Gram-Negative ESKAPE Bacteria Surveillance in COVID-19 Pandemic Exposes High-Risk Sequence Types of Acinetobacter baumannii MDR in a Tertiary Care Hospital
Abstract
:1. Introduction
2. Materials and Methods
2.1. Origin of the Gram-Negative ESKAPE Strains, Bacterial Identification, and Controls
2.2. MDR, XDR, and PDR Classification of Gram-Negative ESKAPE Bacteria
2.3. Carbapenemase Production and Their Relationship with Genotypes
2.3.1. Carbapenemase Detection by mCIM Assay
2.3.2. Screening to Confirm Carbapenemases Production in Gram-Negative ESKAPE Bacteria
2.4. adeABC Operon and Regulator Gene Detection adeRS in A. baumannii
2.5. Detection of High-Risk Sequence Types in Acinetobacter baumannii
2.6. Statistical Analysis
3. Results
3.1. Gram-Negative ESKAPE Bacterial Population Included in This Study
3.2. Clinical Origin of Gram-Negative ESKAPE Bacteria
3.3. MDR, XDR, and PDR Classification of Gram-Negative ESKAPE Bacteria
3.3.1. Antimicrobial Resistance Gram-Negative ESKAPE Bacteria (Enterobacterales)
3.3.2. Antimicrobial Resistance Gram-Negative ESKAPE Bacteria (Non-Lactose Fermenting)
3.3.3. Changes in Antimicrobial Resistance in Enterobacterales during 2021 and 2022
3.3.4. Changes in Antimicrobial Resistance in Non-Fermenters during 2021 and 2022
3.4. Carbapenemase Production and Their Relationship with Genotypes
3.5. Detection of High-Risk Sequence Types in Acinetobacter baumannii
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Primer | Molecular Target | Sequence (5′→3′) | Size (bp) | Reference |
---|---|---|---|---|
IMP-F | blaIMP | TTGACACTCCATTTACDG | 139 | [35] |
IMP-R | GATYGAGAATTAAGCCACYCT | |||
VIM-F | blaVIM | GATGGTGTTTGGTCGCATA | 390 | |
VIM-R | CGAATGCGCAGCACCAG | |||
KPC-F | blaKPC | CATTCAAGGGCTTTCTTGCTGC | 538 | |
KPC-R | ACGACGGCATAGTCATTTGC | |||
OXA-48F | blaOXA-48 | GCACTTCTTTTGTGATGGC | 281 | |
OXA-48R | GAGCACTTCTTTTGTGATGGC | |||
NDM-F | blaNDM | GGTTTGGCGAT CTGGTTTTC | 621 | [36] |
NDM-R | CGGAATGGCTCATCACGATC | |||
OXA-23F | blaOXA-23 | GATGTGTCATAGTATTCGTCG | 1065 | [37] |
OXA-23R | TCACAACAACTAAAAGCACTG | |||
OXA-40F | blaOXA-40 | TCTAGTTTCTCTCAGTGCATGTTCATC | 749 | [38] |
OXA-40R | CATTACGAATAGAACCAGACATTCC | |||
gltA-F | Citrate synthase | AATTTACAGTGGCACATTAGGTCCC | 722 | [39] |
gltA-R | GCAGAGATACCAGCAGAGATACACG | |||
gyrB-F | DNA gyrase subunit B | TGTAAAACGACGGCCAGTGCNGGRTCYTTYTCYTGRCA | 909 | |
gyrB-R | CAGGAAACAGCTATGACCAYGSNGGNGGNAARTTYRA | |||
gdhB-F | Glucose dehydrogenase B | GCTACTTTTATGCAACAGAGCC | 775 | |
gdhB-R | GTTGAGTTGGCGTATGTTGTGC | |||
recA-F | Homologous recombination factor | CCTGAATCTTCYGGTAAAAC | 425 | |
recA-R | GTTTCTGGGCTGCCAAACATTAC | |||
cpn60-F | 60 kDa chaperonin | ACTGTACTTGCTCAAGC | 479 | |
cpn60-R | TTCAGCGATGATAAGAAGTGG | |||
gpi-F | Glucose-6-phosphate isomerase | AATACCGTGGTGCTACGGG | 508 | |
gpi-R | AACTTGATTTTCAGGAGC | |||
rpoD-F | RNA polymerase sigma factor rpoD (Sigma-70) | ACGACTGACCCGGTACGCATGTAYATGMGNGARATCGC NACNCT | 492 | |
rpoD-R | ATAGAAATAACCAGACGTAAGTTNGCYTCNACCATYTG YTTYTT |
Gram-Negative ESKAPE Bacteria Causing Nosocomial Infections | Analyzed Strains by Year n (%) | Total n (%) | |
---|---|---|---|
2021 | 2022 | ||
Escherichia coli | 54 (47.4) | 44 (51.2) | 98 (49.0) |
Klebsiella pneumoniae | 17 (14.9) | 10 (11.6) | 27 (13.5) |
