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Giliazeva A, Akosah Y, Noack J, Mardanova A. Adhesion of Klebsiella oxytoca to bladder or lung epithelial cells is promoted by the presence of other opportunistic pathogens. Microb Pathog 2024; 190:106642. [PMID: 38599551 DOI: 10.1016/j.micpath.2024.106642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2023] [Revised: 04/02/2024] [Accepted: 04/07/2024] [Indexed: 04/12/2024]
Abstract
The intestinal and respiratory tracts of healthy individuals serve as habitats for a diverse array of microorganisms, among which Klebsiella oxytoca holds significance as a causative agent in numerous community- and hospital-acquired infections, often manifesting in polymicrobial contexts. In specific circumstances, K. oxytoca, alongside other constituents of the gut microbiota, undergoes translocation to distinct physiological niches. In these new environments, it engages in close interactions with other microbial community members. As this interaction may progress to co-infection where the virulence of involved pathogens may be promoted and enhance disease severity, we investigated how K. oxytoca affects the adhesion of commonly co-isolated bacteria and vice versa during co-incubation of different biotic and abiotic surfaces. Co-incubation was beneficial for the adhesion of at least one of the two co-cultured strains. K. oxytoca enhanced the adhesion of other enterobacteria strains to polystyrene and adhered more efficiently to bladder or lung epithelial cell lines in the presence of most enterobacteria strains and S. aureus. This effect was accompanied by bacterial coaggregation mediated by carbohydrate-protein interactions occurring between bacteria. These interactions occur only in sessile, but not planktonic populations, and depend on the features of the surface. The data are of particular importance for the risk assessment of the urinary and respiratory tract infections caused by K. oxytoca, including those device-associated. In this paper, we present the first report on K. oxytoca ability to acquire increased adhesive capacities on epithelial cells through interactions with common causal agents of urinary and respiratory tract infections.
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Affiliation(s)
- Adeliia Giliazeva
- Institute of Biotechnology, Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, Universitätsplatz 1, Building 15, 01968, Senftenberg, Germany.
| | - Yaw Akosah
- Department of Molecular Pathobiology, College of Dentistry, New York University, 345 E. 24th St., 10010, New York, USA
| | - Jonas Noack
- Medipan GmbH, Computer Science, Ludwig-Erhard-Ring 3, 15827, Dahlewitz, Germany
| | - Ayslu Mardanova
- Department of Microbiology, Institute of Fundamental Medicine and Biology, Kazan (Volga region) Federal University, Kremlyovskaya 18, 420008, Kazan, Russia
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2
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Schotte U, Ehlers J, Nieter J, Rakotozandrindrainy R, Wolf SA, Semmler T, Frickmann H, Poppert S, Ewers C. ESBL-Type and AmpC-Type Beta-Lactamases in Third Generation Cephalosporin-Resistant Enterobacterales Isolated from Animal Feces in Madagascar. Animals (Basel) 2024; 14:741. [PMID: 38473126 DOI: 10.3390/ani14050741] [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: 01/17/2024] [Revised: 02/23/2024] [Accepted: 02/24/2024] [Indexed: 03/14/2024] Open
Abstract
Third generation cephalosporin-resistant (3GCR) Enterobacterales are known to be prevalent in Madagascar, with high colonization or infection rates in particular in Madagascan patients. Extended spectrum beta-lactamases (ESBLs) have been reported to be the predominant underlying resistance mechanism in human isolates. So far, little is known on antimicrobial resistance and its molecular determinants in Enterobacterales and other bacteria causing enteric colonization of Madagascan wild animals. To address this topic, swabs from 49 animal stool droppings were collected in the Madagascan Tsimanapesotsa National Park and assessed by cultural growth of bacterial microorganisms on elective media. In addition to 7 Acinetobacter spp., a total of 31 Enterobacterales growing on elective agar for Enterobacterales could be isolated and subjected to whole genome sequencing. Enterobacter spp. was the most frequently isolated genus, and AmpC-type beta-lactamases were the quantitatively dominating molecular resistance mechanism. In contrast, the blaCTX-M-15 gene, which has repeatedly been associated with 3GC-resistance in Madagascan Enterobacterales from humans, was detected in a single Escherichia coli isolate only. The identification of the fosfomycin-resistance gene fosA in a high proportion of isolates is concerning, as fosfomycin is increasingly used to treat infections caused by multidrug-resistant bacteria. In conclusion, the proof-of-principle assessment indicated a high colonization rate of resistant bacteria in stool droppings of Madagascan wild animals with a particular focus on 3GCR Enterobacterales. Future studies should confirm these preliminary results in a more systematic way and assess the molecular relationship of animal and human isolates to identify potential routes of transmission.
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Affiliation(s)
- Ulrich Schotte
- Department A-Veterinary Medicine, Central Institute of the Bundeswehr Medical Service Kiel, 24119 Kronshagen, Germany
| | - Julian Ehlers
- Bernhard Nocht Institute for Tropical Medicine Hamburg, 20359 Hamburg, Germany
| | - Johanna Nieter
- Department A-Veterinary Medicine, Central Institute of the Bundeswehr Medical Service Kiel, 24119 Kronshagen, Germany
| | | | - Silver A Wolf
- Genome Competence Centre, Robert Koch Institute, 13353 Berlin, Germany
| | - Torsten Semmler
- Genome Competence Centre, Robert Koch Institute, 13353 Berlin, Germany
| | - Hagen Frickmann
- Department of Microbiology and Hospital Hygiene, Bundeswehr Hospital Hamburg, 20359 Hamburg, Germany
- Institute for Medical Microbiology, Virology and Hygiene, University Medicine Rostock, 18057 Rostock, Germany
| | - Sven Poppert
- Bernhard Nocht Institute for Tropical Medicine Hamburg, 20359 Hamburg, Germany
| | - Christa Ewers
- Institute for Hygiene and Infectious Diseases of Animals, University of Giessen, 35392 Giessen, Germany
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3
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Ikhimiukor OO, Souza SSR, Akintayo IJ, Marcovici MM, Workman A, Martin IW, Andam CP. Phylogenetic lineages and antimicrobial resistance determinants of clinical Klebsiella oxytoca spanning local to global scales. Microbiol Spectr 2023; 11:e0054923. [PMID: 37676032 PMCID: PMC10581156 DOI: 10.1128/spectrum.00549-23] [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: 02/04/2023] [Accepted: 07/19/2023] [Indexed: 09/08/2023] Open
Abstract
Klebsiella oxytoca is an opportunistic pathogen causing serious nosocomial infections. Knowledge about the population structure and diversity of healthcare-associated K. oxytoca from a genomic standpoint remains limited. Here, we characterized the phylogenetic relationships and genomic characteristics of 20 K. oxytoca sensu stricto isolates recovered from bloodstream infections at the Dartmouth-Hitchcock Medical Center, New Hampshire, USA from 2017 to 2021. Results revealed a diverse population consisting of 15 sequence types (STs) that together harbored 10 variants of the intrinsic beta-lactamase gene bla OXY-2, conferring resistance to penicillins. Similar sets of antimicrobial resistance (AMR) determinants reside in multiple distinct lineages, with no one lineage dominating the local population. To place the New Hampshire K. oxytoca in a broader context, we compared them to 304 publicly available genomes of clinical isolates from 18 countries. This global clinical K. oxytoca sensu stricto population is represented by over 65 STs that together harbored resistance genes against 14 antimicrobial classes, including eight bla OXY-2 variants. Three dominant STs in the global population (ST2, ST176, ST199) circulate across multiple countries and were also present in the New Hampshire population. The global K. oxytoca population is genetically diverse, but there is evidence for broad dissemination of a few lineages carrying distinct set of AMR determinants. Our findings reveal the clinical diversity of K. oxytoca sensu stricto and its importance in surveillance efforts aimed at monitoring the evolution of this drug-resistant nosocomial pathogen. IMPORTANCE The opportunistic pathogen Klebsiella oxytoca has been increasingly implicated in patient morbidity and mortality worldwide, including several outbreaks in healthcare settings. The emergence and spread of antimicrobial resistant strains exacerbate the disease burden caused by this species. Our study showed that clinical K. oxytoca sensu stricto is phylogenetically diverse, harboring various antimicrobial resistance determinants and bla OXY-2 variants. Understanding the genomic and population structure of K. oxytoca is important for international initiatives and local epidemiological efforts for surveillance and control of drug-resistant K. oxytoca.
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Affiliation(s)
- Odion O. Ikhimiukor
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Stephanie S. R. Souza
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Ifeoluwa J. Akintayo
- Institute for Infection Prevention and Hospital Epidemiology, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Michael M. Marcovici
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Adrienne Workman
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Isabella W. Martin
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Cheryl P. Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
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Pöltl L, Kitsera M, Raffl S, Schild S, Cosic A, Kienesberger S, Unterhauser K, Raber G, Lembacher-Fadum C, Breinbauer R, Gorkiewicz G, Sebastian C, Hoefler G, Zechner EL. Microbiota-derived genotoxin tilimycin generates colonic stem cell mutations. Cell Rep 2023; 42:112199. [PMID: 36870054 DOI: 10.1016/j.celrep.2023.112199] [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: 04/28/2022] [Revised: 12/19/2022] [Accepted: 02/14/2023] [Indexed: 03/05/2023] Open
Abstract
The DNA-alkylating metabolite tilimycin is a microbial genotoxin. Intestinal accumulation of tilimycin in individuals carrying til+ Klebsiella spp. causes apoptotic erosion of the epithelium and colitis. Renewal of the intestinal lining and response to injury requires the activities of stem cells located at the base of intestinal crypts. This study interrogates the consequences of tilimycin-induced DNA damage to cycling stem cells. We charted the spatial distribution and luminal quantities of til metabolites in Klebsiella-colonized mice in the context of a complex microbial community. Loss of marker gene G6pd function indicates genetic aberrations in colorectal stem cells that became stabilized in monoclonal mutant crypts. Mice colonized with tilimycin-producing Klebsiella displayed both higher frequencies of somatic mutation and more mutations per affected individual than animals carrying a non-producing mutant. Our findings imply that genotoxic til+ Klebsiella may drive somatic genetic change in the colon and increase disease susceptibility in human hosts.
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Affiliation(s)
- Lisa Pöltl
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
| | - Maksym Kitsera
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
| | - Sandra Raffl
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
| | - Stefan Schild
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria; Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria
| | - Amar Cosic
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
| | - Sabine Kienesberger
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria; Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria
| | - Katrin Unterhauser
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria
| | - Georg Raber
- Institute of Chemistry, University of Graz, 8010 Graz, Austria
| | | | - Rolf Breinbauer
- BioTechMed-Graz, 8010 Graz, Austria; Institute of Organic Chemistry, Graz University of Technology, 8010 Graz, Austria
| | - Gregor Gorkiewicz
- BioTechMed-Graz, 8010 Graz, Austria; Diagnostic and Research Institute of Pathology, Medical University of Graz, 8036 Graz, Austria
| | - Carlos Sebastian
- Candiolo Cancer Institute-FPO, IRCCS, 10060 Candiolo, Italy; Departament de Biologia Cellular, Fisiologia i Immunologia, Facultad de Biologia, Universitat de Barcelona (UB), 08028 Barcelona, Spain; Institut de Biomedicina de la Universitat de Barcelona (IBUB), 08028 Barcelona, Spain
| | - Gerald Hoefler
- Diagnostic and Research Institute of Pathology, Medical University of Graz, 8036 Graz, Austria
| | - Ellen L Zechner
- Institute of Molecular Biosciences, University of Graz, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria; Field of Excellence BioHealth, University of Graz, 8010 Graz, Austria.
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Complete Genome Sequence of Klebsiella oxytoca Strain AHC-6, Isolated from a Patient during Acute Antibiotic-Associated Hemorrhagic Colitis. Microbiol Resour Announc 2023; 12:e0135022. [PMID: 36926996 PMCID: PMC10112055 DOI: 10.1128/mra.01350-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023] Open
Abstract
Klebsiella oxytoca is a ubiquitous bacterium that is increasingly associated with inflammatory diseases. Here, we report the hybrid assembled genome for cytotoxic K. oxytoca strain AHC-6. The genome comprises a total of 5.7 Mbp, with a GC content of 55.2% and 5,258 coding sequences after assembly and annotation.
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6
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Cosic A, Leitner E, Petternel C, Galler H, Reinthaler FF, Herzog-Obereder KA, Tatscher E, Raffl S, Feierl G, Högenauer C, Zechner EL, Kienesberger S. Corrigendum: Variation in accessory genes within the Klebsiella oxytoca species complex delineates monophyletic members and simplifies coherent genotyping. Front Microbiol 2023; 14:1155851. [PMID: 36960282 PMCID: PMC10028735 DOI: 10.3389/fmicb.2023.1155851] [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: 01/31/2023] [Accepted: 02/22/2023] [Indexed: 03/09/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fmicb.2021.692453.].
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Affiliation(s)
- Amar Cosic
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Eva Leitner
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Christian Petternel
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Herbert Galler
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Franz F. Reinthaler
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Kathrin A. Herzog-Obereder
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Elisabeth Tatscher
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Sandra Raffl
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Gebhard Feierl
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Christoph Högenauer
- BioTechMed-Graz, Graz, Austria
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Ellen L. Zechner
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
| | - Sabine Kienesberger
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
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Cuetero-Martínez Y, Flores-Ramírez A, De Los Cobos-Vasconcelos D, Aguirre-Garrido JF, López-Vidal Y, Noyola A. Removal of bacterial pathogens and antibiotic resistance bacteria by anaerobic sludge digestion with thermal hydrolysis pre-treatment and alkaline stabilization post-treatment. CHEMOSPHERE 2023; 313:137383. [PMID: 36436581 DOI: 10.1016/j.chemosphere.2022.137383] [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: 11/22/2022] [Accepted: 11/23/2022] [Indexed: 06/16/2023]
Abstract
Primary sludge (PS) is associated with public health and environmental risks, so regulations focus on reducing the pathogenic and heavy metal contents of the treated material (biosolids), intended for soil amendments and land reclamation. The regulations set limits for Escherichia coli (or fecal coliforms), Salmonella spp., helminth eggs and enterovirus. However, the potential risk due to antibiotic resistant bacteria (ARB) and other human potential pathogenic bacteria (HPB) are not considered. In this work, three sludge treatment processes, having in common an anaerobic digestion step, were applied to assess the removal of regulated bacteria (fecal coliforms, Salmonella spp), ARB and HPB. The treatment arrangements, fed with PS from a full-scale wastewater treatment plant were: 1) Mesophilic anaerobic digestion followed by alkaline stabilization post-treatment (MAD-CaO); 2) Thermophilic anaerobic digestion (TAD) and, 3) Pre-treatment (mild thermo-hydrolysis) followed by TAD (PT-TAD). The results address the identification, quantification (colony forming units) and taxonomic characterization of ARB resistant to β-lactams and vancomycin, as well as the taxonomic characterization of HPB by sequencing with PacBio. In addition, quantification based on culture media of fecal coliforms and Salmonella spp. is presented. The capabilities and limitations of microbiological and metataxonomomic analyses based on PacBio sequencing are discussed, emphasizing that they complement each other. Genus Aeromonas, Acinetobacter, Citrobacter, Enterobacter, Escherichia, Klebsiella, Ochrobactrum, Pseudomonas and Raoultella, among others, were found in the PS, which are of clinical or environmental importance, being either HPB, HPB-ARB, or non-pathogenic ARB with the potentiality of horizontal gene transfer. Based on the analysis of fecal coliforms and Salmonella spp., the three processes produced class A (highest) biosolids, suitable for unrestricted agriculture applications. Mild thermo-hydrolisis was effective in decreasing ARB cultivability, but it reappeared after the following TAD. O. intermedium (HPB-ARB) was enriched in MAD and TAD while Laribacter hongkongensis (HPB) did persist after the applied treatments.
