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García-Rivera C, Sánchez-Bautista A, Parra-Grande M, Ricart-Silvestre A, Ventero MP, Tyshkovska I, Merino E, Rodríguez Díaz JC. Comparison of Different Methods for Assaying the In Vitro Activity of Cefiderocol against Carbapenem-Resistant Pseudomonas aeruginosa Strains: Influence of Bacterial Inoculum. Antibiotics (Basel) 2024; 13:663. [PMID: 39061345 PMCID: PMC11273683 DOI: 10.3390/antibiotics13070663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2024] [Revised: 07/03/2024] [Accepted: 07/13/2024] [Indexed: 07/28/2024] Open
Abstract
Carbapenem-resistant Pseudomonas aeruginosa infections represent a critical public health concern, highlighting the need for the development of effective antibiotics. Cefiderocol demonstrated potent in vitro activity against Pseudomonas aeruginosa, particularly in strains that are resistant to other drugs. However, concerns regarding the emergence of drug-resistant strains persist. This study, conducted with 109 carbapenem-resistant Pseudomonas aeruginosa strains from the Spanish Hospital (Dr. Balmis, Alicante). The study evaluated susceptibility to cefiderocol in comparison to alternative antibiotics and including their susceptibility to bacterial inoculum, while assessing various testing methods. Our findings revealed high susceptibility to cefiderocol against carbapenem-resistant strains, with only 2 of 109 strains exhibiting resistance. Comparative analysis demonstrated superiority of cefiderocol towards alternative antibiotics. Both the E-test and disk-diffusion methods showed 100% concordance with the microdilution method in classifying strains as susceptible or resistant. However, 4.6% (5/109) of disc zone diameters fell within the technical uncertainty zone, so the E-test technique was found to be more useful in routine clinical practice. Additionally, escalating bacterial inoculum correlated with decreases in vitro activity, so this parameter should be adjusted very carefully in in vivo studies. This study underscores cefiderocol's potential as a therapeutic option for carbapenem-resistant Pseudomonas aeruginosa infections. However, the emergence of drug-resistant strains emphasizes the critical need for a wise use of antibiotics and a continuous monitoring of resistance to antibiotics. Based on our in vitro data, further investigation concerning the impact of bacterial inoculum on drug efficacy is warranted in order to detect resistance mechanisms and optimize treatment strategies, thereby mitigating the risk of resistance.
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Affiliation(s)
- Celia García-Rivera
- Microbiology Department, Dr. Balmis University General Hospital, Alicante Institute for Health and Biomedical Research (ISABIAL), 03010 Alicante, Spain; (M.P.-G.); (A.R.-S.); (M.P.V.); (I.T.); (J.C.R.D.)
| | - Antonia Sánchez-Bautista
- Microbiology Department, Dr. Balmis University General Hospital, Alicante Institute for Health and Biomedical Research (ISABIAL), 03010 Alicante, Spain; (M.P.-G.); (A.R.-S.); (M.P.V.); (I.T.); (J.C.R.D.)
| | - Mónica Parra-Grande
- Microbiology Department, Dr. Balmis University General Hospital, Alicante Institute for Health and Biomedical Research (ISABIAL), 03010 Alicante, Spain; (M.P.-G.); (A.R.-S.); (M.P.V.); (I.T.); (J.C.R.D.)
| | - Andrea Ricart-Silvestre
- Microbiology Department, Dr. Balmis University General Hospital, Alicante Institute for Health and Biomedical Research (ISABIAL), 03010 Alicante, Spain; (M.P.-G.); (A.R.-S.); (M.P.V.); (I.T.); (J.C.R.D.)
| | - María Paz Ventero
- Microbiology Department, Dr. Balmis University General Hospital, Alicante Institute for Health and Biomedical Research (ISABIAL), 03010 Alicante, Spain; (M.P.-G.); (A.R.-S.); (M.P.V.); (I.T.); (J.C.R.D.)
