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Do DT, Yang MR, Vo TNS, Le NQK, Wu YW. Unitig-centered pan-genome machine learning approach for predicting antibiotic resistance and discovering novel resistance genes in bacterial strains. Comput Struct Biotechnol J 2024; 23:1864-1876. [PMID: 38707536 PMCID: PMC11067008 DOI: 10.1016/j.csbj.2024.04.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Revised: 04/13/2024] [Accepted: 04/13/2024] [Indexed: 05/07/2024] Open
Abstract
In current genomic research, the widely used methods for predicting antimicrobial resistance (AMR) often rely on prior knowledge of known AMR genes or reference genomes. However, these methods have limitations, potentially resulting in imprecise predictions owing to incomplete coverage of AMR mechanisms and genetic variations. To overcome these limitations, we propose a pan-genome-based machine learning approach to advance our understanding of AMR gene repertoires and uncover possible feature sets for precise AMR classification. By building compacted de Brujin graphs (cDBGs) from thousands of genomes and collecting the presence/absence patterns of unique sequences (unitigs) for Pseudomonas aeruginosa, we determined that using machine learning models on unitig-centered pan-genomes showed significant promise for accurately predicting the antibiotic resistance or susceptibility of microbial strains. Applying a feature-selection-based machine learning algorithm led to satisfactory predictive performance for the training dataset (with an area under the receiver operating characteristic curve (AUC) of > 0.929) and an independent validation dataset (AUC, approximately 0.77). Furthermore, the selected unitigs revealed previously unidentified resistance genes, allowing for the expansion of the resistance gene repertoire to those that have not previously been described in the literature on antibiotic resistance. These results demonstrate that our proposed unitig-based pan-genome feature set was effective in constructing machine learning predictors that could accurately identify AMR pathogens. Gene sets extracted using this approach may offer valuable insights into expanding known AMR genes and forming new hypotheses to uncover the underlying mechanisms of bacterial AMR.
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Affiliation(s)
- Duyen Thi Do
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
| | - Ming-Ren Yang
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Department of Electrical Engineering, National Taiwan University of Science and Technology, Taipei, Taiwan
| | - Tran Nam Son Vo
- Department of Business Administration, College of Management, Lunghwa University of Science and Technology, Taoyuan City, Taiwan
| | - Nguyen Quoc Khanh Le
- Professional Master Program in Artificial Intelligence in Medicine, College of Medicine, Taipei Medical University, Taipei, Taiwan
| | - Yu-Wei Wu
- Graduate Institute of Biomedical Informatics, College of Medical Science and Technology, Taipei Medical University, Taipei, Taiwan
- Clinical Big Data Research Center, Taipei Medical University Hospital, Taipei, Taiwan
- TMU Research Center for Digestive Medicine, Taipei Medical University, Taipei, Taiwan
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Vega AD, DeRonde K, Jimenez A, Piazza M, Vu C, Martinez O, Rojas LJ, Marshall S, Yasmin M, Bonomo RA, Abbo LM. Difficult-to-treat (DTR) Pseudomonas aeruginosa harboring Verona-Integron metallo-β-lactamase ( blaVIM): infection management and molecular analysis. Antimicrob Agents Chemother 2024; 68:e0147423. [PMID: 38602418 PMCID: PMC11064525 DOI: 10.1128/aac.01474-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Accepted: 03/11/2024] [Indexed: 04/12/2024] Open
Abstract
Pseudomonas aeruginosa harboring Verona Integron-encoded metallo-β-lactamase enzymes (VIM-CRPA) have been associated with infection outbreaks in several parts of the world. In the US, however, VIM-CRPA remain rare. Starting in December 2018, we identified a cluster of cases in our institution. Herein, we present our epidemiological investigation and strategies to control/manage these challenging infections. This study was conducted in a large academic healthcare system in Miami, FL, between December 2018 and January 2022. Patients were prospectively identified via rapid molecular diagnostics when cultures revealed carbapenem-resistant P. aeruginosa. Alerts were received in real time by the antimicrobial stewardship program and infection prevention teams. Upon alert recognition, a series of interventions were performed as a coordinated effort. A retrospective chart review was conducted to collect patient demographics, antimicrobial therapy, and clinical outcomes. Thirty-nine VIM-CRPA isolates led to infection in 21 patients. The majority were male (76.2%); the median age was 52 years. The majority were mechanically ventilated (n = 15/21; 71.4%); 47.6% (n = 10/21) received renal replacement therapy at the time of index culture. Respiratory (n = 20/39; 51.3%) or bloodstream (n = 13/39; 33.3%) were the most common sources. Most infections (n = 23/37; 62.2%) were treated with an aztreonam-avibactam regimen. Six patients (28.6%) expired within 30 days of index VIM-CRPA infection. Fourteen isolates were selected for whole genome sequencing. Most of them belonged to ST111 (12/14), and they all carried blaVIM-2 chromosomally. This report describes the clinical experience treating serious VIM-CRPA infections with either aztreonam-ceftazidime/avibactam or cefiderocol in combination with other agents. The importance of implementing infection prevention strategies to curb VIM-CRPA outbreaks is also demonstrated.
