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Zagui GS, de Almeida OGG, Moreira NC, Silva NGA, Meschede MSC, Darini ALC, Andrade LN, Segura-Muñoz SI. Hospital wastewater as source of human pathogenic bacteria: A phenotypic and genomic analysis of international high-risk clone VIM-2-producing Pseudomonas aeruginosa ST235/O11. ENVIRONMENTAL RESEARCH 2024; 255:119166. [PMID: 38759772 DOI: 10.1016/j.envres.2024.119166] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2024] [Revised: 05/12/2024] [Accepted: 05/15/2024] [Indexed: 05/19/2024]
Abstract
Pseudomonas aeruginosa belong to the special pathogen group capable of causing serious infections, with high mortality rates. The aim of this study was to describe the antibiotic resistance and genomic characteristics of Pseudomonas aeruginosa belonging to international high-risk clone ST235 (GPAE0131 isolate), obtained from hospital wastewater. P. aeruginosa GPAE0131 was isolated from ward tertiary hospital in Brazil and the antibiotic resistance profile was determined by the disc-diffusion method. Genomic characteristics related to antibiotic resistance and virulence factors were evaluated by genomic DNA sequencing on the Illumina MiSeq platform and bioinformatic analysis. GPAE0131 isolate showed resistance to piperacillin-tazobactam, cefepime, ceftazidime, imipenem, meropenem, ciprofloxacin, levofloxacin and tobramycin. Resistome comprehend of resistance genes to β-lactams (blaVIM-2, blaOXA-4, blaOXA-488, blaPDC-35), aminoglycosides (aph(3')-IIb, aac(6')-IIc, aac(6')-Ib9, aadA1), fosfomycin (fosA), chloramphenicol (catB7) and sulfonamides (sul1). Genome comparisons evidence insertion of blaVIM-2 and blaOXA-4 genes. GPAE0131 isolate was predicted to be pathogenic to humans and several virulence factors were found, including encoding gene for ExoU and exotoxin A. All of these features into a pathogenic international high-risk clone (ST235), classified as critical priority, stands out as public health concern due to the widespread dispersal of human pathogens through wastewater. It is suggested that mitigating measures be implemented, such as the treatment of hospital sewage and the addition of tertiary treatment, to prevent the escape of pathogens at this level into the environment.
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Affiliation(s)
- Guilherme Sgobbi Zagui
- Water Resources Research Group, Postgraduate Program in Environmental Technology, University of Ribeirão Preto, Brazil; School of Medicine, Department of Medicine, University of Ribeirão Preto, Brazil; Laboratory of Ecotoxicology and Environmental Parasitology, Ribeirão Preto College of Nursing, University of São Paulo, Brazil.
| | | | | | | | - Marina Smidt Celere Meschede
- Laboratory of Ecotoxicology and Environmental Parasitology, Ribeirão Preto College of Nursing, University of São Paulo, Brazil; Institute of Collective Health (ISCO), Federal University of Western Pará, Brazil
| | | | | | - Susana Inés Segura-Muñoz
- Laboratory of Ecotoxicology and Environmental Parasitology, Ribeirão Preto College of Nursing, University of São Paulo, Brazil
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Furlan JPR, Lopes R, Ramos MS, Rosa RDS, Dos Santos LDR, Stehling EG. The detection of KPC-2, NDM-1, and VIM-2 carbapenemases in international clones isolated from fresh vegetables highlights an emerging food safety issue. Int J Food Microbiol 2024; 420:110765. [PMID: 38838541 DOI: 10.1016/j.ijfoodmicro.2024.110765] [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: 02/07/2024] [Revised: 05/20/2024] [Accepted: 05/22/2024] [Indexed: 06/07/2024]
Abstract
Resistance to carbapenems emerged in clinical settings and has rapidly spread to other sectors, such as food and the environment, representing a One Health problem. In this regard, vegetables contaminated by critical priority pathogens have raised global concerns. Here, we have performed a whole-genome sequence-based analysis of extensively drug-resistant Klebsiella pneumoniae, Escherichia coli, and Pseudomonas aeruginosa strains isolated from cabbage, spinach, and lettuce, respectively. Genomic analysis revealed the emergence of international and high-risk clones belonging to ST340, ST155, and ST233, harboring a broad resistome to clinically important antimicrobials. In this context, K. pneumoniae, E. coli, and P. aeruginosa strains carried blaKPC-2, blaNDM-1, and blaVIM-2, respectively. The blaKPC-2 gene with a non-Tn4401 element (NTEKPC-Ic) was located on an IncX3-IncU plasmid, while the blaVIM-2 gene was associated with a Tn402-like class 1 integron, In559, on the chromosome. Curiously, the blaNDM-1 gene coexisted with the blaPER-2 gene on an IncC plasmid and the regions harboring both genes contained sequences of Tn3-like element ISKox2-like family transposase. Comparative genomic analysis showed interspecies and clonal transmission of carbapenemase-encoding genes at the human-animal-environmental interface. These findings raise a food safety alert about hospital-associated carbapenemase producers, supporting that fresh vegetables can act as a vehicle for the spread of high-risk clones.
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Affiliation(s)
- João Pedro Rueda Furlan
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Ralf Lopes
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Micaela Santana Ramos
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Rafael da Silva Rosa
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Lucas David Rodrigues Dos Santos
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil
| | - Eliana Guedes Stehling
- Department of Clinical Analyses, Toxicology and Food Science, School of Pharmaceutical Sciences of Ribeirão Preto, University of São Paulo, Ribeirão Preto, São Paulo, Brazil.
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Sendra E, Fernández-Muñoz A, Zamorano L, Oliver A, Horcajada JP, Juan C, Gómez-Zorrilla S. Impact of multidrug resistance on the virulence and fitness of Pseudomonas aeruginosa: a microbiological and clinical perspective. Infection 2024; 52:1235-1268. [PMID: 38954392 PMCID: PMC11289218 DOI: 10.1007/s15010-024-02313-x] [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: 03/22/2024] [Accepted: 05/30/2024] [Indexed: 07/04/2024]
Abstract
Pseudomonas aeruginosa is one of the most common nosocomial pathogens and part of the top emergent species associated with antimicrobial resistance that has become one of the greatest threat to public health in the twenty-first century. This bacterium is provided with a wide set of virulence factors that contribute to pathogenesis in acute and chronic infections. This review aims to summarize the impact of multidrug resistance on the virulence and fitness of P. aeruginosa. Although it is generally assumed that acquisition of resistant determinants is associated with a fitness cost, several studies support that resistance mutations may not be associated with a decrease in virulence and/or that certain compensatory mutations may allow multidrug resistance strains to recover their initial fitness. We discuss the interplay between resistance profiles and virulence from a microbiological perspective but also the clinical consequences in outcomes and the economic impact.
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Affiliation(s)
- Elena Sendra
- Infectious Diseases Service, Hospital del Mar, Infectious Pathology and Antimicrobials Research Group (IPAR), Hospital del Mar Research Institute, Universitat Autònoma de Barcelona (UAB), CEXS-Universitat Pompeu Fabra, Passeig Marítim 25-27, 08003, Barcelona, Spain
| | - Almudena Fernández-Muñoz
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Microbiology Department, University Hospital Son Espases, Crtra. Valldemossa 79, 07010, Palma, Spain
| | - Laura Zamorano
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Microbiology Department, University Hospital Son Espases, Crtra. Valldemossa 79, 07010, Palma, Spain
| | - Antonio Oliver
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Microbiology Department, University Hospital Son Espases, Crtra. Valldemossa 79, 07010, Palma, Spain
- Center for Biomedical Research in Infectious Diseases Network (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Juan Pablo Horcajada
- Infectious Diseases Service, Hospital del Mar, Infectious Pathology and Antimicrobials Research Group (IPAR), Hospital del Mar Research Institute, Universitat Autònoma de Barcelona (UAB), CEXS-Universitat Pompeu Fabra, Passeig Marítim 25-27, 08003, Barcelona, Spain
- Center for Biomedical Research in Infectious Diseases Network (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - Carlos Juan
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Microbiology Department, University Hospital Son Espases, Crtra. Valldemossa 79, 07010, Palma, Spain.
- Center for Biomedical Research in Infectious Diseases Network (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain.
| | - Silvia Gómez-Zorrilla
- Infectious Diseases Service, Hospital del Mar, Infectious Pathology and Antimicrobials Research Group (IPAR), Hospital del Mar Research Institute, Universitat Autònoma de Barcelona (UAB), CEXS-Universitat Pompeu Fabra, Passeig Marítim 25-27, 08003, Barcelona, Spain.
- Center for Biomedical Research in Infectious Diseases Network (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain.
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Royer G, Virieux-Petit M, Aujoulat F, Hersent C, Baranovsky S, Hammer-Dedet F, Masnou A, Marchandin H, Corne P, Jumas-Bilak E, Romano-Bertrand S. Residual risk of Pseudomonas aeruginosa waterborne contamination in an intensive care unit despite the presence of filters at all water points-of-use. J Hosp Infect 2024; 149:155-164. [PMID: 38705477 DOI: 10.1016/j.jhin.2024.04.012] [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: 02/25/2024] [Revised: 04/17/2024] [Accepted: 04/18/2024] [Indexed: 05/07/2024]
Abstract
OBJECTIVE To assess the residual risk of waterborne contamination by Pseudomonas aeruginosa from a water network colonized by a single genotype [sequence type (ST) 299] despite the presence of antimicrobial filters in a medical intensive care unit (ICU). METHODS During the first 19-month period since the ICU opened, contamination of the water network was assessed monthly by collecting water upstream of the filters. Downstream water was also sampled to assess the efficiency of the filters. P. aeruginosa isolates from patients were collected and compared with the waterborne ST299 P. aeruginosa by multiplex-rep polymerase chain reaction (PCR), pulsed-field gel electrophoresis (PFGE) and whole-genome sequencing. Cross-transmission events by other genotypes of P. aeruginosa were also assessed. RESULTS Overall, 1.3% of 449 samples of filtered water were positive for P. aeruginosa in inoculum, varying between 1 and 104 colony-forming units/100 mL according to the tap. All P. aeruginosa hydric isolates belonged to ST299 and displayed fewer than two single nucleotide polymorphisms (SNPs). Among 278 clinical isolates from 122 patients, 10 isolates in five patients showed identical profiles to the hydric ST299 clone on both multiplex-rep PCR and PFGE, and differed by an average of fewer than five SNPs, confirming the water network reservoir as the source of contamination by P. aeruginosa for 4.09% of patients. Cross-transmission events by other genotypes of P. aeruginosa were responsible for the contamination of 1.75% of patients. DISCUSSION/CONCLUSION Antimicrobial filters are not sufficient to protect patients from waterborne pathogens when the water network is highly contaminated. A microbiological survey of filtered water may be needed in units hosting patients at risk of P. aeruginosa infections, even when all water points-of-use are fitted with filters.