Pseudomonas aeruginosa | 25 (21.9) | 24 (27.9) | 49 (24.5) |
Acinetobacter baumannii | 18 (15.8) | 8 (9.30) | 26 (13.0) |
Total | 114 (100) | 86 (100) | 200 (100) |
Clinical Origin | Analyzed Strains by Year n (%) | Total | |
---|---|---|---|
2021 | 2022 | ||
Urinary tract infection (UTI) | 37 (32.4) | 39 (45.3) | 76 (38.0) |
Ventilator-associated pneumonia (VAP) | 50 (43.9) | 29 (33.7) | 79 (39.5) |
Wound infection | 16 (14.0) | 9 (10.5) | 25 (12.5) |
Blood infection (Sepsis) | 11 (9.7) | 9 (10.5) | 20 (10.0) |
Total | 114 (100) | 86 (100) | 200 (100) |
ESKAPE | Carbapenemase Detection (n/%) | Efflux Pump adeABC | ||||||||
---|---|---|---|---|---|---|---|---|---|---|
Phenotype n (%) by | Genotype by End-Point PCR | |||||||||
Disc Diffusion | mCIM Assay | blaNDM | blaVIM | blaIMP | blaKPC | blaOXA-48 | blaOXA-40 | blaOXA-23 | ||
E. coli | 12 (17.6) | 8 (25.85) | 4 (50) | 2 (25) | 0 (0) | 1 (12.5) | 1 (12.5) | NA* | NA | NA |
K. pneumoniae | 11 (16.2) | 4 (12.9) | 1 (25) | 1 (25) | 0 (0) | 0 (0) | 2 (50) | NA | NA | NA |
P. aeruginosa | 21 (30.8) | 2 (6.5) | 0 (0) | 2 (100) | 0 (0) | 0 (0) | 0 (0) | NA | NA | NA |
A. baumannii | 24 (35.4) | 17 (54.8) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 0 (0) | 17 (100) | 0 (0) | 24 (100) |
Total | 68 (100) | 31 (100) |
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Cureño-Díaz, M.A.; Plascencia-Nieto, E.S.; Loyola-Cruz, M.Á.; Cruz-Cruz, C.; Nolasco-Rojas, A.E.; Durán-Manuel, E.M.; Ibáñez-Cervantes, G.; Gómez-Zamora, E.; Tamayo-Ordóñez, M.C.; Tamayo-Ordóñez, Y.d.J.; et al. Gram-Negative ESKAPE Bacteria Surveillance in COVID-19 Pandemic Exposes High-Risk Sequence Types of Acinetobacter baumannii MDR in a Tertiary Care Hospital. Pathogens 2024, 13, 50. https://doi.org/10.3390/pathogens13010050
Cureño-Díaz MA, Plascencia-Nieto ES, Loyola-Cruz MÁ, Cruz-Cruz C, Nolasco-Rojas AE, Durán-Manuel EM, Ibáñez-Cervantes G, Gómez-Zamora E, Tamayo-Ordóñez MC, Tamayo-Ordóñez YdJ, et al. Gram-Negative ESKAPE Bacteria Surveillance in COVID-19 Pandemic Exposes High-Risk Sequence Types of Acinetobacter baumannii MDR in a Tertiary Care Hospital. Pathogens. 2024; 13(1):50. https://doi.org/10.3390/pathogens13010050
Chicago/Turabian StyleCureño-Díaz, Mónica Alethia, Estibeyesbo Said Plascencia-Nieto, Miguel Ángel Loyola-Cruz, Clemente Cruz-Cruz, Andres Emmanuel Nolasco-Rojas, Emilio Mariano Durán-Manuel, Gabriela Ibáñez-Cervantes, Erika Gómez-Zamora, María Concepción Tamayo-Ordóñez, Yahaira de Jesús Tamayo-Ordóñez, and et al. 2024. "Gram-Negative ESKAPE Bacteria Surveillance in COVID-19 Pandemic Exposes High-Risk Sequence Types of Acinetobacter baumannii MDR in a Tertiary Care Hospital" Pathogens 13, no. 1: 50. https://doi.org/10.3390/pathogens13010050
APA StyleCureño-Díaz, M. A., Plascencia-Nieto, E. S., Loyola-Cruz, M. Á., Cruz-Cruz, C., Nolasco-Rojas, A. E., Durán-Manuel, E. M., Ibáñez-Cervantes, G., Gómez-Zamora, E., Tamayo-Ordóñez, M. C., Tamayo-Ordóñez, Y. d. J., Calzada-Mendoza, C. C., & Bello-López, J. M. (2024). Gram-Negative ESKAPE Bacteria Surveillance in COVID-19 Pandemic Exposes High-Risk Sequence Types of Acinetobacter baumannii MDR in a Tertiary Care Hospital. Pathogens, 13(1), 50. https://doi.org/10.3390/pathogens13010050