Finding the Missing IMP Gene: Overcoming the Imipenemase IMP Gene Drop-Out in Automated Molecular Testing for Carbapenem-Resistant Bacteria Circulating in Latin America
Abstract
1. Introduction
2. Materials and Methods
2.1. Bacterial Isolates
2.2. Identification and Antimicrobial Susceptibility Testing
2.3. Automated qPCR Analysis for Carbapenemase Gene Detection
2.4. Genomic DNA Extraction and Quantification
2.5. Redesign of Primers to Extend Detection of IMP Alleles
2.6. Tailored qPCR
2.7. Whole-Genome Sequencing, Assembly, and Annotation
3. Results
4. Discussion
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
Abbreviations
IMP | Imipenemase IMP |
PCR | Polymerase Chain Reaction |
qPCR | Real-time PCR |
References
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Strain | Immuno-Chromatography | MBL Based on Automated qPCR | Whole-Genome Sequencing |
---|---|---|---|
E. cloacae complex R36 | IMP-positive | IMP-negative | IMP-18-positive |
P. aeruginosa R59 | IMP-positive | IMP-negative | IMP-18-positive |
P. aeruginosa AG1 | Not tested | IMP-negative | IMP-18-positive |
Gene | Name | Sequence | Length (pb) |
---|---|---|---|
IMP | IMP-F | GGAATAGAGTGGCTTAAYTCTC | 22 |
IMP-R | CCAAACYACTASGTTATCT | 19 | |
VIM | VIM-F | CGAAAAACACAGCGGCMCTTCT | 22 |
VIM-R | GTGGAGACTGCACGCGTTAC | 20 | |
16S rRNA | 16S-F515 | GTGYCAGCMGCCGCGGTAA | 19 |
16S-R926 | CCGYCAATTYMTTTRAGTTT | 20 |
Study ID | Species | Reception Date | Hospital and Region | MBL-Automated qPCR * | Custom qPCR | ||
---|---|---|---|---|---|---|---|
Ct IMP | Ct VIM | 16S rRNA | |||||
AG1 | P. aeruginosa | 2010 | H1 metropolitan | VIM | 16.9 | 13.36 | + |
RA | P. aeruginosa | 2015 | H1 metropolitan | VIM | 17.57 | 14.23 | + |
RB | P. aeruginosa | 2015 | H1 metropolitan | VIM | 16.36 | 13.95 | + |
R1 | K. pneumoniae | dic-21 | H7 metropolitan | NDM | - | - | + |
R2 | A. baumannii | jul-22 | H7 metropolitan | NDM | - | - | + |
R3 | S. fonticola | jul-22 | H7 metropolitan | NDM | - | - | + |
R4 | P. putida | nov-22 | H1 metropolitan | VIM | 19.01 | 12.65 | + |
R5 | S. marcescens | sept-23 | H1 metropolitan | NDM | - | - | + |
R6 | K. pneumoniae | sept-23 | H1 metropolitan | NDM | - | - | + |
R7 | K. pneumoniae | sept-23 | H1 metropolitan | NDM | - | - | + |
R8 | E. coli | sept-23 | H1 metropolitan | NDM | - | - | + |
R9 | P. mirabilis | sept-23 | H1 metropolitan | NDM | - | - | + |
R10 | P. mirabilis | sept-23 | H1 metropolitan | NDM | - | - | + |
R11 | S. marcescens | sept-23 | H1 metropolitan | NDM | - | - | + |
R12 | P. aeruginosa | sept-23 | H1 metropolitan | VIM | 19.62 | 15.57 | + |
R13 | K. pneumoniae | sept-23 | H1 metropolitan | NDM | - | - | + |
R14 | K. pneumoniae | sept-23 | H1 metropolitan | NDM | - | - | + |