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Affiliation(s)
- Ana D. Vega
- Department of Pharmacy, Jackson Health System, Miami, Florida, USA
| | - Kailynn DeRonde
- Department of Pharmacy, Jackson Health System, Miami, Florida, USA
| | - Adriana Jimenez
- Department of Pharmacy, Jackson Health System, Miami, Florida, USA
- Department of Epidemiology, Florida International University, Miami, Florida, USA
| | - Michael Piazza
- Department of Medicine, Virtua Medical Group, Medford, New Jersey, USA
| | - Christine Vu
- Department of Pharmacy, Jackson Health System, Miami, Florida, USA
| | - Octavio Martinez
- Department of Pharmacy, Jackson Health System, Miami, Florida, USA
- Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida, USA
| | - Laura J. Rojas
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
| | - Steven Marshall
- Department of Medicine, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Mohamad Yasmin
- Department of Medicine, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
| | - Robert A. Bonomo
- Department of Molecular Biology and Microbiology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- CWRU-Cleveland VAMC Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Cleveland, Ohio, USA
- Department of Medicine, Louis Stokes Cleveland Department of Veterans Affairs Medical Center, Cleveland, Ohio, USA
- Departments of Proteomics, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Pharmacology, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
- Department of Biochemistry, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA
| | - Lilian M. Abbo
- Department of Pharmacy, Jackson Health System, Miami, Florida, USA
- Department of Medicine, University of Miami Miller School of Medicine, Miami, Florida, USA
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Gondal AJ, Choudhry N, Niaz A, Yasmin N. Molecular Analysis of Carbapenem and Aminoglycoside Resistance Genes in Carbapenem-Resistant Pseudomonas aeruginosa Clinical Strains: A Challenge for Tertiary Care Hospitals. Antibiotics (Basel) 2024; 13:191. [PMID: 38391577 PMCID: PMC10886086 DOI: 10.3390/antibiotics13020191] [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: 11/25/2023] [Revised: 01/09/2024] [Accepted: 01/23/2024] [Indexed: 02/24/2024] Open
Abstract
Carbapenem-resistant Pseudomonas aeruginosa (P. aeruginosa) strains have become a global threat due to their remarkable capability to survive and disseminate successfully by the acquisition of resistance genes. As a result, the treatment strategies have been severely compromised. Due to the insufficient available data regarding P. aeruginosa resistance from Pakistan, we aimed to investigate the resistance mechanisms of 249 P. aeruginosa strains by antimicrobial susceptibility testing, polymerase chain reaction for the detection of carbapenemases, aminoglycoside resistance genes, extended-spectrum beta-lactamases (ESBLs), sequence typing and plasmid typing. Furthermore, we tested silver nanoparticles (AgNPs) to evaluate their in vitro sensitivity against antimicrobial-resistant P. aeruginosa strains. We observed higher resistance against antimicrobials in the general surgery ward, general medicine ward and wound samples. Phenotypic carbapenemase-producer strains comprised 80.7% (201/249) with 89.0% (179/201) demonstrating genes encoding carbapenemases: blaNDM-1 (32.96%), blaOXA48 (37.43%), blaIMP (7.26%), blaVIM (5.03%), blaKPC-2 (1.12%), blaNDM-1/blaOXA48 (13.97%), blaOXA-48/blaVIM (1.68%) and blaVIM/blaIMP (0.56%). Aminoglycoside-modifying enzyme genes and 16S rRNA methylase variants were detected in 43.8% (109/249) strains: aac(6')-lb (12.8%), aac(3)-lla (12.0%), rmtB (21.1%), rmtC (11.0%), armA (12.8%), rmtD (4.6%), rmtF (6.4%), rmtB/aac(3)-lla (8.2%), rmtB/aac(6')-lla (7.3%) and rmtB/armA (3.6%). In total, 43.0% (77/179) of the strains coharbored carbapenemases and aminoglycoside resistance genes with 83.1% resistant to at least 1 agent in 3 or more classes and 16.9% resistant to every class of antimicrobials tested. Thirteen sequence types (STs) were identified: ST235, ST277, ST234, ST170, ST381, ST175, ST1455, ST1963, ST313, ST207, ST664, ST357 and ST348. Plasmid replicon types IncFI, IncFII, IncA/C, IncL/M, IncN, IncX, IncR and IncFIIK and MOB types F11, F12, H121, P131 and P3 were detected. Meropenem/AgNPs and Amikacin/AgNPs showed enhanced antibacterial activity. We reported the coexistence of carbapenemases and aminoglycoside resistance genes among carbapenem-resistant P. aeruginosa with diverse clonal lineages from Pakistan. Furthermore, we highlighted AgNP's potential role in handling future antimicrobial resistance concerns.
