicine, Taizhou Municipal Hospital, Taizhou, China
| | - Kai Mu
- State Key Laboratory of Pathogen and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, People’s Republic of China
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16
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Wang L, Li Z, Xiao N, Tang J, He Y, Guo J, Zhao X. Genetic Characterization of bla NDM-1-Carrying Citrobacter portucalensis Sequence Type 328 and Citrobacter freundii Sequence Type 98. Infect Drug Resist 2022; 15:2235-2242. [PMID: 35510156 PMCID: PMC9059874 DOI: 10.2147/idr.s361761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2022] [Accepted: 04/16/2022] [Indexed: 11/23/2022] Open
Abstract
Purpose NDM-1-producing Citrobacter portucalensis and Citrobacter freundii simultaneously occurred in a hospital. This study aims to characterize the blaNDM-1-carrying plasmids in these Citrobacter strains. Methods Cf7303, Cf7308, and Cf7313 were recovered from three patients in a teaching hospital from September 24 to October 1, 2021. Bacteria were identified by MALDI-TOF mass spectrometry, and antibiotics susceptibility tests were determined by VITEK® 2 compact system. Whole-genome sequencing (WGS) was performed using the HiSeq Illumina and QNome platform to characterize the genomes. Results Cf7303 was identified as C. portucalensis Sequence Type 328 by WGS, and harbored two plasmids, namely pCf7303 and a novel IncFIB pNDM-Cf7303 on which antibiotic-resistant genes (blaTEM-1, blaCTX-M-14, blaNDM-1, aac (3)-IId, aadA2, fosA3, sul1, sul2, catA2, tetD, dfrA12, qacEdelta1, mph(A), and bleMBL) are located. C. freundii strain Cf7308 and Cf7313 belonged to the same Sequence Type 98. Cf7308 contained two plasmids, pCf7308, and an IncN1 pNDM-Cf7308 with homology to pNDM-BTR in E. coli and pNDM-CWH001 in C. freundii. Conclusion We characterized a putatively novel IncFIB plasmid carrying blaNDM-1 in C. portucalensis. In addition, the closely related blaNDM-1-carrying IncN1 plasmids in E. coli and C. freundii suggest that interspecies or intraspecies horizontal transfer occurs in China.
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Affiliation(s)
- Lijun Wang
- Department of Clinical Laboratory, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, 102218, People's Republic of China
| | - Ziyao Li
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, China-Japan Friendship Hospital, Beijing, 100029, People's Republic of China
| | - Nan Xiao
- Department of Clinical Laboratory, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, 102218, People's Republic of China
| | - Jie Tang
- Department of Clinical Laboratory, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, 102218, People's Republic of China
| | - Yu He
- Qitan Technology Ltd., Chengdu, Sichuan Province, 610044, People's Republic of China
| | - Jun Guo
- Department of Geriatrics, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, 102218, People's Republic of China
| | - Xiuying Zhao
- Department of Clinical Laboratory, Beijing Tsinghua Changgung Hospital, School of Clinical Medicine, Tsinghua University, Beijing, 102218, People's Republic of China
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17
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Phylogeographical Landscape of Citrobacter portucalensis Carrying Clinically Relevant Resistomes. Microbiol Spectr 2022; 10:e0150621. [PMID: 35357225 PMCID: PMC9045157 DOI: 10.1128/spectrum.01506-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
During a surveillance study conducted to assess the occurrence and genomic landscape of critical priority pathogens circulating at the human-animal-environment interface in Brazil, as part of the Grand Challenges Explorations-New Approaches to Characterize the Global Burden of Antimicrobial Resistance program, two multidrug-resistant (MDR) Citrobacter portucalensis carrying blaCTX-M-15 extended-spectrum β-lactamase (ESBL) genes, isolated from green sea turtles, were characterized. Genomic and phylogeographical analysis of C. portucalensis genomes available in public databases revealed the intercontinental dissemination of clades carrying different arrays of clinically relevant genes conferring resistance to carbapenems, broad-spectrum cephalosporins, cephamycins, aminoglycosides and fluoroquinolones, disinfectants, and heavy metals. Our observations suggest that C. portucalensis could be emerging as critical priority bacteria of both public and One Health importance worldwide. IMPORTANCE The global spread of antibiotic-resistant priority pathogens beyond the hospital setting is a critical issue within a One Health context that integrates the human-animal-environment interfaces. On the other hand, next-generation sequencing technologies along with user-friendly and high-quality bioinformatics tools have improved the identification of bacterial species, and bacterial resistance surveillance. The novel Citrobacter portucalensis species was proposed in 2017 after taxonomic reclassification and definition of the strain A60T isolated in 2008. Here, we presented genomic data showing the occurrence of multidrug-resistant C. portucalensis isolates carrying blaCTX-M-15 ESBL genes in South America. Additionally, we observed the intercontinental dissemination of clades harboring a broad resistome to clinically relevant antibiotics. Therefore, these findings highlight that C. portucalensis is a global MDR bacteria that carries intrinsic blaCMY- and qnrB-type genes and has become a critical priority pathogen due to the acquisition of clinically relevant resistance determinants, such as ESBL and carbapenemase-encoding genes.
