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Khoo BY, Hon PY, Leong J, Sai Rama Sridatta P, Thevasagayam NM, Loy SQD, Chua JJY, Ang BSP, Chow A, Marimuthu K, De PP, Ng OT, Vasoo S. Evaluation of NG-Test CARBA 5 version 2, Cepheid Xpert Carba-R, and carbapenem inactivation methods in comparison to whole-genome sequencing for the identification of carbapenemases in non-fermenting Gram-negative bacilli. J Clin Microbiol 2023; 61:e0031623. [PMID: 37671882 PMCID: PMC10512785 DOI: 10.1128/jcm.00316-23] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 07/11/2023] [Indexed: 09/07/2023] Open
Abstract
NG-Test CARBA 5 (NG-Biotech) is a rapid in vitro multiplex immunoassay for the phenotypic detection and differentiation of the "big five" carbapenemase families (KPC, OXA-48-like, VIM, IMP, and NDM). Version 2 of this assay was evaluated alongside the Xpert Carba-R assay (Cepheid, Inc.), the modified carbapenem inactivation method (mCIM), and the CIMTris assay, with a collection of carbapenem-resistant non-fermenting Gram-negative bacilli comprising 138 Pseudomonas aeruginosa and 97 Acinetobacter baumannii isolates. Whole-genome sequencing (WGS) was used as the reference standard. For P. aeruginosa, NG-Test CARBA 5 produced an overall percentage agreement (OPA) with WGS of 97.1%, compared with 92.8% forXpert Carba-R and 90.6% for mCIM. For A. baumannii, as OXA-type carbapenemases (non-OXA-48) are not included, both the NG-Test CARBA 5 and Xpert Carba-R only had an OPA of 6.2%, while the CIMTris performed well with an OPA of 99.0%. The majority of A. baumannii isolates (95.9%) tested falsely positive for IMP on NG-Test CARBA 5; no IMP genes were found on WGS. No clear cause was found for this phenomenon; a cross-reacting protein antigen unique to A. baumannii is a possible culprit. NG-Test CARBA 5 performed well for carbapenemase detection in P. aeruginosa. However, results from A. baumannii isolates should be interpreted with caution.
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Affiliation(s)
- Bo Yan Khoo
- National Centre for Infectious Diseases, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, , Singapore
| | - Pei Yun Hon
- Infectious Diseases Research Laboratory, National Centre for Infectious Diseases, , Singapore
| | - Janice Leong
- Department of Laboratory Medicine, Tan Tock Seng Hospital, , Singapore
| | | | | | - Song Qi Dennis Loy
- Infectious Diseases Research Laboratory, National Centre for Infectious Diseases, , Singapore
| | - Jasmine J. Y. Chua
- Infectious Diseases Research Laboratory, National Centre for Infectious Diseases, , Singapore
| | - Brenda Sze Peng Ang
- National Centre for Infectious Diseases, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, , Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, , Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, , Singapore
- Department of Infection Prevention and Control, Tan Tock Seng Hospital, , Singapore
| | - Angela Chow
- National Centre for Infectious Diseases, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, , Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, , Singapore
- Department of Preventive and Population Medicine, Office of Clinical Epidemiology, Analytics, and Knowledge (OCEAN), Tan Tock Seng Hospital, , Singapore
- Saw Swee Hock School of Public Health, National University of Singapore, , Singapore
| | - Kalisvar Marimuthu
- National Centre for Infectious Diseases, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, , Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, , Singapore
| | - Partha Pratim De
- Department of Laboratory Medicine, Tan Tock Seng Hospital, , Singapore
| | - Oon Tek Ng
- National Centre for Infectious Diseases, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, , Singapore
- Infectious Diseases Research Laboratory, National Centre for Infectious Diseases, , Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, , Singapore
| | - Shawn Vasoo
- National Centre for Infectious Diseases, Singapore
- Department of Infectious Diseases, Tan Tock Seng Hospital, , Singapore
- Infectious Diseases Research Laboratory, National Centre for Infectious Diseases, , Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, , Singapore
- Yong Loo Lin School of Medicine, National University of Singapore, , Singapore
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Octavia S, Kalisvar M, Venkatachalam I, Ng OT, Xu W, Sridatta PSR, Ong YF, Wang LD, Chua A, Cheng B, Lin RTP, Teo JWP. Klebsiella pneumoniae and Klebsiella quasipneumoniae define the population structure of blaKPC-2Klebsiella: a 5 year retrospective genomic study in Singapore. J Antimicrob Chemother 2020; 74:3205-3210. [PMID: 31504571 DOI: 10.1093/jac/dkz332] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/25/2019] [Accepted: 07/04/2019] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To describe the population structure, molecular epidemiology and genetic context of blaKPC-2-bearing Klebsiella pneumoniae. METHODS Isolates (n = 157) were retrospective, phenotypically carbapenem-resistant blaKPC-positive K. pneumoniae, collected from public hospitals. WGS was performed on the Illumina platform. Phylogenomic analysis, screening of resistance and virulence genes, and comparison of the genetic environment of blaKPC were carried out. RESULTS Based on core-tree phylogeny, 67.5% of the isolates were K. pneumoniae and the remainder comprised Klebsiella quasipneumoniae. No Klebsiella variicola strains were observed. Only a single K. pneumoniae carbapenemase (KPC) variant type, blaKPC-2, was seen. MLSTs were diverse and did not comprise the 'traditional' KPC clonal group (CG) 258. blaKPC-2 was associated with a non-Tn4401 element (NTE) in >99% of genomes. Screening for four key virulence loci: yersiniabactin (ybt), aerobactin (iuc), salmochelin (iro) and colibactin (clb) as well as ICEKp (virulence-associated integrative conjugative element of K. pneumoniae), revealed the lack of virulence factors and ICEKp within K. quasipneumoniae. Amongst the K. pneumoniae, there were 32 ybt+ isolates (32/106, 30.2%) and, of these, 8 isolates were also clb+ (7.5%). K. pneumoniae serotypes K1 and K2, the majority of capsular serotype seen in patients with invasive liver abscess syndrome, were detected at 4.5% (7/157). CONCLUSIONS Results suggest that dissemination of blaKPC-2 is driven by NTEKPC in non-ST258 isolates. The detection of blaKPC-2K. pneumoniae serotypes K1/K2 carrying virulence factors, albeit in low numbers, reflects the worrisome convergence of carbapenem resistance and hypervirulence in K. pneumoniae.
