Carbapenemase-Producing <i>Klebsiella pneumoniae</i> in COVID-19 Intensive Care Patients: Identification of IncL-VIM-1 Plasmid in Previously Non-Predominant Sequence Types
During the COVID-19 pandemic, intensive care units (ICUs) operated at or above capacity, and the number of ICU patients coinfected by nosocomial microorganisms increased. Here, we characterize the population structure and resistance mechanisms of carbapenemase-producing <i>Klebsiella pneumonia...
| Main Authors: | , , , , , , , , , , , , , , |
|---|---|
| Format: | Article |
| Language: | English |
| Published: |
MDPI AG
2023-01-01
|
| Series: | Antibiotics |
| Subjects: | |
| Online Access: | https://www.mdpi.com/2079-6382/12/1/107 |
| _version_ | 1797446897030397952 |
|---|---|
| author | Javier E. Cañada-García Eva Ramírez de Arellano Miguel Jiménez-Orellana Esther Viedma Aida Sánchez Almudena Alhambra Jennifer Villa Alberto Delgado-Iribarren Verónica Bautista Noelia Lara Silvia García-Cobos Belén Aracil Emilia Cercenado María Pérez-Vázquez Jesús Oteo-Iglesias |
| author_facet | Javier E. Cañada-García Eva Ramírez de Arellano Miguel Jiménez-Orellana Esther Viedma Aida Sánchez Almudena Alhambra Jennifer Villa Alberto Delgado-Iribarren Verónica Bautista Noelia Lara Silvia García-Cobos Belén Aracil Emilia Cercenado María Pérez-Vázquez Jesús Oteo-Iglesias |
| author_sort | Javier E. Cañada-García |
| collection | DOAJ |
| description | During the COVID-19 pandemic, intensive care units (ICUs) operated at or above capacity, and the number of ICU patients coinfected by nosocomial microorganisms increased. Here, we characterize the population structure and resistance mechanisms of carbapenemase-producing <i>Klebsiella pneumoniae</i> (CP-Kpn) from COVID-19 ICU patients and compare them to pre-pandemic populations of CP-Kpn. We analyzed 84 CP-Kpn isolates obtained during the pandemic and 74 CP-Kpn isolates obtained during the pre-pandemic period (2019) by whole genome sequencing, core genome multilocus sequence typing, plasmid reconstruction, and antibiotic susceptibility tests. More CP-Kpn COVID-19 isolates produced OXA-48 (60/84, 71.4%) and VIM-1 (18/84, 21.4%) than KPC (8/84, 9.5%). Fewer pre-pandemic CP-Kpn isolates produced VIM-1 (7/74, 9.5%). Cefiderocol (97.3–100%) and plazomicin (97.5–100%) had the highest antibiotic activity against pandemic and pre-pandemic isolates. Sequence type 307 (ST307) was the most widely distributed ST in both groups. VIM-1-producing isolates belonging to ST307, ST17, ST321 and ST485, (STs infrequently associated to VIM-1) were detected during the COVID-19 period. Class 1 integron Int1-<i>bla</i><sub>VIM-1</sub>-<i>aac</i>(6<i>′</i>)-1<i>b</i>-<i>dfrB</i>1-<i>aadA</i>I-<i>catB</i>2-<i>qacE</i>Δ1/<i>sul</i>1, found on an IncL plasmid of approximately 70,000 bp, carried <i>bla</i><sub>VIM-1</sub> in ST307, ST17, ST485, and ST321 isolates. Thus, CP-Kpn populations from pandemic and pre-pandemic periods have similarities. However, VIM-1 isolates associated with atypical STs increased during the pandemic, which warrants additional monitoring and surveillance. |
| first_indexed | 2024-03-09T13:48:09Z |
| format | Article |
| id | doaj.art-6ae182353fe041d7be07dd4cc4f3addb |
| institution | Directory Open Access Journal |
| issn | 2079-6382 |
| language | English |
| last_indexed | 2024-03-09T13:48:09Z |
| publishDate | 2023-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Antibiotics |