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Affiliation(s)
- Yovany Cuetero-Martínez
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, 04510 CDMX, Mexico; Doctorado en Ciencias Bioquímicas, Universidad Nacional Autónoma de México, 04510 CDMX, Mexico
| | - Aarón Flores-Ramírez
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, 04510 CDMX, Mexico
| | - Daniel De Los Cobos-Vasconcelos
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, 04510 CDMX, Mexico
| | - José Félix Aguirre-Garrido
- Departamento de Ciencias Ambientales, Universidad Autónoma Metropolitana - Unidad Lerma, 52005 Lerma de Villada, Edo. Mex, Mexico
| | - Yolanda López-Vidal
- Departamento de Microbiología y Parasitología, Facultad de Medicina, Universidad Nacional Autónoma de México, 04510 CDMX, Mexico
| | - Adalberto Noyola
- Subdirección de Hidráulica y Ambiental, Instituto de Ingeniería, Universidad Nacional Autónoma de México, 04510 CDMX, Mexico.
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Smith-Zaitlik T, Shibu P, McCartney AL, Foster G, Hoyles L, Negus D. Extended genomic analyses of the broad-host-range phages vB_KmiM-2Di and vB_KmiM-4Dii reveal slopekviruses have highly conserved genomes. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36156193 DOI: 10.1099/mic.0.001247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
High levels of antimicrobial resistance among members of the Klebsiella oxytoca complex (KoC) have led to renewed interest in the use of bacteriophage (phage) therapy to tackle infections caused by these bacteria. In this study we characterized two lytic phages, vB_KmiM-2Di and vB_KmiM-4Dii, that were isolated from sewage water against two GES-5-positive Klebsiella michiganensis strains (PS_Koxy2 and PS_Koxy4, respectively). ViPTree analysis showed both phages belonged to the genus Slopekvirus. rpoB gene-based sequence analysis of 108 presumptive K. oxytoca isolates (n=59 clinical, n=49 veterinary) found K. michiganensis to be more prevalent (46 % clinical and 43 % veterinary, respectively) than K. oxytoca (40 % clinical and 6 % veterinary, respectively). Host range analysis against these 108 isolates found both vB_KmiM-2Di and vB_KmiM-4Dii showed broad lytic activity against KoC species. Several hypothetical homing endonuclease genes were encoded within the genomes of both phages, which may contribute to their broad host range. Differences in the tail fibre protein may explain the non-identical host range of the two phages. Pangenome analysis of 24 slopekviruses found that genomes within this genus are highly conserved, with more than 50 % of all predicted coding sequences representing core genes at ≥95 % identity and ≥70 % coverage. Given their broad host ranges, our results suggest vB_KmiM-2Di and vB_KmiM-4Dii represent attractive potential therapeutics. In addition, current recommendations for phage-based pangenome analyses may require revision.
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Affiliation(s)
| | - Preetha Shibu
- Life Sciences, University of Westminster, London, UK.,Present address: Berkshire and Surrey Pathology Services, Frimley Health NHS Trust, Wexham Park Hospital, Slough, UK
| | - Anne L McCartney
- Department of Food and Nutritional Sciences, University of Reading, Reading, UK
| | | | - Lesley Hoyles
- Department of Biosciences, Nottingham Trent University, Nottingham NG1 4FQ, UK
| | - David Negus
- Department of Biosciences, Nottingham Trent University, Nottingham NG1 4FQ, UK
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Stewart J, Judd LM, Jenney A, Holt KE, Wyres KL, Hawkey J. Epidemiology and genomic analysis of Klebsiella oxytoca from a single hospital network in Australia. BMC Infect Dis 2022; 22:704. [PMID: 36002802 PMCID: PMC9400251 DOI: 10.1186/s12879-022-07687-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2022] [Accepted: 08/17/2022] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Infections caused by Klebsiella oxytoca are the second most common cause of Klebsiella infections in humans. Most studies have focused on K. oxytoca outbreaks and few have examined the broader clinical context of K. oxytoca. METHODS Here, we collected all clinical isolates identified as K. oxytoca in a hospital microbiological diagnostic lab across a 15-month period (n = 239). Whole genome sequencing was performed on a subset of 92 isolates (all invasive, third-generation cephalosporin resistant (3GCR) and non-urinary isolates collected > 48 h after admission), including long-read sequencing on a further six isolates with extended-spectrum beta-lactamase or carbapenemase genes. RESULTS The majority of isolates were sensitive to antimicrobials, however 22 isolates were 3GCR, of which five were also carbapenem resistant. Genomic analyses showed those identified as K. oxytoca by the clinical laboratory actually encompassed four distinct species (K. oxytoca, Klebsiella michiganensis, Klebsiella grimontii and Klebsiella pasteurii), referred to as the K. oxytoca species complex (KoSC). There was significant diversity within the population, with only 10/67 multi-locus sequence types (STs) represented by more than one isolate. Strain transmission was rare, with only one likely event identified. Six isolates had extended spectrum beta-lactamase (blaSHV-12 and/or blaCTX-M-9) or carbapenemase (blaIMP-4) genes. One pair of K. michiganensis and K. pasteurii genomes carried identical blaIMP-4 IncL/M plasmids, indicative of plasmid transmission. CONCLUSION Whilst antimicrobial resistance was rare, the resistance plasmids were similar to those found in other Enterobacterales, demonstrating that KoSC has access to the same plasmid reservoir and thus there is potential for multi-drug resistance. Further genomic studies are required to improve our understanding of the KoSC population and facilitate investigation into the attributes of successful nosocomial isolates.
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Affiliation(s)
- James Stewart
- grid.413210.50000 0004 4669 2727Department of Infectious Diseases, Cairns Hospital, Cairns, QLD 4870 Australia
| | - Louise M. Judd
- grid.1002.30000 0004 1936 7857Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC 3004 Australia
| | - Adam Jenney
- grid.1002.30000 0004 1936 7857Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC 3004 Australia ,grid.1623.60000 0004 0432 511XMicrobiology Unit, Alfred Pathology Service, The Alfred Hospital Melbourne, Melbourne, VIC 3004 Australia
| | - Kathryn E. Holt
- grid.1002.30000 0004 1936 7857Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC 3004 Australia ,grid.8991.90000 0004 0425 469XDepartment of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT UK
| | - Kelly L. Wyres
- grid.1002.30000 0004 1936 7857Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC 3004 Australia
| | - Jane Hawkey
- grid.1002.30000 0004 1936 7857Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC 3004 Australia
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10
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Leitner E, Bozic M, Kienesberger S, Cosic A, Landt O, Högenauer C, Kessler HH. Improved diagnosis of antibiotic-associated haemorrhagic colitis (AAHC) in faecal specimens by a new qualitative real-time PCR assay detecting relevant toxin genes of Klebsiella oxytoca sensu lato. Clin Microbiol Infect 2022; 28:690-694. [PMID: 34582979 DOI: 10.1016/j.cmi.2021.09.017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 08/27/2021] [Accepted: 09/15/2021] [Indexed: 02/04/2023]
Abstract
OBJECTIVE Toxin-producing Klebsiella oxytoca causes antibiotic-associated haemorrhagic colitis (AAHC). The disease-relevant cytotoxins tilivalline and tilimycine produced by certain K. oxytoca isolates are encoded by the non-ribosomal peptide synthetase genes A (npsA) and B (npsB). In this study, the new LightMix® Modular kit for the detection of relevant K. oxytoca sensu lato (s.l.) toxin genes was evaluated. METHODS DNA was extracted on the automated EMAG® platform. Amplification was done on the Light Cycler® 480 II instrument. In total, 130 residual faecal specimens collected from patients with antibiotic-associated diarrhoea were studied to determine the clinical sensitivity and specificity. Toxigenic culture served as reference method. RESULTS With the new kit, the limit of detection was 15 CFU/mL for all targets. For the pehX target specific to K. oxytoca s.l., 65 of 130 clinical specimens were positive, while toxin-specific targets (npsA/npsB) were positive in 47 of 130. The npsA/npsB PCR targets showed a clinical sensitivity of 100% (95%CI 80.5-100%) and a specificity of 73.5% (95%CI 64.3-81.3%) with a positive predictive value of 16.5% (95%CI 12.7-21.2%) and a negative predictive value of 100%. CONCLUSION Compared with culture, additional clinical specimens positive for K. oxytoca s.l. were detected with real-time PCR. The specificity of the toxin targets appears moderate due to the inferior sensitivity of the culture-based reference method. Since the developed assay is highly sensitive, it may be used as first-line method to improve the diagnosis of AAHC.
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Affiliation(s)
- Eva Leitner
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Austria.
| | - Michael Bozic
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Austria
| | - Sabine Kienesberger
- Institute of Molecular Biosciences, University of Graz, Austria; BioTechMed-Graz, Austria; Field of Excellence BioHealth, University of Graz, Austria
| | - Amar Cosic
- Institute of Molecular Biosciences, University of Graz, Austria
| | | | - Christoph Högenauer
- BioTechMed-Graz, Austria; Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Austria
| | - Harald H Kessler
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Austria
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11
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Hua M, Duan A, Li Q, Yue J, Liu X, Yuan L, Liu J, Chen C. Alteration of microbiota and immune response of mice gavaged with Klebsiella oxytoca. Microbes Infect 2022; 24:104977. [DOI: 10.1016/j.micinf.2022.104977] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 03/30/2022] [Accepted: 03/30/2022] [Indexed: 12/01/2022]
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12
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Shrief R, Hassan RH, Zaki MES, Rizk MA. Molecular Study of Klebsiella Oxytoca Associated with Urinary Tract Infection in Children. Open Microbiol J 2022. [DOI: 10.2174/18742858-v16-e2201070] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Background:
There are scarce reports about the association of Klebsiella oxytoca (K. oxytoca) with urinary tract infection (UTI) in children. We aimed to evaluate the prevalence of fimA, mrkA, matB and pilQ adhesins genes and extended-spectrum beta-lactamase (ESBL) genes blaCTX-M, blaTEM and blaSHV by polymerase chain reaction (PCR) and to study biofilm formation and antibiotics resistance in K. oxytoca from children with UTI.
Methods:
This study was a retrospective cross-sectional study that included 120 children with UTI due to K. oxytoca. The bacteria were subjected to molecular detection of fimA, mrkA, matB and pilQ adhesins genes and ESBL genes blaCTX-M, blaTEM and blaSHV by PCR. Biofilm capacity was determined by the microtiter plate method.
Results:
The isolated K. oxytoca had positive ESBL activity in 45.8% of isolates. About 40% of isolates were biofilm producers. The frequency of adhesion genes among K. oxytoca was 91.7%, 83.3%, 48.3% and 37.5% for matB, pilQ, fimA and mrkA genes, respectively. For ESBL genes, the frequency was 38.3%, 36.7% and 33.3% for blaCTX-M, blaSHV and blaTEM genes, respectively. The commonest genes among ESBL isolates were blaCTX-M (83.6%), blaSHV (80%) then blaTEM gene (72.7%). A significant association (p=0.048) was detected between ESBL activity and biofilm formation by K. oxytoca.
Conclusion:
Present study highlights the emergence of K. oxytoca as a pathogen associated with UTI in children. There was a high prevalence of adhesin genes and ESBL genes among these isolates. The capacity of K. oxytoca to form biofilm was associated with ESBL production.
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13
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Genome analysis of
Klebsiella oxytoca
complex for antimicrobial resistance and virulence genes. Antimicrob Agents Chemother 2022; 66:e0218321. [PMID: 35007133 DOI: 10.1128/aac.02183-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Klebsiella oxytoca
complex comprises nine closely-related species causing human infections. We curated genomes labeled
Klebsiella
(n=14,256) in GenBank and identified 588 belonging to the complex, which were examined for precise species, sequence types, K- and O-antigen types, virulence and antimicrobial resistance genes. The complex and
Klebsiella pneumoniae
share many K- and O-antigen types. Of the complex,
K. oxytoca
and
Klebsiella michiganensis
appear to carry more virulence genes and be more commonly associated with human infections.
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14
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Greimel TM, Stampfer L, Leitner E, Kienesberger S, Zechner EL, Bozic M, Wagner GE, Unterhauser K, Kitsera M, Hauer AC, Gorkiewicz G, Wurm P, Valitutti F, Högenauer C, Hoffmann KM. Toxin-Producing Klebsiella oxytoca in Healthy Infants: Commensal or Pathobiont? J Pediatr Gastroenterol Nutr 2022; 74:e1-e7. [PMID: 34520403 DOI: 10.1097/mpg.0000000000003299] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
OBJECTIVES Klebsiella oxytoca is a gastrointestinal pathobiont with the potential to produce the toxins tilivalline and tilimycin, which cause antibiotic-associated hemorrhagic colitis. Overgrowth of toxigenic K oxytoca has recently been implicated in necrotizing enterocolitis. K oxytoca colonizes 2-9% of healthy adults, however, there is no systematic data on colonization in healthy children. We investigated K oxytoca colonization and its toxigenic properties in healthy infants. METHODS We sampled stool of healthy infants and determined K oxytoca colonization using stool culture and PCR (pehX). Toxin in stool was measured with HPLC/high-resolution mass spectrometry. K oxytoca isolates were typed using multi-locus sequence typing (MLST) and K oxytoca toxin PCR (npsA/B). Cytotoxin production of isolates was analyzed by MTT assay. RESULTS K oxytoca was detected in 30 of 61 infants (49%) using stool culture and in 45 of 61 (73%) using PCR (pehX). Toxin marker PCR (npsA/B) was positive in 66% of stool samples positive for K oxytoca PCR. Stool toxin levels were too low for quantitation but traces of tilivalline were detected. Contrarily, 49% of K oxytoca isolates demonstrated toxicity in the MTT assay. MLST revealed 36 distinct sequence types affiliated with all known K oxytoca sequence type clusters (A, B1 and B2). CONCLUSIONS More than 70% of healthy infants were colonized with K oxytoca. Toxin quantities in stool of colonized healthy infants were below detection level, yet half of the isolates produced toxin in vitro demonstrating their pathobiont potential. The high occurrence of toxigenic K oxytoca in healthy infants has to be considered for future disease association studies.