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Affiliation(s)
- Sophie Octavia
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore
| | - Marimuthu Kalisvar
- Tan Tock Seng Hospital, Department of Infectious Diseases, Singapore.,National Centre for Infectious Diseases, Singapore.,National University of Singapore, Yong Loo Lin School of Medicine, Singapore
| | | | - Oon Tek Ng
- Tan Tock Seng Hospital, Department of Infectious Diseases, Singapore.,National Centre for Infectious Diseases, Singapore.,Nanyang Technological University, Lee Kong Chian School of Medicine, Singapore
| | - Weizhen Xu
- Tan Tock Seng Hospital, Department of Infectious Diseases, Singapore
| | | | - Yi Fa Ong
- Tan Tock Seng Hospital, Department of Infectious Diseases, Singapore
| | - Liang De Wang
- Tan Tock Seng Hospital, Department of Infectious Diseases, Singapore
| | - Amanda Chua
- Tan Tock Seng Hospital, Department of Infectious Diseases, Singapore
| | - Bernadette Cheng
- National University Hospital, Department of Laboratory Medicine, Singapore
| | - Raymond T P Lin
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore.,National University Hospital, Department of Laboratory Medicine, Singapore
| | - Jeanette W P Teo
- National University Hospital, Department of Laboratory Medicine, Singapore
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Komissarov A, Vij S, Yurchenko A, Trifonov V, Thevasagayam N, Saju J, Sridatta PSR, Purushothaman K, Graphodatsky A, Orbán L, Kuznetsova I. B Chromosomes of the Asian Seabass ( Lates calcarifer) Contribute to Genome Variations at the Level of Individuals and Populations. Genes (Basel) 2018; 9:E464. [PMID: 30241368 PMCID: PMC6211105 DOI: 10.3390/genes9100464] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Revised: 09/06/2018] [Accepted: 09/12/2018] [Indexed: 12/01/2022] Open
Abstract
The Asian seabass (Lates calcarifer) is a bony fish from the Latidae family, which is widely distributed in the tropical Indo-West Pacific region. The karyotype of the Asian seabass contains 24 pairs of A chromosomes and a variable number of AT- and GC-rich B chromosomes (Bchrs or Bs). Dot-like shaped and nucleolus-associated AT-rich Bs were microdissected and sequenced earlier. Here we analyzed DNA fragments from Bs to determine their repeat and gene contents using the Asian seabass genome as a reference. Fragments of 75 genes, including an 18S rRNA gene, were found in the Bs; repeats represented 2% of the Bchr assembly. The 18S rDNA of the standard genome and Bs were similar and enriched with fragments of transposable elements. A higher nuclei DNA content in the male gonad and somatic tissue, compared to the female gonad, was demonstrated by flow cytometry. This variation in DNA content could be associated with the intra-individual variation in the number of Bs. A comparison between the copy number variation among the B-related fragments from whole genome resequencing data of Asian seabass individuals identified similar profiles between those from the South-East Asian/Philippines and Indian region but not the Australian ones. Our results suggest that Bs might cause variations in the genome among the individuals and populations of Asian seabass. A personalized copy number approach for segmental duplication detection offers a suitable tool for population-level analysis across specimens with low coverage genome sequencing.
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Affiliation(s)
- Aleksey Komissarov
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg 199004, Russia.
| | - Shubha Vij
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.
- School of Applied Science, Republic Polytechnic 9 Woodlands Avenue 9, Singapore 738964, Singapore.
| | - Andrey Yurchenko
- Theodosius Dobzhansky Center for Genome Bioinformatics, Saint Petersburg State University, St. Petersburg 199004, Russia.
- Institute of Biodiversity, Animal Health & Comparative Medicine, College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow G12 8QQ, UK.
| | - Vladimir Trifonov
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
- Department of Natural Science, Novosibirsk State University, Novosibirsk 630090, Russia.
| | - Natascha Thevasagayam
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.
| | - Jolly Saju
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.
| | | | - Kathiresan Purushothaman
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.
- Faculty of Biosciences and Aquaculture, Nord University, 8049 Bodø, Norway.
| | - Alexander Graphodatsky
- Institute of Molecular and Cellular Biology, Siberian Branch of the Russian Academy of Sciences, Novosibirsk 630090, Russia.
- Department of Natural Science, Novosibirsk State University, Novosibirsk 630090, Russia.
| | - László Orbán
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.
- Department of Animal Sciences, Georgikon Faculty, University of Pannonia, H-8360 Keszthely, Hungary.
- Center for Comparative Genomics, Murdoch University, 6150 Murdoch, Australia.
| | - Inna Kuznetsova
- Reproductive Genomics Group, Temasek Life Sciences Laboratory, Singapore 117604, Singapore.
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