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Affiliation(s)
- Aamir Jamal Gondal
- Department of Biomedical Sciences, King Edward Medical University, Lahore 54000, Pakistan
| | - Nakhshab Choudhry
- Department of Biochemistry, King Edward Medical University, Lahore 54000, Pakistan
| | - Ammara Niaz
- Department of Biochemistry, King Edward Medical University, Lahore 54000, Pakistan
| | - Nighat Yasmin
- Department of Biomedical Sciences, King Edward Medical University, Lahore 54000, Pakistan
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AboElfarh HE, Habib ESE, El-Sokkary MMA. Effect of dexamethasone and tenoxicam on the virulence activities of different Pseudomonas aeruginosa clinical isolates. Germs 2023; 13:321-331. [PMID: 38361541 PMCID: PMC10866164 DOI: 10.18683/germs.2023.1401] [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: 11/26/2022] [Revised: 06/02/2023] [Accepted: 10/31/2023] [Indexed: 02/17/2024]
Abstract
Introduction This study aimed to examine the effect of commonly used non-antibiotic drugs (dexamethasone and tenoxicam), on treatment of Pseudomonas aeruginosa infections, antibiotic resistance and virulence in this pathogen. Methods Four antibiotics (gentamicin, cefepime, ciprofloxacin and meropenem) were investigated. The proteolysis and hemolysis were selected as virulence factors for investigation. In this work, we selected the following final concentrations: dexamethasone (0.0052 μg/mL) and tenoxicam (2.7 μg/mL) to be used in combination with antibiotics or alone for investigation of their effects on antibiotic resistance and virulence in P. aeruginosa isolates. Results The drugs either increased or decreased antibiotic resistance in only 0-3 isolates, which indicates that the investigated drugs did not significantly affect the antibiotic resistance. Interestingly, our study demonstrated that both dexamethasone and tenoxicam increased the hemolytic activity of the investigated isolates. On the other hand, our results indicated that no overall final increasing or decreasing effect could be observed for dexamethasone on the proteolytic activity, while tenoxicam increased the proteolytic activity of the investigated isolates. Interestingly, by real-time PCR dexamethasone has shown significant down-regulation of virulence genes namely algD, plcH and toxA, apparently, in case of combination with ciprofloxacin and with gentamicin in one isolate. However, a negative influence was observed in another isolate. Unfortunately, in the case of tenoxicam the only positive effect was observed in the combination with gentamicin in one isolate. Conclusions Resistance of P. aeruginosa against gentamicin and ciprofloxacin may be affected by combining these antibiotics with dexamethasone or tenoxicam.
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Affiliation(s)
- Heba E. AboElfarh
- MD student, Microbiology and Immunology Department, Faculty of Pharmacy, Mansoura University, 35516, Egypt
| | - El-Sayed E. Habib
- PhD, Professor of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, 35516, Egypt
| | - Mohamed M. A. El-Sokkary
- PhD, Professor of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, 35516, Egypt
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Dos Santos Costa J, Dos Santos PB, de Souza ATHI, Morgado TO, Cândido SL, Silva TRD, Nakazato L, Dutra V. KPC-2-producing Pseudomonas aeruginosa isolated from wild animals in Brazil. Braz J Microbiol 2023; 54:3307-3313. [PMID: 37819609 PMCID: PMC10689335 DOI: 10.1007/s42770-023-01143-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 09/28/2023] [Indexed: 10/13/2023] Open
Abstract
Pseudomonas aeruginosa an opportunistic pathogen that causes infections in hospitals and has high morbidity and mortality rates. In addition, it is a widely distributed environmental bacterium that can colonise a variety of habitats. Although wild animals do not have access to antibiotics, antibacterial resistance in these animals has increasingly been reported worldwide. Although the presence of Klebsiella pneumoniae carbapenemase (KPC) is uncommon in P. aeruginosa, it has been increasingly reported. This study examined KPC-2-producing P. aeruginosa in wild animals. A total of 27 P. aeruginosa isolates were obtained from clinical cases treated at the Microbiology Laboratory of the Veterinary Hospital of UFMT, Brazil. P. aeruginosa and blaKPC-2 carbapenemase resistance genes were identified using PCR. Antimicrobial susceptibility of KPC-producing P. aeruginosa was evaluated using the disk diffusion method. The blaKPC-2 gene was detected in 40.7% of the isolates (11/27). The rates of antimicrobial resistance and intermediate sensitivity were as follows: piperacillin/tazobactam (44.4%), imipenem (29.6%), meropenem (51.8%), amikacin (77.8%), cefepime (85.2%), and ciprofloxacin (70.4%). Twelve isolates were classified as Multidrug-resistant (MDR). This study presents the first report of P. aeruginosa with the blaKPC-2 gene in wild animals in Brazil, highlighting the importance of molecular research on resistance genes in P. aeruginosa from a One-Health perspective.