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Boya BR, Kumar P, Lee JH, Lee J. Diversity of the Tryptophanase Gene and Its Evolutionary Implications in Living Organisms. Microorganisms 2021; 9:microorganisms9102156. [PMID: 34683477 PMCID: PMC8537960 DOI: 10.3390/microorganisms9102156] [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: 08/31/2021] [Revised: 10/09/2021] [Accepted: 10/12/2021] [Indexed: 12/11/2022] Open
Abstract
Tryptophanase encoded by the gene tnaA is a pyridoxal phosphate-dependent enzyme that catalyses the conversion of tryptophan to indole, which is commonly used as an intra- and interspecies signalling molecule, particularly by microbes. However, the production of indole is rare in eukaryotic organisms. A nucleotide and protein database search revealed tnaA is commonly reported in various Gram-negative bacteria, but that only a few Gram-positive bacteria and archaea possess the gene. The presence of tnaA in eukaryotes, particularly protozoans and marine organisms, demonstrates the importance of this gene in the animal kingdom. Here, we document the distribution of tnaA and its acquisition and expansion among different taxonomic groups, many of which are usually categorized as non-indole producers. This study provides an opportunity to understand the intriguing role played by tnaA, and its distribution among various types of organisms.
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Citrobacter arsenatis sp. nov., an arsenate-reducing bacterium isolated from freshwater sediment. Antonie van Leeuwenhoek 2021; 114:1285-1292. [PMID: 34117562 DOI: 10.1007/s10482-021-01601-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 05/27/2021] [Indexed: 10/21/2022]
Abstract
A novel arsenate-reducing bacterium, LY-1T, was isolated from freshwater sediment in Huangshi, China. Morphological analysis indicated that the cells were shaped like rods and were gram-negative. The major fatty acids (> 10%) were C16:0, summed feature 3 (C16:1 ω7c, C16:1 ω6c) and summed feature 8 (C18:1 ω7c, C18:1 ω6c). An assessment of the phylogeny based on 16S rRNA gene sequences indicated that the strain LY-1T belonged to the genus Citrobacter, while further analysis based on the recN gene indicated that LY-1T occupies a distinct phylogenetic niche within the Citrobacter genus. Moreover, average nucleotide identity and digital DNA-DNA hybridization between the strain LY-1T and the type strains of closely related species of the genus Citrobacter (C. europaeus, C. brakii, C. portucalensis, C. freundii, C. werkmanii, C. cronae, C. youngae, C. pasteurii, C. tructae, C. gillenii, and C. murliniae) were 85.8-93.8% and 31.2-56.9%, respectively. In addition, the LY-1T strain's capacity to metabolize various compounds and its characteristic G + C content of 51.9% were also distinct from other species of the Citrobacter genus. These discriminatory features cumulatively indicate the LY-1T strain as a new species within the Citrobacter genus. We propose the species name Citrobacter arsenatis for this new species, with LY-1T (= CCTCC AB 2019169T = KCTC 72440T) as the type strain.