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Affiliation(s)
- Theresa M Greimel
- Division of General Pediatrics, Department of Pediatrics and Adolescent Medicine
| | - Laura Stampfer
- Division of General Pediatrics, Department of Pediatrics and Adolescent Medicine
| | - Eva Leitner
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz
| | - Sabine Kienesberger
- Institute of Molecular Biosciences, University of Graz
- BioTechMed-Graz
- Field of Excellence BioHealth - University of Graz, Graz
| | - Ellen L Zechner
- Institute of Molecular Biosciences, University of Graz
- BioTechMed-Graz
- Field of Excellence BioHealth - University of Graz, Graz
| | - Michael Bozic
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz
| | - Gabriel E Wagner
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz
| | | | | | - Almuthe C Hauer
- Division of General Pediatrics, Department of Pediatrics and Adolescent Medicine
| | - Gregor Gorkiewicz
- Institute of Pathology, Medical University of Graz, Austria
- BioTechMed-Graz
| | - Philipp Wurm
- Institute of Pathology, Medical University of Graz, Austria
| | | | - Christoph Högenauer
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz
- BioTechMed-Graz
| | - Karl Martin Hoffmann
- Division of General Pediatrics, Department of Pediatrics and Adolescent Medicine
- Kinderärzte Zentrum Graz-Raaba, Raaba-Grambach, Austria
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15
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Motamedi H, Fathollahi M, Abiri R, Kadivarian S, Rostamian M, Alvandi A. A worldwide systematic review and meta-analysis of bacteria related to antibiotic-associated diarrhea in hospitalized patients. PLoS One 2021; 16:e0260667. [PMID: 34879104 PMCID: PMC8654158 DOI: 10.1371/journal.pone.0260667] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Accepted: 11/12/2021] [Indexed: 01/05/2023] Open
Abstract
INTRODUCTION Antibiotic-associated diarrhea (AAD) is a major hospital problem and a common adverse effect of antibiotic treatment. The aim of this study was to investigate the prevalence of the most important bacteria that cause AAD in hospitalized patients. MATERIALS AND METHODS PubMed, Web of Science and Scopus databases were searched using multiple relevant keywords and screening carried out based on inclusion/exclusion criteria from March 2001 to October 2021. The random-effects model was used to conduct the meta-analysis. RESULTS Of the 7,377 identified articles, 56 met the inclusion criteria. Pooling all studies, the prevalence of Clostridioides (Clostridium) difficile, Clostridium perfringens, Klebsiella oxytoca, and Staphylococcus aureus as AAD-related bacteria among hospitalized patients were 19.6%, 14.9%, 27%, and 5.2%, respectively. The prevalence of all four bacteria was higher in Europe compared to other continents. The highest resistance of C. difficile was estimated to ciprofloxacin and the lowest resistances were reported to chloramphenicol, vancomycin, and metronidazole. There was no or little data on antibiotic resistance of other bacteria. CONCLUSIONS The results of this study emphasize the need for a surveillance program, as well as timely public and hospital health measures in order to control and treat AAD infections.
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Affiliation(s)
- Hamid Motamedi
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Matin Fathollahi
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Ramin Abiri
- Fertility and Infertility Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Sepide Kadivarian
- Department of Microbiology, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Student Research Committee, School of Medicine, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mosayeb Rostamian
- Infectious Diseases Research Center, Health Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Amirhooshang Alvandi
- Medical Technology Research Center, Health Technology Institute, Kermanshah University of Medical Sciences, Kermanshah, Iran
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16
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Klebsiella oxytoca Complex: Update on Taxonomy, Antimicrobial Resistance, and Virulence. Clin Microbiol Rev 2021; 35:e0000621. [PMID: 34851134 DOI: 10.1128/cmr.00006-21] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Klebsiella oxytoca is actually a complex of nine species-Klebsiella grimontii, Klebsiella huaxiensis, Klebsiella michiganensis, K. oxytoca, Klebsiella pasteurii, Klebsiella spallanzanii, and three unnamed novel species. Phenotypic tests can assign isolates to the complex, but precise species identification requires genome-based analysis. The K. oxytoca complex is a human commensal but also an opportunistic pathogen causing various infections, such as antibiotic-associated hemorrhagic colitis (AAHC), urinary tract infection, and bacteremia, and has caused outbreaks. Production of the cytotoxins tilivalline and tilimycin lead to AAHC, while many virulence factors seen in Klebsiella pneumoniae, such as capsular polysaccharides and fimbriae, have been found in the complex; however, their association with pathogenicity remains unclear. Among the 5,724 K. oxytoca clinical isolates in the SENTRY surveillance system, the rates of nonsusceptibility to carbapenems, ceftriaxone, ciprofloxacin, colistin, and tigecycline were 1.8%, 12.5%, 7.1%, 0.8%, and 0.1%, respectively. Resistance to carbapenems is increasing alarmingly. In addition to the intrinsic blaOXY, many genes encoding β-lactamases with varying spectra of hydrolysis, including extended-spectrum β-lactamases, such as a few CTX-M variants and several TEM and SHV variants, have been found. blaKPC-2 is the most common carbapenemase gene found in the complex and is mainly seen on IncN or IncF plasmids. Due to the ability to acquire antimicrobial resistance and the carriage of multiple virulence genes, the K. oxytoca complex has the potential to become a major threat to human health.
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17
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Osbelt L, Wende M, Almási É, Derksen E, Muthukumarasamy U, Lesker TR, Galvez EJC, Pils MC, Schalk E, Chhatwal P, Färber J, Neumann-Schaal M, Fischer T, Schlüter D, Strowig T. Klebsiella oxytoca causes colonization resistance against multidrug-resistant K. pneumoniae in the gut via cooperative carbohydrate competition. Cell Host Microbe 2021; 29:1663-1679.e7. [PMID: 34610293 DOI: 10.1016/j.chom.2021.09.003] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Revised: 07/27/2021] [Accepted: 09/09/2021] [Indexed: 01/08/2023]
Abstract
Gut colonization with multidrug-resistant (MDR) bacteria enhances the risk of bloodstream infections in susceptible individuals. We demonstrate highly variable degrees of ex vivo colonization resistance against a carbapenem-resistant Klebsiella pneumoniae strain in human feces samples and subsequently isolate diverse K. oxytoca strains from protected donors. Several of these K. oxytoca strains reduce gut colonization of MDR K. pneumoniae strains in antibiotic-treated and gnotobiotic mouse models. Comparative analysis of K. oxytoca strains coupled with CRISPR-Cas9-mediated deletion of casA, a protein essential for utilization of selected beta-glucosides, identified competition for specific carbohydrates as key in promoting colonization resistance. In addition to direct competition between K. oxytoca and K. pneumoniae, cooperation with additional commensals is required to reestablish full colonization resistance and gut decolonization. Finally, humanized microbiota mice generated from K. pneumoniae-susceptible donors are protected by K. oxytoca administration, demonstrating the potential of commensal K. oxytoca strains as next-generation probiotics.
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Affiliation(s)
- Lisa Osbelt
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany; ESF International Graduate School on Analysis, Imaging and Modelling of Neuronal and Inflammatory Processes, Otto-Von-Guericke University, Magdeburg, Germany
| | - Marie Wende
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany; ESF International Graduate School on Analysis, Imaging and Modelling of Neuronal and Inflammatory Processes, Otto-Von-Guericke University, Magdeburg, Germany
| | - Éva Almási
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Elisabeth Derksen
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | | | - Till R Lesker
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Eric J C Galvez
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
| | - Marina C Pils
- Mouse-Pathology Platform, Helmholtz Centre for Infection Research, Braunschweig, Germany
| | - Enrico Schalk
- Department of Hematology and Oncology, University Hospital Magdeburg, Magdeburg, Germany
| | - Patrick Chhatwal
- Department of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Jacqueline Färber
- Department of Medical Microbiology and Hospital Hygiene, University Hospital Magdeburg, Magdeburg, Germany
| | - Meina Neumann-Schaal
- Bacterial Metabolomics, Leibniz Institute DSMZ - German Collection of Microorganisms and Cell Cultures, Braunschweig, Germany
| | - Thomas Fischer
- ESF International Graduate School on Analysis, Imaging and Modelling of Neuronal and Inflammatory Processes, Otto-Von-Guericke University, Magdeburg, Germany; Department of Hematology and Oncology, University Hospital Magdeburg, Magdeburg, Germany
| | - Dirk Schlüter
- ESF International Graduate School on Analysis, Imaging and Modelling of Neuronal and Inflammatory Processes, Otto-Von-Guericke University, Magdeburg, Germany; Department of Medical Microbiology and Hospital Epidemiology, Hannover Medical School, Hannover, Germany
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany; Cluster of Excellence RESIST (EXC 2155), Hannover Medical School, Hannover, Germany; Center for Individualized Infection Medicine, Hannover, Germany; German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany.
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18
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Sun M, Xiao W, Xu Q. IncN1 ST7 Epidemic Plasmid Carrying blaIMP-4 in One ST85-Type Klebsiella oxytoca Clinical Isolate with Porin Deficiency. Infect Drug Resist 2021; 14:3827-3835. [PMID: 34566416 PMCID: PMC8458025 DOI: 10.2147/idr.s330362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Accepted: 09/07/2021] [Indexed: 01/07/2023] Open
Abstract
Purpose Klebsiella oxytoca is an opportunistic pathogen causing nosocomial infections. This study was designed to characterize the genomic features of a carbapenem-resistant K. oxytoca strain and analyze its molecular characteristics. Materials and Methods The strain wzx-IMP was isolated from the blood of a 2-year-old girl diagnosed with acute myeloid leukemia-M7. Species identification was performed, and the minimal inhibitory concentration of the strain was measured. Multilocus sequence typing was performed to identify the subtypes of K. oxytoca. The transfer capacity of the blaIMP-4-harboring plasmid was investigated by conjugation experiments, and the genome characteristics of the strain were examined using whole-genome sequencing. Results wzx-IMP belongs to the ST85 type and is resistant to imipenem and meropenem, which harbored the blaIMP-4 gene. The blaIMP-4 gene was located in an IS26-associated class 1 integron of pwzx_IMP, which contains conserved IncN1-type backbone regions with a replication gene and its accessory structure for plasmid replication. The blaIMP-4-carrying plasmid in wzx-IMP was successfully transferred to Escherichia coli EC600 by conjugation. Whole-genome sequencing showed that the wzx-IMP isolate included the blaOXY-1-1 gene, accompanied by OmpK36 absence. Conclusion We report an ST85-type carbapenem-resistant K. oxytoca strain, which produces blaIMP-4 located in an IncN1-type plasmid and accompanied by OmpK36 porin deficiency.
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Affiliation(s)
- Mingyue Sun
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, People's Republic of China
| | - Weiqiang Xiao
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, People's Republic of China
| | - Qingxia Xu
- Department of Clinical Laboratory, Affiliated Cancer Hospital of Zhengzhou University & Henan Cancer Hospital, Zhengzhou, Henan, People's Republic of China
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19
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Cuénod A, Wüthrich D, Seth-Smith HMB, Ott C, Gehringer C, Foucault F, Mouchet R, Kassim A, Revathi G, Vogt DR, von Felten S, Bassetti S, Tschudin-Sutter S, Hettich T, Schlotterbeck G, Homberger C, Casanova C, Moran-Gilad J, Sagi O, Rodríguez-Sánchez B, Müller F, Aerni M, Gaia V, van Dessel H, Kampinga GA, Müller C, Daubenberger C, Pflüger V, Egli A. Whole-genome sequence-informed MALDI-TOF MS diagnostics reveal importance of Klebsiella oxytoca group in invasive infections: a retrospective clinical study. Genome Med 2021; 13:150. [PMID: 34517886 PMCID: PMC8438989 DOI: 10.1186/s13073-021-00960-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 08/27/2021] [Indexed: 11/13/2022] Open
Abstract
BACKGROUND Klebsiella spp. are opportunistic pathogens which can cause severe infections, are often multi-drug resistant and are a common cause of hospital-acquired infections. Multiple new Klebsiella species have recently been described, yet their clinical impact and antibiotic resistance profiles are largely unknown. We aimed to explore Klebsiella group- and species-specific clinical impact, antimicrobial resistance (AMR) and virulence. METHODS We analysed whole-genome sequence data of a diverse selection of Klebsiella spp. isolates and identified resistance and virulence factors. Using the genomes of 3594 Klebsiella isolates, we predicted the masses of 56 ribosomal subunit proteins and identified species-specific marker masses. We then re-analysed over 22,000 Matrix-Assisted Laser Desorption Ionization - Time Of Flight (MALDI-TOF) mass spectra routinely acquired at eight healthcare institutions in four countries looking for these species-specific markers. Analyses of clinical and microbiological endpoints from a subset of 957 patients with infections from Klebsiella species were performed using generalized linear mixed-effects models. RESULTS Our comparative genomic analysis shows group- and species-specific trends in accessory genome composition. With the identified species-specific marker masses, eight Klebsiella species can be distinguished using MALDI-TOF MS. We identified K. pneumoniae (71.2%; n = 12,523), K. quasipneumoniae (3.3%; n = 575), K. variicola (9.8%; n = 1717), "K. quasivariicola" (0.3%; n = 52), K. oxytoca (8.2%; n = 1445), K. michiganensis (4.8%; n = 836), K. grimontii (2.4%; n = 425) and K. huaxensis (0.1%; n = 12). Isolates belonging to the K. oxytoca group, which includes the species K. oxytoca, K. michiganensis and K. grimontii, were less often resistant to 4th-generation cephalosporins than isolates of the K. pneumoniae group, which includes the species K. pneumoniae, K. quasipneumoniae, K. variicola and "K. quasivariicola" (odds ratio = 0.17, p < 0.001, 95% confidence interval [0.09,0.28]). Within the K. pneumoniae group, isolates identified as K. pneumoniae were more often resistant to 4th-generation cephalosporins than K. variicola isolates (odds ratio = 2.61, p = 0.003, 95% confidence interval [1.38,5.06]). K. oxytoca group isolates were found to be more likely associated with invasive infection to primary sterile sites than K. pneumoniae group isolates (odds ratio = 2.39, p = 0.0044, 95% confidence interval [1.05,5.53]). CONCLUSIONS Currently misdiagnosed Klebsiella spp. can be distinguished using a ribosomal marker-based approach for MALDI-TOF MS. Klebsiella groups and species differed in AMR profiles, and in their association with invasive infection, highlighting the importance for species identification to enable effective treatment options.
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Affiliation(s)
- Aline Cuénod
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Hebelstrasse 20, 4031, Basel, Switzerland.
