Microorganisms (Feb 2023)

Evaluation of a Shotgun Metagenomics Approach for Detection of ESBL- and/or Carbapenemase-Producing <i>Enterobacterales</i> in Culture Negative Patients Recovered from Acute Leukemia

  • Pilar Lumbreras-Iglesias,
  • Carlos Sabater,
  • Ainhoa Fernández Moreno,
  • Paula López de Ugarriza,
  • Ana Fernández-Verdugo,
  • Abelardo Margolles,
  • María Rosario Rodicio,
  • Teresa Bernal,
  • Javier Fernández

DOI
https://doi.org/10.3390/microorganisms11020402
Journal volume & issue
Vol. 11, no. 2
p. 402

Abstract

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Patients diagnosed with acute leukemia (AL) have a weakened immune system. Infections acquired by these patients are cause for concern and especially worrisome when Gram-negative multidrug-resistant (MDR) bacteria are involved, as they are difficult to treat, especially in the case of ESBL- and/or carbapenemase-producing Enterobacterales. Culture-based approaches have been relied on over the past decades as the method of choice for the early detection of gut colonization by MDR Gram-negative bacteria. However, various studies have indicated its limited sensitivity, underlining the need for new screening procedures in onco-hematological patients. Here, we evaluated a shotgun metagenomics approach to detect ESBL- and/or carbapenemase-producing Enterobacterales in the gut of 28 patients who had recovered from AL, which were previously colonized by these bacteria but cured at the time of sampling, as judged by culture-based methods. No ESBL or carbapenemase determinants were detected among the many resistance genes found by the metagenomics approach, supporting that patients were truly decolonized, with considerable consequences for their future clinical management. Due to the relatively low number of patients available for the present investigation, further studies should be conducted to support the utility and applicability of metagenomics for the routine screening of MDR bacteria in onco-hematological patients.

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