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Rivera-Galindo MA, Aguirre-Garrido F, Garza-Ramos U, Villavicencio-Pulido JG, Fernández Perrino FJ, López-Pérez M. Relevance of the Adjuvant Effect between Cellular Homeostasis and Resistance to Antibiotics in Gram-Negative Bacteria with Pathogenic Capacity: A Study of Klebsiella pneumoniae. Antibiotics (Basel) 2024; 13:490. [PMID: 38927157 PMCID: PMC11200652 DOI: 10.3390/antibiotics13060490] [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: 04/05/2024] [Revised: 05/17/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
Antibiotic resistance has become a global issue. The most significant risk is the acquisition of these mechanisms by pathogenic bacteria, which can have a severe clinical impact and pose a public health risk. This problem assumes that bacterial fitness is a constant phenomenon and should be approached from an evolutionary perspective to develop the most appropriate and effective strategies to contain the emergence of strains with pathogenic potential. Resistance mechanisms can be understood as adaptive processes to stressful conditions. This review examines the relevance of homeostatic regulatory mechanisms in antimicrobial resistance mechanisms. We focus on the interactions in the cellular physiology of pathogenic bacteria, particularly Gram-negative bacteria, and specifically Klebsiella pneumoniae. From a clinical research perspective, understanding these interactions is crucial for comprehensively understanding the phenomenon of resistance and developing more effective drugs and treatments to limit or attenuate bacterial sepsis, since the most conserved adjuvant phenomena in bacterial physiology has turned out to be more optimized and, therefore, more susceptible to alterations due to pharmacological action.
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Affiliation(s)
- Mildred Azucena Rivera-Galindo
- Doctorado en Ciencias Biológicas y de la Salud Universidad Autónoma Metropolitana, Ciudad de México, México Universidad Autónoma Metropolitana-Unidad Xochimilco Calz, del Hueso 1100, Coapa, Villa Quietud, Coyoacán CP 04960, Mexico;
| | - Félix Aguirre-Garrido
- Environmental Sciences Department, Division of Biological and Health Sciences, Autonomous Metropolitan University (Lerma Unit), Av. de las Garzas N◦ 10, Col. El Panteón, Lerma de Villada CP 52005, Mexico; (F.A.-G.); (J.G.V.-P.)
| | - Ulises Garza-Ramos
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca CP 62100, Mexico;
| | - José Geiser Villavicencio-Pulido
- Environmental Sciences Department, Division of Biological and Health Sciences, Autonomous Metropolitan University (Lerma Unit), Av. de las Garzas N◦ 10, Col. El Panteón, Lerma de Villada CP 52005, Mexico; (F.A.-G.); (J.G.V.-P.)
| | - Francisco José Fernández Perrino
- Department of Biotechnology, Division of Biological and Health Sciences, Universidad Autónoma Metropolitana-Unidad Iztapalapa, Av. San Rafael Atlixco 186, Leyes de Reforma, México City CP 09340, Mexico;
| | - Marcos López-Pérez
- Environmental Sciences Department, Division of Biological and Health Sciences, Autonomous Metropolitan University (Lerma Unit), Av. de las Garzas N◦ 10, Col. El Panteón, Lerma de Villada CP 52005, Mexico; (F.A.-G.); (J.G.V.-P.)
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Marais G, Moodley C, Claassen-Weitz S, Patel F, Prentice E, Tootla H, Nyakutira N, Lennard K, Reddy K, Bamford C, Niehaus A, Whitelaw A, Brink A. Carbapenem-resistant Klebsiella pneumoniae among hospitalized patients in Cape Town, South Africa: molecular epidemiology and characterization. JAC Antimicrob Resist 2024; 6:dlae050. [PMID: 38529003 PMCID: PMC10963078 DOI: 10.1093/jacamr/dlae050] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 03/03/2024] [Indexed: 03/27/2024] Open
Abstract
Background The molecular epidemiology of carbapenem-resistant Enterobacterales in Cape Town remains largely unknown. Objectives This study aimed to describe the molecular epidemiology, resistome, virulome and mobilome of carbapenem-resistant Klebsiella pneumoniae (CRKP) within Cape Town to guide therapy, antimicrobial stewardship and infection prevention and control practices. Methods Eighty-five CRKP isolates from hospitalized patients underwent WGS as part of a prospective, multicentre, cross-sectional study, conducted between 1 November 2020 and 30 November 2022, across public-sector and private-sector hospitals in Cape Town, South Africa. Results MLST revealed three novel types, ST6785, ST6786 and ST6787, while the most common were ST219, ST307, ST17, ST13 and ST2497. Different predominant clones were noted in each hospital. The most common carbapenemase gene was blaOXA-48-like, detected in 71% of isolates, with blaNDM detected in 5%. Notably, co-detection of two carbapenemase genes (blaOXA-48-like and blaNDM) occurred in 13% of isolates. The yersiniabactin siderophore was detected in 73% of isolates, and was most commonly associated with the ICEKp5 mobile element. All carbapenemases were located on plasmids. The genes blaOXA-181 and blaOXA-232 colocalized with a ColKP3 replicon type on assembled contigs in 83% and 100% of cases, respectively. Conclusions CRKP epidemiology in Cape Town reflects institutionally dominant, rather than regional, clones. The most prevalent carbapenemase gene was blaOXA-48-like, in keeping with CRKP epidemiology in South Africa in general. Emerging clones harbouring both blaOXA-48-like and blaNDM, such as ST17, ST2497 and the novel ST6787, are a concern due to the limited availability of appropriate antimicrobial agents in South Africa.
