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Sim EM, Koh B, Ng J, Nguyen T, Wang Q, Ginn AN, Brown M, Pham D, Sintchenko V. Case report: a genomics-guided reclassification of a blood culture isolate misassigned by MALDI-TOF as Yersinia pestis. Access Microbiol 2022; 4:acmi000422. [PMID: 36415732 PMCID: PMC9675175 DOI: 10.1099/acmi.0.000422] [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: 05/15/2022] [Accepted: 08/18/2022] [Indexed: 01/25/2023] Open
Abstract
In this report, we describe a case where Gram-negative rods were isolated from a blood culture which subsequently presented a discordant Yersinia species result by MALDI-TOF. Rapid sequencing provided high-resolution identification of the isolate as Yersinia pseudotuberculosis , which was subsequently confirmed by biochemical tests.
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Affiliation(s)
- Eby M. Sim
- Centre for Infectious Diseases and Microbiology- Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, New South Wales, Australia,*Correspondence: Eby M. Sim,
| | - Bryant Koh
- Centre for Infectious Diseases and Microbiology- Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, New South Wales, Australia
| | - Jimmy Ng
- Centre for Infectious Diseases and Microbiology- Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, New South Wales, Australia
| | - Trang Nguyen
- Centre for Infectious Diseases and Microbiology- Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, New South Wales, Australia
| | - Qinning Wang
- Centre for Infectious Diseases and Microbiology- Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, New South Wales, Australia
| | - Andrew N. Ginn
- Centre for Infectious Diseases and Microbiology- Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, New South Wales, Australia,Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, New South Wales, Australia
| | - Mitchell Brown
- Centre for Infectious Diseases and Microbiology- Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, New South Wales, Australia
| | - David Pham
- Centre for Infectious Diseases and Microbiology- Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, New South Wales, Australia
| | - Vitali Sintchenko
- Centre for Infectious Diseases and Microbiology- Laboratory Services, Institute of Clinical Pathology and Medical Research, NSW Health Pathology, Sydney, New South Wales, Australia,Sydney Institute for Infectious Diseases, The University of Sydney, Sydney, New South Wales, Australia,Centre for Infectious Diseases and Microbiology- Public Health, Westmead Hospital, Sydney, New South Wales, Australia
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Extraintestinal Manifestation of Yersinia pseudotuberculosis Bacteremia as Acute Hepatitis: Case Report and Review of the Literature. Pathogens 2021; 10:pathogens10101255. [PMID: 34684204 PMCID: PMC8539584 DOI: 10.3390/pathogens10101255] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2021] [Revised: 09/14/2021] [Accepted: 09/24/2021] [Indexed: 11/17/2022] Open
Abstract
Yersinia pseudotuberculosis is a causative agent of foodborne zoonosis that usually causes self-limiting pseudoappendicitis. Y. pseudotuberculosis infection also causes systemic spread or extraintestinal manifestations in patients with predisposing conditions. Here, we present a case of acute hepatitis with Y. pseudotuberculosis bacteremia in a 30-year-old man. He was previously healthy without significant medical history other than obesity and current smoking. At the time of admission, he presented with high fever accompanied by chills, jaundice, abdominal pain, and watery diarrhea. Laboratory studies revealed leukocytosis and elevated liver function parameters. A stool culture showed no causative pathogens. Empiric antibiotic therapy with ceftriaxone and metronidazole was administered. Y. pseudotuberculosis was later isolated from the initial blood culture performed on the day of admission using MALDI-TOF mass spectrometry. Antibiotic treatment was continued based on the susceptibility testing results from MALDI-TOF MS and VITEk®2, as well as clinical and laboratory improvements. The patient was discharged on the tenth day of admission and remained healthy with no recurrence during the 12-month follow-up. Here, we review the literature on the systemic infection caused by Y. pseudotuberculosis, including extraintestinal manifestations. This case highlights that Y. pseudotuberculosis may be considered a differential causative organism in patients with acute colitis and hepatitis.
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Obtaining Specific Sequence Tags for Yersinia pestis and Visually Detecting Them Using the CRISPR-Cas12a System. Pathogens 2021; 10:pathogens10050562. [PMID: 34066578 PMCID: PMC8148545 DOI: 10.3390/pathogens10050562] [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] [Received: 03/24/2021] [Revised: 04/30/2021] [Accepted: 04/30/2021] [Indexed: 12/18/2022] Open
Abstract
Three worldwide historical plague pandemics resulted in millions of deaths. Yersinia pestis, the etiologic agent of plague, is also a potential bioterrorist weapon. Simple, rapid, and specific detection of Y. pestis is important to prevent and control plague. However, the high similarity between Y. pestis and its sister species within the same genus makes detection work problematic. Here, the genome sequence from the Y. pestis CO92 strain was electronically separated into millions of fragments. These fragments were analyzed and compared with the genome sequences of 539 Y. pestis strains and 572 strains of 20 species within the Yersinia genus. Altogether, 97 Y. pestis-specific tags containing two or more single nucleotide polymorphism sites were screened out. These 97 tags efficiently distinguished Y. pestis from all other closely related species. We chose four of these tags to design a Cas12a-based detection system. PCR–fluorescence methodology was used to test the specificity of these tags, and the results showed that the fluorescence intensity produced by Y. pestis was significantly higher than that of non-Y. pestis (p < 0.0001). We then employed recombinase polymerase amplification and lateral flow dipsticks to visualize the results. Our newly developed plasmid-independent, species-specific library of tags completely and effectively screened chromosomal sequences. The detection limit of our four-tag Cas12a system reached picogram levels.