| spelling | doaj.art-6ae182353fe041d7be07dd4cc4f3addb2023-11-30T20:55:48ZengMDPI AGAntibiotics2079-63822023-01-0112110710.3390/antibiotics12010107Carbapenemase-Producing <i>Klebsiella pneumoniae</i> in COVID-19 Intensive Care Patients: Identification of IncL-VIM-1 Plasmid in Previously Non-Predominant Sequence TypesJavier E. Cañada-García0Eva Ramírez de Arellano1Miguel Jiménez-Orellana2Esther Viedma3Aida Sánchez4Almudena Alhambra5Jennifer Villa6Alberto Delgado-Iribarren7Verónica Bautista8Noelia Lara9Silvia García-Cobos10Belén Aracil11Emilia Cercenado12María Pérez-Vázquez13Jesús Oteo-Iglesias14Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28222 Madrid, SpainLaboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28222 Madrid, SpainLaboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28222 Madrid, SpainServicio de Microbiología, Hospital Universitario 12 de Octubre, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, SpainLaboratorio de Microbiología, URSalud UTE, Hospital Infanta Sofía, San Sebastián de los Reyes, 28702 Madrid, SpainServicio de Microbiología, Laboratorios ABACID, HM Hospitales, 28050 Madrid, SpainServicio de Microbiología, Hospital Universitario 12 de Octubre, Instituto de Investigación Hospital 12 de Octubre (imas12), 28041 Madrid, SpainServicio de Microbiología Clínica, Hospital Clínico San Carlos, 28040 Madrid, SpainLaboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28222 Madrid, SpainLaboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28222 Madrid, SpainLaboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28222 Madrid, SpainLaboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28222 Madrid, SpainServicio de Microbiología, Hospital General Universitario Gregorio Marañón, 28007 Madrid, SpainLaboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28222 Madrid, SpainLaboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, 28222 Madrid, SpainDuring the COVID-19 pandemic, intensive care units (ICUs) operated at or above capacity, and the number of ICU patients coinfected by nosocomial microorganisms increased. Here, we characterize the population structure and resistance mechanisms of carbapenemase-producing <i>Klebsiella pneumoniae</i> (CP-Kpn) from COVID-19 ICU patients and compare them to pre-pandemic populations of CP-Kpn. We analyzed 84 CP-Kpn isolates obtained during the pandemic and 74 CP-Kpn isolates obtained during the pre-pandemic period (2019) by whole genome sequencing, core genome multilocus sequence typing, plasmid reconstruction, and antibiotic susceptibility tests. More CP-Kpn COVID-19 isolates produced OXA-48 (60/84, 71.4%) and VIM-1 (18/84, 21.4%) than KPC (8/84, 9.5%). Fewer pre-pandemic CP-Kpn isolates produced VIM-1 (7/74, 9.5%). Cefiderocol (97.3–100%) and plazomicin (97.5–100%) had the highest antibiotic activity against pandemic and pre-pandemic isolates. Sequence type 307 (ST307) was the most widely distributed ST in both groups. VIM-1-producing isolates belonging to ST307, ST17, ST321 and ST485, (STs infrequently associated to VIM-1) were detected during the COVID-19 period. Class 1 integron Int1-<i>bla</i><sub>VIM-1</sub>-<i>aac</i>(6<i>′</i>)-1<i>b</i>-<i>dfrB</i>1-<i>aadA</i>I-<i>catB</i>2-<i>qacE</i>Δ1/<i>sul</i>1, found on an IncL plasmid of approximately 70,000 bp, carried <i>bla</i><sub>VIM-1</sub> in ST307, ST17, ST485, and ST321 isolates. Thus, CP-Kpn populations from pandemic and pre-pandemic periods have similarities. However, VIM-1 isolates associated with atypical STs increased during the pandemic, which warrants additional monitoring and surveillance.https://www.mdpi.com/2079-6382/12/1/107<i>Klebsiella pneumoniae</i>carbapenemasesCOVID-19antibiotic resistanceintensive care units (ICUs)outbreaks |
| spellingShingle | Javier E. Cañada-García Eva Ramírez de Arellano Miguel Jiménez-Orellana Esther Viedma Aida Sánchez Almudena Alhambra Jennifer Villa Alberto Delgado-Iribarren Verónica Bautista Noelia Lara Silvia García-Cobos Belén Aracil Emilia Cercenado María Pérez-Vázquez Jesús Oteo-Iglesias Carbapenemase-Producing <i>Klebsiella pneumoniae</i> in COVID-19 Intensive Care Patients: Identification of IncL-VIM-1 Plasmid in Previously Non-Predominant Sequence Types Antibiotics <i>Klebsiella pneumoniae</i> carbapenemases COVID-19 antibiotic resistance intensive care units (ICUs) outbreaks |