R15 | K. pneumoniae | sept-23 | H1 metropolitan | NDM | - | - | + |
R16 | P. aeruginosa | oct-23 | H1 metropolitan | VIM | 15.99 | 13.46 | + |
R17 | P. aeruginosa | oct-23 | H1 metropolitan | VIM | 15.97 | 15.97 | + |
R18 | A. baumannii | oct-23 | H1 metropolitan | NDM | - | - | + |
R19 | K. pneumoniae | dic-23 | H7 metropolitan | No MBL | - | - | + |
R20 | K. pneumoniae | ene-24 | H2 regional | No MBL | - | - | + |
R21 | M. morganii | ene-24 | H2 regional | No MBL | - | - | + |
R22 | E. coli | ene-24 | H2 regional | No MBL | - | - | + |
R23 | E. coli | ene-24 | H2 regional | No MBL | - | - | + |
R24 | E. cloacae complex | ene-24 | H2 regional | No MBL | - | - | + |
R25 | P. mirabilis | ene-24 | H2 regional | No MBL | - | - | + |
R26 | E. coli | ene-24 | H2 regional | No MBL | - | - | + |
R27 | E. coli | ene-24 | H2 regional | No MBL | - | - | + |
R28 | P. aeruginosa | feb-24 | H2 regional | No MBL | - | - | + |
R29 | E. coli | feb-24 | H2 regional | No MBL | - | - | + |
R30 | E. coli | feb-24 | H2 regional | No MBL | - | - | + |
R31 | K. pneumoniae | feb-24 | H2 regional | No MBL | - | - | + |
R32 | K. pneumoniae | feb-24 | H2 regional | No MBL | - | - | + |
R33 | E. cloacae | mar-24 | H2 regional | No MBL | - | - | + |
R34 | P. aeruginosa | jun-24 | H3 metropolitan | No MBL | - | - | + |
R35 | P. aeruginosa | jun-24 | H3 metropolitan | No MBL | - | - | + |
R36 | E. cloacae complex | jun-24 | H4 metropolitan | No MBL (IC: IMP-pos) | 18.24 | - | + |
R37 | S. marcescens | jun-24 | H4 metropolitan | NDM | - | - | + |
R38 | C. youngae | jun-24 | H4 metropolitan | NDM | - | - | + |
R39 | S. marcescens | jun-24 | H4 metropolitan | NDM | - | - | + |
R40 | K. aerogenes | jun-24 | H4 metropolitan | NDM | - | - | + |
R41 | E. coli | jun-24 | H4 metropolitan | NDM | - | - | + |
R42 | E. coli | jun-24 | H4 metropolitan | NDM | - | - | + |
R43 | C. freundii | jun-24 | H4 metropolitan | NDM | - | - | + |
R44 | E. cloacae complex | jun-24 | H4 metropolitan | NDM | - | - | + |
R45 | K. pneumoniae | jun-24 | H4 metropolitan | NDM | - | - | + |
R46 | K. pneumoniae | jun-24 | H4 metropolitan | NDM | - | - | + |
R47 | K. aerogenes | jun-24 | H4 metropolitan | NDM | - | - | + |
R48 | K. pneumoniae | jun-24 | H4 metropolitan | NDM | - | - | + |
R49 | K. aerogenes | jun-24 | H4 metropolitan | NDM | - | - | + |
R50 | C. youngae | jun-24 | H4 metropolitan | NDM | - | - | + |
R51 | E. coli | jun-24 | H4 metropolitan | NDM | - | - | + |
R52 | K. aerogenes | jun-24 | H4 metropolitan | NDM | - | - | + |
R53 | K. aerogenes | jun-24 | H4 metropolitan | NDM | - | - | + |
R54 | K. aerogenes | jun-24 | H4 metropolitan | NDM | - | - | + |
R55 | K. oxytoca | jun-24 | H4 metropolitan | NDM | - | - | + |