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Affiliation(s)
- Jackeliny Dos Santos Costa
- Laboratório de Microbiologia e Biologia Molecular Veterinária, Universidade Federal do Mato Grosso, Av. Fernando Corrêa da Costa 2367, Bairro Boa Esperança, Cuiabá, MT, 78060-900, Brazil
| | - Paulo Batista Dos Santos
- Laboratório de Microbiologia e Biologia Molecular Veterinária, Universidade Federal do Mato Grosso, Av. Fernando Corrêa da Costa 2367, Bairro Boa Esperança, Cuiabá, MT, 78060-900, Brazil
| | - Alessandra Tammy Hayakawa Ito de Souza
- Laboratório de Microbiologia e Biologia Molecular Veterinária, Universidade Federal do Mato Grosso, Av. Fernando Corrêa da Costa 2367, Bairro Boa Esperança, Cuiabá, MT, 78060-900, Brazil
| | - Thais Oliveira Morgado
- Laboratório de Microbiologia e Biologia Molecular Veterinária, Universidade Federal do Mato Grosso, Av. Fernando Corrêa da Costa 2367, Bairro Boa Esperança, Cuiabá, MT, 78060-900, Brazil
| | - Stéfhano Luís Cândido
- Laboratório de Microbiologia e Biologia Molecular Veterinária, Universidade Federal do Mato Grosso, Av. Fernando Corrêa da Costa 2367, Bairro Boa Esperança, Cuiabá, MT, 78060-900, Brazil
| | - Thais Rosso da Silva
- Laboratório de Microbiologia e Biologia Molecular Veterinária, Universidade Federal do Mato Grosso, Av. Fernando Corrêa da Costa 2367, Bairro Boa Esperança, Cuiabá, MT, 78060-900, Brazil
| | - Luciano Nakazato
- Laboratório de Microbiologia e Biologia Molecular Veterinária, Universidade Federal do Mato Grosso, Av. Fernando Corrêa da Costa 2367, Bairro Boa Esperança, Cuiabá, MT, 78060-900, Brazil.
| | - Valeria Dutra
- Laboratório de Microbiologia e Biologia Molecular Veterinária, Universidade Federal do Mato Grosso, Av. Fernando Corrêa da Costa 2367, Bairro Boa Esperança, Cuiabá, MT, 78060-900, Brazil
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Tickler IA, Kawa D, Obradovich AE, Fang FC, Tenover FC. Characterization of Carbapenemase- and ESBL-Producing Gram-Negative Bacilli Isolated from Patients with Urinary Tract and Bloodstream Infections. Antibiotics (Basel) 2023; 12:1386. [PMID: 37760683 PMCID: PMC10525328 DOI: 10.3390/antibiotics12091386] [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: 07/31/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 09/29/2023] Open
Abstract
A total of 199 Gram-negative bacterial isolates from urinary tract infections and 162 from bloodstream infections were collected from 12 healthcare systems throughout the United States between May 2021 and August 2022. The isolates, phenotypically non-susceptible to 2nd or 3rd generation cephalosporins or carbapenems, were characterized through antimicrobial susceptibility testing and whole genome sequence analysis to obtain a broad snapshot of beta-lactamase-mediated resistance among these two sample types. Overall, 23 different carbapenemase genes were detected among 13 species (20.5% of isolates). The blaKPC-3 and blaKPC-2 subtypes were the most common carbapenemase genes identified, followed by blaNDM and the co-carriage of two different blaOXA carbapenemases by Acinetobacter baumannii isolates. All carbapenemase-producing A. baumannii isolates were mCIM negative. Extended-spectrum beta-lactamase genes were identified in 66.2% of isolates; blaCTX-M-15 was the most common. AmpC genes, both plasmid and chromosomal, were detected in 33.2% of isolates. Importantly, 2.8%, 8.3%, and 22.2% of blaKPC-positive organisms were susceptible to ertapenem, imipenem, and meropenem, respectively. The correlation between broth microdilution and disk diffusion results was high for most drugs except cefepime, where the detection of resistance was statistically lower by disk diffusion. Thus, there were gaps in the accuracy of susceptibility testing for some mechanisms of resistance.
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Affiliation(s)
| | | | - Anne E. Obradovich
- Department of Medical Microbiology and Immunology, School of Medicine, Creighton University, Omaha, NE 68178, USA
| | - Ferric C. Fang
- Departments of Laboratory Medicine and Microbiology, University of Washington, Seattle, WA 98195, USA
| | - Fred C. Tenover
- College of Arts & Sciences, University of Dayton, Dayton, OH 45469, USA
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Forero-Hurtado D, Corredor-Rozo ZL, Ruiz-Castellanos JS, Márquez-Ortiz RA, Abril D, Vanegas N, Lafaurie GI, Chambrone L, Escobar-Pérez J. Worldwide Dissemination of blaKPC Gene by Novel Mobilization Platforms in Pseudomonas aeruginosa: A Systematic Review. Antibiotics (Basel) 2023; 12:antibiotics12040658. [PMID: 37107020 PMCID: PMC10134989 DOI: 10.3390/antibiotics12040658] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/11/2023] [Accepted: 03/12/2023] [Indexed: 03/30/2023] Open
Abstract
The dissemination of blaKPC-harboring Pseudomonas aeruginosa (KPC-Pa) is considered a serious public health problem. This study provides an overview of the epidemiology of these isolates to try to elucidate novel mobilization platforms that could contribute to their worldwide spread. A systematic review in PubMed and EMBASE was performed to find articles published up to June 2022. In addition, a search algorithm using NCBI databases was developed to identify sequences that contain possible mobilization platforms. After that, the sequences were filtered and pair-aligned to describe the blaKPC genetic environment. We found 691 KPC-Pa isolates belonging to 41 different sequence types and recovered from 14 countries. Although the blaKPC gene is still mobilized by the transposon Tn4401, the non-Tn4401 elements (NTEKPC) were the most frequent. Our analysis allowed us to identify 25 different NTEKPC, mainly belonging to the NTEKPC-I, and a new type (proposed as IVa) was also observed. This is the first systematic review that consolidates information about the behavior of the blaKPC acquisition in P. aeruginosa and the genetic platforms implied in its successful worldwide spread. Our results show high NTEKPC prevalence in P. aeruginosa and an accelerated dynamic of unrelated clones. All information collected in this review was used to build an interactive online map.