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Detection of a clinical carbapenem-resistant Citrobacter portucalensis strain and the dissemination of Citrobacter portucalensis in clinical settings. J Glob Antimicrob Resist 2021; 27:79-81. [PMID: 34048980 DOI: 10.1016/j.jgar.2021.04.027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 04/12/2021] [Accepted: 04/22/2021] [Indexed: 11/22/2022] Open
Abstract
OBJECTIVE A clinically isolated carbapenem-resistant Citrobacter portucalensis was characterized by whole genome sequencing (WGS). METHODS Strain 3839 was identified by Vitek 2.0 and matrix-associated laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS). Antibiotic susceptibility testing was performed by microbroth dilution method. WGS followed by bioinformatics analysis was conducted. RESULTS Strain 3839 was initially identified as C. freundii by Vitek and MALDI-TOF MS, and later was demonstrated as C. portucalensis by WGS analysis. Through average-nucleotide identity analysis, we further detected 55 C. portucalensis genomes which were misidentified as C. freundii in GenBank, and at least 22 were clinical-associated, suggesting that the occurrence of C. portucalensis in the clinical setting might be underestimated by the conventional method. Strain 3839 was extremely drug-resistant, and the presence of multiple resistance determinants was detected by WGS, including blaNDM-1, blaSHV-12, blaCMY-150, blaOXA-1, qnrB9, qnrA1, aac(6')Ib-cr; aph(6)-Id_1, aph(3'')-Ib, aac(6')Ib-cr, tetA, tet34, and catB3. Forty-five insertion sequences, 8 phages, and 1 integron gene cassette were identified in this strain. The blaNDM-1 gene was carried by an IncX3 plasmid, which was identical to a plasmid detected in a C. freundii strain. The genetic context of blaNDM-1 was IS30-blaNDM-1-bleMBL-trpF-dsbD-cutA1-groES-groEL-IS91. CONCLUSION To our knowledge, this is the first report of carbapenem-resistant C. portucalensis isolated from clinical samples. The blaNDM-1 gene carried by C. portucalensis may transmit among Citrobacter spp. mediated by plasmids. Together with the underestimation of clinical occurrence caused by the misidentification, our study warrants the necessity of preventing the dissemination of such emerging drug-resistant species in clinical settings.
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Jung WJ, Kim HJ, Giri SS, Kim SG, Kim SW, Kang JW, Kwon J, Lee SB, Oh WT, Jun JW, Park SC. Citrobacter tructae sp. nov. Isolated from Kidney of Diseased Rainbow Trout ( Oncorhynchus mykiss). Microorganisms 2021; 9:microorganisms9020275. [PMID: 33525640 PMCID: PMC7912136 DOI: 10.3390/microorganisms9020275] [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: 01/06/2021] [Revised: 01/25/2021] [Accepted: 01/26/2021] [Indexed: 12/02/2022] Open
Abstract
A novel Citrobacter species was isolated from the kidney of diseased rainbow trout (Oncorhynchus mykiss) reared on a trout farm. Biochemical characterization and phylogenetic analysis were performed for bacterial identification. Sequencing of the 16S rRNA gene and five housekeeping genes indicated that the strain belongs to the Citrobacter genus. However, multilocus sequence analysis, a comparison of average nucleotide identity, and genome-to-genome distance values revealed that strain SNU WT2 is distinct and forms a separate clade from other Citrobacter species. Additionally, the phenotype characteristics of the strain differed from those of other Citrobacter species. Quinone analysis indicated that the predominant isoprenoid quinone is Q-10. Furthermore, strain virulence was determined by a rainbow trout challenge trial, and the strain showed resistance to diverse antibiotics including β-lactams, quinolone, and aminoglycosides. The complete genome of strain SNU WT2 is 4,840,504 bp with a DNA G + C content of 51.94% and 106,068-bp plasmid. Genome analysis revealed that the strain carries virulence factors on its chromosome and antibiotic resistance genes on its plasmid. This strain represents a novel species in the genus Citrobacter for which the name C. tructae has been proposed, with SNU WT2 (=KCTC 72517 = JCM 33612) as the type strain.