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Affiliation(s)
- G Royer
- Hydrosciences Montpellier, IRD, CNRS, Univ Montpellier, Service de Prévention des Infections et de la Résistance, CHU Montpellier, Montpellier, France; Département de prévention, diagnostic et traitement des infections, Hôpital Henri Mondor, AP-HP, Créteil, France
| | - M Virieux-Petit
- Hydrosciences Montpellier, IRD, CNRS, Univ Montpellier, Service de Prévention des Infections et de la Résistance, CHU Montpellier, Montpellier, France; Hydrosciences Montpellier, Univ Montpellier, IRD, CNRS, Montpellier, France
| | - F Aujoulat
- Hydrosciences Montpellier, Univ Montpellier, IRD, CNRS, Montpellier, France
| | - C Hersent
- Service de Prévention des Infections et de la Résistance, CHU Montpellier, France
| | - S Baranovsky
- Service de Prévention des Infections et de la Résistance, CHU Montpellier, France
| | - F Hammer-Dedet
- Hydrosciences Montpellier, Univ Montpellier, IRD, CNRS, Montpellier, France
| | - A Masnou
- Hydrosciences Montpellier, Univ Montpellier, IRD, CNRS, Montpellier, France
| | - H Marchandin
- Hydrosciences Montpellier, Univ Montpellier, IRD, CNRS, Montpellier, France; Service de Microbiologie et Hygiène hospitalière, CHU Nîmes, Nîmes, France
| | - P Corne
- Département de Médecine Intensive et Réanimation, CHU Montpellier, Montpellier, France
| | - E Jumas-Bilak
- Hydrosciences Montpellier, IRD, CNRS, Univ Montpellier, Service de Prévention des Infections et de la Résistance, CHU Montpellier, Montpellier, France
| | - S Romano-Bertrand
- Hydrosciences Montpellier, IRD, CNRS, Univ Montpellier, Service de Prévention des Infections et de la Résistance, CHU Montpellier, Montpellier, France.
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Daaboul D, Osman M, Kassem II, Yassine I, Girlich D, Proust A, Mounir C, Zerouali K, Raymond J, Naas T, Oueslati S. Neonatal sepsis due to NDM-1 and VIM-2 co-producing Pseudomonas aeruginosa in Morocco. J Antimicrob Chemother 2024; 79:1614-1618. [PMID: 38804143 DOI: 10.1093/jac/dkae153] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/26/2024] [Indexed: 05/29/2024] Open
Abstract
BACKGROUND Carbapenem-resistant Pseudomonas aeruginosa are being increasingly described worldwide. Here, we investigated the molecular mechanisms underlying carbapenem resistance in an extremely drug-resistant P. aeruginosa isolate from a neonatal intensive care unit in Morocco. MATERIALS AND METHODS P. aeruginosa strain O82J1 was identified using MALDI-TOF-MS. Carba NP, immunochromatographic assay NG Carba5 and antimicrobial susceptibility testing using disc diffusion and microbroth were performed. Whole-genome sequencing using the Illumina and MinION technologies and different software packages available at the Center of Genomic Epidemiology were used to predict the resistome, sequence type and plasmid types. RESULTS P. aeruginosa O82J1 co-expressed two metallo-β-lactamases, blaNDM-1 and blaVIM-2, and was susceptible to colistin and apramycin only. It belonged to ST773 that is frequently reported worldwide as a high-risk P. aeruginosa clone. The blaVIM-2 gene was integron-borne on a IncP-2 465-kb plasmid, whereas the blaNDM-1 gene was chromosomally encoded and embedded in an integrative conjugative element, probably at the origin of its acquisition. A total of 23 antimicrobial resistance genes were detected including a blaPER-1 ESBL gene, and an 16S-rRNA methyltransferase gene rmtB. CONCLUSIONS The isolation of XDR P. aeruginosa isolates expressing several carbapenemases in a neonatal intensive care unit is of great concern due to the reduced treatment options, relying only on colistin, but not recommended in neonates, and apramycin, not yet approved for human therapy. Concerns were further elevated due to the resistance to cefiderocol and ATM/AVI, two novel and last-resort antibiotics recommended to treat infections caused by Gram-negative bacteria, particularly XDR P. aeruginosa in adults.
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Affiliation(s)
- Dina Daaboul
- Team ReSIST, UMR1184, INSERM, Université Paris-Saclay, CEA, School of Medicine, OI HEALTHI, Le Kremlin-Bicêtre, France
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon
| | - Marwan Osman
- Department of Neurosurgery, Yale University School of Medicine, New Haven, CT 06510, USA
| | - Issmat I Kassem
- Center for Food Safety and Department of Food Science and Technology, University of Georgia, 1109 Experiment Street, Griffin, GA 30223-1797, USA
| | - Iman Yassine
- Laboratoire Microbiologie Santé et Environnement (LMSE), Doctoral School of Sciences and Technology, Faculty of Public Health, Lebanese University, Tripoli 1300, Lebanon
| | - Delphine Girlich
- Team ReSIST, UMR1184, INSERM, Université Paris-Saclay, CEA, School of Medicine, OI HEALTHI, Le Kremlin-Bicêtre, France
| | - Alexis Proust
- Department of Hormonal Biochemistry, Hôpital de Bicêtre, Assistance Publique-Hôpitaux de Paris, Le Kremlin-Bicêtre, France
| | - Chemsi Mounir
- Service de néonatalogie, CHU Ibn Rochd, Faculté de Médecine et de Pharmacie de Casablanca, Université Hassan II, Casablanca, Morocco
| | - Khalid Zerouali
- Service de Microbiologie, CHU Ibn Rochd, Faculté de Médecine et de Pharmacie de Casablanca, Université Hassan II, Casablanca, Morocco
| | - Josette Raymond
- Bacteriology-Hygiene Unit, Bicêtre Hospital, APHP Paris-Saclay, Le Kremlin-Bicêtre 94270, France
| | - Thierry Naas
- Team ReSIST, UMR1184, INSERM, Université Paris-Saclay, CEA, School of Medicine, OI HEALTHI, Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene Unit, Bicêtre Hospital, APHP Paris-Saclay, Le Kremlin-Bicêtre 94270, France
- French National Reference Center for Antibiotic Resistance: Carbapenemase-producing Enterobacterales, Le Kremlin-Bicêtre, France
| | - Saoussen Oueslati
- Team ReSIST, UMR1184, INSERM, Université Paris-Saclay, CEA, School of Medicine, OI HEALTHI, Le Kremlin-Bicêtre, France
- Bacteriology-Hygiene Unit, Bicêtre Hospital, APHP Paris-Saclay, Le Kremlin-Bicêtre 94270, France
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Jasim AS, Mohammed AL, Abbas WH, Ibraheim HK, Gharban HA. Identification of bla OXA-23 gene in resistant Pseudomonas aeruginosa strains isolated from cows and humans in Basra province, Iraq. Vet World 2024; 17:1629-1636. [PMID: 39185049 PMCID: PMC11344103 DOI: 10.14202/vetworld.2024.1629-1636] [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: 05/03/2024] [Accepted: 07/01/2024] [Indexed: 08/27/2024] Open
Abstract
Background and Aim Pseudomonas aeruginosa is an infectious agent of great importance for animals and humans. It causes serious infections that show high resistance to antibiotics. This study investigated the molecular detection of blaOXA-23 gene in antibiotic-resistant P. aeruginosa strains isolated from cows and humans. Materials and Methods In total, 120 samples, comprised 60 from cows (30 milk and 30 nasal discharge) and 60 from their owners (30 urine and 30 sputum), were individually collected, cultured, and tested for P. aeruginosa through molecular analysis targeting the blaOXA-23 gene. P. aeruginosa antibiotic-resistant isolates were identified by performing antibiotic susceptibility testing and detecting biofilm formation. Results In total, 74.17% positive P. aeruginosa isolates, including 66.67% and 81.67% for cows and humans, respectively. Subsequently, positive cow isolates were detected in 60% of milk samples and 73.33% of nasal discharge samples; while positive human isolates were detected in 76.67% of urine samples and 86.66% of sputum samples. Targeting blaOXA-23 gene, 58.43% of cultured isolates were positive for P. aeruginosa by polymerase chain reaction. Respectively, positive isolates were detected in 66.67% and 45.46% of cow milk and nasal discharges as well as in 60.87% and 61.54% of human urine and sputum. The antibiotic susceptibility test revealed that all isolates were resistant to all applied antibiotics, particularly imipenem. Results of biofilm formation revealed 67.31% total positives, including 51.43% strong, 34.285% moderate, and 14.285% weak reactions. In addition, although values of the total positive cows and humans differed insignificantly, total positives showed insignificant variation between values of milk and nasal discharges of cows as well as between urine and sputum of humans; however, significant differences were identified in the distribution of strong, moderate, and weak positivity of these samples. Conclusion Antibiotic overuse contributes extensively to increasing the prevalence of resistant P. aeruginosa isolates carrying the blaOXA-23 gene in both cows and humans. Furthermore, studies in other Iraqi areas are necessary to support our findings. The main limitations include that the number of tested samples is relatively low, and there is a need to use a large number of samples from different sources. Also, the current methods for detection of resistant isolates are still culture-based approaches.
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Affiliation(s)
- Alyaa Sabti Jasim
- Department of Microbiology, College of Veterinary Medicine, University of Basrah, Basra, Iraq
| | - Abeer Laily Mohammed
- Department of Microbiology, Al-Zahraa College of Medicine, University of Basrah, Basra, Iraq
| | - Wameedh Hashim Abbas
- Department of Microbiology, Al-Zahraa College of Medicine, University of Basrah, Basra, Iraq
| | - Hanaa Khaleel Ibraheim
- Department of Microbiology, College of Veterinary Medicine, University of Basrah, Basra, Iraq
| | - Hasanain A.J. Gharban
- Department of Internal and Preventive Veterinary Medicine, College of Veterinary Medicine, University of Wasit, Wasit, Iraq
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Opazo-Capurro A, Aguilar-Vera OA, González-Muñoz P, Amsteins-Romero L, Quiroga M, Encina A, Herrera-Chávez N, Quezada-Aguiluz M, Aguayo-Reyes A, Morales-León F, Illesca V, Vera R, Salgado F, Suazo P, Fuenzalida LM, Bello-Toledo H, Castillo-Ramírez S, González-Rocha G. Genomic and Phylogenomic Characterization of Carbapenem-resistant Pseudomonas aeruginosa 'High-risk' Clone O4/ExoS+/ST654 Circulating in Chilean Hospitals. J Glob Antimicrob Resist 2024; 38:205-211. [PMID: 38849115 DOI: 10.1016/j.jgar.2024.05.015] [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: 12/19/2023] [Revised: 04/22/2024] [Accepted: 05/23/2024] [Indexed: 06/09/2024] Open
Abstract
INTRODUCTION Carbapenem-resistant Pseudomonas aeruginosa (CRPA) is a serious threat to public health. Globally, carbapenemases-producing CRPA isolates mainly belong to 'high-risk' clones; however, the molecular epidemiology of CRPA isolates circulating in Chile are scarce, where this pathogen is the main aetiological agent of ventilator-associated pneumonia. OBJECTIVES To characterize the phylogenomics and molecular features of ST654 CRPA isolates collected in Chile between 2016 and 2022. METHODS Eighty-nine CRPA isolates collected in different Chilean hospitals from clinical specimens between 2005 and 2022 were analysed. Antibiotic susceptibility tests and carbapenemases production were carried out on the CRPA ST654 isolates. Also, they were subjected to whole-genome sequencing, from which in silico analyses were performed. RESULTS Thirty-four strains (38.2%) belonged to the ST654 high-risk clone, being the most predominant lineage of the collection. Most of these isolates belonged to a subclade including KPC producers that also clustered with strains from Argentina and the United States, whereas few VIM and NDM co-producers clustered in two different smaller subclades. The isolates exhibited a broad resistome encompassing genes mediating resistance to several other clinically relevant drugs. Additionally, all the 34 ST654 isolates were ExoS+ as a virulence factor and associated to the O4-serotype. CONCLUSIONS Our report represents the most comprehensive phylogenomic study of a CRPA high-risk clone ST654 to date. Our analyses suggest that this lineage is undergoing a divergent evolutionary path in Chile, because most of the isolates were KPC producers and were O4 serotype, differing from previous descriptions, which underline the relevance of performing molecular surveillance on this pathogen.