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Zhao Y, Chen D, Ji B, Zhang X, Anbo M, Jelsbak L. Whole-genome sequencing reveals high-risk clones of Pseudomonas aeruginosa in Guangdong, China. Front Microbiol 2023; 14:1117017. [PMID: 37125174 PMCID: PMC10140354 DOI: 10.3389/fmicb.2023.1117017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2022] [Accepted: 03/27/2023] [Indexed: 05/02/2023] Open
Abstract
The ever-increasing prevalence of infections produced by multidrug-resistant or extensively drug-resistant Pseudomonas aeruginosa is commonly linked to a limited number of aptly-named epidemical 'high-risk clones' that are widespread among and within hospitals worldwide. The emergence of new potential high-risk clone strains in hospitals highlights the need to better and further understand the underlying genetic mechanisms for their emergence and success. P. aeruginosa related high-risk clones have been sporadically found in China, their genome sequences have rarely been described. Therefore, the large-scale sequencing of multidrug-resistance high-risk clone strains will help us to understand the emergence and transmission of antibiotic resistances in P. aeruginosa high-risk clones. In this study, 212 P. aeruginosa strains were isolated from 2 tertiary hospitals within 3 years (2018-2020) in Guangdong Province, China. Whole-genome sequencing, multi-locus sequence typing (MLST) and antimicrobial susceptibility testing were applied to analyze the genomic epidemiology of P. aeruginosa in this region. We found that up to 130 (61.32%) of the isolates were shown to be multidrug resistant, and 196 (92.45%) isolates were Carbapenem-Resistant Pseudomonas aeruginosa. MLST analysis demonstrated high diversity of sequence types, and 18 reported international high-risk clones were identified. Furthermore, we discovered the co-presence of exoU and exoS genes in 5 collected strains. This study enhances insight into the regional research of molecular epidemiology and antimicrobial resistance of P. aeruginosa in China. The high diversity of clone types and regional genome characteristics can serve as a theoretical reference for public health policies and help guide measures for the prevention and control of P. aeruginosa resistance.
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Affiliation(s)
- Yonggang Zhao
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Dingqiang Chen
- Department of Laboratory Medicine, Microbiome Medicine Center, Zhujiang Hospital, Southern Medical University, Guangzhou, Guangdong, China
| | - Boyang Ji
- Department of Biology and Biological Engineering, Chalmers University of Technology, Gothenburg, Sweden
| | | | - Mikkel Anbo
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Lars Jelsbak
- Department of Biotechnology and Biomedicine, Technical University of Denmark, Kongens Lyngby, Denmark
- *Correspondence: Lars Jelsbak,
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9
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Hammoudi Halat D, Ayoub Moubareck C. The Intriguing Carbapenemases of Pseudomonas aeruginosa: Current Status, Genetic Profile, and Global Epidemiology. THE YALE JOURNAL OF BIOLOGY AND MEDICINE 2022; 95:507-515. [PMID: 36568831 PMCID: PMC9765337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Worldwide, Pseudomonas aeruginosa remains a leading nosocomial pathogen that is difficult to treat and constitutes a challenging menace to healthcare systems. P. aeruginosa shows increased and alarming resistance to carbapenems, long acknowledged as last-resort antibiotics for treatment of resistant infections. Varied and recalcitrant pathways of resistance to carbapenems can simultaneously occur in P. aeruginosa, including the production of carbapenemases, broadest spectrum types of β-lactamases that hydrolyze virtually almost all β-lactams, including carbapenems. The organism can produce chromosomal, plasmid-encoded, and integron- or transposon-mediated carbapenemases from different molecular classes. These include Ambler class A (KPC and some types of GES enzymes), class B (different metallo-β-lactamases such as IMP, VIM, and NDM), and class D (oxacillinases with carbapenem-hydrolyzing capacity like OXA-198) enzymes. Additionally, derepression of chromosomal AmpC cephalosporinases in P. aeruginosa contributes to carbapenem resistance in the presence of other concomitant mechanisms such as impermeability or efflux overexpression. Epidemiologic and molecular evidence of carbapenemases in P. aeruginosa has been long accumulating, and reports of their existence in different geographical areas of the world currently exist. Such reports are continuously being updated and reveal emerging varieties of carbapenemases and/or new genetic environments. This review summarizes carbapenemases of importance in P. aeruginosa, highlights their genetic profile, and presents current knowledge about their global epidemiology.