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Affiliation(s)
- Won Joon Jung
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (W.J.J.); (H.J.K.); (S.S.G.); (S.G.K.); (S.W.K.); (J.W.K.); (J.K.); (S.B.L.); (W.T.O.)
| | - Hyoun Joong Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (W.J.J.); (H.J.K.); (S.S.G.); (S.G.K.); (S.W.K.); (J.W.K.); (J.K.); (S.B.L.); (W.T.O.)
| | - Sib Sankar Giri
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (W.J.J.); (H.J.K.); (S.S.G.); (S.G.K.); (S.W.K.); (J.W.K.); (J.K.); (S.B.L.); (W.T.O.)
| | - Sang Guen Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (W.J.J.); (H.J.K.); (S.S.G.); (S.G.K.); (S.W.K.); (J.W.K.); (J.K.); (S.B.L.); (W.T.O.)
| | - Sang Wha Kim
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (W.J.J.); (H.J.K.); (S.S.G.); (S.G.K.); (S.W.K.); (J.W.K.); (J.K.); (S.B.L.); (W.T.O.)
| | - Jeong Woo Kang
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (W.J.J.); (H.J.K.); (S.S.G.); (S.G.K.); (S.W.K.); (J.W.K.); (J.K.); (S.B.L.); (W.T.O.)
| | - Jun Kwon
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (W.J.J.); (H.J.K.); (S.S.G.); (S.G.K.); (S.W.K.); (J.W.K.); (J.K.); (S.B.L.); (W.T.O.)
| | - Sung Bin Lee
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (W.J.J.); (H.J.K.); (S.S.G.); (S.G.K.); (S.W.K.); (J.W.K.); (J.K.); (S.B.L.); (W.T.O.)
| | - Woo Taek Oh
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (W.J.J.); (H.J.K.); (S.S.G.); (S.G.K.); (S.W.K.); (J.W.K.); (J.K.); (S.B.L.); (W.T.O.)
| | - Jin Woo Jun
- Department of Aquaculture, Korea National College of Agriculture and Fisheries, Jeonju 54874, Korea
- Correspondence: (J.W.J.); (S.C.P.); Tel.: +82-63-238-9253 (J.W.J.); Tel.: +82-2-880-1282 (S.C.P.)
| | - Se Chang Park
- Laboratory of Aquatic Biomedicine, College of Veterinary Medicine and Research Institute for Veterinary Science, Seoul National University, Seoul 08826, Korea; (W.J.J.); (H.J.K.); (S.S.G.); (S.G.K.); (S.W.K.); (J.W.K.); (J.K.); (S.B.L.); (W.T.O.)
- Correspondence: (J.W.J.); (S.C.P.); Tel.: +82-63-238-9253 (J.W.J.); Tel.: +82-2-880-1282 (S.C.P.)
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Thomas SG, Abajorga M, Glover MA, Wengert PC, Parthasarathy A, Savka MA, Wadsworth CB, Shipman PA, Hudson AO. Aeromonas hydrophila RIT668 and Citrobacter portucalensis RIT669-Potential Zoonotic Pathogens Isolated from Spotted Turtles. Microorganisms 2020; 8:microorganisms8111805. [PMID: 33212916 PMCID: PMC7698337 DOI: 10.3390/microorganisms8111805] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2020] [Revised: 11/06/2020] [Accepted: 11/13/2020] [Indexed: 11/16/2022] Open
Abstract
Antimicrobial resistance (AMR) is one of the biggest challenges of the 21st century, and biofilm formation enables bacteria to resist antibiotic at much higher concentrations than planktonic cells. Earlier, we showed that the Gram-negative Aeromonas hydrophila RIT668 and Citrobacter portucalensis RIT669 (closely related to C. freundii NBRC 12681) from infected spotted turtles (Clemmys guttata), formed biofilms and upregulated toxin expression on plastic surfaces, and were predicted to possess multiple antibiotic resistance genes. Here, we show that they each resist several antibiotics in the planktonic phase, but were susceptible to neomycin, and high concentrations of tetracycline and cotrimoxazole. The susceptibility of their biofilms to neomycin and cotrimoxazole was tested using the Calgary device. For A. hydrophila, the minimum inhibitory concentration (MIC) = 500-1000, and the minimum biofilm eradication concentration (MBEC) > 1000 μg/mL, using cotrimoxazole, and MIC = 32.3-62.5, and MBEC > 1000 μg/mL, using neomycin. For C. freundii MIC = 7.8-15.6, and, MBEC > 1000 μg/mL, using cotrimoxazole, and MIC = 7.8, and MBEC > 1000 μg/mL, using neomycin. Both A. hydrophila and C. portucalensis activated an acyl homoserine lactone (AHL) dependent biosensor, suggesting that quorum sensing could mediate biofilm formation. Their multidrug resistance in the planktonic form, and weak biofilm eradication even with neomycin and cotrimoxazole, indicate that A. hydrophila and C. portucalensis are potential zoonotic pathogens, with risks for patients living with implants.