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Affiliation(s)
- Andrés Opazo-Capurro
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile; Grupo de Estudio en Resistencia Antimicrobiana (GRAM), Universidad de Concepción, Concepción, Chile
| | - Omar Alejandro Aguilar-Vera
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Paulina González-Muñoz
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile; Grupo de Estudio en Resistencia Antimicrobiana (GRAM), Universidad de Concepción, Concepción, Chile; Departamento de Ciencias Biológicas y Químicas, Facultad de Medicina y Ciencia, Universidad San Sebastián, Concepción, Chile
| | - Luis Amsteins-Romero
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile; Grupo de Estudio en Resistencia Antimicrobiana (GRAM), Universidad de Concepción, Concepción, Chile
| | - Monserrat Quiroga
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Antonia Encina
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile
| | - Néstor Herrera-Chávez
- Laboratorio de Microbiología, Hospital Regional Guillermo Grant Benavente, Concepción, Chile
| | - Mario Quezada-Aguiluz
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile; Grupo de Estudio en Resistencia Antimicrobiana (GRAM), Universidad de Concepción, Concepción, Chile; Grupo de Estudio de Enfermedades Infecciosas de la Universidad de Concepción (GrEEn-UdeC), Departamento de Medicina Interna, Facultad de Medicina, Universidad de Concepción, Concepción, Chile
| | - Alejandro Aguayo-Reyes
- Grupo de Estudio en Resistencia Antimicrobiana (GRAM), Universidad de Concepción, Concepción, Chile; Grupo de Estudio de Enfermedades Infecciosas de la Universidad de Concepción (GrEEn-UdeC), Departamento de Medicina Interna, Facultad de Medicina, Universidad de Concepción, Concepción, Chile
| | - Felipe Morales-León
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile; Grupo de Estudio en Resistencia Antimicrobiana (GRAM), Universidad de Concepción, Concepción, Chile; Departamento de Farmacia, Facultad de Farmacia, Universidad de Concepción, Concepción, Chile
| | - Vijna Illesca
- Hospital Hernán Henríquez Aravena, Laboratorio Clínico, Temuco, Chile
| | - Rodrigo Vera
- Hospital de Urgencia Asistencia Pública, Santiago de Chile, Chile
| | | | | | | | - Helia Bello-Toledo
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile; Grupo de Estudio en Resistencia Antimicrobiana (GRAM), Universidad de Concepción, Concepción, Chile
| | - Santiago Castillo-Ramírez
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, México
| | - Gerardo González-Rocha
- Laboratorio de Investigación en Agentes Antibacterianos (LIAA), Facultad de Ciencias Biológicas, Universidad de Concepción, Concepción, Chile; Grupo de Estudio en Resistencia Antimicrobiana (GRAM), Universidad de Concepción, Concepción, Chile.
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Chebotar I, Savinova T, Bocharova J, Korostin D, Evseev P, Mayanskiy N. Genetic Alternatives for Experimental Adaptation to Colistin in Three Pseudomonas aeruginosa Lineages. Antibiotics (Basel) 2024; 13:452. [PMID: 38786180 PMCID: PMC11117860 DOI: 10.3390/antibiotics13050452] [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: 04/08/2024] [Revised: 05/13/2024] [Accepted: 05/14/2024] [Indexed: 05/25/2024] Open
Abstract
Pseudomonas aeruginosa is characterized by a high adaptive potential, developing resistance in response to antimicrobial pressure. We employed a spatiotemporal evolution model to disclose the pathways of adaptation to colistin, a last-resort polymyxin antimicrobial, among three unrelated P. aeruginosa lineages. The P. aeruginosa ATCC-27833 reference strain (Pa_ATCC), an environmental P. aeruginosa isolate (Pa_Environment), and a clinical isolate with multiple drug resistance (Pa_MDR) were grown over an increasing 5-step colistin concentration gradient from 0 to 400 mg/L. Pa_Environment demonstrated the highest growth pace, achieving the 400 mg/L band in 15 days, whereas it took 37 and 60 days for Pa_MDR and Pa_ATCC, respectively. To identify the genome changes that occurred during adaptation to colistin, the isolates selected during the growth of the bacteria (n = 185) were subjected to whole genome sequencing. In total, 17 mutation variants in eight lipopolysaccharide-synthesis-associated genes were detected. phoQ and lpxL/PA0011 were affected in all three lineages, whereas changes in pmrB were found in Pa_Environment and Pa_MDR but not in Pa_ATCC. In addition, mutations were detected in 34 general metabolism genes, and each lineage developed mutations in a unique set of such genes. Thus, the three examined distinct P. aeruginosa strains demonstrated different capabilities and genetic pathways of colistin adaptation.
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Affiliation(s)
- Igor Chebotar
- Laboratory of Molecular Microbiology, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia (J.B.); (D.K.); (N.M.)
| | | | | | | | - Peter Evseev
- Laboratory of Molecular Microbiology, Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Pirogov Russian National Research Medical University, Ostrovityanova 1, 117997 Moscow, Russia (J.B.); (D.K.); (N.M.)
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9
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Morgado S, Freitas F, Rodrigues C, Fonseca E, Vicente AC. Metallo-beta-lactamase bla NDM-1 in extremely drug-resistant high-risk Pseudomonas aeruginosa clone ST235 and non-high-risk clone ST2407 in Brazil. J Glob Antimicrob Resist 2024; 38:69-70. [PMID: 38723709 DOI: 10.1016/j.jgar.2024.04.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Revised: 02/27/2024] [Accepted: 04/11/2024] [Indexed: 06/22/2024] Open
Affiliation(s)
- Sergio Morgado
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Avenida Brasil 4365, Manguinhos, Rio de Janeiro, RJ, 21040-900, Brazil.
| | - Fernanda Freitas
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Avenida Brasil 4365, Manguinhos, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Caio Rodrigues
- Laboratório de Bacteriologia - Laboratório Central, Hospital Federal dos Servidores do Estado, Rio de Janeiro, RJ, 20221-161, Brazil
| | - Erica Fonseca
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Avenida Brasil 4365, Manguinhos, Rio de Janeiro, RJ, 21040-900, Brazil
| | - Ana Carolina Vicente
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz (FIOCRUZ), Avenida Brasil 4365, Manguinhos, Rio de Janeiro, RJ, 21040-900, Brazil
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10
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Jung H, Pitout JDD, Matsumura Y, Strydom KA, Kingsburgh C, Ehlers MM, Kock MM. Genomic epidemiology and molecular characteristics of bla NDM-1-positive carbapenem-resistant Pseudomonas aeruginosa belonging to international high-risk clone ST773 in the Gauteng region, South Africa. Eur J Clin Microbiol Infect Dis 2024; 43:627-640. [PMID: 38265603 DOI: 10.1007/s10096-024-04763-5] [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: 10/12/2023] [Accepted: 01/12/2024] [Indexed: 01/25/2024]
Abstract
PURPOSE The emergence of carbapenem-resistant P. aeruginosa (CRPA) harbouring acquired carbapenemase genes (blaVIM, blaIMP and blaNDM) has become a global public health threat. Three CRPA isolates included in the study had an extensively drug-resistant phenotype with susceptibility to colistin only and were positive for the blaNDM-1 gene. The current study aimed to investigate the genomic epidemiology and molecular characteristics of the blaNDM-1-positive CRPA isolates collected from the Gauteng region, South Africa. METHODS Short read whole genome sequencing (WGS) was performed to determine sequence types (STs), genetic relatedness, resistome, virulome and the genetic environment of the blaNDM-1 gene. RESULTS The WGS and phylogenetic analyses revealed that the study isolates belonged to an international high-risk clone ST773 and belonged to the same clade with eight blaNDM-1-positive ST773 isolates from Hungary, India, Nigeria, South Korea and USA. The study isolates harboured a wide repertoire of intrinsic and acquired antibiotic resistance genes (ARGs) related with mobile genetic elements, porins and efflux pumps, as well as virulence factor genes. The clade-specific ARGs (blaNDM-1, floR2/cmlA9, rmtB4, tetG) were found in a putative integrative and conjugative element (ICE) region similar to ICE6660-like. CONCLUSION As ICE carrying the blaNDM-1 gene can easily spread to other P. aeruginosa isolates and other Gram-negative bacteria, the findings in this study highlight the need for appropriate management strategies and active surveillance of CRPA isolates in the Gauteng region, South Africa.
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Affiliation(s)
- Hyunsul Jung
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
| | - Johann D D Pitout
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
- Division of Microbiology, Alberta Public Laboratories, Cummings School of Medicine, University of Calgary, Calgary, Canada
| | - Yasufumi Matsumura
- Department of Clinical Laboratory Medicine, Kyoto University Graduate School of Medicine, Kyoto, Japan
| | - Kathy-Anne Strydom
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
- Ampath National Reference Laboratory, Centurion, South Africa
| | - Chanel Kingsburgh
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
- Ampath National Reference Laboratory, Centurion, South Africa
| | - Marthie M Ehlers
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa
- Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service (NHLS), Pretoria, South Africa
| | - Marleen M Kock
- Department of Medical Microbiology, University of Pretoria, Pretoria, South Africa.
- Department of Medical Microbiology, Tshwane Academic Division, National Health Laboratory Service (NHLS), Pretoria, South Africa.
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11
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Martínez-Gallardo MJ, Villicaña C, Yocupicio-Monroy M, Alcaraz-Estrada SL, Salazar-Salinas J, Mendoza-Vázquez OF, Damazo-Hernández G, León-Félix J. Comparative genomic analysis of Pseudomonas aeruginosa strains susceptible and resistant to carbapenems and aztreonam isolated from patients with healthcare-associated infections in a Mexican hospital. Mol Genet Genomics 2024; 299:29. [PMID: 38472486 DOI: 10.1007/s00438-024-02122-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Accepted: 02/02/2024] [Indexed: 03/14/2024]
Abstract
Pseudomonas aeruginosa (PA) is an important opportunistic pathogen that causes different infections on immunocompromised patients. Within PA accessory genome, differences in virulence, antibiotic resistance and biofilm formation have been described between strains, leading to the emergence of multidrug-resistant strains. The genome sequences of 17 strains isolated from patients with healthcare-associated infections in a Mexican hospital were genomically and phylogenetically analyzed and antibiotic resistance genes, virulence genes, and biofilm formation genes were detected. Fifteen of the 17 strains were resistant to at least two of the carbapenems meropenem, imipenem, and the monobactam aztreonam. The antibiotic resistance (mexA, mexB, and oprM) and the biofilm formation (pslA and pslD) genes were detected in all strains. Differences were found between strains in accessory genome size. The strains had different sequence types, and seven strains had sequence types associated with global high risk epidemic PA clones. All strains were represented in two groups among PA global strains. In the 17 strains, horizontally acquired resistance genes to aminoglycosides and beta-lactams were found, mainly, and between 230 and 240 genes that encode virulence factors. The strains under study were variable in terms of their accessory genome, antibiotic resistance, and virulence genes. With these characteristics, we provide information about the genomic diversity of clinically relevant PA strains.
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Affiliation(s)
- María José Martínez-Gallardo
- Laboratory of Molecular Biology and Functional Genomics, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Culiacán, Sinaloa, Mexico
| | - Claudia Villicaña
- CONACYT-Centro de Investigación en Alimentación y Desarrollo A.C. (CIAD), Culiacán, Sinaloa, Mexico
| | - Martha Yocupicio-Monroy
- Postgraduate in Genomic Sciences, Universidad Autónoma de la Ciudad de México (UACM), Mexico City, Mexico
| | | | | | | | | | - Josefina León-Félix
- Laboratory of Molecular Biology and Functional Genomics, Centro de Investigación en Alimentación y Desarrollo, A.C. (CIAD), Culiacán, Sinaloa, Mexico.
