Evaluation of a Shotgun Metagenomics Approach for Detection of ESBL- and/or Carbapenemase-Producing Enterobacterales in Culture Negative Patients Recovered from Acute Leukemia
Abstract
:1. Introduction
2. Materials and Methods
3. Results
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Patient | Age/ Gender | Underlying Disease/ Status | Sample | Previous ESBL- and/or Carbapenemase-Producing Enterobacterales Gut Colonization | Time from Last Gut Colonization (days)/Time from Administration of the Last Cycle of Chemotherapy (Days) | Current Detection of ESBL- and/or Carbapenemase-Producing Enterobacterales by Culture/PCR/Metagenomic Shotgun Sequencing | Other Antibiotic Resistant Genes Detected by Metagenomic Approach |
---|---|---|---|---|---|---|---|
SMet_1 | 53/M | AML/CR | Feces | Klebsiella pneumoniae ESBL | 1047/1293 | No | cfxA5, cepA, ant(3″)-Ia, ant(6)-Ia, aph(3′)-III, tet(Q), tet(W), tet(X), tet(40), catS, erm(B), erm(F), erm(G), mef(A), msr(D), dfrA1 |
SMet_2 | 57/F | AML/CR | Rectal swab | Enterobacter cloacae ESBL + OXA-48 | 542/537 | No | blaTEM-1A, blaACI-1, cfxA3, ant(6)-Ia, aph(3′)-III, tet(M), tet(O), tet(Q), tet(W), erm(A), erm(F) |
SMet_3 | 59/M | AML/CR | Rectal swab | K. pneumoniae ESBL | 1246/1215 | No | cfxA6, sul2, tet(Q), tet(W), lnu(C) |
SMet_4 | 69/F | AML/CR | Rectal swab | Citrobacter freundii OXA-48 | 790/795 | No | ant(6)-Ia, aph(3′)-III, tet(O), tet(Q), tet(W), tet(40), cat, erm(B) |
SMet_5 1 | 70/F | AML/Relapse | Rectal swab | Escherichia coli ESBL | 0/537 | Yes | blaCTX-M-15, cfxA3, blaOXA-1, aac(6′)-Ib-cr, erm(F), mph(A), dfrA17 |
SMet_6 | 47/F | AML/CR | Rectal swab | E. coli ESBL + OXA-48 | 433/477 | No | blaZ, cfxA4, cepA, blaOXA-85, aac(6′)-II, ant(6)-Ia, ant(6)-Ib, aph(3′)-III, aph(3″)-Ib, tetB(46), tet(M), tet(Q), tet(T), tet(W), tet(X), tet(40), erm(A), erm(B), erm(F), lnu(C), lsa(A), mef(A), mph(C), msr(C), msr(D), dfrG, fosB |
SMet_7 | 74/F | AML/CR | Rectal swab | E. cloacae ESBL + OXA-48 | 806/834 | No | cfxA5, ant(6)-Ia, aph(3′)-III, tet(M), tet(O), tet(W), tet(X), tet(40), cat, erm(A), erm(B), erm(F), erm(G), mdf(A), mef(A), msr(D) |
SMet_8 | 47/F | AML/CR | Rectal swab | K. pneumoniae ESBL | 578/588 | No | blaTEM-1C, cfxA5, sul2, ant(6)-Ia, aph(3′)-III, aph(3″)-Ib, aph(6)-Id, tet(M), tet(Q), tet(W), floR, erm(A), erm(B), erm(F), erm(G), erm(X), erm(X), lnu(C), lsa(C), mdf(A) |
SMet_9 | 31/M | AML/CR | Rectal swab | K. pneumoniae ESBL | 1464/1359 | No | cfxA3, cfxA6, ant(6)-Ia, aph(3′)-III, tet(O), tet(Q), tet(Q), tet(W), tet(X), tet(32), erm(A), erm(B), erm(F), erm(G), erm(X), mef(A), msr(D) |
SMet_10 | 46/F | AML/CR | Rectal swab | K. pneumoniae ESBL | 1365/1377 | No | blaTEM-1C, blaACI-1, cfxA3, sul2, aph(3′)-Ia, aph(3″)-Ib, aph(6)-Id, tet(B), tet(O), tet(Q), tet(Q), tet(X), floR, erm(F), mdf(A), mef(A), mph(A), msr(D), dfrA14 |
SMet_11 | 70/M | AML/CR | Rectal swab | K. pneumoniae ESBL | 1375/1263 | No | blaTEM-1B, cfxA3, sul2, aph(3″)-Ib, aph(6)-Id, tet(A), tet(M), tet(Q), mdf(A), qnrB19, dfrA5 |