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland.
| | - Daniel Wüthrich
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Hebelstrasse 20, 4031, Basel, Switzerland
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland
- Swiss Institute for Bioinformatics, Basel, Switzerland
| | - Helena M B Seth-Smith
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Hebelstrasse 20, 4031, Basel, Switzerland
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland
- Swiss Institute for Bioinformatics, Basel, Switzerland
| | - Chantal Ott
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Hebelstrasse 20, 4031, Basel, Switzerland
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland
| | - Christian Gehringer
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Hebelstrasse 20, 4031, Basel, Switzerland
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland
- Division of Internal Medicine, University Hospital Basel, Basel, Switzerland
| | | | | | - Ali Kassim
- Aga Khan University Hospital, Nairobi, Kenya
| | | | - Deborah R Vogt
- Department of Clinical Research, University of Basel and University Hospital Basel, Basel, Switzerland
| | - Stefanie von Felten
- Department of Clinical Research, University of Basel and University Hospital Basel, Basel, Switzerland
- Department of Biostatistics, Epidemiology, Biostatistics and Prevention Institute (EBPI), University of Zurich, Zurich, Switzerland
| | - Stefano Bassetti
- Division of Internal Medicine, University Hospital Basel, Basel, Switzerland
| | - Sarah Tschudin-Sutter
- Division of Infectious Diseases and Hospital Epidemiology, University Hospital Basel, Basel, Switzerland
- Department of Clinical Research, University of Basel, Basel, Switzerland
| | - Timm Hettich
- Division of Instrumental Analytics, School of Applied Sciences (FHNW), Muttenz, Switzerland
| | - Götz Schlotterbeck
- Division of Instrumental Analytics, School of Applied Sciences (FHNW), Muttenz, Switzerland
| | - Christina Homberger
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Hebelstrasse 20, 4031, Basel, Switzerland
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland
| | - Carlo Casanova
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Jacob Moran-Gilad
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- Soroka University Medical Center, Beer Sheva, Israel
| | - Orli Sagi
- Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer Sheva, Israel
- Soroka University Medical Center, Beer Sheva, Israel
| | - Belén Rodríguez-Sánchez
- Hospital General Universitario Gregorio Marañón, Madrid, Spain
- Servicio de Microbiología Clínica y Enfermedades Infecciosas, Hospital General Universitario Gregorio Marañón, Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain. Instituto de Investigación Sanitaria Gregorio Marañón, Madrid, Spain
| | | | | | - Valeria Gaia
- Servizio di microbiologia EOLAB, Ente Ospedaliero Cantonale, Bellinzona, Switzerland
| | - Helke van Dessel
- Department of Medical Microbiology, Maastricht University Medical Center, Maastricht, the Netherlands
| | - Greetje A Kampinga
- Department of Medical Microbiology & Infection prevention, University of Groningen, Groningen, the Netherlands
- University Medical Center Groningen (UMCG), Groningen, the Netherlands
| | | | - Claudia Daubenberger
- Swiss Tropical and Public Health Institute, Basel, Switzerland
- Department of Sciences, University of Basel, Basel, Switzerland
| | | | - Adrian Egli
- Applied Microbiology Research, Department of Biomedicine, University of Basel, Hebelstrasse 20, 4031, Basel, Switzerland.
- Division of Clinical Bacteriology and Mycology, University Hospital Basel, Petersgraben 4, 4031, Basel, Switzerland.
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20
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Liu F, Tang C, Wang D, Sun Z, Du L, Wang D. The synergistic effects of phenyllactic acid and slightly acid electrolyzed water to effectively inactivate Klebsiella oxytoca planktonic and biofilm cells. Food Control 2021. [DOI: 10.1016/j.foodcont.2020.107804] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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21
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Shibu P, McCuaig F, McCartney AL, Kujawska M, Hall LJ, Hoyles L. Improved molecular characterization of the Klebsiella oxytoca complex reveals the prevalence of the kleboxymycin biosynthetic gene cluster. Microb Genom 2021; 7. [PMID: 34142942 PMCID: PMC8461473 DOI: 10.1099/mgen.0.000592] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
As part of the ongoing studies with clinically relevant Klebsiella spp., we characterized the genomes of three clinical GES-5-positive ST138 strains originally identified as Klebsiella oxytoca. blaOXY gene, average nucleotide identity and phylogenetic analyses showed the strains to be Klebsiella michiganensis. Affiliation of the strains to ST138 led us to demonstrate that the current multi-locus sequence typing scheme for K. oxytoca can be used to distinguish members of this genetically diverse complex of bacteria. The strains encoded the kleboxymycin biosynthetic gene cluster (BGC), previously only found in K. oxytoca strains and one strain of Klebsiella grimontii. The finding of this BGC, associated with antibiotic-associated haemorrhagic colitis, in K. michiganensis led us to carry out a wide-ranging study to determine the prevalence of this BGC in Klebsiella spp. Of 7170 publicly available Klebsiella genome sequences screened, 88 encoded the kleboxymycin BGC. All BGC-positive strains belonged to the K. oxytoca complex, with strains of four (K. oxytoca, K. pasteurii, K. grimontii, K. michiganensis) of the six species of complex found to encode the complete BGC. In addition to being found in K. grimontii strains isolated from preterm infants, the BGC was found in K. oxytoca and K. michiganensis metagenome-assembled genomes recovered from neonates. Detection of the kleboxymycin BGC across the K. oxytoca complex may be of clinical relevance and this cluster should be included in databases characterizing virulence factors, in addition to those characterizing BGCs.
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Affiliation(s)
- Preetha Shibu
- Life Sciences, University of Westminster, UK.,Present address: Berkshire and Surrey Pathology Services, Frimley Health NHS Trust, Wexham Park Hospital, Slough, UK
| | - Frazer McCuaig
- Department of Biosciences, Nottingham Trent University, UK
| | - Anne L McCartney
- Department of Food and Nutritional Sciences, University of Reading, UK
| | - Magdalena Kujawska
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Lindsay J Hall
- Gut Microbes & Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.,Chair of Intestinal Microbiome, ZIEL - Institute for Food & Health, Technical University of Munich, Freising, Germany
| | - Lesley Hoyles
- Department of Biosciences, Nottingham Trent University, UK.,Department of Surgery and Cancer, Imperial College London, UK
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22
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Paveglio S, Ledala N, Rezaul K, Lin Q, Zhou Y, Provatas AA, Bennett E, Lindberg T, Caimano M, Matson AP. Cytotoxin-producing Klebsiella oxytoca in the preterm gut and its association with necrotizing enterocolitis. Emerg Microbes Infect 2021; 9:1321-1329. [PMID: 32525754 PMCID: PMC7473113 DOI: 10.1080/22221751.2020.1773743] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Necrotizing enterocolitis (NEC) is a devastating intestinal inflammatory disease of premature infants associated with gut bacterial dysbiosis. Using 16S rRNA-based methods, our laboratory identified an unclassified Enterobacteriaceae sequence (NEC_unk_OTU) with high abundance in NEC fecal samples. We aimed to identify this bacterium and determine its potential role in the disease. NCBI database searches for the 16S sequence, selective culture systems, biotyping and polymerase chain reaction were employed to refine classification of NEC_unk_OTU and identify toxin-encoding genes from the index NEC case. Bacterial cytotoxin production was confirmed by mass spectrometry and apoptosis assays. Additional fecal samples from 9 NEC and 5 non-NEC controls were analyzed using similar methods and multi-locus sequence typing (MLST) was performed to investigate clonal relationships and define sequence types of the isolates. NEC_unk_OTU was identified as Klebsiella oxytoca, a pathobiont known to cause antibiotic-associated hemorrhagic colitis, but not previously linked to NEC. Including the index case, cytotoxin-producing strains of K. oxytoca were isolated from 6 of 10 subjects with NEC; in these, the K. oxytoca 16S sequence predominated the fecal microbiota. Cytotoxin-producing strains of K. oxytoca also were isolated from 4 of 5 controls; in these, however, the abundance of the corresponding 16S sequence was very low. MLST analysis of the toxin-positive isolates demonstrated no clonal relationships and similar genetic clustering between cases and controls. These results suggest cytotoxin-producing strains of K. oxytoca colonize a substantial proportion of premature infants. Some, perhaps many, cases of NEC may be precipitated by outgrowth of this opportunistic pathogen.
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Affiliation(s)
- Sara Paveglio
- Division of Neonatology, Connecticut Children's Medical Center, Hartford, CT, USA.,Department of Pediatrics, UConn Health, Farmington, CT, USA
| | | | - Karim Rezaul
- Department of Pediatrics, UConn Health, Farmington, CT, USA
| | - Qingqi Lin
- Department of Computer Science and Engineering, University of Connecticut, Storrs, CT, USA
| | - Yanjiao Zhou
- Department of Medicine, UConn Health, Farmington, CT, USA.,The Jackson Laboratory for Genomic Medicine, Farmington, CT, USA
| | - Anthony A Provatas
- Center for Environmental Sciences and Engineering, University of Connecticut, Storrs, CT, USA
| | - Erin Bennett
- Department of Research, Connecticut Children's Medical Center, Hartford, CT, USA
| | - Tristan Lindberg
- Division of Neonatology, Connecticut Children's Medical Center, Hartford, CT, USA
| | - Melissa Caimano
- Department of Pediatrics, UConn Health, Farmington, CT, USA.,Department of Medicine, UConn Health, Farmington, CT, USA.,Department of Molecular Biology and Biophysics, UConn Health, Farmington, CT, USA
| | - Adam P Matson
- Division of Neonatology, Connecticut Children's Medical Center, Hartford, CT, USA.,Department of Pediatrics, UConn Health, Farmington, CT, USA.,Department of Immunology, UConn Health, Farmington, CT, USA
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23
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Munson E, Carroll KC. Summary of Novel Bacterial Isolates Derived from Human Clinical Specimens and Nomenclature Revisions Published in 2018 and 2019. J Clin Microbiol 2021; 59:e01309-20. [PMID: 32967902 PMCID: PMC8111135 DOI: 10.1128/jcm.01309-20] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Knowledge of novel prokaryotic taxon discovery and nomenclature revisions is of importance to clinical microbiology laboratory practice, infectious disease epidemiology, and studies of microbial pathogenesis. Relative to bacterial isolates derived from human clinical specimens, we present an in-depth summary of novel taxonomic designations and revisions to prokaryotic taxonomy that were published in 2018 and 2019. Included are several changes pertinent to former designations of or within Propionibacterium spp., Corynebacterium spp., Clostridium spp., Mycoplasma spp., Methylobacterium spp., and Enterobacteriaceae Future efforts to ascertain clinical relevance for many of these changes may be augmented by a document development committee that has been appointed by the Clinical and Laboratory Standards Institute.
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Affiliation(s)
- Erik Munson
- College of Health Sciences, Marquette University, Milwaukee, Wisconsin, USA
| | - Karen C Carroll
- Division of Medical Microbiology, Department of Pathology, the Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
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24
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Simultaneous quantification of enterotoxins tilimycin and tilivalline in biological matrices using HPLC high resolution ESMS 2 based on isotopically 15N-labeled internal standards. Talanta 2021; 222:121677. [PMID: 33167283 DOI: 10.1016/j.talanta.2020.121677] [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: 06/26/2020] [Revised: 09/11/2020] [Accepted: 09/15/2020] [Indexed: 12/20/2022]
Abstract
Non-ribosomal peptides are one class of bacterial metabolites formed by gut microbiota. Intestinal resident Klebsiella oxytoca produces two pyrrolobenzodiazepines, tilivalline and tilimycin, via the same nonribosomal biosynthesis platform. These molecules cause human disease by genotoxic and tubulin inhibitory activities resulting in apoptosis of the intestinal epithelium, loss of barrier integrity and ultimately colitis. Here we report a fast, reliable, HPLC-HR-ESMS2 method for quantifying simultaneously the bacterial enterotoxins tilimycin and tilivalline in complex biological matrices. We synthesized and applied stable isotopically labeled internal standards for precise quantification of the metabolites. Sample preparation was optimized using clinical and laboratory specimens including serum, colonic fluid and stool. The developed method overcame the disadvantage of low selectivity by applying high resolution mass spectrometry in MS2 mode. High sensitivity and low interference from matrices were achieved and validated. We show that the approach is suitable for detection and quantification of the enterotoxic metabolites produced in vivo, in infected human or animal hosts, and in bacterial culture in vitro.
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25
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Cosic A, Leitner E, Petternel C, Galler H, Reinthaler FF, Herzog-Obereder KA, Tatscher E, Raffl S, Feierl G, Högenauer C, Zechner EL, Kienesberger S. Variation in Accessory Genes Within the Klebsiella oxytoca Species Complex Delineates Monophyletic Members and Simplifies Coherent Genotyping. Front Microbiol 2021; 12:692453. [PMID: 34276625 PMCID: PMC8283571 DOI: 10.3389/fmicb.2021.692453] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2021] [Accepted: 05/28/2021] [Indexed: 02/03/2023] Open
Abstract
Members of the Klebsiella oxytoca species complex (KoSC) are emerging human pathogens causing infections of increasing significance especially in healthcare settings. KoSC strains are affiliated with distinct phylogroups based on genetic variation at the beta-lactamase gene (bla OXY) and it has been proposed that each major phylogroup represents a unique species. However, since the typing methods applied in clinical settings cannot differentiate every species within the complex, existing clinical, epidemiological and DNA sequence data is frequently misclassified. Here we systematically examined the phylogenetic relationship of KoSC strains to evaluate robustness of existing typing methods and to provide a simple typing strategy for KoSC members that cannot be differentiated biochemically. Initial analysis of a collection of K. oxytoca, K. michiganensis, K. pasteurii, and K. grimontii strains of environmental origin showed robust correlation of core phylogeny and blaOXY grouping. Moreover, we identified species-specific accessory gene loci for these strains. Extension of species correlation using database entries initially failed. However, assessment of average nucleotide identities (ANI) and phylogenetic validations showed that nearly one third of isolates in public databases have been misidentified. Reclassification resulted in a robust reference strain set for reliable species identification of new isolates or for retyping of strains previously analyzed by multi-locus sequence typing (MLST). Finally, we show convergence of ANI, core gene phylogeny, and accessory gene content for available KoSC genomes. We conclude that also the monophyletic members K. oxytoca, K. michiganensis, K. pasteurii and K. grimontii can be simply differentiated by a PCR strategy targeting bla OXY and accessory genes defined here.
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Affiliation(s)
- Amar Cosic
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
| | - Eva Leitner
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Christian Petternel
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Herbert Galler
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Franz F. Reinthaler
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Kathrin A. Herzog-Obereder
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Elisabeth Tatscher
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Sandra Raffl
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Gebhard Feierl
- Diagnostic and Research Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Christoph Högenauer
- BioTechMed-Graz, Graz, Austria
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Ellen L. Zechner
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
| | - Sabine Kienesberger
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
- BioTechMed-Graz, Graz, Austria
- Field of Excellence BioHealth, University of Graz, Graz, Austria
- *Correspondence: Sabine Kienesberger,
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26
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Li J, Oh J, Kienesberger S, Kim NY, Clarke DJ, Zechner EL, Crawford JM. Making and Breaking Leupeptin Protease Inhibitors in Pathogenic Gammaproteobacteria. Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202005506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Jhe‐Hao Li
- Department of Chemistry Yale University New Haven CT 06520 USA
- Chemical Biology Institute Yale University West Haven CT 06516 USA
| | - Joonseok Oh
- Department of Chemistry Yale University New Haven CT 06520 USA
- Chemical Biology Institute Yale University West Haven CT 06516 USA
| | | | - Nam Yoon Kim
- Department of Chemistry Yale University New Haven CT 06520 USA
- Chemical Biology Institute Yale University West Haven CT 06516 USA
| | - David J. Clarke
- School of Microbiology and APC Microbiome Ireland University College Cork Cork Ireland
| | - Ellen L. Zechner
- Institute of Molecular Biosciences University of Graz 8010 Graz Austria
- BioTechMed-Graz 8010 Graz Austria
| | - Jason M. Crawford
- Department of Chemistry Yale University New Haven CT 06520 USA
- Chemical Biology Institute Yale University West Haven CT 06516 USA
- Department of Microbial Pathogenesis Yale University School of Medicine New Haven CT 06536 USA
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27
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Li JH, Oh J, Kienesberger S, Kim NY, Clarke DJ, Zechner EL, Crawford JM. Making and Breaking Leupeptin Protease Inhibitors in Pathogenic Gammaproteobacteria. Angew Chem Int Ed Engl 2020; 59:17872-17880. [PMID: 32609431 DOI: 10.1002/anie.202005506] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 06/29/2020] [Indexed: 12/12/2022]
Abstract
Leupeptin is a bacterial small molecule that is used worldwide as a protease inhibitor. However, its biosynthesis and genetic distribution remain unknown. We identified a family of leupeptins in gammaproteobacterial pathogens, including Photorhabdus, Xenorhabdus, and Klebsiella species, amongst others. Through genetic, metabolomic, and heterologous expression analyses, we established their construction by discretely expressed ligases and accessory enzymes. In Photorhabdus species, a hypothetical protein required for colonizing nematode hosts was established as a new class of proteases. This enzyme cleaved the tripeptide aldehyde protease inhibitors, leading to the formation of "pro-pyrazinones" featuring a hetero-tricyclic architecture. In Klebsiella oxytoca, the pathway was enriched in clinical isolates associated with respiratory tract infections. Thus, the bacterial production and proteolytic degradation of leupeptins can be associated with animal colonization phenotypes.