R56 | K. aerogenes | jun-24 | H4 metropolitan | NDM | - | - | + |
R57 | E. coli | jun-24 | H3 metropolitan | No MBL | - | - | + |
R58 | P. mirabilis | jun-24 | H3 metropolitan | No MBL | - | - | + |
R59 | P. aeruginosa | jul-24 | H5 metropolitan | No MBL (IC: IMP-pos) | 18.16 | - | + |
R60 | P. aeruginosa | jul-24 | H5 metropolitan | NT | 20.17 | - | + |
R61 | P. aeruginosa | jul-24 | H3 metropolitan | VIM | 18.13 | 11.88 | + |
R62 | P. aeruginosa | jul-24 | H3 metropolitan | No MBL | - | - | + |
R63 | P. aeruginosa | jul-24 | H3 metropolitan | VIM | - | - | + |
R64 | K. pneumoniae | ago-24 | H6 metropolitan | NT | - | - | + |
R65 | P. aeruginosa | ago-24 | H6 metropolitan | NT | - | - | + |
R66 | P. aeruginosa | ago-24 | H6 metropolitan | NT | - | - | + |
R67 | K. pneumoniae | ago-24 | H6 metropolitan | NT | - | - | + |
R68 | Salmonella sp | ago-24 | H6 metropolitan | NT | - | - | + |
R69 | K. pneumoniae | ago-24 | H6 metropolitan | NT | - | - | + |
R70 | K. aerogenes | ago-24 | H6 metropolitan | NT | - | - | + |
R71 | P. aeruginosa | ago-24 | H3 metropolitan | No MBL | - | - | + |
R72 | P. aeruginosa | sept-24 | H3 metropolitan | No MBL | - | - | + |
R73 | P. aeruginosa | sept-24 | H3 metropolitan | No MBL | - | - | + |
R74 | P. aeruginosa | sept-24 | H3 metropolitan | No MBL | - | - | + |
R75 | E. coli | sept-24 | H7 metropolitan | No MBL | - | - | + |
R76 | E. aerogenes | sept-24 | H7 metropolitan | No MBL | - | - | + |
R77 | E. coli | sept-24 | H7 metropolitan | NDM | - | - | + |
R78 | E. cloacae complex | oct-24 | H7 metropolitan | No MBL | - | - | + |
R79 | K. aerogenes | oct-24 | H7 metropolitan | No MBL | - | - | + |
R80 | E. coli | oct-24 | H8 regional | No MBL | - | - | + |
R81 | K. pneumoniae | oct-24 | H8 regional | NDM | - | - | + |
R82 | S. marcescens | oct-24 | H5 metropolitan | NDM | - | - | + |
R83 | S. marcescens | oct-24 | H5 metropolitan | NDM | - | - | + |
R84 | E. coli | oct-24 | H8 regional | NDM | - | - | + |
R85 | K. pneumoniae | oct-24 | H8 regional | NDM | - | - | + |
R86 | P. aeruginosa | nov-24 | H7 metropolitan | VIM (IC: VIM and IMP-pos) | 18.01 | 12.71 | + |
R87 | E. cloacae | nov-24 | H6 metropolitan | NT | - | - | + |
R88 | P. aeruginosa | nov-24 | H6 metropolitan | NT | 21.76 | 11.31 | + |
R89 | K. pneumoniae | nov-24 | H5 metropolitan | NDM | - | - | + |
R90 | P. aeruginosa | nov-24 | H5 metropolitan | VIM | 21.11 | 13.62 | + |
R91 | M. morganii | nov-24 | H8 regional | NDM | - | - | + |
R92 | S. marcescens | nov-24 | H8 regional | NDM | - | - | + |
R93 | K. pneumoniae | nov-24 | H8 regional | NDM | - | - | + |
R94 | E. coli | nov-24 | H8 regional | NDM | - | - | + |