SMet_12 | 39/F | AML/CR | Rectal swab | E. coli ESBL | 728/867 | No | cfxA3, ant(6)-Ia, aph(3′)-III, tet(M), tet(Q), tet(X), erm(A), erm(F), mdf(A), msr(D) |
SMet_13 | 56/F | AML/CR | Rectal swab | K. pneumoniae ESBL | 267/729 | No | blaTEM-1B, cfxA3, sul2, sul3, aadA2, ant(3″)-Ia, ant(6)-Ia, aph(3′)-III, aph(3″)-Ib, aph(6)-Id, tet(A), tet(O), tet(Q), tet(W), tet(X), tet(32), tet(40), catP, cmlA1, floR, erm(B), erm(F), erm(X), lnu(C), mdf(A), mef(B), dfrA1, dfrA12 |
SMet_14 | 50/F | AML/CR | Rectal swab | E. coli OXA-48 | 333/351 | No | cfxA3, tet(O), tet(Q), erm(A), erm(F), lsa(C) |
SMet_15 | 49/F | AML/CR | Rectal swab | K. pneumoniae ESBL | 1211/1098 | No | cfxA5, ant(3″)-Ia, ant(6)-Ia, aph(3′)-III, tet(Q), tet(W), tet(40), cat, erm(A), erm(G), erm(X), mdf(A), mef(A), msr(D) |
SMet_16 | 43/M | AML/CR | Rectal swab | K. pneumoniae ESBL | 224/405 | No | blaTEM-1B, cfxA3, sul3, ant(3″)-Ia, ant(6)-Ia, aph(3′)-III, aph(3″)-Ib, aph(6)-Id, tet(A), tet(O), tet(Q), tet(W), tet(X), tet(32), tet(40), cmx, erm(A), erm(B), erm(F), erm(X), lnu(C), mdf(A), dfrA1 |
SMet_17 | 68/F | AML/CR | Rectal swab | K. pneumoniae ESBL | 1230/1419 | No | cfxA5, sul2, aac(6′)-Im, ant(6)-Ia, aph(2″)-Ib, aph(2″)-Ig, aph(3′)-III, aph(3″)-Ib, aph(6)-Id, tet(W), tet(40), erm(F) |
SMet_18 | 51/M | MDS/CR | Rectal swab | K. pneumoniae ESBL | 720/630 | No | blaTEM-1B, cfxA3, cfxA5, blaDHA-14, blaOXA-347, sul1, sul2, aac(3)-IId, aac(3)-XI, aadA2, aph(3′)-Ia, aph(3′)-III, aph(3″)-Ib, aph(6)-Id, tet(B), tet(M), tet(O), tet(Q), tet(X), tet(32), tet(40), catA1, cmx, erm(A), erm(B), erm(F), erm(X), lnu(C), mph(A), dfrA12 |
SMet_19 | 61/F | AML/CR | Rectal swab | K. pneumoniae ESBL | 987/831 | No | blaTEM-1B, cfxA5, sul2, ant(3″)-Ia, ant(6)-Ia, aph(3′)-III, aph(3″)-Ib, tet(M), tet(Q), tet(W), tet(X), catS, erm(B), erm(F), erm(G), lnu(C), mdf(A), dfrA1, dfrA14 |
SMet_20 | 58/M | ALL/CR | Rectal swab | K. pneumoniae ESBL | 1218 | No | cfxA3, sul1, sul2, ant(3″)-Ia, ant(6)-Ia, aph(3′)-III, aph(3″)-Ib, aph(6)-Id, tet(C), tet(O), tet(Q), tet(W), erm(B), lnu(C), mdf(A), dfrA1 |
SMet_21 | 39/F | ALL/CR | Rectal swab | E. coli ESBL | 85/51 | No | blaTEM-1B, cfxA3, cfxA5, sul2, ant(6)-Ia, aph(3′)-Ia, aph(3′)-III, aph(6)-Id, tet(A), tet(M), tet(O), tet(Q), tet(Q), tet(X), erm(A), erm(B), erm(X), lnu(C), mef(A), mph(A), dfrA14 |
SMet_22 | 67/M | AML/CR | Rectal swab | K. pneumoniae OXA-48 | 715/864 | No | blaSHV-145, tet(M), erm(B), lsa(A), oqxA, oqxB, fosA |
SMet_23 | 72/F | AML/CR | Rectal swab | K. pneumoniae ESBL | 288/303 | No | cfxA3, blaDHA-1, sul1, ant(6)-Ia, aph(3′)-III, tet(O), tet(Q), tet(W), tet(X), cat, erm(A), erm(B), erm(F), mdf(A), mph(A), qnrB4 |
SMet_24 | 54/M | AML/CR | Feces | K. pneumoniae ESBL | 1362/1398 | No | cfxA3, cepA, sul2, aac(6′)-Im, ant(3″)-Ia, ant(6)-Ia, aph(3″)-Ib, aph(6)-Id, tet(M), tet(O), tet(W), tet(32), catP, erm(B), erm(F), erm(G), lnu(C) |