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Affiliation(s)
- Jhe-Hao Li
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA.,Chemical Biology Institute, Yale University, West Haven, CT, 06516, USA
| | - Joonseok Oh
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA.,Chemical Biology Institute, Yale University, West Haven, CT, 06516, USA
| | | | - Nam Yoon Kim
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA.,Chemical Biology Institute, Yale University, West Haven, CT, 06516, USA
| | - David J Clarke
- School of Microbiology and APC Microbiome Ireland, University College Cork, Cork, Ireland
| | - Ellen L Zechner
- Institute of Molecular Biosciences, University of Graz, 8010, Graz, Austria.,BioTechMed-Graz, 8010, Graz, Austria
| | - Jason M Crawford
- Department of Chemistry, Yale University, New Haven, CT, 06520, USA.,Chemical Biology Institute, Yale University, West Haven, CT, 06516, USA.,Department of Microbial Pathogenesis, Yale University School of Medicine, New Haven, CT, 06536, USA
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28
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Tominaga T. Rapid quantification of coliforms in ready‐to‐eat foods using lateral‐flow immunochromatographic assay. J Food Saf 2020. [DOI: 10.1111/jfs.12835] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Tatsuya Tominaga
- Division of Food Science and Biotechnology Saitama Industrial Technology Center North Institute Saitama Japan
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29
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Chen Y, Brook TC, Soe CZ, O'Neill I, Alcon-Giner C, Leelastwattanagul O, Phillips S, Caim S, Clarke P, Hall LJ, Hoyles L. Preterm infants harbour diverse Klebsiella populations, including atypical species that encode and produce an array of antimicrobial resistance- and virulence-associated factors. Microb Genom 2020; 6:e000377. [PMID: 32436839 PMCID: PMC7371107 DOI: 10.1099/mgen.0.000377] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2019] [Accepted: 04/26/2020] [Indexed: 01/08/2023] Open
Abstract
Klebsiella spp. are frequently enriched in the gut microbiota of preterm neonates, and overgrowth is associated with necrotizing enterocolitis (NEC), nosocomial infections and late-onset sepsis. Little is known about the genomic and phenotypic characteristics of preterm-associated Klebsiella, as previous studies have focused on the recovery of antimicrobial-resistant isolates or culture-independent molecular analyses. The aim of this study was to better characterize preterm-associated Klebsiella populations using phenotypic and genotypic approaches. Faecal samples from a UK cohort of healthy and sick preterm neonates (n=109) were screened on MacConkey agar to isolate lactose-positive Enterobacteriaceae. Whole-genome sequences were generated for Klebsiella spp., and virulence and antimicrobial resistance genes identified. Antibiotic susceptibility profiling and in vitro macrophage and iron assays were undertaken for the Klebsiella strains. Metapangenome analyses with a manually curated genome dataset were undertaken to examine the diversity of Klebsiella oxytoca and related bacteria in a publicly available shotgun metagenome dataset. Approximately one-tenth of faecal samples harboured Klebsiella spp. (Klebsiella pneumoniae, 7.3 %; Klebsiella quasipneumoniae, 0.9 %; Klebsiella grimontii, 2.8 %; Klebsiella michiganensis, 1.8 %). Isolates recovered from NEC- and sepsis-affected infants and those showing no signs of clinical infection (i.e. 'healthy') encoded multiple β-lactamases. No difference was observed between isolates recovered from healthy and sick infants with respect to in vitro siderophore production (all encoded enterobactin in their genomes). All K. pneumoniae, K. quasipneumoniae, K. grimontii and K. michiganensis faecal isolates tested were able to reside and persist in macrophages, indicating their immune evasion abilities. Metapangenome analyses of published metagenomic data confirmed our findings regarding the presence of K. michiganensis in the preterm gut. There is little difference in the phenotypic and genomic characteristics of Klebsiella isolates recovered from healthy and sick infants. Identification of β-lactamases in all isolates may prove problematic when defining treatment regimens for NEC or sepsis, and suggests that healthy preterm infants contribute to the resistome. Refined analyses with curated sequence databases are required when studying closely related species present in metagenomic data.
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Affiliation(s)
- Yuhao Chen
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
| | - Thomas C. Brook
- Department of Biomedical Sciences, Faculty of Science and Technology, University of Westminster, London, UK
| | - Cho Zin Soe
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Ian O'Neill
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Cristina Alcon-Giner
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Onnicha Leelastwattanagul
- Bioinformatics and Systems Biology Program, School of Bioresources and Technology, King Mongkut's University of Technology Thonburi (Bang Khun Thian Campus), Bangkok, Thailand
| | - Sarah Phillips
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Shabhonam Caim
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Paul Clarke
- Neonatal Intensive Care Unit, Norfolk and Norwich University Hospitals NHS Foundation Trust, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Lindsay J. Hall
- Gut Microbes and Health, Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | - Lesley Hoyles
- Department of Surgery and Cancer, Faculty of Medicine, Imperial College London, London, UK
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
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30
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Herridge WP, Shibu P, O’Shea J, Brook TC, Hoyles L. Bacteriophages of Klebsiella spp., their diversity and potential therapeutic uses. J Med Microbiol 2020; 69:176-194. [PMID: 31976857 PMCID: PMC7431098 DOI: 10.1099/jmm.0.001141] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Accepted: 12/20/2019] [Indexed: 12/16/2022] Open
Abstract
Klebsiella spp. are commensals of the human microbiota, and a leading cause of opportunistic nosocomial infections. The incidence of multidrug resistant (MDR) strains of Klebsiella pneumoniae causing serious infections is increasing, and Klebsiella oxytoca is an emerging pathogen. Alternative strategies to tackle infections caused by these bacteria are required as strains become resistant to last-resort antibiotics such as colistin. Bacteriophages (phages) are viruses that can infect and kill bacteria. They and their gene products are now being considered as alternatives or adjuncts to antimicrobial therapies. Several in vitro and in vivo studies have shown the potential for lytic phages to combat MDR K. pneumoniae infections. Ready access to cheap sequencing technologies has led to a large increase in the number of genomes available for Klebsiella-infecting phages, with these phages being heterogeneous at the whole-genome level. This review summarizes our current knowledge on phages of Klebsiella spp. and highlights technological and biological issues relevant to the development of phage-based therapies targeting these bacteria.
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Affiliation(s)
- Warren P. Herridge
- Department of Biosciences, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Preetha Shibu
- Life Sciences, University of Westminster, 115 Cavendish Street, London W1W 6UW, UK
| | - Jessica O’Shea
- Department of Biosciences, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
| | - Thomas C. Brook
- Life Sciences, University of Westminster, 115 Cavendish Street, London W1W 6UW, UK
| | - Lesley Hoyles
- Department of Biosciences, Nottingham Trent University, Clifton Lane, Nottingham NG11 8NS, UK
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31
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Hering NA, Fromm A, Bücker R, Gorkiewicz G, Zechner E, Högenauer C, Fromm M, Schulzke JD, Troeger H. Tilivalline- and Tilimycin-Independent Effects of Klebsiella oxytoca on Tight Junction-Mediated Intestinal Barrier Impairment. Int J Mol Sci 2019; 20:E5595. [PMID: 31717457 PMCID: PMC6888351 DOI: 10.3390/ijms20225595] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 02/06/2023] Open
Abstract
Klebsiella oxytoca causes antibiotic-associated hemorrhagic colitis and diarrhea. This was attributed largely to its secreted cytotoxins tilivalline and tilimycin, inductors of epithelial apoptosis. To study whether Klebsiella oxytoca exerts further barrier effects, T84 monolayers were challenged with bacterial supernatants derived from tilivalline/tilimycin-producing AHC6 or its isogeneic tilivalline/tilimycin-deficient strain Mut-89. Both preparations decreased transepithelial resistance, enhanced fluorescein and FITC-dextran-4kDa permeabilities, and reduced expression of barrier-forming tight junction proteins claudin-5 and -8. Laser scanning microscopy indicated redistribution of both claudins off the tight junction region in T84 monolayers as well as in colon crypts of mice infected with AHC6 or Mut-89, indicating that these effects are tilivalline/tilimycin-independent. Furthermore, claudin-1 was affected, but only in a tilivalline/tilimycin-dependent manner. In conclusion, Klebsiella oxytoca induced intestinal barrier impairment by two mechanisms: the tilivalline/tilimycin-dependent one, acting by increasing cellular apoptosis and a tilivalline/tilimycin-independent one, acting by weakening the paracellular pathway through the tight junction proteins claudin-5 and -8.
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Affiliation(s)
- Nina A. Hering
- Medical Department of General, Visceral and Vascular Surgery, Charité – Universitätsmedizin Berlin, 12203 Berlin, Germany
| | - Anja Fromm
- Institute of Clinical Physiology/Nutritional Medicine, Medical Department, Division of Gastroenterology, Infectiology and Rheumatology, Charité – Universitätsmedizin Berlin, 12203 Berlin, Germany; (A.F.); (R.B.); (M.F.); (J.-D.S.)
| | - Roland Bücker
- Institute of Clinical Physiology/Nutritional Medicine, Medical Department, Division of Gastroenterology, Infectiology and Rheumatology, Charité – Universitätsmedizin Berlin, 12203 Berlin, Germany; (A.F.); (R.B.); (M.F.); (J.-D.S.)
| | - Gregor Gorkiewicz
- Institute of Pathology, Medical University of Graz, A-8036 Graz, Austria;
| | - Ellen Zechner
- BioTechMed-Graz, Institute of Molecular Biosciences, University of Graz, A-8010 Graz, Austria;
| | - Christoph Högenauer
- Division of Gastroenterology and Hepatology, Medical University of Graz, A-8036 Graz, Austria;
| | - Michael Fromm
- Institute of Clinical Physiology/Nutritional Medicine, Medical Department, Division of Gastroenterology, Infectiology and Rheumatology, Charité – Universitätsmedizin Berlin, 12203 Berlin, Germany; (A.F.); (R.B.); (M.F.); (J.-D.S.)
| | - Jörg-Dieter Schulzke
- Institute of Clinical Physiology/Nutritional Medicine, Medical Department, Division of Gastroenterology, Infectiology and Rheumatology, Charité – Universitätsmedizin Berlin, 12203 Berlin, Germany; (A.F.); (R.B.); (M.F.); (J.-D.S.)
| | - Hanno Troeger
- Medical Department, Division of Gastroenterology, Infectiology and Rheumatology, Charité – Universitätsmedizin Berlin, 12203 Berlin, Germany;
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32
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The Washing Machine as a Reservoir for Transmission of Extended-Spectrum-Beta-Lactamase (CTX-M-15)-Producing Klebsiella oxytoca ST201 to Newborns. Appl Environ Microbiol 2019; 85:AEM.01435-19. [PMID: 31562168 PMCID: PMC6821978 DOI: 10.1128/aem.01435-19] [Citation(s) in RCA: 30] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2019] [Accepted: 09/04/2019] [Indexed: 12/18/2022] Open
Abstract
Washing machines should be further investigated as possible sites for horizontal gene transfer (ESBL genes) and cross-contamination with clinically important Gram-negative strains. Particularly in the health care sector, the knowledge of possible (re-)contamination of laundry (patients’ clothes and staff uniforms) with multidrug-resistant Gram-negative bacteria could help to prevent and to control nosocomial infections. This report describes an outbreak with a single strain of a multidrug-resistant bacterium (Klebsiella oxytoca sequence type 201) in a neonatal intensive care unit that was terminated only when the washing machine was removed. In addition, the study implies that changes in washing machine design and processing are required to prevent accumulation of residual water where microbial growth can occur and contaminate clothes. During the period from April 2012 to May 2013, 13 newborns (1 to 4 weeks of age) and 1 child in a pediatric hospital ward in Germany were colonized with Klebsiella oxytoca producing an extended-spectrum beta-lactamase (ESBL) (CTX-M-15). A microbiological source-tracking analysis with human and environmental samples was carried out to identify the source and transmission pathways of the K. oxytoca clone. In addition, different hygienic intervention methods were evaluated. K. oxytoca isolates were detected in the detergent drawer and on the rubber door seal of a domestic washer-extractor machine that was used in the same ward to wash laundry for the newborns, as well as in two sinks. These strains were typed using pulsed-field gel electrophoresis (PFGE) and multilocus sequence typing. The environmental findings were compared with those for the human strains and the isolates detected on clothing. The results from both techniques showed that the strains were identical (sequence type 201 and PFGE type 00531, a clone specific to this hospital and not previously isolated in Germany), emphasizing the washing machine as a reservoir and fomite for the transmission of these multidrug-resistant bacteria. After the washing machine was taken out of use, no further colonizations were detected during the subsequent 4-year period. IMPORTANCE Washing machines should be further investigated as possible sites for horizontal gene transfer (ESBL genes) and cross-contamination with clinically important Gram-negative strains. Particularly in the health care sector, the knowledge of possible (re-)contamination of laundry (patients’ clothes and staff uniforms) with multidrug-resistant Gram-negative bacteria could help to prevent and to control nosocomial infections. This report describes an outbreak with a single strain of a multidrug-resistant bacterium (Klebsiella oxytoca sequence type 201) in a neonatal intensive care unit that was terminated only when the washing machine was removed. In addition, the study implies that changes in washing machine design and processing are required to prevent accumulation of residual water where microbial growth can occur and contaminate clothes.