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12
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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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13
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Burke KA, Urick CD, Mzhavia N, Nikolich MP, Filippov AA. Correlation of Pseudomonas aeruginosa Phage Resistance with the Numbers and Types of Antiphage Systems. Int J Mol Sci 2024; 25:1424. [PMID: 38338703 PMCID: PMC10855318 DOI: 10.3390/ijms25031424] [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: 12/14/2023] [Revised: 01/18/2024] [Accepted: 01/22/2024] [Indexed: 02/12/2024] Open
Abstract
Phage therapeutics offer a potentially powerful approach for combating multidrug-resistant bacterial infections. However, to be effective, phage therapy must overcome existing and developing phage resistance. While phage cocktails can reduce this risk by targeting multiple receptors in a single therapeutic, bacteria have mechanisms of resistance beyond receptor modification. A rapidly growing body of knowledge describes a broad and varied arsenal of antiphage systems encoded by bacteria to counter phage infection. We sought to understand the types and frequencies of antiphage systems present in a highly diverse panel of Pseudomonas aeruginosa clinical isolates utilized to characterize novel antibacterials. Using the web-server tool PADLOC (prokaryotic antiviral defense locator), putative antiphage systems were identified in these P. aeruginosa clinical isolates based on sequence homology to a validated and curated catalog of known defense systems. Coupling this host bacterium sequence analysis with host range data for 70 phages, we observed a correlation between existing phage resistance and the presence of higher numbers of antiphage systems in bacterial genomes. We were also able to identify antiphage systems that were more prevalent in highly phage-resistant P. aeruginosa strains, suggesting their importance in conferring resistance.
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Affiliation(s)
| | | | | | | | - Andrey A. Filippov
- Wound Infections Department, Bacterial Diseases Branch, Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA; (K.A.B.); (C.D.U.); (N.M.); (M.P.N.)
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14
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Ali MG, Almoneim ZA, Kareem SM. Evaluated gene expressions of Metallo beta lactamase genes GIM and , VIM, SPM in Pseudomonas aeruginosa clinical isolates. Mol Biol Rep 2023; 50:10111-10120. [PMID: 37917414 DOI: 10.1007/s11033-023-08883-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 10/03/2023] [Indexed: 11/04/2023]
Abstract
Pseudomonas aeruginosa is considered as one of the human health care problems, P. aeruginosa's carbapenem resistance emerges by several different mechanisms, some of which include carbapenems genes. P. aeruginosa's carbapenem resistance is a significant health concern, So this study aims to evaluate MBL gene expressions. The study was conducted at the Department of Microbiology, AL-Mahmoodia Hospital, over one year from January to December 2022. The samples were collected from patients with different clinical sources (Burn, Urine, Wound, Sputum, Ear, and Blood), from different ages while. Samples were collected from three hospitals in Baghdad including Al-Yarmouk Teaching Hospital, AL-Mahmmodiya Hospital, and Child's Central Teaching Hospital. A study analyzed 55 P. aeruginosa strains from various clinical sources, the study utilizes the chemical characterization, VITEK 2 system, 16s rRNA, antibiogram sensitivity tests, antibiotic susceptibility using eight antibiotics, including Amikacin, Ciprofloxacin, Levofloxacin, Imipenem Meropenem, Piperacillin, Cefepim and Aztreonam. The test of bacterial susceptibility revealed that each isolate was highly resistant to piperacillin, which are 96.36%, and lower resistance to Ciprofloxacin, which are 32%. Phenotypic screening carbapenem resistance methods combined the disk synergy test and conventional PCR that were used to detect isolates by using 16 S rRNA. This proves that the bacteria is P. aeruginosa and computed by measuring gene expression of the target genes (GIM, VIM, SPM) by using the real-time PCR, which is employed for twenty-five isolates. The result indicates that the expression level of the VIM gene is highly regulated in carbapenem-resistance isolates compared to control isolates that is 1.00. While the expression level of gene GIM and SPM is downregulated in carbapenem-resistance isolates compared to control isolates that is 6. The carbapenem VIM and GIM, SPM (class B) genes are essential for resistance in P. aeruginosa induced by chromosomal changes that modify membrane permeability efflux pump overexpression for genes. As a result, many studies require for discovering new strategies to reduce the threat to public health through preventing the spread of these isolates via tight infections, control measures, and the reduction of the danger to public health.
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Affiliation(s)
- Marwa Ghalib Ali
- Department of Medical Laboratory, AL-Mahmmodiya Hospital, Ministry of Health, Baghdad, Iraq
| | | | - Sawsan M Kareem
- Branch of Biotechnology, Department of Biology, College of Science, Mustansiriyah University, POX 10244, Baghdad, Iraq.
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15
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de Sousa T, Silva C, Alves O, Costa E, Igrejas G, Poeta P, Hébraud M. Determination of Antimicrobial Resistance and the Impact of Imipenem + Cilastatin Synergy with Tetracycline in Pseudomonas aeruginosa Isolates from Sepsis. Microorganisms 2023; 11:2687. [PMID: 38004699 PMCID: PMC10673103 DOI: 10.3390/microorganisms11112687] [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: 09/29/2023] [Revised: 10/24/2023] [Accepted: 11/01/2023] [Indexed: 11/26/2023] Open
Abstract
Pseudomonas aeruginosa is among the most ubiquitous bacteria in the natural world, exhibiting metabolic and physiological versatility, which makes it highly adaptable. Imipenem + cilastatin and tetracycline are antibiotic combinations commonly used to treat infections caused by P. aeruginosa, including serious infections such as sepsis. In the context of bacterial infections, biofilm, formed by bacterial cells surrounded by extracellular substances forming a matrix, plays a pivotal role in the resistance of P. aeruginosa to antibiotics. This study aimed to characterize a representative panel of P. aeruginosa isolates from septicemias, assessing their susceptibility to various antibiotics, specifically, imipenem + cilastatin and tetracycline, and the impact of these treatments on biofilm formation. Results from antibiotic susceptibility tests revealed sensitivity in most isolates to six antibiotics, with four showing near or equal to 100% sensitivity. However, resistance was observed in some antibiotics, albeit at minimal levels. Notably, tetracycline showed a 100% resistance phenotype, while imipenem + cilastatin predominantly displayed an intermediate phenotype (85.72%), with some resistance (38.1%). Microdilution susceptibility testing identified effective combinations against different isolates. Regarding biofilm formation, P. aeruginosa demonstrated the ability to produce biofilms. The staining of microtiter plates confirmed that specific concentrations of imipenem + cilastatin and tetracycline could inhibit biofilm production. A significant proportion of isolates exhibited resistance to aminoglycoside antibiotics because of the presence of modifying genes (aac(3)-II and aac(3)-III), reducing their effectiveness. This study also explored various resistance genes, unveiling diverse resistance mechanisms among P. aeruginosa isolates. Several virulence genes were detected, including the las quorum-sensing system genes (lasI and lasR) in a significant proportion of isolates, contributing to virulence factor activation. However, genes related to the type IV pili (T4P) system (pilB and pilA) were found in limited isolates. In conclusion, this comprehensive study sheds light on the intricate dynamics of P. aeruginosa, a remarkably adaptable bacterium with a widespread presence in the natural world. Our findings provide valuable insights into the ongoing battle against P. aeruginosa infections, highlighting the need for tailored antibiotic therapies and innovative approaches to combat biofilm-related resistance.
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Affiliation(s)
- Telma de Sousa
- MicroART-Antibiotic Resistance Team, Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; (T.d.S.); (C.S.); (P.P.)
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal;
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry, University NOVA of Lisbon, 1099-085 Caparica, Portugal
| | - Catarina Silva
- MicroART-Antibiotic Resistance Team, Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; (T.d.S.); (C.S.); (P.P.)
| | - Olimpia Alves
- Hospital Centre of Trás-os-Montes and Alto Douro, Clinical Pathology Department, 5000-801 Vila Real, Portugal; (O.A.); (E.C.)
| | - Eliana Costa
- Hospital Centre of Trás-os-Montes and Alto Douro, Clinical Pathology Department, 5000-801 Vila Real, Portugal; (O.A.); (E.C.)
| | - Gilberto Igrejas
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal;
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry, University NOVA of Lisbon, 1099-085 Caparica, Portugal
| | - Patricia Poeta
- MicroART-Antibiotic Resistance Team, Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal; (T.d.S.); (C.S.); (P.P.)
- Associated Laboratory for Green Chemistry, University NOVA of Lisbon, 1099-085 Caparica, Portugal
- CECAV—Veterinary and Animal Research Centre, University of Trás-os-Montes and Alto Douro, 5000-801 Vila Real, Portugal
- Veterinary and Animal Research Centre, Associate Laboratory for Animal and Veterinary Science (AL4AnimalS), 5000-801 Vila Real, Portugal
| | - Michel Hébraud
- INRAE, Université Clermont Auvergne, UMR Microbiologie Environnement Digestif Santé (MEDiS), 63122 Saint-Genès-Champanelle, France
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16
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Gray HK, Beaird OE, Smith EA, Schaenman JM, Yang S. Domestically Acquired NDM-1-Producing Pseudomonas aeruginosa, Southern California, USA, 2023. Emerg Infect Dis 2023; 29:2382-2385. [PMID: 37877613 PMCID: PMC10617354 DOI: 10.3201/eid2911.230646] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2023] Open
Abstract
We describe a case of New Delhi metallo-β-lactamase 1-producing carbapenem-resistant Pseudomonas aeruginosa (CRPA) in a transplant patient with multiple hospitalizations in California, USA. Whole-genome sequencing revealed the isolate was genetically distinctive, despite ≈95% similarity to other global strains. The patient's lack of international travel suggests this CRPA was acquired domestically.
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17
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Eladawy M, Thomas JC, Hoyles L. Phenotypic and genomic characterization of Pseudomonas aeruginosa isolates recovered from catheter-associated urinary tract infections in an Egyptian hospital. Microb Genom 2023; 9:001125. [PMID: 37902186 PMCID: PMC10634444 DOI: 10.1099/mgen.0.001125] [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: 07/20/2023] [Accepted: 10/12/2023] [Indexed: 10/31/2023] Open
Abstract
Catheter-associated urinary tract infections (CAUTIs) represent one of the major healthcare-associated infections, and Pseudomonas aeruginosa is a common Gram-negative bacterium associated with catheter infections in Egyptian clinical settings. The present study describes the phenotypic and genotypic characteristics of 31 P. aeruginosa isolates recovered from CAUTIs in an Egyptian hospital over a 3 month period. Genomes of isolates were of good quality and were confirmed to be P. aeruginosa by comparison to the type strain (average nucleotide identity, phylogenetic analysis). Clonal diversity among the isolates was determined; eight different sequence types were found (STs 244, 357, 381, 621, 773, 1430, 1667 and 3765), of which ST357 and ST773 are considered to be high-risk clones. Antimicrobial resistance (AMR) testing according to European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines showed that the isolates were highly resistant to quinolones [ciprofloxacin (12/31, 38.7 %) and levofloxacin (9/31, 29 %) followed by tobramycin (10/31, 32.5 %)] and cephalosporins (7/31, 22.5 %). Genotypic analysis of resistance determinants predicted all isolates to encode a range of AMR genes, including those conferring resistance to aminoglycosides, β-lactamases, fluoroquinolones, fosfomycin, sulfonamides, tetracyclines and chloramphenicol. One isolate was found to carry a 422 938 bp pBT2436-like megaplasmid encoding OXA-520, the first report from Egypt of this emerging family of clinically important mobile genetic elements. All isolates were able to form biofilms and were predicted to encode virulence genes associated with adherence, antimicrobial activity, anti-phagocytosis, phospholipase enzymes, iron uptake, proteases, secretion systems and toxins. The present study shows how phenotypic analysis alongside genomic analysis may help us understand the AMR and virulence profiles of P. aeruginosa contributing to CAUTIs in Egypt.