| | - Iryna Tyshkovska
- Microbiology Department, Dr. Balmis University General Hospital, Alicante Institute for Health and Biomedical Research (ISABIAL), 03010 Alicante, Spain; (M.P.-G.); (A.R.-S.); (M.P.V.); (I.T.); (J.C.R.D.)
| | - Esperanza Merino
- Infectious Diseases Unit, Dr. Balmis University General Hospital, Alicante Institute for Health and Biomedical Research (ISABIAL), 03010 Alicante, Spain;
- División de Microbiología, Universidad Miguel Hernández, Apartado 18, 03550 San Juan de Alicante, Spain
| | - Juan Carlos Rodríguez Díaz
- Microbiology Department, Dr. Balmis University General Hospital, Alicante Institute for Health and Biomedical Research (ISABIAL), 03010 Alicante, Spain; (M.P.-G.); (A.R.-S.); (M.P.V.); (I.T.); (J.C.R.D.)
- División de Microbiología, Universidad Miguel Hernández, Apartado 18, 03550 San Juan de Alicante, Spain
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Nozick SH, Ozer EA, Medernach R, Kochan TJ, Kumar R, Mills JO, Wunderlink RG, Qi C, Hauser AR. Phenotypes of a Pseudomonas aeruginosa hypermutator lineage that emerged during prolonged mechanical ventilation in a patient without cystic fibrosis. mSystems 2024; 9:e0048423. [PMID: 38132670 PMCID: PMC10804958 DOI: 10.1128/msystems.00484-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2023] [Accepted: 11/13/2023] [Indexed: 12/23/2023] Open
Abstract
Hypermutator lineages of Pseudomonas aeruginosa arise frequently during the years of airway infection experienced by patients with cystic fibrosis and bronchiectasis but are rare in the absence of chronic infection and structural lung disease. Since the onset of the COVID-19 pandemic, large numbers of patients have remained mechanically ventilated for extended periods of time. These patients are prone to acquire bacterial pathogens that persist for many weeks and have the opportunity to evolve within the pulmonary environment. However, little is known about what types of adaptations occur in these bacteria and whether these adaptations mimic those observed in chronic infections. We describe a COVID-19 patient with a secondary P. aeruginosa lung infection in whom the causative bacterium persisted for >50 days. Over the course of this infection, a hypermutator lineage of P. aeruginosa emerged and co-existed with a non-hypermutator lineage. Compared to the parental lineage, the hypermutator lineage evolved to be less cytotoxic and less virulent. Genomic analyses of the hypermutator lineage identified numerous mutations, including in the mismatch repair gene mutL and other genes frequently mutated in individuals with cystic fibrosis. Together, these findings demonstrate that hypermutator lineages can emerge when P. aeruginosa persists following acute infections such as ventilator-associated pneumonia and that these lineages have the potential to affect patient outcomes.IMPORTANCEPseudomonas aeruginosa may evolve to accumulate large numbers of mutations in the context of chronic infections such as those that occur in individuals with cystic fibrosis. However, these "hypermutator" lineages are rare following acute infections. Here, we describe a non-cystic fibrosis patient with COVID-19 pneumonia who remained mechanically ventilated for months. The patient became infected with a strain of P. aeruginosa that evolved to become a hypermutator. We demonstrate that hypermutation led to changes in cytotoxicity and virulence. These findings are important because they demonstrate that P. aeruginosa hypermutators can emerge following acute infections and that they have the potential to affect patient outcomes in this setting.