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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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Draft Genome Sequence of the Redox-Active Enteric Bacterium Citrobacter portucalensis Strain MBL. Microbiol Resour Announc 2020; 9:9/32/e00695-20. [PMID: 32763937 PMCID: PMC7409854 DOI: 10.1128/mra.00695-20] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
We grew a soil enrichment culture to identify organisms that anaerobically oxidize phenazine-1-carboxylic acid. A strain of Citrobacter portucalensis was isolated from this enrichment and sequenced by both Illumina and PacBio technologies. It has a genome with a length of 5.3 Mb, a G+C content of 51.8%, and at least one plasmid.
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Expression of a Shiga-Like Toxin during Plastic Colonization by Two Multidrug-Resistant Bacteria, Aeromonas hydrophila RIT668 and Citrobacter freundii RIT669, Isolated from Endangered Turtles ( Clemmys guttata). Microorganisms 2020; 8:microorganisms8081172. [PMID: 32752245 PMCID: PMC7465454 DOI: 10.3390/microorganisms8081172] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 07/23/2020] [Accepted: 07/30/2020] [Indexed: 12/12/2022] Open
Abstract
Aeromonas hydrophila RIT668 and Citrobacter freundii RIT669 were isolated from endangered spotted turtles (Clemmys guttata). Whole-genome sequencing, annotation and phylogenetic analyses of the genomes revealed that the closest relative of RIT668 is A. hydrophila ATCC 7966 and Citrobacter portucalensis A60 for RIT669. Resistome analysis showed that A. hydrophila and C. freundii harbor six and 19 different antibiotic resistance genes, respectively. Both bacteria colonize polyethylene and polypropylene, which are common plastics, found in the environment and are used to fabricate medical devices. The expression of six biofilm-related genes—biofilm peroxide resistance protein (bsmA), biofilm formation regulatory protein subunit R (bssR), biofilm formation regulatory protein subunit S (bssS), biofilm formation regulator (hmsP), toxin-antitoxin biofilm protein (tabA) and transcriptional activator of curli operon (csgD)—and two virulence factors—Vi antigen-related gene (viaB) and Shiga-like toxin (slt-II)—was investigated by RT-PCR. A. hydrophila displayed a > 2-fold increase in slt-II expression in cells adhering to both polymers, C. freundii adhering on polyethylene displayed a > 2-fold, and on polypropylene a > 6-fold upregulation of slt-II. Thus, the two new isolates are potential pathogens owing to their drug resistance, surface colonization and upregulation of a slt-II-type diarrheal toxin on polymer surfaces.
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Oberhettinger P, Schüle L, Marschal M, Bezdan D, Ossowski S, Dörfel D, Vogel W, Rossen JW, Willmann M, Peter S. Description of Citrobacter cronae sp. nov., isolated from human rectal swabs and stool samples. Int J Syst Evol Microbiol 2020; 70:2998-3003. [PMID: 32375941 PMCID: PMC7395625 DOI: 10.1099/ijsem.0.004100] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2020] [Accepted: 02/19/2020] [Indexed: 12/19/2022] Open
Abstract
Nine independent Gram-negative bacterial strains were isolated from rectal swabs or stool samples of immunocompromised patients from two different wards of a university hospital. All isolates were phylogenetically analysed based on their 16S rRNA gene sequence, housekeeping gene recN, multilocus sequence analysis of concatenated partial fusA, leuS, pyrG and rpoB sequences, and by whole genome sequencing data. The analysed strains of the new species cluster together and form a separate branch with Citrobacter werkmanii NBRC105721T as the most closely related species. An average nucleotide identity value of 95.9-96% and computation of digital DNA-DNA hybridization values separate the new species from all other type strains of the genus Citrobacter. Biochemical characteristics further delimit the isolates from closely related Citrobacter type strains. As a result of the described data, a new Citrobacter species is introduced, for which the name Citrobacter cronae sp. nov. is proposed. The type strain is Tue2-1T with a G+C DNA content of 52.2 mol%.