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Berendsen EM, Levin E, Braakman R, Prodan A, van Leeuwen HC, Paauw A. Untargeted accurate identification of highly pathogenic bacteria directly from blood culture flasks. Int J Med Microbiol 2019; 310:151376. [PMID: 31784214 DOI: 10.1016/j.ijmm.2019.151376] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 08/22/2019] [Accepted: 10/29/2019] [Indexed: 10/25/2022] Open
Abstract
To improve the preparedness against exposure to highly pathogenic bacteria and to anticipate the wide variety of bacteria that can cause bloodstream infections (BSIs), a safe, unbiased and highly accurate identification method was developed. Our liquid chromatography-tandem mass spectrometry (LC-MS/MS)-based method can identify highly pathogenic bacteria, their near-neighbors and bacteria that are common causes of BSIs directly from positive blood culture flasks. The developed Peptide-Based Microbe Detection Engine (http://proteome2pathogen.com) relies on a two-step workflow: a genus-level search followed by a species-level search. This strategy enables the rapid identification of microorganisms based on the analyzed proteome. This method was successfully used to identify strains of Bacillus anthracis, Brucella abortus, Brucella melitensis, Brucella suis, Burkholderia pseudomallei, Burkholderia mallei, Francisella tularensis, Yersinia pestis and closely related species from simulated blood culture flasks. This newly developed LC-MS/MS method is a safe and rapid method for accurately identifying bacteria directly from positive blood culture flasks.
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Affiliation(s)
- Erwin M Berendsen
- Netherlands Organization for Applied Scientific Research TNO, Department of CBRN Protection, Rijswijk, The Netherlands
| | - Evgeni Levin
- HORAIZON Technology BV., Rotterdam, The Netherlands; Amsterdam Diabetes Center, Department of Internal Medicine, Academic Medical Center, VU University Medical Center, Amsterdam, The Netherlands
| | - René Braakman
- Netherlands Organization for Applied Scientific Research TNO, Department of CBRN Protection, Rijswijk, The Netherlands
| | - Andrei Prodan
- HORAIZON Technology BV., Rotterdam, The Netherlands; Amsterdam Diabetes Center, Department of Internal Medicine, Academic Medical Center, VU University Medical Center, Amsterdam, The Netherlands
| | - Hans C van Leeuwen
- Netherlands Organization for Applied Scientific Research TNO, Department of CBRN Protection, Rijswijk, The Netherlands
| | - Armand Paauw
- Netherlands Organization for Applied Scientific Research TNO, Department of CBRN Protection, Rijswijk, The Netherlands.
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Savin C, Criscuolo A, Guglielmini J, Le Guern AS, Carniel E, Pizarro-Cerdá J, Brisse S. Genus-wide Yersinia core-genome multilocus sequence typing for species identification and strain characterization. Microb Genom 2019; 5:e000301. [PMID: 31580794 PMCID: PMC6861861 DOI: 10.1099/mgen.0.000301] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2019] [Accepted: 09/16/2019] [Indexed: 11/18/2022] Open
Abstract
The genus Yersinia comprises species that differ widely in their pathogenic potential and public-health significance. Yersinia pestis is responsible for plague, while Yersinia enterocolitica is a prominent enteropathogen. Strains within some species, including Y. enterocolitica, also vary in their pathogenic properties. Phenotypic identification of Yersinia species is time-consuming, labour-intensive and may lead to incorrect identifications. Here, we developed a method to automatically identify and subtype all Yersinia isolates from their genomic sequence. A phylogenetic analysis of Yersinia isolates based on a core subset of 500 shared genes clearly demarcated all existing Yersinia species and uncovered novel, yet undefined Yersinia taxa. An automated taxonomic assignment procedure was developed using species-specific thresholds based on core-genome multilocus sequence typing (cgMLST). The performance of this method was assessed on 1843 isolates prospectively collected by the French National Surveillance System and analysed in parallel using phenotypic reference methods, leading to nearly complete (1814; 98.4 %) agreement at species and infra-specific (biotype and serotype) levels. For 29 isolates, incorrect phenotypic assignments resulted from atypical biochemical characteristics or lack of phenotypic resolution. To provide an identification tool, a database of cgMLST profiles and reference taxonomic information has been made publicly accessible (https://bigsdb.pasteur.fr/yersinia). Genomic sequencing-based identification and subtyping of any Yersinia is a powerful and reliable novel approach to define the pathogenic potential of isolates of this medically important genus.
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Affiliation(s)
- Cyril Savin
- Yersinia Research Unit, Institut Pasteur, Paris, France
- National Reference Laboratory for Plague and Other Yersinioses, Institut Pasteur, Paris, France
- WHO Collaborating Centre for Yersinia, Institut Pasteur, Paris, France
| | - Alexis Criscuolo
- Hub de Bioinformatique et Biostatistique – Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Julien Guglielmini
- Hub de Bioinformatique et Biostatistique – Département Biologie Computationnelle, Institut Pasteur, USR 3756 CNRS, Paris, France
| | - Anne-Sophie Le Guern
- Yersinia Research Unit, Institut Pasteur, Paris, France
- National Reference Laboratory for Plague and Other Yersinioses, Institut Pasteur, Paris, France
- WHO Collaborating Centre for Yersinia, Institut Pasteur, Paris, France
| | - Elisabeth Carniel
- Yersinia Research Unit, Institut Pasteur, Paris, France
- National Reference Laboratory for Plague and Other Yersinioses, Institut Pasteur, Paris, France
- WHO Collaborating Centre for Yersinia, Institut Pasteur, Paris, France
| | - Javier Pizarro-Cerdá
- Yersinia Research Unit, Institut Pasteur, Paris, France
- National Reference Laboratory for Plague and Other Yersinioses, Institut Pasteur, Paris, France
- WHO Collaborating Centre for Yersinia, Institut Pasteur, Paris, France
| | - Sylvain Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
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