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Oli AN, Itumo CJ, Okam PC, Ezebialu IU, Okeke KN, Ifezulike CC, Ezeobi I, Emechebe GO, Okezie UM, Adejumo SA, Okoyeh JN. Carbapenem-Resistant Enterobacteriaceae Posing a Dilemma in Effective Healthcare Delivery. Antibiotics (Basel) 2019; 8:antibiotics8040156. [PMID: 31547023 PMCID: PMC6963482 DOI: 10.3390/antibiotics8040156] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 08/27/2019] [Accepted: 08/28/2019] [Indexed: 12/14/2022] Open
Abstract
The emergence and spread of Carbapenem-resistant Enterobacteriaceae (CRE) is seriously posing threats in effective healthcare delivery. The aim of this study was to ascertain the emergence of CRE at Chukwuemeka Odumegwu Ojukwu University Teaching Hospital (COOUTH) Awka. Biological samples were collected from 153 consenting patient from 5 clinics in the hospital. The isolates were identified using standard microbiological protocols. Susceptibility to meropenem was done using Kirby-Bauer disc diffusion method on Mueller Hinton Agar. A total of 153 patients were recruited in this study. About one half of those from rural, 63.64% from Sub-urban and 42.27% from urban areas had significant E. coli and Klebsiella spp infections. The male: female ratio of the Enterobacteriaceae infection was 1:1. Almost as much inpatient as outpatient study participants had the infections. The infections were observed mostly on participants with lower educational status. The unmarried individuals were most infected compared to their married counterparts. Enterobacteriaceae infection rate was 50.98%. Of this, 28.21% had CRE infection while the overall prevalence of the CRE in the studied population was 14.38% (22/153). This study shows that CRE is quickly emerging in both community and hospital environments. Klebsiella spp was the most common CRE in this hospital especially Klebsiella oxytoca. Hospitalization was a strong risk factor in the CRE infections. Rapid and accurate detection is critical for their effective management and control.
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Affiliation(s)
- Angus Nnamdi Oli
- Department of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharmaceutical Sciences, Agulu, Nnamdi Azikiwe University, Awka 420108, Anambra State, Nigeria.
| | - Chimaobi Johnpaul Itumo
- Department of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharmaceutical Sciences, Agulu, Nnamdi Azikiwe University, Awka 420108, Anambra State, Nigeria
| | - Princeston Chukwuemeka Okam
- Department of Pharmacology and Therapeutics, College of Health Sciences, Faculty of Medicine, Nnamdi Azikiwe University, Nnewi Campus, Nnewi 435101, Nigeria
| | - Ifeanyichukwu U Ezebialu
- Department of Obstetrics and Gynaecology, Faculty of Clinical Medicine, Chukwuemeka Odumegwu Ojukwu University, Awka Campus, Awka 420108, Anambra state, Nigeria
| | - Kenneth Nchekwube Okeke
- Department of Pediatrics, Faculty of Medicine, Nnamdi Azikiwe University, Nnewi Campus, Nnewi 435101, Anambra State, Nigeria
| | - Christian Chukwuemeka Ifezulike
- Department of Pediatrics, Faculty of Clinical Medicine, Chukwuemeka Odumegwu Ojukwu University, Awka Campus, Awka 420108, Anambra State, Nigeria
| | - Ifeanyi Ezeobi
- Department of Orthopaedic Surgery, Faculty of Clinical Medicine, Chukwuemeka Odumegwu Ojukwu University, Awka Campus, Awka 420108, Anambra State, Nigeria
| | - George Ogonna Emechebe
- Department of Pediatrics, Faculty of Clinical Medicine, Chukwuemeka Odumegwu Ojukwu University, Awka Campus, Awka 420108, Anambra State, Nigeria
| | - Ugochukwu Moses Okezie
- Department of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharmaceutical Sciences, Agulu, Nnamdi Azikiwe University, Awka 420108, Anambra State, Nigeria
| | - Samson A Adejumo
- Department of Pharmaceutical Microbiology and Biotechnology, Faculty of Pharmaceutical Sciences, Agulu, Nnamdi Azikiwe University, Awka 420108, Anambra State, Nigeria
| | - Jude Nnaemeka Okoyeh
- Department of Biology and Clinical Laboratory Science, Division of Arts and Sciences, Neumann University, One Neumann Drive, Aston, PA 19014-1298, USA
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Shnaiderman-Torban A, Paitan Y, Arielly H, Kondratyeva K, Tirosh-Levy S, Abells-Sutton G, Navon-Venezia S, Steinman A. Extended-Spectrum β-Lactamase-Producing Enterobacteriaceae in Hospitalized Neonatal Foals: Prevalence, Risk Factors for Shedding and Association with Infection. Animals (Basel) 2019; 9:ani9090600. [PMID: 31450865 PMCID: PMC6770135 DOI: 10.3390/ani9090600] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2019] [Revised: 08/16/2019] [Accepted: 08/20/2019] [Indexed: 12/31/2022] Open
Abstract
Simple Summary Multidrug-resistant (MDR) Enterobacteriaceae are becoming a major worldwide concern in human and veterinary medicine, mainly due to the production of extended-spectrum β-lactamases (ESBLs). These bacteria have been investigated in adult horses, but not in neonatal foals. In this study, we investigated extended-spectrum β-lactamase Enterobacteriaceae (ESBL-E) shedding and infection in hospitalized mares and their neonatal foals. Overall, we sampled rectal swabs from 55 pairs of mares and their foals on admission, and 33 of them were re-sampled on the 3rd day of hospitalization. We also collected clinical samples, when available. We found that shedding rates and bacterial species diversity increased significantly during hospitalization, both in mares and foals. On admission to hospital, foals’ shedding was associated with umbilical infection. During hospitalization, it was associated with ampicillin treatment. Foals’ shedding was independent of their mares’ shedding. Four foals were infected with ESBL-E strains, including umbilical infections and wounds. We suggest further investigation and surveillance of ESBL-E in neonatal foals, in order to reduce resistance rates and infections. Abstract Extended-spectrum β-lactamase Enterobacteriaceae (ESBL-E) have been investigated in adult horses, but not in foals. We aimed to determine shedding and infection in neonatal foals and mares. Rectal swabs were sampled from mare and foal pairs on admission and on the 3rd day of hospitalization; enriched, plated, and bacteria were verified for ESBL production. Identification and antibiotic susceptibility profiles were determined (Vitek2). Genotyping was performed by multilocus sequence typing (MLST). Genes were identified by PCR and Sanger sequencing. Medical data were analyzed for risk factors (SPSS). On admission, 55 pairs were sampled, of which 33 pairs were re-sampled. Shedding rates on admission in foals and mares were 33% (95% CI 21–47%) and 16% (95% CI 8–29%), respectively, and during hospitalization, these increased significantly to 85% (95% CI 70–94%) and 58% (95% CI 40–73%), respectively. Foal shedding was associated with umbilical infection on admission (P = 0.016) and with ampicillin treatment during hospitalization (p = 0.011), and was independent of the mare’s shedding. The most common ESBL-E was Escherichia coli. During hospitalization, species diversity increased. Four foals were infected with ESBL-E strains, including umbilical infections and wounds. This study substantiates an alarming prevalence of shedding in neonatal foals, which should be further investigated in order to reduce resistance rates.
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Affiliation(s)
- Anat Shnaiderman-Torban
- Koret School of Veterinary Medicine (KSVM), The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 761001, Israel
| | - Yossi Paitan
- Department of Clinical Microbiology and Immunology, Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv 6997801, Israel
- Clinical Microbiology Lab, Meir Medical Center, Kfar Saba 4428164, Israel
| | - Haia Arielly
- Clinical Microbiology Lab, Meir Medical Center, Kfar Saba 4428164, Israel
| | - Kira Kondratyeva
- Department of Molecular Biology, Faculty of Natural Science, Ariel University, Ariel 40700, Israel
| | - Sharon Tirosh-Levy
- Koret School of Veterinary Medicine (KSVM), The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 761001, Israel
| | - Gila Abells-Sutton
- Koret School of Veterinary Medicine (KSVM), The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 761001, Israel
| | - Shiri Navon-Venezia
- Department of Molecular Biology, Faculty of Natural Science, Ariel University, Ariel 40700, Israel
| | - Amir Steinman
- Koret School of Veterinary Medicine (KSVM), The Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot 761001, Israel.
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Characterization of Carbapenemase-Producing Klebsiella oxytoca in Spain, 2016-2017. Antimicrob Agents Chemother 2019; 63:AAC.02529-18. [PMID: 30936106 DOI: 10.1128/aac.02529-18] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Accepted: 03/23/2019] [Indexed: 11/20/2022] Open
Abstract
There is little information about carbapenemase-producing (CP) Klebsiella oxytoca, an important nosocomial pathogen. We characterized CP K. oxytoca isolates collected from different Spanish hospitals between January 2016 and October 2017. During the study period, 139 nonduplicate CP K. oxytoca isolates were identified; of these, 80 were studied in detail. Carbapenemase and extended-spectrum β-lactamase genes were identified by PCR and sequencing. Genetic relatedness was studied by pulsed-field gel electrophoresis (PFGE). Whole-genome sequencing (WGS), carried out on 12 representative isolates, was used to identify the resistome, to elucidate the phylogeny, and to determine the plasmids harboring carbapenemase genes. Forty-eight (60%) isolates produced VIM-1, 30 (37.5%) produced OXA-48, 3 (3.7%) produced KPC-2, 2 (2.5%) produced KPC-3, and 1 (1.2%) produced NDM-1; 4 isolates coproduced two carbapenemases. By PFGE, 69 patterns were obtained from the 80 CP K. oxytoca isolates, and four well-defined clusters were detected: cluster 1 consisted of 11 OXA-48-producing isolates, and the other three clusters included VIM-1-producing isolates (5, 3, and 3 isolates, respectively). In the 12 sequenced isolates, the average number of acquired resistance genes was significantly higher in VIM-1-producing isolates (10.8) than in OXA-48-producing isolates (2.3). All 12 isolates had chromosomally encoded genes of the bla OXY-2 genotype, and by multilocus sequence typing, most belonged to sequence type 2 (ST2). Carbapenemase genes were carried by IncL, IncHI2, IncFII, IncN, IncC, and IncP6 plasmid types. The emergence of CP K. oxytoca was principally due to the spread of VIM-1- and OXA-48-producing isolates in which VIM-1- and OXA-48 were carried by IncL, IncHI2, IncFII, and IncN plasmids. ST2 and the genotype bla OXY-2 predominated among the 12 sequenced isolates.
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Hamner S, Brown BL, Hasan NA, Franklin MJ, Doyle J, Eggers MJ, Colwell RR, Ford TE. Metagenomic Profiling of Microbial Pathogens in the Little Bighorn River, Montana. INTERNATIONAL JOURNAL OF ENVIRONMENTAL RESEARCH AND PUBLIC HEALTH 2019; 16:ijerph16071097. [PMID: 30934749 PMCID: PMC6479903 DOI: 10.3390/ijerph16071097] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2019] [Revised: 03/21/2019] [Accepted: 03/22/2019] [Indexed: 12/26/2022]
Abstract
The Little Bighorn River is the primary source of water for water treatment plants serving the local Crow Agency population, and has special significance in the spiritual and ceremonial life of the Crow tribe. Unfortunately, the watershed suffers from impaired water quality, with high counts of fecal coliform bacteria routinely measured during run-off events. A metagenomic analysis was carried out to identify potential pathogens in the river water. The Oxford Nanopore MinION platform was used to sequence DNA in near real time to identify both uncultured and a coliform-enriched culture of microbes collected from a popular summer swimming area of the Little Bighorn River. Sequences were analyzed using CosmosID bioinformatics and, in agreement with previous studies, enterohemorrhagic and enteropathogenic Escherichia coli and other E. coli pathotypes were identified. Noteworthy was detection and identification of enteroaggregative E. coli O104:H4 and Vibrio cholerae serotype O1 El Tor, however, cholera toxin genes were not identified. Other pathogenic microbes, as well as virulence genes and antimicrobial resistance markers, were also identified and characterized by metagenomic analyses. It is concluded that metagenomics provides a useful and potentially routine tool for identifying in an in-depth manner microbial contamination of waterways and, thereby, protecting public health.
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Affiliation(s)
- Steve Hamner
- Department of Environmental Health Sciences, School of Public Health & Health Sciences, University of Massachusetts Amherst, Amherst, MA 01003, USA 2 Department of Microbiology, Montana State University, Bozeman, MT 59717, USA.
- Department of Microbiology, Montana State University, Bozeman, MT 59717, USA.
| | - Bonnie L Brown
- Department of Biological Sciences, University of New Hampshire, Durham, NH 03824, USA.
| | - Nur A Hasan
- CosmosID Inc., 1600 East Gude Drive, Rockville, MD 20850, USA.
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA.
| | - Michael J Franklin
- Department of Microbiology, Montana State University, Bozeman, MT 59717, USA.
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, USA.
| | - John Doyle
- Crow Water Quality Project, Crow Agency, Little Big Horn College, MT 59022, USA.
- Crow Environmental Health Steering Committee, Crow Agency, Little Big Horn College, MT 59022, USA.
| | - Margaret J Eggers
- Department of Microbiology, Montana State University, Bozeman, MT 59717, USA.
- Center for Biofilm Engineering, Montana State University, Bozeman, MT 59717, USA.
- Crow Environmental Health Steering Committee, Crow Agency, Little Big Horn College, MT 59022, USA.
| | - Rita R Colwell
- CosmosID Inc., 1600 East Gude Drive, Rockville, MD 20850, USA.
- Center for Bioinformatics and Computational Biology, University of Maryland, College Park, MD 20742, USA.
| | - Timothy E Ford
- Department of Environmental Health Sciences, School of Public Health & Health Sciences, University of Massachusetts Amherst, Amherst, MA 01003, USA 2 Department of Microbiology, Montana State University, Bozeman, MT 59717, USA.
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Klebsiella oxytoca enterotoxins tilimycin and tilivalline have distinct host DNA-damaging and microtubule-stabilizing activities. Proc Natl Acad Sci U S A 2019; 116:3774-3783. [PMID: 30808763 PMCID: PMC6397511 DOI: 10.1073/pnas.1819154116] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Human gut microbes form a complex community with vast biosynthetic potential. Microbial products and metabolites released in the gut impact human health and disease. However, defining causative relationships between specific bacterial products and disease initiation and progression remains an immense challenge. This study advances understanding of the functional capacity of the gut microbiota by determining the presence, concentration, and spatial and temporal variability of two enterotoxic metabolites produced by the gut-resident Klebsiella oxytoca. We present a detailed mode of action for the cytotoxins and recapitulate their functionalities in disease models in vivo. The findings provide distinct molecular mechanisms for the enterotoxicity of the metabolites allowing them to act in tandem to damage the intestinal epithelium and cause colitis. Establishing causal links between bacterial metabolites and human intestinal disease is a significant challenge. This study reveals the molecular basis of antibiotic-associated hemorrhagic colitis (AAHC) caused by intestinal resident Klebsiella oxytoca. Colitogenic strains produce the nonribosomal peptides tilivalline and tilimycin. Here, we verify that these enterotoxins are present in the human intestine during active colitis and determine their concentrations in a murine disease model. Although both toxins share a pyrrolobenzodiazepine structure, they have distinct molecular targets. Tilimycin acts as a genotoxin. Its interaction with DNA activates damage repair mechanisms in cultured cells and causes DNA strand breakage and an increased lesion burden in cecal enterocytes of colonized mice. In contrast, tilivalline binds tubulin and stabilizes microtubules leading to mitotic arrest. To our knowledge, this activity is unique for microbiota-derived metabolites of the human intestine. The capacity of both toxins to induce apoptosis in intestinal epithelial cells—a hallmark feature of AAHC—by independent modes of action, strengthens our proposal that these metabolites act collectively in the pathogenicity of colitis.