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Affiliation(s)
- Dalal Hammoudi Halat
- Department of Pharmaceutical Sciences, School of
Pharmacy, Lebanese International University, Beirut and Bekaa Campuses,
Lebanon,To whom all correspondence should be addressed:
Dr. Dalal Hammoudi Halat, Lebanese International University, School of Pharmacy,
West Bekaa, Lebanon; ; ORCID:
https://www.orcid.org/0000-0001-6907-4110
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Dong N, Liu C, Hu Y, Lu J, Zeng Y, Chen G, Chen S, Zhang R. Emergence of an Extensive Drug Resistant Pseudomonas aeruginosa Strain of Chicken Origin Carrying blaIMP-45, tet(X6), and tmexCD3- toprJ3 on an Inc pRBL16 Plasmid. Microbiol Spectr 2022; 10:e0228322. [PMID: 36301093 PMCID: PMC9769874 DOI: 10.1128/spectrum.02283-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/13/2022] [Indexed: 01/06/2023] Open
Abstract
This study reports an extensively drug resistant Pseudomonas aeruginosa strain PA166-2 which was of chicken origin and carrying blaIMP-45, tet(X6) and tmexCD3-toprJ3 on a single plasmid. The strain was characterized by antimicrobial susceptibility testing, resistance gene screening, conjugation assay, whole-genome sequencing, and bioinformatics analysis. Strain PA166-2 was resistant to tigecycline and carbapenems. It belonged to ST313 and carried a plasmid pPA166-2-MDR, which belongs to the incompatibility group IncpRBL16. pPA166-2-MDR harbored a 78 Kb multidrug resistance (MDR) region carrying an array of antimicrobial resistance genes, including blaIMP-45, tet(X6), and tmexCD3-toprJ3. The gene blaIMP-45 was inserted into the backbone of plasmid pPA166-2-MDR within a class 1 integron, In786. tmexCD3-toprJ3 in plasmid pPA166-2-MDR was inserted in umuC, constituting the genetic context of ISCfr1-tnfxB3-tmexC3-tmexD3-toprJ3-△umuC. The genetic context of tet(X6) in this plasmid was identical to that of other reported plasmid-borne tet(X) variants, namely, tet(X6)-abh-guaA-ISVsa3. To the best of our knowledge, this is the first report of the cooccurrence of blaIMP-45, tet(X6), and tmexCD3-toprJ3 in one plasmid in Pseudomonas sp. The emergence of plasmid-mediated tigecycline resistance genes tmexCD3-toprJ3 and tet(X6), as well as carbapenemase genes from chickens expanded the global transmission of vital resistance genes. Findings from us and from others indicate that plasmids of the incompatibility group IncpRBL16 may serve as a reservoir for carbapenem and tigecycline resistance determinants. IMPORTANCE Pseudomonas aeruginosa is an opportunistic pathogen that causes infections that are difficult to treat. This study reported, for the first time, the occurrence of last-resort antibiotic resistance determinants blaIMP-45, tet(X6), and tmexCD3-toprJ3 on a single plasmid in P. aeruginosa from chickens. The P. aeruginosa strain belonged to ST313 and was resistant to last-line antibiotics, namely, carbapenems and tigecycline. The plasmid carrying the last-line resistance genes belonged to the incompatibility group IncpRBL16, which was reported to contain different profiles of accessory modules and thus carried diverse collections of resistance genes. The emergence of plasmid-mediated tigecycline resistance genes tmexCD3-toprJ3 and tet(X6), as well as carbapenemase genes, from chickens expanded the global transmission of vital resistance genes. The results in this study highlighted that IncpRBL16 plasmids may serve as a reservoir for the dissemination of resistance genes. Control measures should be implemented to prevent the further dissemination of such strains.
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Affiliation(s)
- Ning Dong
- Department of Medical Microbiology, School of Biology and Basic Medical Science, Medical College of Soochow University, Suzhou, China
- Suzhou Key Laboratory of Pathogen Bioscience and Anti-infective Medicine, Soochow University, Suzhou, China
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Congcong Liu
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China
| | - Yanyan Hu
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China
| | - Jiayue Lu
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China
| | - Yu Zeng
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China
| | - Gongxiang Chen
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Rong Zhang
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China
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Efficacy of Vaporized Hydrogen Peroxide Combined with Silver Ions against Multidrug-Resistant Gram-Negative and Gram-Positive Clinical Isolates. Int J Mol Sci 2022; 23:ijms232415826. [PMID: 36555465 PMCID: PMC9779286 DOI: 10.3390/ijms232415826] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 11/19/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022] Open
Abstract
Antimicrobial resistance (AMR) is a serious public health problem that results in high morbidity and mortality rates. In particular, multidrug-resistant (MDR) strains circulating in hospital settings pose a major threat as they are associated with serious nosocomial infections. Therefore, regular cleaning and disinfection procedures, usually using chemical disinfectants, must be implemented in these facilities. Hydrogen peroxide (HP)-based disinfectants have proven high microbicidal activity and several comparative advantages over conventional disinfectants. We assessed the in vitro biocidal activity of an 8% HP solution combined with 30 mg/L silver ions (HP + Ag) against MDR clinical isolates of Klebsiella pneumoniae (MDRKp) and Pseudomonas aeruginosa (MDRPa), and methicillin-resistant Staphylococcus aureus (MRSA). Accordingly, the in vitro antibacterial activity was determined using the macrodilution method, and the efficacy was determined for 30 min in terms of (1) activity on bacteria in suspension and (2) activity on surfaces using vaporized HP + Ag on a 20 cm2 stainless steel surface. A strong bactericidal effect of HP + Ag was observed against MDRKp, MDRPa, and MRSA strains, with minimum inhibitory concentrations and minimum bactericidal concentrations between 362.5 and 5800 mg/L. A strong effect was observed during the 30 min of HP + Ag exposure to the resistant clinical isolates, with over 4-Log10 reduction in CFUs. Regarding the efficacy of the disinfectant on surfaces, bacterial load reductions of >99% were observed. These results suggest that HP + Ag is potentially useful as an effective disinfectant for decontaminating surfaces in hospital settings suspected of contamination with MDR bacteria.