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Affiliation(s)
- Mohamed Eladawy
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
- Department of Microbiology and Immunology, Faculty of Pharmacy, Mansoura University, Mansoura, Egypt
| | - Jonathan C. Thomas
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
| | - Lesley Hoyles
- Department of Biosciences, School of Science and Technology, Nottingham Trent University, Nottingham, UK
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18
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Jordana-Lluch E, Barceló IM, Escobar-Salom M, Estévez MA, Zamorano L, Gómez-Zorrilla S, Sendra E, Oliver A, Juan C. The balance between antibiotic resistance and fitness/virulence in Pseudomonas aeruginosa: an update on basic knowledge and fundamental research. Front Microbiol 2023; 14:1270999. [PMID: 37840717 PMCID: PMC10569695 DOI: 10.3389/fmicb.2023.1270999] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Accepted: 09/15/2023] [Indexed: 10/17/2023] Open
Abstract
The interplay between antibiotic resistance and bacterial fitness/virulence has attracted the interest of researchers for decades because of its therapeutic implications, since it is classically assumed that resistance usually entails certain biological costs. Reviews on this topic revise the published data from a general point of view, including studies based on clinical strains or in vitro-evolved mutants in which the resistance phenotype is seen as a final outcome, i.e., a combination of mechanisms. However, a review analyzing the resistance/fitness balance from the basic research perspective, compiling studies in which the different resistance pathways and respective biological costs are individually approached, was missing. Here we cover this gap, specifically focusing on Pseudomonas aeruginosa, a pathogen that stands out because of its extraordinary capacity for resistance development and for which a considerable number of recent and particular data on the interplay with fitness/virulence have been released. The revised information, split into horizontally-acquired vs. mutation-driven resistance, suggests a great complexity and even controversy in the resistance-fitness/virulence balance in the acute infection context, with results ranging from high costs linked to certain pathways to others that are seemingly cost-free or even cases of resistance mechanisms contributing to increased pathogenic capacities. The elusive mechanistic basis for some enigmatic data, knowledge gaps, and possibilities for therapeutic exploitation are discussed. The information gathered suggests that resistance-fitness/virulence interplay may be a source of potential antipseudomonal targets and thus, this review poses the elementary first step for the future development of these strategies harnessing certain resistance-associated biological burdens.
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Affiliation(s)
- Elena Jordana-Lluch
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Department of Microbiology, University Hospital Son Espases, Palma, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Isabel Mª Barceló
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Department of Microbiology, University Hospital Son Espases, Palma, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - María Escobar-Salom
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Department of Microbiology, University Hospital Son Espases, Palma, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Miguel A. Estévez
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Department of Microbiology, University Hospital Son Espases, Palma, Spain
| | - Laura Zamorano
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Department of Microbiology, University Hospital Son Espases, Palma, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Silvia Gómez-Zorrilla
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
- Infectious Diseases Service, Hospital del Mar, Hospital del Mar Research Institute, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Universitat Autònoma de Barcelóna (UAB), Barcelona, Spain
| | - Elena Sendra
- Infectious Diseases Service, Hospital del Mar, Hospital del Mar Research Institute, Barcelona, Spain
- Universitat Pompeu Fabra (UPF), Universitat Autònoma de Barcelóna (UAB), Barcelona, Spain
| | - Antonio Oliver
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Department of Microbiology, University Hospital Son Espases, Palma, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Carlos Juan
- Research Unit, University Hospital Son Espases-Health Research Institute of the Balearic Islands (IdISBa), Palma, Spain
- Department of Microbiology, University Hospital Son Espases, Palma, Spain
- Centro de Investigación Biomédica en Red, Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
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Silva A, Silva V, López M, Rojo-Bezares B, Carvalho JA, Castro AP, Sáenz Y, Igrejas G, Poeta P. Antimicrobial Resistance, Genetic Lineages, and Biofilm Formation in Pseudomonas aeruginosa Isolated from Human Infections: An Emerging One Health Concern. Antibiotics (Basel) 2023; 12:1248. [PMID: 37627668 PMCID: PMC10451160 DOI: 10.3390/antibiotics12081248] [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: 06/05/2023] [Revised: 07/17/2023] [Accepted: 07/25/2023] [Indexed: 08/27/2023] Open
Abstract
Pseudomonas aeruginosa (PA) is a leading nosocomial pathogen and has great versatility due to a complex interplay between antimicrobial resistance and virulence factors. PA has also turned into one the most relevant model organisms for the study of biofilm-associated infections. The objective of the study focused on analyzing the antimicrobial susceptibility, resistance genes, virulence factors, and biofilm formation ability of thirty-two isolates of PA. PA isolates were characterized by the following analyses: susceptibility to 12 antimicrobial agents, the presence of resistance genes and virulence factors in PCR assays, and the quantification of biofilm production as evaluated by two distinct assays. Selected PA isolates were analyzed through multilocus sequence typing (MLST). Thirty PA isolates have a multi-resistant phenotype, and most of the isolates showed high levels of resistance to the tested antibiotics. Carbapenems showed the highest prevalence of resistance. Various virulence factors were detected and, for the quantification of biofilm production, the effectiveness of different methods was assessed. The microtiter plate method showed the highest accuracy and reproducibility for detecting biofilm-producing bacteria. MLST revealed four distinct sequence types (STs) in clinical PA, with three of them considered high-risk clones of PA, namely ST175, ST235, and ST244. These clones are associated with multidrug resistance and are prevalent in hospitals worldwide. Overall, the study highlights the high prevalence of antibiotic resistance, the presence of carbapenemase genes, the diversity of virulence factors, and the importance of biofilm formation in PA clinical isolates. Understanding these factors is crucial for effective infection control measures and the development of targeted treatment strategies.
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Affiliation(s)
- Adriana Silva
- MicroART-Microbiology and Antibiotic Resistance Team, Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal (V.S.)
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 1099-085 Lisboa, Portugal
| | - Vanessa Silva
- MicroART-Microbiology and Antibiotic Resistance Team, Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal (V.S.)
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 1099-085 Lisboa, Portugal
| | - María López
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), 26006 Logroño, Spain
| | - Beatriz Rojo-Bezares
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), 26006 Logroño, Spain
| | | | - Ana Paula Castro
- Medical Center of Trás-os-Montes e Alto Douro E.P.E., 5000-508 Vila Real, Portugal
| | - Yolanda Sáenz
- Área de Microbiología Molecular, Centro de Investigación Biomédica de La Rioja (CIBIR), 26006 Logroño, Spain
| | - Gilberto Igrejas
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 1099-085 Lisboa, Portugal
| | - Patrícia Poeta
- MicroART-Microbiology and Antibiotic Resistance Team, Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal (V.S.)
- Associated Laboratory for Green Chemistry (LAQV-REQUIMTE), University NOVA of Lisboa, 1099-085 Lisboa, Portugal
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), 5000-801 Vila Real, Portugal
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de Sousa T, Garcês A, Silva A, Lopes R, Alegria N, Hébraud M, Igrejas G, Poeta P. The Impact of the Virulence of Pseudomonas aeruginosa Isolated from Dogs. Vet Sci 2023; 10:vetsci10050343. [PMID: 37235426 DOI: 10.3390/vetsci10050343] [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: 03/29/2023] [Revised: 05/09/2023] [Accepted: 05/10/2023] [Indexed: 05/28/2023] Open
Abstract
Pseudomonas aeruginosa is a pathogenic bacterium that can cause serious infections in both humans and animals, including dogs. Treatment of this bacterium is challenging because some strains have developed multi-drug resistance. This study aimed to evaluate the antimicrobial resistance patterns and biofilm production of clinical isolates of P. aeruginosa obtained from dogs. The study found that resistance to various β-lactam antimicrobials was widespread, with cefovecin and ceftiofur showing resistance in 74% and 59% of the isolates tested, respectively. Among the aminoglycosides, all strains showed susceptibility to amikacin and tobramycin, while gentamicin resistance was observed in 7% of the tested isolates. Furthermore, all isolates carried the oprD gene, which is essential in governing the entry of antibiotics into bacterial cells. The study also investigated the presence of virulence genes and found that all isolates carried exoS, exoA, exoT, exoY, aprA, algD, and plcH genes. This study compared P. aeruginosa resistance patterns worldwide, emphasizing regional understanding and responsible antibiotic use to prevent multi-drug resistance from emerging. In general, the results of this study emphasize the importance of the continued monitoring of antimicrobial resistance in veterinary medicine.
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Affiliation(s)
- Telma de Sousa
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Green Chemistry (LAQV), Chemistry Department, Faculty of Science and Technology, University Nova of Lisbon, 2829-516 Lisbon, Portugal
| | - Andreia Garcês
- CRL-CESPU, Cooperativa de Ensino Superior Politécnico e Universitário, R. Central Dada Gandra, 1317, 4585-116 Gandra, Portugal
- CITAB, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Augusto Silva
- INNO-Veterinary Laboratory, R. Cândido de Sousa 15, 4710-503 Braga, Portugal
| | - Ricardo Lopes
- INNO-Veterinary Laboratory, R. Cândido de Sousa 15, 4710-503 Braga, Portugal
| | - Nuno Alegria
- Department of Veterinary Sciences, School of Agrarian and Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
| | - Michel Hébraud
- UMR Microbiologie Environnement Digestif Santé (MEDiS), INRAE, Université Clermont Auvergne, 60122 Saint-Genès-Champanelle, France
| | - Gilberto Igrejas
- Department of Genetics and Biotechnology, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Functional Genomics and Proteomics Unit, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Green Chemistry (LAQV), Chemistry Department, Faculty of Science and Technology, University Nova of Lisbon, 2829-516 Lisbon, Portugal
| | - Patricia Poeta
- Microbiology and Antibiotic Resistance Team (MicroART), Department of Veterinary Sciences, University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Green Chemistry (LAQV), Chemistry Department, Faculty of Science and Technology, University Nova of Lisbon, 2829-516 Lisbon, Portugal
- Veterinary and Animal Research Centre (CECAV), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
- Associate Laboratory for Animal and Veterinary Sciences (AL4AnimalS), University of Trás-os-Montes and Alto Douro (UTAD), 5000-801 Vila Real, Portugal
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Fortunato G, Vaz-Moreira I, Gajic I, Manaia CM. Insight into phylogenomic bias of bla VIM-2 or bla NDM-1 dissemination amongst carbapenem-resistant Pseudomonas aeruginosa. Int J Antimicrob Agents 2023; 61:106788. [PMID: 36924802 DOI: 10.1016/j.ijantimicag.2023.106788] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2022] [Revised: 02/06/2023] [Accepted: 03/08/2023] [Indexed: 03/17/2023]
Abstract
OBJECTIVES Pseudomonas aeruginosa (P. aeruginosa) are ubiquitous opportunistic pathogens that combine intrinsic and acquired multidrug resistance phenotypes. Due to different types of acquired genes, carbapenem resistance has been expanding in this species. This study hypothesised that the spread of carbapenem resistance among P. aeruginosa is influenced by phylogenomic features, being distinct for different genes. METHODS To test this hypothesis, the genomes of P. aeruginosa harbouring blaVIM-2 or blaNDM-1 genes were compared. The blaVIM-2 gene was selected because, although frequent, it is almost restricted to this species and blaNDM-1 gene due to its wide interspecies distribution. A group of genomes harbouring the genes blaVIM-2 (n = 116) or blaNDM-1 (n = 27), available in GenBank, was characterised based on core phylogenomic analysis, functional categories in the accessory genome and mobile genetic elements flanking the selected genes. RESULTS Most blaVIM-2 gene hosts belonged to multilocus sequence types (ST) ST111 (n = 32 of 116) and ST233 (n = 27 of 116) and were reported in Europe (n = 75 of 116). The blaNDM-1 gene hosts were distributed by different STs (ST38, ST773, ST235, ST357 and ST654), frequently from Asia (n = 11 of 27). Significant differences in the prevalence of functional protein/enzyme annotations per number of accessory genomes were observed between blaVIM-2+ and blaNDM-1+. The blaVIM-2 gene was frequently inserted in the Tn402-like and Tn21 transposons family and rarely in IS6100, while blaNDM-1 gene was preferentially flanked by ISAba125 and bleMBL genes or associated with IS91 insertion sequence. CONCLUSION The hypothesis that carbapenem resistance gene acquisition is not random among phylogenomic lineages was confirmed, suggesting the importance of phylogeny in the dissemination of antibiotic resistance genes.