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Affiliation(s)
- Philipp Oberhettinger
- Institute of Medical Microbiology and Hygiene, University of Tuebingen, Tuebingen, Germany
- German Center for Infection Research (DZIF), Tuebingen, Germany
| | - Leonard Schüle
- Institute of Medical Microbiology and Hygiene, University of Tuebingen, Tuebingen, Germany
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
| | - Matthias Marschal
- Institute of Medical Microbiology and Hygiene, University of Tuebingen, Tuebingen, Germany
- German Center for Infection Research (DZIF), Tuebingen, Germany
| | - Daniela Bezdan
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, New York, USA
| | - Stephan Ossowski
- Institute of Medical Genetics and Applied Genomics, University of Tuebingen, Tuebingen, Germany
| | - Daniela Dörfel
- Medical Center, Department of Hematology, Oncology, Immunology and Rheumatology, University of Tuebingen, Tuebingen, Germany
- Clinical Collaboration Unit Translational Immunology, German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ), Tuebingen, Germany
| | - Wichard Vogel
- Medical Center, Department of Hematology, Oncology, Immunology and Rheumatology, University of Tuebingen, Tuebingen, Germany
| | - John W. Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
| | - Matthias Willmann
- Institute of Medical Microbiology and Hygiene, University of Tuebingen, Tuebingen, Germany
- German Center for Infection Research (DZIF), Tuebingen, Germany
| | - Silke Peter
- Institute of Medical Microbiology and Hygiene, University of Tuebingen, Tuebingen, Germany
- German Center for Infection Research (DZIF), Tuebingen, Germany
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In Vitro Susceptibility and Florfenicol Resistance in Citrobacter Isolates and Whole-Genome Analysis of Multidrug-Resistant Citrobacter freundii. Int J Genomics 2019; 2019:7191935. [PMID: 31828082 PMCID: PMC6885840 DOI: 10.1155/2019/7191935] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 09/17/2019] [Indexed: 01/06/2023] Open
Abstract
The genus Citrobacter is an opportunistic pathogen causing infections in animals, and the published data for its resistance to florfenicol are scarce. In this study, we investigated the antimicrobial susceptibility and molecular characteristics of florfenicol resistance genes among Citrobacter isolates from animal and relevant environmental samples and conducted a comparative analysis of a multidrug-resistant Citrobacter freundii strain isolated from a rabbit. Among 20 Citrobacter strains isolated from animal samples, resistance was most commonly observed to ampicillin (100%), tetracycline (75%), streptomycin (65%), florfenicol (60%), chloramphenicol (60%), and aztreonam (50%), while all the strains found in environmental samples were resistant to few antibiotics. The florfenicol resistance gene floR was detected in 12 isolates (48%, 12/25) from animal samples, and all of the floR-positive isolates were resistant to florfenicol with minimum inhibitory concentration (MIC) values ≥256 μg/mL. Sequencing and comparative analysis of the plasmids from a multidrug-resistant C. freundii isolate named R47 showed that the floR-containing region in the plasmid pR47-54 was a truncated transposon-like structure and could be found on both plasmids and chromosomes of bacteria of either animal or human origin. Furthermore, a range of antimicrobial and metal resistance genes associated with mobile genetic elements could be identified in pR47-54 and the other plasmid pR47-309 of C. freundii R47. These results provide in-depth views into the phenotypic and molecular characteristics of Citrobacter isolates recovered from animal and relevant environmental samples, as well as highlight the role horizontal gene transfer plays in the dissemination of plasmid-encoded resistance genes.
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Draft Genome Sequence of a Bioflocculant-Producing Bacterium, Citrobacter freundii IFO 13545. Microbiol Resour Announc 2019; 8:8/29/e00524-19. [PMID: 31320412 PMCID: PMC6639614 DOI: 10.1128/mra.00524-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Here, we report the 5.2-Mb genome sequence of a bioflocculant-producing bacterial strain, Citrobacter freundii IFO 13545, which consists of 5,209,670 bp with a G+C content of 51.5% and 4,853 predicted coding sequences (CDSs). The genes related to the biosynthetic pathway of the bioflocculant were localized on the genome map. Here, we report the 5.2-Mb genome sequence of a bioflocculant-producing bacterial strain, Citrobacter freundii IFO 13545, which consists of 5,209,670 bp with a G+C content of 51.5% and 4,853 predicted coding sequences (CDSs). The genes related to the biosynthetic pathway of the bioflocculant were localized on the genome map.