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Mojica MF, De La Cadena E, Ríos R, García-Betancur JC, Díaz L, Reyes J, Hernández-Gómez C, Radice M, Gales AC, Castañeda Méndez P, Munita JM, Pallares CJ, Martínez JRW, Villegas MV. Molecular mechanisms leading to ceftolozane/tazobactam resistance in clinical isolates of Pseudomonas aeruginosa from five Latin American countries. Front Microbiol 2022; 13:1035609. [PMID: 36353456 PMCID: PMC9638110 DOI: 10.3389/fmicb.2022.1035609] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2022] [Accepted: 09/30/2022] [Indexed: 12/03/2022] Open
Abstract
Objectives Identify molecular mechanisms responsible for the in vitro non-susceptibility to ceftolozane/tazobactam (TOL) in a group of 158 clinical isolates of Pseudomonas aeruginosa from five Latin American countries collected before the introduction of TOL into the clinical practice. Methods Clinical isolates of P. aeruginosa (n = 504) were collected between January 2016 and October 2017 from 20 hospitals located in Argentina, Brazil, Chile, Colombia, and Mexico. Minimum inhibitory concentrations (MICs) to TOL were determined by standard broth microdilution and interpreted according to CLSI breakpoints. Initially, production of carbapenemases in TOL non-susceptible isolates was assessed by Rapidec® followed by qPCR to detect blaKPC, blaNDM-1, blaVIM, and blaIMP. Illumina® WGS was performed for isolates in which non-susceptibility to TOL was not mediated by carbapenemases. Results A total of 158 (31.3%) isolates were non-susceptible to TOL. In 74 (46.8%) of these isolates, non-susceptibility to TOL was explained by the production of at least one carbapenemase. WGS revealed that some isolates carried ESBLs, mutated blaPDC and ampD, associated with decreased susceptibility to TOL. Conclusion Substitutions found in PDC and carbapenemase production were the most common presumed mechanisms of resistance to TOL detected in this study. This study shows that epidemiological surveillance is warranted to monitor the emergence of novel mechanisms of resistance to TOL that might compromise its clinical utility.
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Affiliation(s)
- María F. Mojica
- Grupo de Investigación en Resistencia Antimicrobiana y Epidemiologia Hospitalaria, Universidad El Bosque, Bogotá, Colombia
- Department of Molecular Biology and Microbiology, School of Medicine, Case Western Reserve University, Cleveland, OH, United States
- Cleveland VA Medical Center for Antimicrobial Resistance and Epidemiology (Case VA CARES), Case Western Reserve University, Cleveland, OH, United States
- Research Service, VA Northeast Ohio Healthcare System, Cleveland, OH, United States
- *Correspondence: María F. Mojica,
| | - Elsa De La Cadena
- Grupo de Investigación en Resistencia Antimicrobiana y Epidemiologia Hospitalaria, Universidad El Bosque, Bogotá, Colombia
| | - Rafael Ríos
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogotá, Colombia
| | - Juan Carlos García-Betancur
- Grupo de Investigación en Resistencia Antimicrobiana y Epidemiologia Hospitalaria, Universidad El Bosque, Bogotá, Colombia
| | - Lorena Díaz
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogotá, Colombia
- Millenium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
| | - Jinnethe Reyes
- Molecular Genetics and Antimicrobial Resistance Unit, Universidad El Bosque, Bogotá, Colombia
| | - Cristhian Hernández-Gómez
- Grupo de Investigación en Resistencia Antimicrobiana y Epidemiologia Hospitalaria, Universidad El Bosque, Bogotá, Colombia
| | - Marcela Radice
- Universidad de Buenos Aires, Facultad de Farmacia y Bioquímica, Buenos Aires, Argentina
- Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), Buenos Aires, Argentina
| | - Ana C. Gales
- Universidade Federal de São Paulo, Division of Infectious Diseases, Brazil
| | | | - José M. Munita
- Millenium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- Genomics and Resistant Microbes (GeRM) Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina, Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Christian José Pallares
- Grupo de Investigación en Resistencia Antimicrobiana y Epidemiologia Hospitalaria, Universidad El Bosque, Bogotá, Colombia
- Clínica Imbanaco, Grupo Quiron, Cali, Colombia
| | - José R. W. Martínez
- Millenium Initiative for Collaborative Research on Bacterial Resistance (MICROB-R), Santiago, Chile
- Genomics and Resistant Microbes (GeRM) Instituto de Ciencias e Innovación en Medicina, Facultad de Medicina, Clínica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - María Virginia Villegas
- Grupo de Investigación en Resistencia Antimicrobiana y Epidemiologia Hospitalaria, Universidad El Bosque, Bogotá, Colombia
- Clínica Imbanaco, Grupo Quiron, Cali, Colombia