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Affiliation(s)
- Gert Marais
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
- National Health Laboratory Service Laboratory, Groote Schuur Hospital, Cape Town, Western Cape, South Africa
| | - Clinton Moodley
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
- National Health Laboratory Service Laboratory, Groote Schuur Hospital, Cape Town, Western Cape, South Africa
| | - Shantelle Claassen-Weitz
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Fadheela Patel
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Elizabeth Prentice
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
- National Health Laboratory Service Laboratory, Groote Schuur Hospital, Cape Town, Western Cape, South Africa
| | - Hafsah Tootla
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
- Medical Microbiology, National Health Laboratory Service, Red Cross War Memorial Children’s Hospital, Cape Town, South Africa
| | - Nyasha Nyakutira
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Katie Lennard
- Division of Computational Biology, University of Cape Town, Cape Town, Western Cape, South Africa
| | - Kessendri Reddy
- Division of Medical Microbiology, Stellenbosch University, Cape Town, Western Cape, South Africa
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, Western Cape, South Africa
| | - Colleen Bamford
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
- Division of Medical Microbiology, Pathcare, Cape Town, South Africa
| | - Abraham Niehaus
- Division of Medical Microbiology, Ampath, Cape Town, South Africa
| | - Andrew Whitelaw
- Division of Medical Microbiology, Stellenbosch University, Cape Town, Western Cape, South Africa
- National Health Laboratory Service, Tygerberg Hospital, Cape Town, Western Cape, South Africa
| | - Adrian Brink
- Division of Medical Microbiology, University of Cape Town, Cape Town, Western Cape, South Africa
- National Health Laboratory Service Laboratory, Groote Schuur Hospital, Cape Town, Western Cape, South Africa
- Institute of Infectious Disease and Molecular Medicine, University of Cape Town, Cape Town, Western Cape, South Africa
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3
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Gato E, Rodiño-Janeiro BK, Gude MJ, Fernández-Cuenca F, Pascual Á, Fernández A, Pérez A, Bou G. Diagnostic tool for surveillance, detection and monitoring of the high-risk clone K. pneumoniae ST15. J Hosp Infect 2023; 142:18-25. [PMID: 37802237 DOI: 10.1016/j.jhin.2023.09.015] [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: 08/02/2023] [Revised: 09/13/2023] [Accepted: 09/17/2023] [Indexed: 10/08/2023]
Abstract
BACKGROUND The global spread of Klebsiella pneumoniae ST15, causing multi-continental outbreaks, contributes to the movement of resistance genes between clones increasing the antimicrobial resistance crisis. The genomic traits providing it with the ability to outcompete other bacteria and cause epidemics remain unclear. AIM To identify the specific genomic traits of K. pneumoniae ST15 to develop a diagnostic test. METHODS An outbreak caused by K. pneumoniae occurred in Hospital A Coruña, Spain. Antimicrobial susceptibility analysis and molecular typing (PGFE and MLST) were performed. One isolate of each sequence type was selected for whole-genome sequencing analysis. Comparative analysis of genomes was performed using RAST. BLASTn was used to evaluate the presence of the fhaC and kpiD genes. Two hundred and ninety-four K. pneumoniae from a Spanish nationwide collection were analysed by PCR. FINDINGS Genotyping showed that 87.5% of the isolates tested belonged to a clone with a unique PFGE pattern which corresponded to ST15. Comparative genomic analysis of the different STs enabled us to determine the specific genomic traits of K. pneumoniae ST15. Two adherence-related systems (Kpi and KpFhaB/FhaC) were specific markers of this clone. Multiplex-PCR analysis with kpiD and fhaC oligonucleotides revealed that K. pneumoniae ST15 is specifically detected with a sensitivity of 100% and a specificity of 97.76%. The PCR results showed 100% concordance with the MLST and whole-genome sequencing data. CONCLUSION K. pneumoniae ST15 possesses specific genomic traits that could favour its dissemination. They could be used as targets to detect K. pneumoniae ST15 with high sensitivity and specificity.