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Complete genome arrangement revealed the emergence of a poultry origin superbug Citrobacter portucalensis strain NR-12. J Glob Antimicrob Resist 2019; 18:126-129. [PMID: 31185330 DOI: 10.1016/j.jgar.2019.05.031] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 05/13/2019] [Accepted: 05/30/2019] [Indexed: 11/20/2022] Open
Abstract
OBJECTIVES Citrobacter spp. are part of normal human and animal intestinal flora. Citrobacter portucalensis (C. portucalensis) is closely related to Citrobacter freundii, which is an emerging opportunistic nosocomial pathogen. The aim of this study was to retrieve colistin-resistant Citrobacter spp. from poultry in Bangladesh. METHODS The C. portucalensis strain NR-12 was isolated from poultry droppings and subjected to antibiotic susceptibility testing. Complete genome analysis of NR-12 was performed followed by bioinformatics. It is believed that this is one of first reports of its kind of complete genome sequence of multidrug-resistant (MDR) C. portucalensis isolated from veterinary samples. RESULTS The C. portucalensis strain NR-12 showed resistance to polymyxin, sulfonamide, tetracycline, fluoroquinolone, and macrolide. Its complete genome revealed 13 acquired antimicrobial resistance gene markers (AMRs) conferring resistance to eight different antibiotic groups: dfrA12 (trimethoprim); sul1 and sul2 (sulfonamide); mph (A) (macrolide); tet (A) (tetracycline); qnrS1 and qnrB13 (fluoroquinolone); blaCMY-39 (extended-spectrum β-lactamase (ESBL)), blaTEM-176 (non-ESBL) and aadA2, aph (3')-Ia, aph (3″)-Ib, aph (3')-Ic, aph (3')-Id, strA, strB) (aminoglycoside). The genome possessed a class 1 integron (IntI1) gene cassette harbouring four different antibiotic resistance genes (dfrA12, aadA2, sul1, mph (A)). The organisation of class 1 integron (IntI1) carrying MDR determinants in C. portucalensis strain NR-12 was also first reported here. Colistin-resistant genes such as mgrB, phoP, phoQ, pmrA, pmrB, eptB and arnB were also present within NR-12. CONCLUSION C. portucalensis NR-12 was resistant to eight different antibiotics from six antimicrobial groups. To formulate a control strategy, it is important to understand this resistant mechanism.
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Characterization of Antimicrobial Resistance in Serratia spp. and Citrobacter spp. Isolates from Companion Animals in Japan: Nosocomial Dissemination of Extended-Spectrum Cephalosporin-Resistant Citrobacter freundii. Microorganisms 2019; 7:microorganisms7030064. [PMID: 30823419 PMCID: PMC6462910 DOI: 10.3390/microorganisms7030064] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2019] [Revised: 02/27/2019] [Accepted: 02/27/2019] [Indexed: 01/28/2023] Open
Abstract
In many countries including Japan, the status of emerging antimicrobial resistance among Serratia spp. and Citrobacter spp. in companion animals remains unknown because these genera are rarely isolated from animals. In this study, 30 Serratia spp. and 23 Citrobacter spp. isolates from companion animals underwent susceptibility testing for 10 antimicrobials. Phenotypic and genetic approaches were used to identify the mechanisms of extended-spectrum cephalosporins (ESC). Subsequently, ESC-resistant Citrobacter spp. strains underwent multilocus sequence typing and pulsed-field gel electrophoresis (PFGE). A significantly higher rate (34.8%) of ESC resistance was observed in Citrobacter spp. isolates than in Serratia spp. isolates (0%). ESC resistance was detected in five C. freundii strains, two C. portucalensis strains, and one C. koseri strain. All of the ESC-resistant Citrobacter spp. strains harbored CMY-type and/or DHA-type AmpC β-lactamases. Three C. freundii strains harbored the CTX-M-3-type extended-spectrum β-lactamases. Notably, the three blaCTX-3-producing and two blaCMY-117-bearing C. freundii strains (obtained from different patients in one hospital) had the same sequence type (ST156 and ST18, respectively) and similar PFGE profiles. We believe that ESC-resistant Citrobacter spp. are important nosocomial pathogens in veterinary medicine. Therefore, infection control in animal hospitals is essential to prevent dissemination of these resistant pathogens.