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Miao M, Wen H, Xu P, Niu S, Lv J, Xie X, Mediavilla JR, Tang YW, Kreiswirth BN, Zhang X, Zhang H, Du H, Chen L. Genetic Diversity of Carbapenem-Resistant Enterobacteriaceae (CRE) Clinical Isolates From a Tertiary Hospital in Eastern China. Front Microbiol 2019; 9:3341. [PMID: 30697205 PMCID: PMC6340961 DOI: 10.3389/fmicb.2018.03341] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2018] [Accepted: 12/27/2018] [Indexed: 12/05/2022] Open
Abstract
The prevalence of carbapenem-resistant Enterobacteriaceae (CRE) is increasing globally, with different molecular mechanisms described. Here we studied the molecular mechanisms of carbapenem resistance, including clonal and plasmid dissemination, of 67 CRE isolates collected between 2012 and 2016 from a tertiary hospital in Eastern China, an CRE endemic region. Species identification and susceptibility testing were performed using the BD Phoenix Automated Microbiology System. Isolates were characterized by PCR (for carbapenemases, ESBLs, AmpC and porin genes), multilocus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), and conjugation transfer experiments. Selected blaKPC-2 -harboring plasmids were subjected to next-generation sequencing using the Illumina Miseq platform. Among the 67 CRE isolates, 42 Klebsiella pneumoniae, 10 Serratia marcescens, 6 Enterobacter cloacae, 2 Raoultella ornithinolytica, 2 K. oxytoca, 1 K. aerogenes, and 4 Escherichia coli isolates were identified. Six different carbapenemases were detected, including blaKPC-2 (n = 45), blaKPC-3 (n = 1), blaNDM-1 (n = 6), blaNDM-5 (n = 1), blaIMP-4 (n = 2), and blaVIM-1 (n = 2); blaOXA-48-like genes were not detected. One E. cloacae strain possessed both blaNDM-1 and blaKPC-3, while two E. cloacae isolates harbored blaNDM-1 and blaVIM-1. ESBLs (CTX-M, SHV, and TEM) and/or AmpC (CMY, DHA, and ACT/MIR) genes were also identified in 59 isolates, including 13 strains that lacked carbapenemases. Several insertions or stop codon mutations were found within porin genes of K. pneumoniae, E. coli and S. marcescens isolates, both with and without carbapenemases. The 42 K. pneumoniae isolates belonged to 12 different sequence types (ST), with ST11 being the most common, while the 6 E. cloacae isolates comprised 4 different STs. The 10 S. marcescens all shared the same PFGE pulsotype, suggestive of clonal spread. Complete plasmid sequencing and PCR screening revealed both intra-strain and inter-species spread of a common blaKPC-2-harboring plasmid in our hospital. Taken together, our study revealed extensive genetic diversity among CRE isolates form a single Chinese hospital. CRE isolates circulating in the hospital differ significantly in their species, STs, porin genes, carbapenemase genes, and their plasmid content, highlighting the complex dissemination of CRE in this endemic region.
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Affiliation(s)
- Minhui Miao
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China.,Department of Clinical Laboratory, Jiangyin Hospital of Traditional Chinese Medicine, Jiangyin, China
| | - Huiyan Wen
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Ping Xu
- Department of Clinical Laboratory, The Fifth People's Hospital of Suzhou, Suzhou, China
| | - Siqiang Niu
- Department of Laboratory Medicine, The First Affiliated Hospital of Chongqing Medical University, Chongqing, China
| | - Jingnan Lv
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Xiaofang Xie
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - José R Mediavilla
- Public Health Research Institute Tuberculosis Center, New Jersey Medical School, Rutgers University, Newark, NJ, United States
| | - Yi-Wei Tang
- Memorial Sloan Kettering Cancer Center, New York, NY, United States
| | - Barry N Kreiswirth
- Public Health Research Institute Tuberculosis Center, New Jersey Medical School, Rutgers University, Newark, NJ, United States
| | - Xia Zhang
- Department of Clinical Laboratory, The North District of Affiliated Suzhou Hospital, Nanjing Medical University, Suzhou, China
| | - Haifang Zhang
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Hong Du
- Department of Clinical Laboratory, The Second Affiliated Hospital of Soochow University, Suzhou, China
| | - Liang Chen
- Public Health Research Institute Tuberculosis Center, New Jersey Medical School, Rutgers University, Newark, NJ, United States
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Liu L, Feng Y, Hu Y, Kang M, Xie Y, Zong Z. Klebsiella grimontii, a New Species Acquired Carbapenem Resistance. Front Microbiol 2018; 9:2170. [PMID: 30271396 PMCID: PMC6142883 DOI: 10.3389/fmicb.2018.02170] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2018] [Accepted: 08/23/2018] [Indexed: 02/05/2023] Open
Abstract
Klebsiella grimontii is a newly identified species closely related to Klebsiella oxytoca, but carbapenem resistance was not identified in the species before. We found a carbapenem-resistant K. oxytoca-like clinical strain, WCHKG020121. The strain was subjected to whole genome sequencing using Illumina HiSeq X10. The precise species identification was established based on average nucleotide identity (ANI) and in silico DNA-DNA hybridization (isDDH) between strain WCHKG020121 and type strains of Klebsiella species. Antimicrobial resistance genes were identified from the genome sequence. The sequence of the bla KPC-2-carrying plasmid was completed using PCR and Sanger sequencing. Conjugation experiments were performed to obtain the plasmid carrying bla KPC-2. All K. grimontii genomes were retrieved from GenBank and were analyzed for antimicrobial resistance genes. Strain WCHKG020121 was resistant to imipenem and meropenem (MIC for both, 32 μg/ml) but was susceptible to colistin (1 μg/ml). Strain WCHKG020121 was initially identified as K. oxytoca using Vitek II but it actually belongs to K. grimontii as it had a 98.81% ANI and 83.4% isDDH value with K. grimontii type strain. Strain WCHKG020121 had bla KPC-2; by contrast, none of other K. grimontii genomes carry any known carbapenemase genes. bla KPC-2 was carried by a 95,734-bp plasmid, designated pKPC2_020121, which contained two different FII(Y) replicons. pKPC2_020121 was closest (93% coverage, 99% identity) to bla KPC-2-carrying plasmids from Enterobacter hormaechei recovered in 2014 at the same hospital. pKPC2_020121 was not self-transmissible, which could be explained by the absence of a conjugation essential gene, traY. In conclusion, we reported the first K. grimontii strain that produced the KPC carbapenemase. Carbapenem resistant K. grimontii may represent a new threat.
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Affiliation(s)
- Lu Liu
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.,Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Yu Feng
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.,Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Yiyi Hu
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.,Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China
| | - Mei Kang
- Laboratory of Clinical Microbiology, Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Yi Xie
- Laboratory of Clinical Microbiology, Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China
| | - Zhiyong Zong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.,Division of Infectious Diseases, State Key Laboratory of Biotherapy, Chengdu, China.,Laboratory of Clinical Microbiology, Department of Laboratory Medicine, West China Hospital, Sichuan University, Chengdu, China.,Department of Infection Control, West China Hospital, Sichuan University, Chengdu, China
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Paskova V, Medvecky M, Skalova A, Chudejova K, Bitar I, Jakubu V, Bergerova T, Zemlickova H, Papagiannitsis CC, Hrabak J. Characterization of NDM-Encoding Plasmids From Enterobacteriaceae Recovered From Czech Hospitals. Front Microbiol 2018; 9:1549. [PMID: 30042758 PMCID: PMC6048247 DOI: 10.3389/fmicb.2018.01549] [Citation(s) in RCA: 48] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2018] [Accepted: 06/21/2018] [Indexed: 01/11/2023] Open
Abstract
The aim of the present study was to characterize sporadic cases and an outbreak of NDM-like-producing Enterobacteriaceae recovered from hospital settings, in Czechia. During 2016, 18 Entrobacteriaceae isolates including 10 Enterobacter cloacae complex (9 E. xiangfangensis and 1 E. asburiae), 4 Escherichia coli, 1 Kluyvera intermedia, 1 Klebsiella pneumoniae, 1 Klebsiella oxytoca, and 1 Raoultella ornithinolytica that produced NDM-like carbapenemases were isolated from 15 patients. Three of the patients were colonized or infected by two different NDM-like producers. Moreover, an NDM-4-producing isolate of E. cloacae complex, isolated in 2012, was studied for comparative purposes. All isolates of E. cloacae complex, except the E. asburiae, recovered from the same hospital, were assigned to ST182. Additionally, two E. coli belonged to ST167, while the remaining isolates were not clonally related. Thirteen isolates carried blaNDM-4, while six isolates carried blaNDM-1 (n = 3) or blaNDM-5 (n = 3). Almost all isolates carried blaNDM-like-carrying plasmids being positive for the IncX3 allele, except ST58 E. coli and ST14 K. pneumoniae isolates producing NDM-1. Analysis of plasmid sequences revealed that all IncX3 blaNDM-like-carrying plasmids exhibited a high similarity to each other and to previously described plasmids, like pNDM-QD28, reported from worldwide. However, NDM-4-encoding plasmids differed from other IncX3 plasmids by the insertion of a Tn3-like transposon. On the other hand, the ST58 E. coli and ST14 K. pneumoniae isolates carried two novel NDM-1-encoding plasmids, pKpn-35963cz, and pEsco-36073cz. Plasmid pKpn-35963cz that was an IncFIB(K) molecule contained an acquired sequence, encoding NDM-1 metallo-β-lactamase (MβL), which exhibited high similarity to the mosaic region of pS-3002cz from an ST11 K. pneumoniae from Czechia. Finally, pEsco-36073cz was a multireplicon A/C2+R NDM-1-encoding plasmid. Similar to other type 1 A/C2 plasmids, the blaNDM-1 gene was located within the ARI-A resistance island. These findings underlined that IncX3 plasmids have played a major role in the dissemination of blaNDM-like genes in Czech hospitals. In combination with further evolvement of NDM-like-encoding MDR plasmids through reshuffling, NDM-like producers pose an important public threat.
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Affiliation(s)
- Veronika Paskova
- Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Plzen, Czechia
- Faculty of Medicine, Biomedical Center, Charles University, Plzen, Czechia
| | - Matej Medvecky
- Veterinary Research Institute, Brno, Czechia
- Faculty of Science, National Centre for Biomolecular Research, Masaryk University, Brno, Czechia
| | - Anna Skalova
- Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Plzen, Czechia
- Faculty of Medicine, Biomedical Center, Charles University, Plzen, Czechia
| | - Katerina Chudejova
- Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Plzen, Czechia
- Faculty of Medicine, Biomedical Center, Charles University, Plzen, Czechia
| | - Ibrahim Bitar
- Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Plzen, Czechia
- Faculty of Medicine, Biomedical Center, Charles University, Plzen, Czechia
| | - Vladislav Jakubu
- National Reference Laboratory for Antibiotics, National Institute of Public Health, Prague, Czechia
| | - Tamara Bergerova
- Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Plzen, Czechia
- Faculty of Medicine, Biomedical Center, Charles University, Plzen, Czechia
| | - Helena Zemlickova
- National Reference Laboratory for Antibiotics, National Institute of Public Health, Prague, Czechia
- Department of Clinical Microbiology, University Hospital and Faculty of Medicine in Hradec Kralove, Charles University, Hradec Kralove, Czechia
| | - Costas C. Papagiannitsis
- Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Plzen, Czechia
- Faculty of Medicine, Biomedical Center, Charles University, Plzen, Czechia
| | - Jaroslav Hrabak
- Department of Microbiology, Faculty of Medicine and University Hospital in Plzen, Charles University, Plzen, Czechia
- Faculty of Medicine, Biomedical Center, Charles University, Plzen, Czechia
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Dieckmann R, Hammerl JA, Hahmann H, Wicke A, Kleta S, Dabrowski PW, Nitsche A, Stämmler M, Al Dahouk S, Lasch P. Rapid characterisation of Klebsiella oxytoca isolates from contaminated liquid hand soap using mass spectrometry, FTIR and Raman spectroscopy. Faraday Discuss 2018; 187:353-75. [PMID: 27053001 DOI: 10.1039/c5fd00165j] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Microbiological monitoring of consumer products and the efficiency of early warning systems and outbreak investigations depend on the rapid identification and strain characterisation of pathogens posing risks to the health and safety of consumers. This study evaluates the potential of three rapid analytical techniques for identification and subtyping of bacterial isolates obtained from a liquid hand soap product, which has been recalled and reported through the EU RAPEX system due to its severe bacterial contamination. Ten isolates recovered from two bottles of the product were identified as Klebsiella oxytoca and subtyped using matrix-assisted laser desorption/ionisation time-of-flight mass spectrometry (MALDI TOF MS), near-infrared Fourier transform (NIR FT) Raman spectroscopy and Fourier transform infrared (FTIR) spectroscopy. Comparison of the classification results obtained by these phenotype-based techniques with outcomes of the DNA-based methods pulsed-field gel electrophoresis (PFGE), multi-locus sequence typing (MLST) and single nucleotide polymorphism (SNP) analysis of whole-genome sequencing (WGS) data revealed a high level of concordance. In conclusion, a set of analytical techniques might be useful for rapid, reliable and cost-effective microbial typing to ensure safe consumer products and allow source tracking.