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García P, Brito B, Alcalde-Rico M, Munita JM, Martínez JRW, Olivares-Pacheco J, Quiroz V, Wozniak A. Acquisition of resistance to ceftazidime-avibactam during infection treatment in Pseudomonas aeruginosa through D179Y mutation in one of two blaKPC-2 gene copies without losing carbapenem resistance. Front Cell Infect Microbiol 2022; 12:981792. [PMID: 36118031 PMCID: PMC9478442 DOI: 10.3389/fcimb.2022.981792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 08/12/2022] [Indexed: 11/24/2022] Open
Abstract
Ceftazidime/Avibactam (CAZ/AVI) is frequently used to treat KPC-producing Pseudomonas aeruginosa (KPC-PA) and Enterobacterales. CAZ/AVI resistance is driven by several mechanisms. In P. aeruginosa this mainly occurs through alteration of AmpC, porins, and/or efflux pump overexpression, whereas in Enterobacterales it frequently occurs through D179Y substitution in the active site of KPC enzyme. This aminoacid change abolishes AVI binding to the KPC active site, hence inhibition is impaired. However, this substitution also decreases KPC-mediated resistance to carbapenems (“see-saw” effect). The goal of this work was to characterize the in vivo acquisition of CAZ/AVI resistance through D179Y substitution in a KPC-PA isolated from a hospitalized patient after CAZ/AVI treatment. Two KPC-PA isolates were obtained. The first isolate, PA-1, was obtained before CAZ/AVI treatment and was susceptible to CAZ/AVI. The second isolate, PA-2, was obtained after CAZ/AVI treatment and exhibited high-level CAZ/AVI resistance. Characterization of isolates PA-1 and PA-2 was performed through short and long-read whole genome sequencing analysis. The hybrid assembly showed that PA-1 and PA-2A had a single plasmid of 54,030 bp, named pPA-1 and pPA-2 respectively. Each plasmid harbored two copies of the blaKPC-containing Tn4401b transposon. However, while pPA-1 carried two copies of blaKPC-2, pPA-2 had one copy of blaKPC-2 and one copy of blaKPC-33, the allele with the D179Y substitution. Interestingly, isolate PA-2 did not exhibit the “see-saw” effect. The blaKPC-33 allele was detected only through hybrid assembly using a long-read-first approach. The present work describes a KPC-PA isolate harboring a plasmid-borne CAZ/AVI resistance mechanism based on two copies of blaKPC-2-Tn4401b and D179Y mutation in one of them, that is not associated with loss of resistance to carbapenems. These findings highlight the usefulness of a fine-tuned combined analysis of short and long-read data to detect similar emerging resistance mechanisms.
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Affiliation(s)
- Patricia García
- Laboratory of Microbiology, Department of Clinical Laboratories, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Universidad del Desarrollo, Santiago, Chile
- Clinical Laboratories Network, Red de Salud UC-CHRISTUS, Santiago, Chile
| | - Bárbara Brito
- Australian Institute for Microbiology & Infection, Faculty of Science, University of Technology, Sydney, Australia
| | - Manuel Alcalde-Rico
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Universidad del Desarrollo, Santiago, Chile
- Grupo de Resistencia Antimicrobiana en Bacterias Patógenas y Ambientales (GRABPA), Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
- Genomics & Resistant Microbes group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - José M. Munita
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Universidad del Desarrollo, Santiago, Chile
- Genomics & Resistant Microbes group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Jose R. W. Martínez
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Universidad del Desarrollo, Santiago, Chile
- Genomics & Resistant Microbes group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Jorge Olivares-Pacheco
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Universidad del Desarrollo, Santiago, Chile
- Grupo de Resistencia Antimicrobiana en Bacterias Patógenas y Ambientales (GRABPA), Instituto de Biología, Pontificia Universidad Católica de Valparaíso, Valparaíso, Chile
| | - Valeria Quiroz
- Laboratory of Microbiology, Department of Clinical Laboratories, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Genomics & Resistant Microbes group (GeRM), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina Clinica Alemana, Universidad del Desarrollo, Santiago, Chile
| | - Aniela Wozniak
- Laboratory of Microbiology, Department of Clinical Laboratories, Escuela de Medicina, Pontificia Universidad Católica de Chile, Santiago, Chile
- Millennium Initiative for Collaborative Research On Bacterial Resistance (MICROB-R), Instituto de Ciencias e Innovación en Medicina (ICIM), Facultad de Medicina, Universidad del Desarrollo, Santiago, Chile
- Clinical Laboratories Network, Red de Salud UC-CHRISTUS, Santiago, Chile
- *Correspondence: Aniela Wozniak, ;
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