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Draft Genome Sequence of Citrobacter gillenii MBT-C3, Isolated from Lamb's Lettuce. Microbiol Resour Announc 2018; 7:MRA01177-18. [PMID: 30533725 PMCID: PMC6256432 DOI: 10.1128/mra.01177-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 09/23/2018] [Indexed: 11/20/2022] Open
Abstract
The genome of the streptomycin-resistant Citrobacter gillenii strain MBT-C3, isolated from lamb's lettuce in Germany, was sequenced. Sequence analysis showed the assembled draft genome size to be 5,167,205 bp, containing a predicted total of 5,011 protein-encoding genes, 8 rRNAs, and 71 tRNAs.
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Huang CH, Li SW, Huang L, Watanabe K. Identification and Classification for the Lactobacillus casei Group. Front Microbiol 2018; 9:1974. [PMID: 30186277 PMCID: PMC6113361 DOI: 10.3389/fmicb.2018.01974] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 08/06/2018] [Indexed: 12/14/2022] Open
Abstract
Lactobacillus casei, Lactobacillus paracasei, and Lactobacillus rhamnosus are phenotypically and genotypically closely related, and together comprise the L. casei group. Although the strains of this group are commercially valuable as probiotics, the taxonomic status and nomenclature of the L. casei group have long been contentious because of the difficulties in identifying these three species by using the most frequently used genotypic methodology of 16S rRNA gene sequencing. Long used as the gold standard for species classification, DNA–DNA hybridization is laborious, requires expert skills, and is difficult to use routinely in laboratories. Currently, genome-based comparisons, including average nucleotide identity (ANI) and digital DNA–DNA hybridization (dDDH), are commonly applied to bacterial taxonomy as alternatives to the gold standard method for the demarcating phylogenetic relationships. To establish quick and accurate methods for identifying strains in the L. casei group at the species and subspecies levels, we developed species- and subspecies-specific identification methods based on housekeeping gene sequences and whole-cell matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) spectral pattern analysis. By phylogenetic analysis based on concatenated housekeeping gene sequences (dnaJ, dnaK, mutL, pheS, and yycH), 53 strains were separated into four clusters corresponding to the four species: L. casei, L. paracasei and L. rhamnosus, and Lactobacillus chiayiensis sp. nov. A multiplex minisequencing assay using single nucleotide polymorphism (SNP)-specific primers based on the dnaK gene sequences and species-specific primers based on the mutL gene sequences provided high resolution that enabled the strains at the species level to be identified as L. casei, L. paracasei, and L. rhamnosus. By MALDI-TOF MS analysis coupled with an internal database and ClinProTools software, species- and subspecies-level L. casei group strains were identified based on reliable scores and species- and subspecies-specific MS peaks. The L. paracasei strains were distinguished clearly at the subspecies level based on subspecies-specific MS peaks. This article describes the rapid and accurate methods used for identification and classification of strains in the L. casei group based on housekeeping gene sequences and MALDI-TOF MS analysis as well as the novel speciation of this group including L. chiayiensis sp. nov. and ‘Lactobacillus zeae’ by genome-based methods.
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Affiliation(s)
- Chien-Hsun Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Shiao-Wen Li
- Molecular Medicine Research Center, Chang Gung University, Taoyuan, Taiwan
| | - Lina Huang
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan
| | - Koichi Watanabe
- Bioresource Collection and Research Center, Food Industry Research and Development Institute, Hsinchu, Taiwan.,Department of Animal Science and Technology, College of Bioresources and Agriculture, National Taiwan University, Taipei, Taiwan
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Draft Genome Sequence of Multidrug-Resistant Strain Citrobacter portucalensis MBTC-1222, Isolated from Uziza (Piper guineense) Leaves in Nigeria. GENOME ANNOUNCEMENTS 2018; 6:6/9/e00123-18. [PMID: 29496838 PMCID: PMC5834338 DOI: 10.1128/genomea.00123-18] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In this work, we report the draft whole-genome sequence of the multiply antibiotic-resistant Citrobacter portucalensis strain MBTC-1222 isolated from the uziza leafy vegetable in Nigeria. Sequence analysis showed the assembled genome size to be 4,881,935 bp, containing 4,603 protein-coding genes, 131 pseudogenes, 7 rRNAs, 74 tRNAs, and 9 noncoding RNAs (ncRNAs).
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