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Citrobacter telavivum sp. nov. with chromosomal mcr-9 from hospitalized patients

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Abstract

Strains 6105T and 6106, recovered from colonized patients in a hospital in Tel-Aviv, Israel, were compared with currently known species of the genus Citrobacter by a polyphasic taxonomic approach. Strains were characterized by whole-genome sequencing, 16S rRNA and recN gene sequencing, multilocus sequence analysis (MLSA), average nucleotide identity (ANI), Genome-to-Genome Distance Calculator (GGDC), and biochemical tests. The location and genetic surrounding of antibiotic resistance genes were investigated, and antibiotic susceptibility profiles were determined by broth microdilution or agar dilution methods. Phylogenetic analysis based on recN and MLSA revealed that both strains formed a distinct cluster from all currently recognized species. The ANI and GGDC were 90.7% and 54.3% with Citrobacter farmeri, respectively. The ability to metabolize various compounds also differentiated both strains from closely related Citrobacter species. Chromosomes of the isolates contained locus encoding a novel class A β-lactamase (TEL-1; 90.5% amino acid identity with CdiA of Citrobacter koseri) plus a LysR-like transcriptional regulator (TEL-R) and an ~ 25.5-kb mcr-9 mosaic region. The direct mcr-9 context matched with those previously identified in several plasmids and chromosomes of diverse Enterobacteriaceae, yet similarity with the plasmidic loci extended further. Untypeable plasmids, pCTEL-2 (~ 235 kb) and pCTEL-1 (~ 114 kb), devoid of resistance genes, were identified in the strains. The isolates were non-susceptible to β-lactams. The name Citrobacter telavivum sp. nov. is proposed, with 6105T (CECT 9989T or DSM 110286T) as the type strain. C. telavivum may represent a bacterial species adapting to hospital settings, able to disseminate and acquire antimicrobial resistance genes.

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Funding

The study isolates were collected within activities of the MOSAR project (LSHP-CT-2007-037941) supported by the European Commission. This work received financial support from Applied Molecular Biosciences Unit UCIBIO, supported by national funds from FCT/MCTES (UIDB/04378/2020), and from the National Medicines Institute in Warsaw, Poland (grant no. DS-4.41/2018-19).

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Author notes

  1. Luísa Peixe

    Present address: UCIBIO-REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal

  2. Teresa Gonçalves Ribeiro and Radosław Izdebski contributed equally to this work.

Authors and Affiliations

  1. UCIBIO-REQUIMTE, Laboratório de Microbiologia, Faculdade de Farmácia, Universidade do Porto, Porto, Portugal

    Teresa Gonçalves Ribeiro

  2. Department of Molecular Microbiology, National Medicines Institute, Warsaw, Poland

    Radosław Izdebski, Paweł Urbanowicz & Marek Gniadkowski

  3. Division of Epidemiology, Tel-Aviv Sourasky Medical Centre, Tel-Aviv, Israel

    Yehuda Carmeli

Authors
  1. Teresa Gonçalves Ribeiro
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  2. Radosław Izdebski
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  4. Yehuda Carmeli
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  6. Luísa Peixe
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Correspondence to Luísa Peixe.

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The study was approved by the Ethic Committee of the Tel Aviv Sourasky Medical Center, Tel-Aviv, Israel.

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Ribeiro, T.G., Izdebski, R., Urbanowicz, P. et al. Citrobacter telavivum sp. nov. with chromosomal mcr-9 from hospitalized patients. Eur J Clin Microbiol Infect Dis 40, 123–131 (2021). https://doi.org/10.1007/s10096-020-04003-6

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  • DOI: https://doi.org/10.1007/s10096-020-04003-6

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