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Affiliation(s)
- Ralf Dieckmann
- Federal Institute for Risk Assessment, Department of Biological Safety, Max-Dohrn-Str. 8-10, D-10589 Berlin, Germany.
| | - Jens Andre Hammerl
- Federal Institute for Risk Assessment, Department of Biological Safety, Max-Dohrn-Str. 8-10, D-10589 Berlin, Germany.
| | - Hartmut Hahmann
- Landesamt für Verbraucherschutz Sachsen-Anhalt, Fachbereich Lebensmittelsicherheit, Freiimfelder Str. 68, D-06112 Halle, Germany
| | - Amal Wicke
- Landesamt für Verbraucherschutz Sachsen-Anhalt, Fachbereich Lebensmittelsicherheit, Freiimfelder Str. 68, D-06112 Halle, Germany
| | - Sylvia Kleta
- Federal Institute for Risk Assessment, Department of Biological Safety, Max-Dohrn-Str. 8-10, D-10589 Berlin, Germany.
| | | | - Andreas Nitsche
- Robert Koch-Institut, ZBS 1 - Highly Pathogenic Viruses, Seestraße 10, D-13353 Berlin, Germany
| | - Maren Stämmler
- Robert Koch-Institut, ZBS 6 - Proteomics and Spectroscopy, Seestraße 10, D-13353 Berlin, Germany
| | - Sascha Al Dahouk
- Federal Institute for Risk Assessment, Department of Biological Safety, Max-Dohrn-Str. 8-10, D-10589 Berlin, Germany.
| | - Peter Lasch
- Robert Koch-Institut, ZBS 6 - Proteomics and Spectroscopy, Seestraße 10, D-13353 Berlin, Germany
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42
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Müller H, Sib E, Gajdiss M, Klanke U, Lenz-Plet F, Barabasch V, Albert C, Schallenberg A, Timm C, Zacharias N, Schmithausen RM, Engelhart S, Exner M, Parcina M, Schreiber C, Bierbaum G. Dissemination of multi-resistant Gram-negative bacteria into German wastewater and surface waters. FEMS Microbiol Ecol 2018; 94:4963742. [DOI: 10.1093/femsec/fiy057] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2018] [Accepted: 04/05/2018] [Indexed: 12/19/2022] Open
Affiliation(s)
- Heike Müller
- University of Bonn, University Hospital, Institute for Hygiene and Public Health, 53105 Bonn, Sigmund-Freud-Str. 25, Germany
| | - Esther Sib
- University of Bonn, University Hospital, Institute of Medical Microbiology, Immunology and Parasitology, Sigmund-Freud-Str. 25, 53105 Bonn, Germany
| | - Mike Gajdiss
- University of Bonn, University Hospital, Institute of Medical Microbiology, Immunology and Parasitology, Sigmund-Freud-Str. 25, 53105 Bonn, Germany
| | - Ursula Klanke
- University of Bonn, University Hospital, Institute of Medical Microbiology, Immunology and Parasitology, Sigmund-Freud-Str. 25, 53105 Bonn, Germany
| | - Franziska Lenz-Plet
- University of Bonn, University Hospital, Institute of Medical Microbiology, Immunology and Parasitology, Sigmund-Freud-Str. 25, 53105 Bonn, Germany
| | - Vanessa Barabasch
- University of Bonn, University Hospital, Institute of Medical Microbiology, Immunology and Parasitology, Sigmund-Freud-Str. 25, 53105 Bonn, Germany
| | - Cathrin Albert
- University of Bonn, University Hospital, Institute of Medical Microbiology, Immunology and Parasitology, Sigmund-Freud-Str. 25, 53105 Bonn, Germany
| | - Anna Schallenberg
- University of Bonn, University Hospital, Institute of Medical Microbiology, Immunology and Parasitology, Sigmund-Freud-Str. 25, 53105 Bonn, Germany
| | - Christian Timm
- University of Bonn, University Hospital, Institute for Hygiene and Public Health, 53105 Bonn, Sigmund-Freud-Str. 25, Germany
| | - Nicole Zacharias
- University of Bonn, University Hospital, Institute for Hygiene and Public Health, 53105 Bonn, Sigmund-Freud-Str. 25, Germany
| | - Ricarda Maria Schmithausen
- University of Bonn, University Hospital, Institute for Hygiene and Public Health, 53105 Bonn, Sigmund-Freud-Str. 25, Germany
| | - Steffen Engelhart
- University of Bonn, University Hospital, Institute for Hygiene and Public Health, 53105 Bonn, Sigmund-Freud-Str. 25, Germany
| | - Martin Exner
- University of Bonn, University Hospital, Institute for Hygiene and Public Health, 53105 Bonn, Sigmund-Freud-Str. 25, Germany
| | - Marijo Parcina
- University of Bonn, University Hospital, Institute of Medical Microbiology, Immunology and Parasitology, Sigmund-Freud-Str. 25, 53105 Bonn, Germany
| | - Christiane Schreiber
- University of Bonn, University Hospital, Institute for Hygiene and Public Health, 53105 Bonn, Sigmund-Freud-Str. 25, Germany
| | - Gabriele Bierbaum
- University of Bonn, University Hospital, Institute of Medical Microbiology, Immunology and Parasitology, Sigmund-Freud-Str. 25, 53105 Bonn, Germany
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Passet V, Brisse S. Description of Klebsiella grimontii sp. nov. Int J Syst Evol Microbiol 2018; 68:377-381. [DOI: 10.1099/ijsem.0.002517] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Virginie Passet
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
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44
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Identification of cytotoxin-producing Klebsiella oxytoca strains isolated from clinical samples with cell culture assays. Microb Pathog 2017; 113:1-4. [DOI: 10.1016/j.micpath.2017.09.063] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 09/27/2017] [Accepted: 09/28/2017] [Indexed: 11/21/2022]
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Zarfel G, Lipp M, Gürtl E, Folli B, Baumert R, Kittinger C. Troubled water under the bridge: Screening of River Mur water reveals dominance of CTX-M harboring Escherichia coli and for the first time an environmental VIM-1 producer in Austria. THE SCIENCE OF THE TOTAL ENVIRONMENT 2017; 593-594:399-405. [PMID: 28351808 DOI: 10.1016/j.scitotenv.2017.03.138] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 03/14/2017] [Accepted: 03/15/2017] [Indexed: 06/06/2023]
Abstract
Antibiotic resistant bacteria (ARB) in the aquatic environment are reported from all over the world and their presence in the environment has become quite common. The current most prominent example is the presence of beta-lactamases harboring Enterobacteriaceae. The aim of this study was to investigate the presence and diversity (on the genetic and phenotypic levels) of extended spectrum beta-lactamases (ESBL) and carbapenemases harboring Enterobacteriaceae from the River Mur in the center of Graz, Austria's second largest city. Thus over a period of four months water samples were taken, filtrated and screened for these bacteria. All samples revealed ESBL harboring Enterobacteriaceae, of which all with only one exception were Escherichia coli. Dominant ESBL gene family was CTX-M, represented by subgroups CTX-M-1 group, CTX-M-2 group and CTX-M-9 group. Surprisingly co-resistances to non-beta-lactam antibiotics were low, only resistance to trimethoprim was detected in 50% of all (70) isolates. One Klebsiella oxytoca with GES-1 was isolated. To date, GES ESBL has never been reported from Austria before and only rarely from other European countries. Screening for carbapenemase harboring Enterobacteriaceae revealed one Enterobacter cloacae with the gene for VIM-1. Members sharing the same multi-locus-sequence-type (MLST) as well as members of the same rep PCR clusters occurred at different sampling time points. ESBL-harboring Enterobacteriaceae are common in Austrian river water, is dominated by Escherichia coli and CTX-M enzymes. Furthermore, some of the isolates could be linked to different origins.
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Affiliation(s)
- Gernot Zarfel
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria
| | - Michaela Lipp
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria
| | - Elena Gürtl
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria
| | - Bettina Folli
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria
| | - Rita Baumert
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria
| | - Clemens Kittinger
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University Graz, Graz, Austria.
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46
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Characterization of Piperacillin/Tazobactam-Resistant Klebsiella oxytoca Recovered from a Nosocomial Outbreak. PLoS One 2015; 10:e0142366. [PMID: 26539828 PMCID: PMC4634934 DOI: 10.1371/journal.pone.0142366] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2015] [Accepted: 10/21/2015] [Indexed: 11/19/2022] Open
Abstract
We characterized 12 clinical isolates of Klebsiella oxytoca with the extended-spectrum β-lactamase (ESBL) phenotype (high minimum inhibitory concentration [MIC] values of ceftriaxone) recovered over 9 months at a university hospital in Japan. To determine the clonality of the isolates, we used pulsed-field gel electrophoresis (PFGE), multi-locus sequence typing (MLST), and PCR analyses to detect blaRBI, which encodes the β-lactamase RbiA, OXY-2-4 with overproduce-type promoter. Moreover, we performed the isoelectric focusing (IEF) of β-lactamases, and the determination of the MICs of β-lactams including piperacillin/tazobactam for 12 clinical isolates and E. coli HB101 with pKOB23, which contains blaRBI, by the agar dilution method. Finally, we performed the initial screening and phenotypic confirmatory tests for ESBLs. Each of the 12 clinical isolates had an identical PFGE pulsotype and MLST sequence type (ST9). All 12 clinical isolates harbored identical blaRBI. The IEF revealed that the clinical isolate produced only one β-lactamase. E. coli HB101 (pKOB23) and all 12 isolates demonstrated equally resistance to piperacillin/tazobactam (MICs, >128 μg/ml). The phenotypic confirmatory test after the initial screening test for ESBLs can discriminate β-lactamase RbiA-producing K. oxytoca from β-lactamase CTX-M-producing K. oxytoca. Twelve clinical isolates of K. oxytoca, which were recovered from an outbreak at one university hospital, had identical genotypes and produced β-lactamase RbiA that conferred resistance to piperacillin/tazobactam. In order to detect K. oxytoca isolates that produce RbiA to promote research concerning β-lactamase RbiA-producing K. oxytoca, the phenotypic confirmatory test after the initial screening test for ESBLs would be useful.
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47
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Zollner-Schwetz I, Herzog KAT, Feierl G, Leitner E, Schneditz G, Sprenger H, Prattes J, Petritsch W, Wenzl H, Kump P, Gorkiewicz G, Zechner E, Högenauer C. The Toxin-Producing Pathobiont Klebsiella oxytoca Is Not Associated with Flares of Inflammatory Bowel Diseases. Dig Dis Sci 2015; 60:3393-8. [PMID: 26091802 DOI: 10.1007/s10620-015-3765-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/04/2015] [Accepted: 06/11/2015] [Indexed: 12/31/2022]
Abstract
BACKGROUND Alterations in the intestinal microbiota are thought to be involved in the pathogenesis of inflammatory bowel diseases (IBD). Klebsiella oxytoca is an intestinal pathobiont that can produce a cytotoxin (tillivaline). AIM We aimed to elucidate the pathogenetic relevance of toxin-producing K. oxytoca in patients with IBD flares and investigated the clonal relationship of K. oxytoca isolates from IBD patients using multilocus sequence typing (MLST). METHODS Fecal samples of 235 adult IBD patients were collected from January 2008 to May 2009 and were tested for K. oxytoca, C. difficile toxin, and other pathogens by standard microbiological methods. Clinical data and disease activity scores were collected. K. oxytoca isolates were tested for toxin production using cell culture assays. A total of 45 K. oxytoca isolates from IBD patients, healthy, asymptomatic carriers and from patients with antibiotic-associated hemorrhagic colitis in part from our strain collection were tested for their clonal relationship using MLST. RESULTS The prevalence of K. oxytoca in IBD overall was 4.7%. Eleven K. oxytoca isolates were detected. Two of 11 isolates were tested positive for toxin production. There was no significant difference in the distribution of K. oxytoca isolates between the groups (active vs. remission in UC and CD). MLST yielded 33 sequence types. K. oxytoca isolates from IBD did not cluster separately from isolates from asymptomatic carriers. CONCLUSIONS Our data demonstrate that toxin (tilivalline)-producing K. oxytoca is not associated with IBD flares.
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Affiliation(s)
- Ines Zollner-Schwetz
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036, Graz, Austria.
| | - Kathrin A T Herzog
- Institute of Molecular Biosciences, University of Graz, Graz, Austria.,Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Gebhard Feierl
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Eva Leitner
- Institute of Hygiene, Microbiology and Environmental Medicine, Medical University of Graz, Graz, Austria
| | - Georg Schneditz
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Hanna Sprenger
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Jürgen Prattes
- Section of Infectious Diseases and Tropical Medicine, Department of Internal Medicine, Medical University of Graz, Auenbruggerplatz 15, 8036, Graz, Austria
| | - Wolfgang Petritsch
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Heimo Wenzl
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | - Patrizia Kump
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
| | | | - Ellen Zechner
- Institute of Molecular Biosciences, University of Graz, Graz, Austria
| | - Christoph Högenauer
- Division of Gastroenterology and Hepatology, Department of Internal Medicine, Medical University of Graz, Graz, Austria
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48
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Baraniak A, Izdebski R, Fiett J, Gawryszewska I, Bojarska K, Herda M, Literacka E, Żabicka D, Tomczak H, Pewińska N, Szarata M, Ozorowski T, Milner A, Hryniewicz W, Gniadkowski M. NDM-producing Enterobacteriaceae in Poland, 2012–14: inter-regional outbreak ofKlebsiella pneumoniaeST11 and sporadic cases. J Antimicrob Chemother 2015; 71:85-91. [DOI: 10.1093/jac/dkv282] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Accepted: 08/11/2015] [Indexed: 11/13/2022] Open
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Izdebski R, Fiett J, Urbanowicz P, Baraniak A, Derde LPG, Bonten MJM, Carmeli Y, Goossens H, Hryniewicz W, Brun-Buisson C, Brisse S, Gniadkowski M. Phylogenetic lineages, clones and β-lactamases in an international collection of Klebsiella oxytoca isolates non-susceptible to expanded-spectrum cephalosporins. J Antimicrob Chemother 2015; 70:3230-7. [PMID: 26318191 DOI: 10.1093/jac/dkv273] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Accepted: 08/10/2015] [Indexed: 12/26/2022] Open
Abstract
OBJECTIVES The objective of this study was to examine Klebsiella oxytoca clonal and phylogenetic diversity, based on an international collection of carriage isolates non-susceptible to expanded-spectrum cephalosporins (ESCs). METHODS The study material comprised 68 rectal carriage K. oxytoca isolates non-susceptible to ESCs recovered in 2008-11 from patients in 14 hospitals across Europe and Israel. ESC resistance was tested phenotypically; genes encoding ESBLs, AmpC cephalosporinases and carbapenemases were amplified and sequenced. The isolates were typed by PFGE and MLST, followed by sequencing of blaOXY genes. RESULTS MLST and PFGE distinguished 34 STs and 47 pulsotypes among the isolates, respectively. Six STs were split into several pulsotypes each. Five STs were more prevalent (n = 2-9) and occurred in several countries each, including ST2, ST9 and ST141, which belong to a growing international clonal complex (CC), CC2. Four phylogenetic lineages were distinguished, each with another type of chromosomal OXY-type β-lactamase. Three of these, with OXY-1/-5, OXY-2 types and OXY-4, corresponded to previously described phylogroups KoI, KoII and KoIV, respectively. A single isolate from Israel represented a distinct lineage with a newly defined OXY-7 type. The phylogroups showed interesting differences in mechanisms of ESC resistance; KoI strains rarely overexpressed the OXY enzymes but commonly produced ESBLs, whereas KoII strains often were OXY hyperproducers and carried ESBLs much less frequently. AmpCs (DHA-1) and carbapenemases (VIM-1) occurred sporadically. CONCLUSIONS The study confirmed the high genetic diversity of the collection of K. oxytoca ESC-non-susceptible isolates, composed of phylogroups with distinct types of OXY-type β-lactamases, and revealed some STs of broad geographical distribution.
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Affiliation(s)
- R Izdebski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - J Fiett
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - P Urbanowicz
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - A Baraniak
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - L P G Derde
- Department of Medical Microbiology and Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - M J M Bonten
- Department of Medical Microbiology and Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Y Carmeli
- Division of Epidemiology and Preventive Medicine, Tel-Aviv Sourasky Medical Center, Tel-Aviv, Israel
| | - H Goossens
- Department of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium
| | - W Hryniewicz
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
| | - C Brun-Buisson
- Service de reanimation médicale, INSERM, U957 & Université Paris-Est, Créteil, France
| | - S Brisse
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France
| | - M Gniadkowski
- Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland
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50
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Klebsiella oxytoca with reduced sensitivity to chlorhexidine isolated from a diabetic foot ulcer. Int J Infect Dis 2015; 34:112-6. [DOI: 10.1016/j.ijid.2015.03.021] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2015] [Revised: 03/25/2015] [Accepted: 03/26/2015] [Indexed: 01/19/2023] Open
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