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Affiliation(s)
- Gianuario Fortunato
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
| | - Ivone Vaz-Moreira
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal
| | - Ina Gajic
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Belgrade, Belgrade, Serbia
| | - Célia M Manaia
- Universidade Católica Portuguesa, CBQF - Centro de Biotecnologia e Química Fina - Laboratório Associado, Escola Superior de Biotecnologia, Porto, Portugal.
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Molecular Mechanisms of Resistance to Ceftazidime/Avibactam in Clinical Isolates of Enterobacterales and Pseudomonas aeruginosa in Latin American Hospitals. mSphere 2023; 8:e0065122. [PMID: 36877058 PMCID: PMC10117078 DOI: 10.1128/msphere.00651-22] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023] Open
Abstract
Ceftazidime-avibactam (CZA) is the combination of a third-generation cephalosporin and a new non-β-lactam β-lactamase inhibitor capable of inactivating class A, C, and some D β-lactamases. From a collection of 2,727 clinical isolates of Enterobacterales (n = 2,235) and P. aeruginosa (n = 492) that were collected between 2016 and 2017 from five Latin American countries, we investigated the molecular resistance mechanisms to CZA of 127 (18/2,235 [0.8%] Enterobacterales and 109/492 [22.1%] P. aeruginosa). First, by qPCR for the presence of genes encoding KPC, NDM, VIM, IMP, OXA-48-like, and SPM-1 carbapenemases, and second, by whole-genome sequencing (WGS). From the CZA-resistant isolates, MBL-encoding genes were detected in all 18 Enterobacterales and 42/109 P. aeruginosa isolates, explaining their resistant phenotype. Resistant isolates that yielded a negative qPCR result for any of the MBL encoding genes were subjected to WGS. The WGS analysis of the 67 remaining P. aeruginosa isolates showed mutations in genes previously associated with reduced susceptibility to CZA, such as those involved in the MexAB-OprM efflux pump and AmpC (PDC) hyperproduction, PoxB (blaOXA-50-like), FtsI (PBP3), DacB (PBP4), and OprD. The results presented here offer a snapshot of the molecular epidemiological landscape for CZA resistance before the introduction of this antibiotic into the Latin American market. Therefore, these results serve as a valuable comparison tool to trace the evolution of the resistance to CZA in this carbapenemase-endemic geographical region. IMPORTANCE In this manuscript, we determine the molecular mechanisms of ceftazidime-avibactam resistance in Enterobacterales and P. aeruginosa isolates from five Latin American countries. Our results reveal a low rate of resistance to ceftazidime-avibactam among Enterobacterales; in contrast, resistance in P. aeruginosa has proven to be more complex, as it might involve multiple known and possibly unknown resistance mechanisms.
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Wang Y, Li Y, Li H, Zhou J, Wang T. Seasonal dissemination of antibiotic resistome from livestock farms to surrounding soil and air: Bacterial hosts and risks for human exposure. JOURNAL OF ENVIRONMENTAL MANAGEMENT 2023; 325:116638. [PMID: 36335698 DOI: 10.1016/j.jenvman.2022.116638] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2022] [Revised: 10/19/2022] [Accepted: 10/24/2022] [Indexed: 06/16/2023]
Abstract
Feces in livestock farms is a reservoir of antibiotic resistance genes (ARGs), which can disseminate into surrounding soil and air, bringing risks to human health. In this study, seasonal dissemination of ARGs in a livestock farm and implications for human exposure was explored. The experimental results showed that ARGs abundance basically ranked as feces > soil > air, and significant seasonal dependence was observed. The total ARGs in pig feces was relatively higher in autumn (109.7 copies g-1) and winter (1010.0 copies g-1), and lower in summer (105.0 copies g-1). Similarly, the lowest total ARGs in soil and air were also observed in summer. There were correlations among ARGs, integron intI1, and bacterial community. Total organic carbon was an important factor affecting ARGs distribution in the feces, and pH and moisture content significantly affected soil ARGs. The daily intakes of integron intI1 and ARGs from air were 10°.5 copies h-1 and 102.3 copies h-1 for human exposure, respectively. Pseudomonas was a potential pathogenic host of blaTEM-1 in feces, Pseudomonas and Acinetobacter were potential pathogenic hosts of multiple ARGs in soil, while ARGs in air did not migrate into pathogens.
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Affiliation(s)
- Yangyang Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, 712100, PR China
| | - Yingwei Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, 712100, PR China
| | - Hu Li
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, 712100, PR China
| | - Jian Zhou
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, 712100, PR China
| | - Tiecheng Wang
- College of Natural Resources and Environment, Northwest A&F University, Yangling, Shaanxi Province, 712100, PR China; Key Laboratory of Plant Nutrition and the Agri-environment in Northwest China, Ministry of Agriculture, Yangling, Shaanxi, 712100, PR China.
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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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Tickler IA, Torre JCGDL, Alvarado L, Obradovich AE, Tenover FC. Mechanisms of carbapenemase-mediated resistance among high-risk Pseudomonas aeruginosa lineages in Peru. J Glob Antimicrob Resist 2022; 31:135-140. [PMID: 36055547 DOI: 10.1016/j.jgar.2022.08.018] [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: 06/16/2022] [Revised: 08/18/2022] [Accepted: 08/19/2022] [Indexed: 12/31/2022] Open
Abstract
OBJECTIVES Pseudomonas aeruginosa is one of the leading causes of healthcare-associated infections globally. High-risk carbapenemase-encoding P. aeruginosa clones are disseminating in many regions. The aim of this study was to learn more about the lineages and mechanisms of resistance of P. aeruginosa circulating in Peru. METHODS A total of 141 carbapenemase-producing isolates recovered from hospitalized and ambulatory patients in Lima were sequenced and analyzed to infer their lineages through whole-genome sequence typing (wgST) and to identify their antimicrobial resistance genes. RESULTS wgST identified nine sequence types (STs); ST111 and ST357 were the most frequently encountered (44.0% and 38.3%, respectively), followed by ST179 (8.5%), with the remaining six detected only sporadically. Among ST357 isolates, 96.3% carried the novel blaIMP-93 allele, whereas the remainder harbored blaIMP-74. 74.2% of ST111 isolates co-harbored blaIMP-18 and blaVIM-2, while the rest carried either of these genes individually. All other ST lineages carried a single carbapenemase, which was either blaIMP-16, blaIMP-74, or blaVIM-2. CONCLUSION Our study shows that the high-risk P. aeruginosa clones ST357, which harbors the novel blaIMP-93, and ST111, which carries blaIMP-18 and blaVIM-2, have apparently become endemic in the region.
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El-Badawy MF, Eed EM, Sleem AS, El-Sheikh AAK, Maghrabi IA, Abdelwahab SF. The First Saudi Report of Novel and Common Mutations in the gyrA and parC Genes Among Pseudomonas Spp. Clinical Isolates Recovered from Taif Area. Infect Drug Resist 2022; 15:3801-3814. [PMID: 35875614 PMCID: PMC9300750 DOI: 10.2147/idr.s372027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 07/01/2022] [Indexed: 11/23/2022] Open
Abstract
Background and Aims Reports examine quinolone resistance mechanisms among Pseudomonas spp. are sporadic in the Kingdom of Saudi Arabia (KSA). We previously examined the genetic bases of plasmid-mediated quinolone resistance among Pseudomonas spp. clinical isolates. This study investigated chromosomally mediated quinolone resistance mechanisms via investigation of the mutations in the gyrA and parC genes. Methods The minimum inhibitory concentration (MIC) to different quinolones was determined. Twenty-nine quinolone resistant Pseudomonas spp. clinical isolates were included. The gyrA and parC genes were sequenced by Sanger capillary electrophoresis. Multiple sequence alignment for the translated gyrA and parC genes was performed to identify mutation sites. Results Of the 29 isolates, 27 isolates were P. aeruginosa and two were P. putida. The cluster analysis of the quinolone susceptibility pattern revealed seven susceptibility phenotypes (A-G) based on susceptibility patterns rather than the MIC values. Also, 22 different susceptibility phenotypes were detected based on MIC values. All isolates exhibited a missense mutation at position 83 (S83I/T/F) of the gyrA gene in addition to six missense mutations at positions outside the QRDR of this gene. In addition, 82.8% (24/29) of the isolates harbored a missense mutation in the parC gene at position 87 (S87L), along with six novel mutations outside the QRDR of the parC gene. Haplotyping of the gyrA, parC, and the overall QRDR revealed six, 10, and 13 different haplotypes, respectively. Conclusion This study documents the incidence of the commonly reported mutations in the gyrA and parC genes in addition to novel mutations in these genes among Pseudomonas spp. clinical isolates recovered from KSA. Together with our previous findings, these data provide an insight into the genetic background of quinolone resistance among Pseudomonas spp. clinical isolates in KSA.
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Affiliation(s)
- Mohamed F El-Badawy
- Department of Microbiology and Immunology, Faculty of Pharmacy, University of Sadat City, Sadat City, Menoufia, 32897, Egypt
| | - Emad M Eed
- Department of Clinical Laboratory Sciences, College of Applied Medical Sciences, Taif University, Taif, 21944, Saudi Arabia
| | - Asmaa S Sleem
- Department of Medical Microbiology and Immunology, Faculty of Medicine, Menoufia University, Menoufia, 32511, Egypt
| | - Azza A K El-Sheikh
- Basic Health Sciences Department, College of Medicine, Princess Nourah bint Abdulrahman University, Riyadh, 11671, Saudi Arabia
| | - Ibrahim A Maghrabi
- Department of Clinical Pharmacy, College of Pharmacy, Taif University, Taif, 21944, Saudi Arabia
| | - Sayed F Abdelwahab
- Department of Pharmaceutics and Industrial Pharmacy, College of Pharmacy, Taif University, Taif, 21944, Kingdom of Saudi Arabia
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Torres RT, Cunha MV, Ferreira H, Fonseca C, Palmeira JD. A high-risk carbapenem-resistant Pseudomonas aeruginosa clone detected in red deer (Cervus elaphus) from Portugal. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 829:154699. [PMID: 35318052 DOI: 10.1016/j.scitotenv.2022.154699] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2021] [Revised: 03/15/2022] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Pseudomonas aeruginosa is a ubiquitous bacterium, successfully exploiting a variety of environmental niches due to its remarkable metabolic versatility. The World Health Organization classifies P. aeruginosa as a "priority pathogen" due to its a great ability to overcome the action of antimicrobials, including carbapenems. Hitherto, most studies have focused on clinical settings from humans, but much less on animal and environmental settings, particularly on wildlife. In this work, we report the isolation of a carbapenem-resistant Pseudomonas aeruginosa strain recovered from the faeces of a red deer adult female sampled in a humanized area. This isolate was obtained during a nationwide survey on antimicrobial resistance in wildlife aimed to determine the occurrence of carbapenem-resistant bacteria among 181 widely distributed wild ungulates. This P. aeruginosa isolate was found to be a high-risk clone, belonging to the sequence type (ST) 274. The genomic analysis of P. aeruginosa isolate UP4, classified this isolate as belonging to serogroup O3, which was also found to harbour the genes blaPAO, blaPDC-24, blaOXA-486 (encoding resistance to beta-lactams), aph(3')-IIb (aminoglycosides resistance), fosA (fosfomycin resistance) and catB7 (chloramphenicol resistance). Antimicrobial susceptibility screening, according to EUCAST, showed resistance to imipenem and intermediate resistance to meropenem and doripenem. To our knowledge, this is the first description of carbapenem-resistant P. aeruginosa in deer in Europe. Our results highlight the importance of wild ungulates either as victims of human activity or amplifiers of AMR, either way with potential impacts on animal, human and ecosystem health, since excretion of AMR bacteria might directly or indirectly contaminate other animals and the surrounding environment, perpetuating the spill-over and chain dissemination of AMR determinants.