R95 | E. coli | nov-24 | H5 metropolitan | NDM | - | - | + |
R96 | K. pneumoniae | nov-24 | H5 metropolitan | NDM | - | - | + |
R97 | C. freundii | dic-24 | H5 metropolitan | NDM | - | - | + |
R98 | E. coli | dic-24 | H5 metropolitan | NDM | - | - | + |
R99 | K. aerogenes | ene-25 | H7 metropolitan | No MBL | - | - | + |
R100 | C. freundii | ene-25 | H7 metropolitan | NDM | - | - | + |
R101 | E. aerogenes | ene-25 | H7 metropolitan | NDM | - | - | + |
R102 | S. fonticola | feb-25 | H7 metropolitan | NDM | - | - | + |
R103 | E. coli | mar-25 | H7 metropolitan | NDM | - | - | + |
R104 | K. pneumoniae | abr-25 | H8 regional | NDM | - | - | + |
R105 | K. pneumoniae | abr-25 | H8 regional | NDM | - | - | + |
R106 | E. coli | abr-25 | H8 regional | NDM | - | - | + |
R107 | C. freundii | abr-25 | H8 regional | NDM | - | - | + |
R108 | K. pneumoniae | abr-25 | H8 regional | NDM | - | - | + |
R109 | K. pneumoniae | abr-25 | H8 regional | NDM | - | - | + |
R110 | A. baumannii | may-25 | H6 metropolitan | NDM | - | - | + |
R111 | A. baumannii | may-25 | H6 metropolitan | NDM | - | - | + |
R112 | A. baumannii | may-25 | H6 metropolitan | NDM | - | - | + |
R113 | A. baumannii | may-25 | H6 metropolitan | NDM | - | - | + |
R114 | A. baumannii | may-25 | H6 metropolitan | NDM | - | - | + |
R115 | K. pneumoniae | may-25 | H6 metropolitan | NT | - | - | + |
R116 | E. cloacae complex | may-25 | H8 regional | NDM | - | - | + |
Isolates | Phenotypic Profile * | Genomic Profile | |||||||
---|---|---|---|---|---|---|---|---|---|
Species (Strain/ID) | Hospital (H) | Meropenem | Imipenem | qPCR | Whole-Genome Sequencing Analyses | ||||
MIC (µg/mL) | Profile | MIC (µg/mL) | Profile | Ct IMP | Ct VIM | MLST | bla Genes | ||
P. aeruginosa AG1 | H1 metropolitan | ≥16 | R | ≥16 | R | 16.90 | 13.36 | ST-111 | IMP-18, VIM-2, OXA-2, OXA-395, PDC-55 |
P. aeruginosa RA | H1 metropolitan | ≥16 | R | ≥16 | R | 17.57 | 14.23 | ST-111 | IMP-18, VIM-2, OXA-2, OXA-395, PDC-55 |
P. aeruginosa RB | H1 metropolitan | ≥16 | R | ≥16 | R | 16.36 | 13.95 | ST-111 | IMP-18, VIM-62, OXA-2, OXA-395, PDC-55 |
P. putida R4 | H1 metropolitan | ≥16 | R | ≥16 | R | 19.01 | 12.65 | Unassigned | IMP-18, VIM-2 |
P. aeruginosa R12 | H1 metropolitan | ≥16 | R | NT | NT | 19.62 | 15.57 | ST-111 | IMP-18, VIM-2, OXA-2, OXA-395, PDC-55 |
P. aeruginosa R16 | H1 metropolitan | ≥16 | R | ≥16 | R | 15.99 | 13.46 | ST-111 | IMP-18, VIM-2, OXA-2, OXA-395, PDC-55 |
P. aeruginosa R17 | H1 metropolitan | ≥16 | R | ≥16 | R | 15.97 | 15.97 | ST-111 | IMP-18, VIM-2, OXA-2, OXA-395, PDC-55 |
E. cloacae complex R36 | H4 metropolitan | 8 | R | ≥16 | R | 18.24 | - | ST-90 | IMP-18, OXA-2, SHV-12 |
P. aeruginosa R59 | H5 metropolitan | 8 | R | ≥16 | R | 18.16 | - | ST-179 | IMP-18, OXA-2, OXA-396, PDC-374 |