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Affiliation(s)
- Sophia H. Nozick
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Egon A. Ozer
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Center for Pathogen Genomics and Microbial Evolution, Robert J. Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Rachel Medernach
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Travis J. Kochan
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Rebecca Kumar
- />Department of Medicine, Division of Infectious Diseases, Georgetown University, Washington, DC, USA
| | - Jori O. Mills
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Richard G. Wunderlink
- Department of Medicine, Division of Pulmonary and Critical Care, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Chao Qi
- Department of Pathology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
| | - Alan R. Hauser
- Department of Microbiology-Immunology, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
- Department of Medicine, Division of Infectious Diseases, Northwestern University Feinberg School of Medicine, Chicago, Illinois, USA
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Shen C, Zeng J, Zheng D, Xiao Y, Pu J, Luo L, Zhou H, Cai Y, Zhang L, Wu M, Zhang X, Deng G, Li S, Li Q, Zeng J, Sun Z, Huang B, Chen C. Molecular epidemiology and genomic dynamics of Pseudomonas aeruginosa isolates causing relapse infections. Microbiol Spectr 2023; 11:e0531222. [PMID: 37768065 PMCID: PMC10581123 DOI: 10.1128/spectrum.05312-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2023] [Accepted: 08/11/2023] [Indexed: 09/29/2023] Open
Abstract
Pseudomonas aeruginosa (P. aeruginosa) is one of the leading causes of chronic infections, including reinfection, relapse, and persistent infection, especially in cystic fibrosis patients. Relapse P. aeruginosa infections are more harmful because of repeated hospitalization and undertreatment of antimicrobials. However, relapse P. aeruginosa infection in China remains largely unknown. Herein, we performed a 3-year retrospective study from 2019 to 2022 in a tertiary hospital, which included 442 P. aeruginosa isolates from 196 patients. Relapse infection was identified by screening clinical records and whole-genome sequencing (WGS). We found that 31.6% (62/196) of patients had relapsed infections. The relapse incidence of carbapenem-resistant P. aeruginosa infection (51.4%) is significantly higher than that of carbapenem-susceptible P. aeruginosa infection (20.2%, P < 0.0001). These isolates were assigned to 50 distinct sequence types and sporadically distributed in phylogeny, indicating that relapsed infections were not caused by certain lineages. Fast adaptation and evolution of P. aeruginosa isolates were reflected by dynamic changes of antimicrobial resistance, gene loss and acquisition, and single-nucleotide polymorphisms during relapse episodes. Remarkably, a convergent non-synonymous mutation that occurs in a pyochelin-associated virulence gene fptA (T1056C, M252T) could be a considerable target for the diagnosis and treatment of relapse P. aeruginosa infection. These findings suggest that integrated utilization of WGS and medical records provides opportunities for improved diagnostics of relapsed infections. Continued surveillance of the genomic dynamics of relapse P. aeruginosa infection will generate further knowledge for optimizing treatment and prevention in the future.IMPORTANCEPseudomonas aeruginosa is a predominant pathogen that causes various chronic infections. Relapse infections promote the adaptation and evolution of antimicrobial resistance and virulence of P. aeruginosa, which obscure evolutionary trends and complicate infection management. We observed a high incidence of relapse P. aeruginosa infection in this study. Whole-genome sequencing (WGS) revealed that relapse infections were not caused by certain lineages of P. aeruginosa isolates. Genomic dynamics of relapse P. aeruginosa among early and later stages reflected a plasticity scattered through the entire genome and fast adaptation and genomic evolution in different ways. Remarkably, a convergent evolution was found in a significant virulence gene fptA, which could be a considerable target for diagnosis and treatment. Taken together, our findings highlight the importance of longitudinal surveillance of relapse P. aeruginosa infection in China since cystic fibrosis is rare in Chinese. Integrated utilization of WGS and medical records provides opportunities for improved diagnostics of relapse infections.
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Affiliation(s)
- Cong Shen
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Jinxiang Zeng
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Dexiang Zheng
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Yinglun Xiao
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Jieying Pu
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Li Luo
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Hongyun Zhou
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Yimei Cai
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Liling Zhang
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Meina Wu
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Xuan Zhang
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Guangyuan Deng
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Song Li
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Qiwei Li
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Jianming Zeng
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
| | - Zhaohui Sun
- Department of Laboratory Medicine, General Hospital of Southern Theater Command, Guangzhou, China
| | - Bin Huang
- Department of Clinical Laboratory, The First Affiliated Hospital of Sun Yat-sen University, Guangzhou, China
| | - Cha Chen
- The Second Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou, China
- Department of Clinical Laboratory, The Second Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangdong Provincial Hospital of Traditional Chinese Medicine, Guangzhou, China
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