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Affiliation(s)
- Rita Tinoco Torres
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal.
| | - Mónica V Cunha
- Centre for Ecology, Evolution and Environmental Changes (cE3c), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal; Biosystems & Integrative Sciences Institute (BioISI), Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisbon, Portugal
| | - Helena Ferreira
- UCIBIO - Applied Molecular Biosciences Unit, REQUIMTE - University of Porto, Porto, Portugal; Microbiology, Biological Sciences Department, Faculty of Pharmacy of University of Porto, Porto, Portugal
| | - Carlos Fonseca
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal; ForestWISE - Collaborative Laboratory for Integrated Forest & Fire Management, Quinta de Prados, 5001-801 Vila Real, Portugal
| | - Josman Dantas Palmeira
- Departamento de Biologia & CESAM, Universidade de Aveiro, Campus de Santiago, 3810-193 Aveiro, Portugal
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Synergistic Activity of Imipenem in Combination with Ceftazidime/Avibactam or Avibactam against Non-MBL-Producing Extensively Drug-Resistant Pseudomonas aeruginosa. Microbiol Spectr 2022; 10:e0274021. [PMID: 35315696 PMCID: PMC9045292 DOI: 10.1128/spectrum.02740-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Extensively drug-resistant Pseudomonas aeruginosa (XDRPA) infection is a significant public health threat due to a lack of effective therapeutic options. New β-lactam-β-lactamase inhibitor combinations, including ceftazidime-avibactam (CZA), have shown a high resistance rate to XDRPA. This study was therefore conducted to describe the underlying genomic mechanism of resistance for CZA nonsusceptible XDRPA strains that are non-metallo-β-lactamase (MBL) producers as well as to examine synergism of CZA and other antipseudomonal agents. Furthermore, the synergistic antibacterial activity of the most effective antimicrobial combination against non-MBL-producing XDRPA was evaluated through in vitro experiments. The resistance profiles of 15 CZA-resistant XDRPA strains isolated from clinical specimens in China-Japan Friendship Hospital between January 2017 to December 2020 were obtained by whole-genome sequencing (WGS) analysis. MBL genes blaIMP-1 and blaIMP-45 were found in 2 isolates (2/15, 13.3%); the other underlying CZA-resistance mechanisms involved the decreased OprD porin (13/13), blaAmpC overexpression (8/13) or mutation (13/13), and upregulated efflux pumps (13/13). CZA-imipenem (CZA-IPM) combination was identified to be the most effective against non-MBL-producing XDRPA according to the results of WGS analysis and combined antimicrobial susceptibility tests, with an approximately 16.62-fold reduction in MICs compared to CZA alone. Furthermore, the results of checkerboard analysis and growth curve displayed the synergistic antimicrobial activity of CZA and IPM against non-MBL-producing XDRPA. Electron microscopy also revealed that CZA-IPM combination might lead to more cellular structural alterations than CZA or IPM alone. This study suggested that the CZA-IPM combination has potential for non-MBL-producing XDRPA with blaAmpC overexpression or mutation, decreased OprD porin, and upregulated efflux pumps. IMPORTANCE Handling the infections by extensively drug-resistant Pseudomonas aeruginosa (XDRPA) strains is challenging due to their complicated antibiotic resistance mechanisms in immunosuppressed patients with pulmonary diseases (e.g., cystic fibrosis, chronic obstructive pulmonary disease, and lung transplant), ventilator-associated pneumonia, and bloodstream infections. The current study suggested the potentiality of the ceftazidime-avibactam-imipenem combination against XDRPA with blaAmpC overexpression or mutation, decreased OprD porin, and/or upregulated efflux pumps. Our findings indicate the necessity of combined drug sensitivity tests against XDRPA and also lay a foundation for the development of prevention, control, and treatment strategies in XDRPA infections.
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Doumith M, Alhassinah S, Alswaji A, Alzayer M, Alrashidi E, Okdah L, Aljohani S, Balkhy HH, Alghoribi MF. Genomic Characterization of Carbapenem-Non-susceptible Pseudomonas aeruginosa Clinical Isolates From Saudi Arabia Revealed a Global Dissemination of GES-5-Producing ST235 and VIM-2-Producing ST233 Sub-Lineages. Front Microbiol 2022; 12:765113. [PMID: 35069471 PMCID: PMC8770977 DOI: 10.3389/fmicb.2021.765113] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Accepted: 12/13/2021] [Indexed: 11/21/2022] Open
Abstract
Carbapenem-resistant P. aeruginosa has become a major clinical problem due to limited treatment options. However, studies assessing the trends in the molecular epidemiology and mechanisms of antibiotic resistance in this pathogen are lacking in Saudi Arabia. Here, we reported the genome characterization in a global context of carbapenem non-susceptible clinical isolates from a nationally representative survey. The antibiotic resistance profiles of the isolates (n = 635) collected over 14 months between March 2018 and April 2019 from different geographical regions of Saudi Arabia showed resistance rates to relevant β-lactams, aminoglycosides and quinolones ranging between 6.93 and 27.56%. Overall, 22.52% (143/635) of the isolates exhibited resistance to both imipenem and meropenem that were mainly explained by porin loss and efflux overexpression. However, 18.18% of resistant isolates harbored genes encoding GES (69.23%), VIM (23.07%), NDM (3.85%) or OXA-48-like (3.85%) carbapenemases. Most common GES-positive isolates produced GESs −5, −15 or −1 and all belonged to ST235 whereas the VIM-positive isolates produced mainly VIM-2 and belonged to ST233 or ST257. GES and VIM producers were detected at different sampling periods and in different surveyed regions. Interestingly, a genome-wide comparison revealed that the GES-positive ST235 and VIM-2-positive ST233 genomes sequenced in this study and those available through public databases from various locations worldwide, constituted each a phylogenetically closely related sub-lineage. Profiles of virulence determinants, antimicrobial resistance genes and associated mobile elements confirmed relatedness within each of these two different sub-lineages. Sequence analysis located the blaGES gene in nearly all studied genomes (95.4%) in the same integrative conjugative element that also harbored the acc(6′)-Ib, aph(3′)-XV, aadA6, sul1, tet(G), and catB resistance genes while blaVIM–2 in most (98.89%) ST233-positive genomes was co-located with aac(6′)-I1, dfrB-5, and aac(3′)-Id in the same class I integron. The study findings revealed the global spread of GES-5 ST235 and VIM-2 ST233 sub-lineages and highlighted the importance of routine detection of rare β-lactamases.
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Affiliation(s)
- Michel Doumith
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Sarah Alhassinah
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Abdulrahman Alswaji
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Maha Alzayer
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Essa Alrashidi
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Liliane Okdah
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
| | - Sameera Aljohani
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City (KAMC), Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
| | | | | | - Majed F Alghoribi
- Infectious Diseases Research Department, King Abdullah International Medical Research Center, Riyadh, Saudi Arabia.,King Saud bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia.,Department of Pathology and Laboratory Medicine, King Abdulaziz Medical City (KAMC), Ministry of National Guard Health Affairs (MNGHA), Riyadh, Saudi Arabia
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Wendel AF, Malecki M, Mattner F, Xanthopoulou K, Wille J, Seifert H, Higgins PG. OUP accepted manuscript. JAC Antimicrob Resist 2022; 4:dlac057. [PMID: 35611260 PMCID: PMC9122648 DOI: 10.1093/jacamr/dlac057] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 05/03/2022] [Indexed: 11/24/2022] Open
Abstract
Objectives To describe the propensity of carbapenem-resistant Pseudomonas aeruginosa to spread within a hospital critical care setting. Methods The study was conducted in a 700-bed tertiary centre in Cologne, Germany. P. aeruginosa resistant to piperacillin, ceftazidime, cefepime, imipenem, meropenem and ciprofloxacin, isolated from clinical and screening specimens from four critical care units from 2015 to 2020 were analysed. Genotyping was carried out by WGS (Illumina and MinION). MLST, core genome MLST (cgMLST) and resistome analysis was performed and merged with epidemiological data. Results Fifty-five out of 79 non-duplicate P. aeruginosa isolates were available, of which 20 were carbapenemase producers as follows: blaVIM-1 (n = 1), blaVIM-2 (n = 17), blaVIM-4 (n = 1), and blaNDM-1/blaGES-5 (n = 1). Forty-two of 55 isolates were hospital-acquired. cgMLST revealed three clusters: Cluster 1 (n = 15, ST111, blaVIM-2, recovered between 2015 and 2020); Cluster 2 (n = 4, ST970, carbapenemase negative); and Cluster 3 (n = 2, ST357, carbapenemase negative). The blaVIM-2 gene of Cluster 1 was integrated on the chromosome in a class 1 integron (type In59). Using conventional epidemiology, we were only able to confirm two patient-to-patient transmissions and one room-to-patient transmission on three different ICUs within Cluster 1. Isolates from Cluster 2 represented an outbreak occurring in 2019. Conclusions These data give insight into the epidemiology of carbapenem-resistant P. aeruginosa. Transmission dynamics differed between carbapenemase- and non-carbapenemase-producing isolates. A continuous acquisition of clonally related ST111 VIM-2 P. aeruginosa, being the main carbapenemase-producing strain, was observed over the whole study period, as well as an overall higher genomic diversity among non-carbapenemase-producing P. aeruginosa.