P. aeruginosa R60 | H5 metropolitan | 2 | S | ≥16 | R | 20.17 | - | ST-179 | IMP-18, OXA-2, OXA-396, PDC-374 |
P. aeruginosa R61 | H3 metropolitan | ≥16 | R | ≥16 | R | 18.13 | 11.88 | ST-111 | IMP-18, VIM-2, OXA-2, OXA-395, PDC-55 |
P. aeruginosa R86 | H7 metropolitan | 4 | I | ≥16 | R | 18.01 | 12.71 | ST-111 | IMP-18, VIM-2, OXA-2, OXA-395, PDC-55 |
P. aeruginosa R88 | H6 metropolitan | ≥16 | R | ≥16 | R | 21.76 | 11.31 | ST-111 | IMP-18, VIM-2, OXA-2, OXA-395, PDC-55 |
P. aeruginosa R90 | H5 metropolitan | ≥16 | R | ≥16 | R | 21.11 | 13.62 | ST-111 | IMP-18, VIM-2, OXA-2, OXA-395, PDC-55 |
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Molina-Mora, J.A.; Rojas-Varela, Á.; Martínez-Arana, C.; Portilla-Victor, L.; Quirós-Fallas, I.; Sánchez-Fonseca, M.; Araya, X.; Cascante-Serrano, D.; Segura-Retana, E.; Espinoza-Solís, C.; et al. Finding the Missing IMP Gene: Overcoming the Imipenemase IMP Gene Drop-Out in Automated Molecular Testing for Carbapenem-Resistant Bacteria Circulating in Latin America. Antibiotics 2025, 14, 772. https://doi.org/10.3390/antibiotics14080772
Molina-Mora JA, Rojas-Varela Á, Martínez-Arana C, Portilla-Victor L, Quirós-Fallas I, Sánchez-Fonseca M, Araya X, Cascante-Serrano D, Segura-Retana E, Espinoza-Solís C, et al. Finding the Missing IMP Gene: Overcoming the Imipenemase IMP Gene Drop-Out in Automated Molecular Testing for Carbapenem-Resistant Bacteria Circulating in Latin America. Antibiotics. 2025; 14(8):772. https://doi.org/10.3390/antibiotics14080772
Chicago/Turabian StyleMolina-Mora, Jose Arturo, Ángel Rojas-Varela, Christopher Martínez-Arana, Lucia Portilla-Victor, Isaac Quirós-Fallas, Miryana Sánchez-Fonseca, Xavier Araya, Daniel Cascante-Serrano, Elvira Segura-Retana, Carlos Espinoza-Solís, and et al. 2025. "Finding the Missing IMP Gene: Overcoming the Imipenemase IMP Gene Drop-Out in Automated Molecular Testing for Carbapenem-Resistant Bacteria Circulating in Latin America" Antibiotics 14, no. 8: 772. https://doi.org/10.3390/antibiotics14080772
APA StyleMolina-Mora, J. A., Rojas-Varela, Á., Martínez-Arana, C., Portilla-Victor, L., Quirós-Fallas, I., Sánchez-Fonseca, M., Araya, X., Cascante-Serrano, D., Segura-Retana, E., Espinoza-Solís, C., Uribe-Calvo, M. J., Villalobos-Alfaro, V., Estrada-Murillo, H., Montoya-Madriz, S., Madrigal, W., Lizano, M., Lozada-Alvarado, S., Alvarado-Rodríguez, M., Bolaños-Muñoz, M., ... García-Santamaría, F. (2025). Finding the Missing IMP Gene: Overcoming the Imipenemase IMP Gene Drop-Out in Automated Molecular Testing for Carbapenem-Resistant Bacteria Circulating in Latin America. Antibiotics, 14(8), 772. https://doi.org/10.3390/antibiotics14080772