| title | Carbapenemase-Producing <i>Klebsiella pneumoniae</i> in COVID-19 Intensive Care Patients: Identification of IncL-VIM-1 Plasmid in Previously Non-Predominant Sequence Types |
| title_full | Carbapenemase-Producing <i>Klebsiella pneumoniae</i> in COVID-19 Intensive Care Patients: Identification of IncL-VIM-1 Plasmid in Previously Non-Predominant Sequence Types |
| title_fullStr | Carbapenemase-Producing <i>Klebsiella pneumoniae</i> in COVID-19 Intensive Care Patients: Identification of IncL-VIM-1 Plasmid in Previously Non-Predominant Sequence Types |
| title_full_unstemmed | Carbapenemase-Producing <i>Klebsiella pneumoniae</i> in COVID-19 Intensive Care Patients: Identification of IncL-VIM-1 Plasmid in Previously Non-Predominant Sequence Types |
| title_short | Carbapenemase-Producing <i>Klebsiella pneumoniae</i> in COVID-19 Intensive Care Patients: Identification of IncL-VIM-1 Plasmid in Previously Non-Predominant Sequence Types |
| title_sort | carbapenemase producing i klebsiella pneumoniae i in covid 19 intensive care patients identification of incl vim 1 plasmid in previously non predominant sequence types |
| topic | <i>Klebsiella pneumoniae</i> carbapenemases COVID-19 antibiotic resistance intensive care units (ICUs) outbreaks |
| url | https://www.mdpi.com/2079-6382/12/1/107 |
| work_keys_str_mv | AT javierecanadagarcia carbapenemaseproducingiklebsiellapneumoniaeiincovid19intensivecarepatientsidentificationofinclvim1plasmidinpreviouslynonpredominantsequencetypes AT evaramirezdearellano carbapenemaseproducingiklebsiellapneumoniaeiincovid19intensivecarepatientsidentificationofinclvim1plasmidinpreviouslynonpredominantsequencetypes AT migueljimenezorellana carbapenemaseproducingiklebsiellapneumoniaeiincovid19intensivecarepatientsidentificationofinclvim1plasmidinpreviouslynonpredominantsequencetypes AT estherviedma carbapenemaseproducingiklebsiellapneumoniaeiincovid19intensivecarepatientsidentificationofinclvim1plasmidinpreviouslynonpredominantsequencetypes AT aidasanchez carbapenemaseproducingiklebsiellapneumoniaeiincovid19intensivecarepatientsidentificationofinclvim1plasmidinpreviouslynonpredominantsequencetypes AT almudenaalhambra carbapenemaseproducingiklebsiellapneumoniaeiincovid19intensivecarepatientsidentificationofinclvim1plasmidinpreviouslynonpredominantsequencetypes AT jennifervilla carbapenemaseproducingiklebsiellapneumoniaeiincovid19intensivecarepatientsidentificationofinclvim1plasmidinpreviouslynonpredominantsequencetypes AT albertodelgadoiribarren carbapenemaseproducingiklebsiellapneumoniaeiincovid19intensivecarepatientsidentificationofinclvim1plasmidinpreviouslynonpredominantsequencetypes AT veronicabautista carbapenemaseproducingiklebsiellapneumoniaeiincovid19intensivecarepatientsidentificationofinclvim1plasmidinpreviouslynonpredominantsequencetypes AT noelialara carbapenemaseproducingiklebsiellapneumoniaeiincovid19intensivecarepatientsidentificationofinclvim1plasmidinpreviouslynonpredominantsequencetypes AT silviagarciacobos carbapenemaseproducingiklebsiellapneumoniaeiincovid19intensivecarepatientsidentificationofinclvim1plasmidinpreviouslynonpredominantsequencetypes AT belenaracil carbapenemaseproducingiklebsiellapneumoniaeiincovid19intensivecarepatientsidentificationofinclvim1plasmidinpreviouslynonpredominantsequencetypes AT emiliacercenado carbapenemaseproducingiklebsiellapneumoniaeiincovid19intensivecarepatientsidentificationofinclvim1plasmidinpreviouslynonpredominantsequencetypes AT mariaperezvazquez carbapenemaseproducingiklebsiellapneumoniaeiincovid19intensivecarepatientsidentificationofinclvim1plasmidinpreviouslynonpredominantsequencetypes AT jesusoteoiglesias carbapenemaseproducingiklebsiellapneumoniaeiincovid19intensivecarepatientsidentificationofinclvim1plasmidinpreviouslynonpredominantsequencetypes |