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Affiliation(s)
- Andreas F. Wendel
- Institute of Hygiene, Cologne Merheim Medical Centre, University Hospital of Witten/Herdecke, Cologne, Germany
- Division of Hygiene and Environmental Medicine, Department of Human Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany
- Corresponding author. E-mail: ; @AndyFW; @docpolski
| | - Monika Malecki
- Institute of Hygiene, Cologne Merheim Medical Centre, University Hospital of Witten/Herdecke, Cologne, Germany
- Division of Hygiene and Environmental Medicine, Department of Human Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany
| | - Frauke Mattner
- Institute of Hygiene, Cologne Merheim Medical Centre, University Hospital of Witten/Herdecke, Cologne, Germany
- Division of Hygiene and Environmental Medicine, Department of Human Medicine, Faculty of Health, Witten/Herdecke University, Witten, Germany
| | - Kyriaki Xanthopoulou
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Centre for Infection Research, Partner site Bonn-Cologne, Cologne, Germany
| | - Julia Wille
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Centre for Infection Research, Partner site Bonn-Cologne, Cologne, Germany
| | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Centre for Infection Research, Partner site Bonn-Cologne, Cologne, Germany
| | - Paul G. Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, Cologne, Germany
- German Centre for Infection Research, Partner site Bonn-Cologne, Cologne, Germany
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Selection of AmpC β-lactamase variants and metallo-β-lactamases leading to ceftolozane/tazobactam and ceftazidime/avibactam-resistance during treatment of MDR/XDR Pseudomonas aeruginosa infections. Antimicrob Agents Chemother 2021; 66:e0206721. [PMID: 34930034 DOI: 10.1128/aac.02067-21] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Infections caused by ceftolozane/tazobactam and ceftazidime/avibactam-resistant P. aeruginosa infections are an emerging concern. We aimed to analyze the underlying ceftolozane/tazobactam and ceftazidime/avibactam resistance mechanisms in all MDR/XDR P. aeruginosa isolates recovered during one year (2020) from patients with a documented P. aeruginosa infection. Fifteen isolates showing ceftolozane/tazobactam and ceftazidime/avibactam resistance were evaluated. Clinical conditions, previous positive cultures and β-lactams received in the previous month were reviewed for each patient. MICs were determined by broth microdilution. MLSTs and resistance mechanisms were determined using short- and long-read WGS. The impact of PDCs on β-lactam resistance was demonstrated by cloning into an ampC-deficient PAO1 derivative (PAOΔC) and construction of 3D models. Genetic support of acquired β-lactamases was determined in silico from high-quality hybrid assemblies. In most cases, the isolates were recovered after treatment with ceftolozane/tazobactam or ceftazidime/avibactam. Seven isolates from different STs owed their β-lactam resistance to chromosomal mutations and all displayed specific substitutions in PDC: Phe121Leu and Gly222Ser, Pro154Leu, Ala201Thr, Gly214Arg, ΔGly203-Glu219 and Glu219Lys. In the other eight isolates, the ST175 clone was overrepresented (6 isolates) and associated with IMP-28 and IMP-13, whereas two ST1284 isolates produced VIM-2. The cloned PDCs conferred enhanced cephalosporin resistance. 3D PDC models revealed rearrangements affecting residues involved in cephalosporin hydrolysis. Carbapenemases were chromosomal (VIM-2) or plasmid-borne (IMP-28, IMP-13), and associated with class-1 integrons located in Tn402-like transposition modules. Our findings highlight that cephalosporin/ß-lactamase inhibitors are potential selectors of MDR/XDR P. aeruginosa strains producing PDC variants or metallo-ß-lactamases. Judicious use of these agents is encouraged.
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Tyumentseva M, Mikhaylova Y, Prelovskaya A, Karbyshev K, Tyumentsev A, Petrova L, Mironova A, Zamyatin M, Shelenkov A, Akimkin V. CRISPR Element Patterns vs. Pathoadaptability of Clinical Pseudomonas aeruginosa Isolates from a Medical Center in Moscow, Russia. Antibiotics (Basel) 2021; 10:antibiotics10111301. [PMID: 34827239 PMCID: PMC8615150 DOI: 10.3390/antibiotics10111301] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2021] [Revised: 10/15/2021] [Accepted: 10/22/2021] [Indexed: 11/24/2022] Open
Abstract
Pseudomonas aeruginosa is a member of the ESKAPE opportunistic pathogen group, which includes six species of the most dangerous microbes. This pathogen is characterized by the rapid acquisition of antimicrobial resistance, thus causing major healthcare concerns. This study presents a comprehensive analysis of clinical P. aeruginosa isolates based on whole-genome sequencing data. The isolate collection studied was characterized by a variety of clonal lineages with a domination of high-risk epidemic clones and different CRISPR/Cas element patterns. This is the first report on the coexistence of two and even three different types of CRISPR/Cas systems simultaneously in Russian clinical strains of P. aeruginosa. The data include molecular typing and genotypic antibiotic resistance determination, as well as the phylogenetic analysis of the full-length cas gene and anti-CRISPR genes sequences, predicted prophage sequences, and conducted a detailed CRISPR array analysis. The differences between the isolates carrying different types and quantities of CRISPR/Cas systems were investigated. The pattern of virulence factors in P. aeruginosa isolates lacking putative CRISPR/Cas systems significantly differed from that of samples with single or multiple putative CRISPR/Cas systems. We found significant correlations between the numbers of prophage sequences, antibiotic resistance genes, and virulence genes in P. aeruginosa isolates with different patterns of CRISPR/Cas-elements. We believe that the data presented will contribute to further investigations in the field of bacterial pathoadaptability, including antimicrobial resistance and the role of CRISPR/Cas systems in the plasticity of the P. aeruginosa genome.
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Affiliation(s)
- Marina Tyumentseva
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (M.T.); (Y.M.); (A.P.); (K.K.); (A.T.); (V.A.)
| | - Yulia Mikhaylova
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (M.T.); (Y.M.); (A.P.); (K.K.); (A.T.); (V.A.)
| | - Anna Prelovskaya
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (M.T.); (Y.M.); (A.P.); (K.K.); (A.T.); (V.A.)
| | - Konstantin Karbyshev
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (M.T.); (Y.M.); (A.P.); (K.K.); (A.T.); (V.A.)
| | - Aleksandr Tyumentsev
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (M.T.); (Y.M.); (A.P.); (K.K.); (A.T.); (V.A.)
| | - Lyudmila Petrova
- National Medical and Surgical Center Named after N.I. Pirogov, Nizhnyaya Pervomayskaya Str., 70, 105203 Moscow, Russia; (L.P.); (A.M.); (M.Z.)
| | - Anna Mironova
- National Medical and Surgical Center Named after N.I. Pirogov, Nizhnyaya Pervomayskaya Str., 70, 105203 Moscow, Russia; (L.P.); (A.M.); (M.Z.)
| | - Mikhail Zamyatin
- National Medical and Surgical Center Named after N.I. Pirogov, Nizhnyaya Pervomayskaya Str., 70, 105203 Moscow, Russia; (L.P.); (A.M.); (M.Z.)
| | - Andrey Shelenkov
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (M.T.); (Y.M.); (A.P.); (K.K.); (A.T.); (V.A.)
- Correspondence: or
| | - Vasiliy Akimkin
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia; (M.T.); (Y.M.); (A.P.); (K.K.); (A.T.); (V.A.)
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Esposito F, Cardoso B, Fontana H, Fuga B, Cardenas-Arias A, Moura Q, Fuentes-Castillo D, Lincopan N. Genomic Analysis of Carbapenem-Resistant Pseudomonas aeruginosa Isolated From Urban Rivers Confirms Spread of Clone Sequence Type 277 Carrying Broad Resistome and Virulome Beyond the Hospital. Front Microbiol 2021; 12:701921. [PMID: 34539602 PMCID: PMC8446631 DOI: 10.3389/fmicb.2021.701921] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Accepted: 07/20/2021] [Indexed: 11/13/2022] Open
Abstract
The dissemination of antibiotic-resistant priority pathogens beyond hospital settings is both a public health and an environmental problem. In this regard, high-risk clones exhibiting a multidrug-resistant (MDR) or extensively drug-resistant (XDR) phenotype have shown rapid adaptation at the human-animal-environment interface. In this study, we report genomic data and the virulence potential of the carbapenemase, São Paulo metallo-β-lactamase (SPM-1)-producing Pseudomonas aeruginosa strains (Pa19 and Pa151) isolated from polluted urban rivers, in Brazil. Bioinformatic analysis revealed a wide resistome to clinically relevant antibiotics (carbapenems, aminoglycosides, fosfomycin, sulfonamides, phenicols, and fluoroquinolones), biocides (quaternary ammonium compounds) and heavy metals (copper), whereas the presence of exotoxin A, alginate, quorum sensing, types II, III, and IV secretion systems, colicin, and pyocin encoding virulence genes was associated with a highly virulent behavior in the Galleria mellonella infection model. These results confirm the spread of healthcare-associated critical-priority P. aeruginosa belonging to the MDR sequence type 277 (ST277) clone beyond the hospital, highlighting that the presence of these pathogens in environmental water samples can have clinical implications for humans and other animals.
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Affiliation(s)
- Fernanda Esposito
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
| | - Brenda Cardoso
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Herrison Fontana
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
| | - Bruna Fuga
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Adriana Cardenas-Arias
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
| | - Quézia Moura
- Federal Institute of Education, Science and Technology of Espírito Santo, Vila Velha, Brazil
| | - Danny Fuentes-Castillo
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Pathology, School of Veterinary Medicine and Animal Sciences, University of São Paulo, São Paulo, Brazil
| | - Nilton Lincopan
- Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
- One Health Brazilian Resistance Project (OneBR), São Paulo, Brazil
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil
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Tran HA, Vu TNB, Trinh ST, Tran DL, Pham HM, Ngo THH, Nguyen MT, Tran ND, Pham DT, Dang DA, Shibayama K, Suzuki M, Yoshida LM, Trinh HS, Le VT, Vu PT, Luu TVN, Bañuls AL, Trinh KL, Tran VA, Tran HH, van Doorn HR. Resistance mechanisms and genetic relatedness among carbapenem-resistant Pseudomonas aeruginosa isolates from three major hospitals in Hanoi, Vietnam (2011-15). JAC Antimicrob Resist 2021; 3:dlab103. [PMID: 34322671 PMCID: PMC8313516 DOI: 10.1093/jacamr/dlab103] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2021] [Accepted: 06/22/2021] [Indexed: 01/18/2023] Open
Abstract
Background MDR bacteria including carbapenem-resistant Pseudomonas aeruginosa are recognized as an important cause of hospital-acquired infections worldwide. This investigation seeks to determine the molecular characterization and antibiotic resistance genes associated with carbapenem-resistant P. aeruginosa. Methods We conducted WGS and phylogenetic analysis of 72 carbapenem-resistant P. aeruginosa isolated from hospital-acquired infection patients from August 2011 to March 2015 in three major hospitals in Hanoi, Vietnam. Results We identified three variants of IMP gene, among which blaIMP-15 was the most frequent (n = 34) in comparison to blaIMP-26 (n = 2) and blaIMP-51 (n = 12). We observed two isolates with imipenem MIC >128 mg/L that co-harboured blaIMP-15 and blaDIM-1 genes and seven isolates (imipenem MIC > 128 mg/L) with a blaKPC-1 gene from the same hospital. MLST data shows that these 72 isolates belong to 18 STs and phylogenetic tree analysis has divided these isolates into nine groups. Conclusions Our results provide evidence that not only blaIMP-26 but other IMP variants such as blaIMP-15 and blaIMP-51 genes and several STs (ST235, ST244, ST277, ST310, ST773 and ST3151) have been disseminating in healthcare settings in Vietnam. In addition, we report the emergence of two isolates belonging to ST1240 and ST3340 that harboured two important carbapenemase genes (blaIMP-15 and blaDIM-1) and seven isolates belonging to ST3151 of P. aeruginosa that carried the blaKPC-1 gene in Vietnam, which could potentially cause serious restricted availability of treatment options in healthcare settings.
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Affiliation(s)
| | | | - Son Tung Trinh
- Oxford University Clinical Research Unit, Hanoi, Vietnam
| | - Dieu Linh Tran
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Ha My Pham
- Oxford University Clinical Research Unit, Hanoi, Vietnam
| | | | | | - Nhu Duong Tran
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Duy Thai Pham
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - Duc Anh Dang
- National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | | | - Masato Suzuki
- National Institute of Infectious Diseases, Tokyo, Japan
| | - Lay-Myint Yoshida
- Institute of Tropical Medicine, Nagasaki University, Nagasaki, Japan
| | | | - Viet Thanh Le
- Oxford University Clinical Research Unit, Hanoi, Vietnam.,Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | | | | | - Anne-Laure Bañuls
- MIVEGEC Univ Montpellier-IRD-CNRS, Centre IRD, Montpellier, France.,LMI DRISA, Hanoi, Vietnam
| | | | | | - Huy Hoang Tran
- Hanoi Medical University, Hanoi, Vietnam.,National Institute of Hygiene and Epidemiology, Hanoi, Vietnam
| | - H Rogier van Doorn
- Oxford University Clinical Research Unit, Hanoi, Vietnam.,Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford, UK
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