SMet_25 | 65/F | AML/CR | Feces | K. pneumoniae ESBL | 612/588 | No | cfxA3, cepA, sul2, ant(6)-Ia, aph(3′)-III, aph(3″)-Ib, aph(6)-Id, tet(M), tet(O), tet(Q), tet(X), tet(32), tet(40), cat, erm(B), erm(F), erm(G), lnu(C), lnu(C), mef(A) |
SMet_26 | 57/F | AML/CR | Feces | K. pneumoniae ESBL | 1356/1314 | No | cfxA3, cepA, sul2, ant(6)-Ia, aph(3′)-III, aph(6)-Id, tet(Q), tet(X), tet(40), cat, catS, erm(B), erm(F), erm(G), lnu(C), mef(A) |
SMet_28 | 60/F | AML/CR | Feces | K. pneumoniae ESBL | 1471/1428 | No | blaTEM-1B, cfxA5, cfxA6, sul2, ant(3″)-Ia, ant(6)-Ia, aph(3′)-III, aph(3″)-Ib, aph(6)-Id, tet(A), tet(B), tet(O), tet(Q), tet(W), tet(X), tet(40), tet(44), cat, catS, erm(B), erm(F), erm(G), lnu(C), mdf(A), mef(A), msr(D), dfrA1 |
SMet_29 | 69/F | AML/CR | Feces | K. pneumoniae ESBL | 1334/1341 | No | cfxA3, cfxA6, ant(6)-Ia, tet(Q), tet(W), tet(X), tet(32), tet(40), cat, catP, erm(B), erm(F), erm(G), lnu(C), mef(A), msr(D) |
SMet_30 | 48/M | AML/CR | Feces | K. pneumoniae ESBL | 463/411 | No | cfxA4, sul1, aadA5, ant(6)-Ia, tet(A), tet(O), tet(Q), tet(W), tet(X), cat, erm(F), erm(G), lnu(C), mdf(A), mef(A), mph(A), msr(D), dfrA17 |
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Lumbreras-Iglesias, P.; Sabater, C.; Fernández Moreno, A.; López de Ugarriza, P.; Fernández-Verdugo, A.; Margolles, A.; Rodicio, M.R.; Bernal, T.; Fernández, J. Evaluation of a Shotgun Metagenomics Approach for Detection of ESBL- and/or Carbapenemase-Producing Enterobacterales in Culture Negative Patients Recovered from Acute Leukemia. Microorganisms 2023, 11, 402. https://doi.org/10.3390/microorganisms11020402
Lumbreras-Iglesias P, Sabater C, Fernández Moreno A, López de Ugarriza P, Fernández-Verdugo A, Margolles A, Rodicio MR, Bernal T, Fernández J. Evaluation of a Shotgun Metagenomics Approach for Detection of ESBL- and/or Carbapenemase-Producing Enterobacterales in Culture Negative Patients Recovered from Acute Leukemia. Microorganisms. 2023; 11(2):402. https://doi.org/10.3390/microorganisms11020402
Chicago/Turabian StyleLumbreras-Iglesias, Pilar, Carlos Sabater, Ainhoa Fernández Moreno, Paula López de Ugarriza, Ana Fernández-Verdugo, Abelardo Margolles, María Rosario Rodicio, Teresa Bernal, and Javier Fernández. 2023. "Evaluation of a Shotgun Metagenomics Approach for Detection of ESBL- and/or Carbapenemase-Producing Enterobacterales in Culture Negative Patients Recovered from Acute Leukemia" Microorganisms 11, no. 2: 402. https://doi.org/10.3390/microorganisms11020402
APA StyleLumbreras-Iglesias, P., Sabater, C., Fernández Moreno, A., López de Ugarriza, P., Fernández-Verdugo, A., Margolles, A., Rodicio, M. R., Bernal, T., & Fernández, J. (2023). Evaluation of a Shotgun Metagenomics Approach for Detection of ESBL- and/or Carbapenemase-Producing Enterobacterales in Culture Negative Patients Recovered from Acute Leukemia. Microorganisms, 11(2), 402. https://doi.org/10.3390/microorganisms11020402