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Affiliation(s)
- E Gato
- Institute for Biomedical Research of A Coruña (INIBIC), A Coruña, Spain; Carlos III Health Institute (ISCIII), Madrid, Spain
| | | | - M J Gude
- University Hospital Lucus Augusti (HULA), Lugo, Spain
| | - F Fernández-Cuenca
- University Hospital Virgen Macarena, Seville, Spain; Institute of Biomedicine of Sevilla, Seville, Spain; University of Sevilla, Seville, Spain
| | - Á Pascual
- University Hospital Virgen Macarena, Seville, Spain; Institute of Biomedicine of Sevilla, Seville, Spain; University of Sevilla, Seville, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
| | - A Fernández
- University Hospital of A Coruña (HUAC), A Coruña, Spain
| | - A Pérez
- Institute for Biomedical Research of A Coruña (INIBIC), A Coruña, Spain; Carlos III Health Institute (ISCIII), Madrid, Spain.
| | - G Bou
- University Hospital of A Coruña (HUAC), A Coruña, Spain; CIBER de Enfermedades Infecciosas (CIBERINFEC), Instituto de Salud Carlos III, Madrid, Spain
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Rahman MH, Al Azad S, Uddin MF, Farzana M, Sharmeen IA, Kabbo KS, Jabin A, Rahman A, Jamil F, Srishti SA, Riya FH, Khan T, Ahmed R, Nurunnahar, Rahman S, Khan MFR, Rahman MB. WGS-based screening of the co-chaperone protein DjlA-induced curved DNA binding protein A (CbpA) from a new multidrug-resistant zoonotic mastitis-causing Klebsiella pneumoniae strain: a novel molecular target of selective flavonoids. Mol Divers 2023:10.1007/s11030-023-10731-6. [PMID: 37902899 DOI: 10.1007/s11030-023-10731-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2023] [Accepted: 09/11/2023] [Indexed: 11/01/2023]
Abstract
The research aimed to establish a multidrug-resistant Klebsiella pneumoniae-induced genetic model for mastitis considering the alternative mechanisms of the DjlA-mediated CbpA protein regulation. The Whole Genome Sequencing of the newly isolated K. pneumoniae strain was conducted to annotate the frequently occurring antibiotic resistance and virulence factors following PCR and MALDI-TOF mass-spectrophotometry. Co-chaperon DjlA was identified and extracted via restriction digestion on PAGE. Based on the molecular string property analysis of different DnaJ and DnaK type genes, CbpA was identified to be regulated most by the DjlA protein during mastitis. Based on the quantum tunnel-cluster profiles, CbpA was modeled as a novel target for diversified biosynthetic, and chemosynthetic compounds. Pharmacokinetic and pharmacodynamic analyses were conducted to determine the maximal point-specificity of selective flavonoids in complexing with the CbpA macromolecule at molecular docking. The molecular dynamic simulation (100 ns) of each of the flavonoid-protein complexes was studied regarding the parameters RMSD, RMSF, Rg, SASA, MMGBSA, and intramolecular hydrogen bonds; where all of them resulted significantly. To ratify all the molecular dynamic simulation outputs, the potential stability of the flavonoids in complexing with CbpA can be remarked as Quercetin > Biochanin A > Kaempherol > Myricetin, which were all significant in comparison to the control Galangin. Finally, a comprehensive drug-gene interaction pathway for each of the flavonoids was developed to determine the simultaneous and quantitative-synergistic effects of different operons belonging to the DnaJ-type proteins on the metabolism of the tested pharmacophores in CbpA. Considering all the in vitro and in silico parameters, DjlA-mediated CbpA can be a novel target for the tested flavonoids as the potential therapeutics of mastitis as futuristic drugs.
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Affiliation(s)
- Mohammad Habibur Rahman
- Molecular Microbiology and Vaccinology Lab, Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Salauddin Al Azad
- Key Laboratory of Industrial Biotechnology, Ministry of Education, School of Biotechnology, Jiangnan University, Wuxi, 214122, Jiangsu, People's Republic of China
- Immunoinformatics and Vaccinomics Research Unit, RPG Interface Lab, Jashore, 7400, Bangladesh
| | - Mohammad Fahim Uddin
- College of Material Science and Engineering, Zhejiang Sci-Tech University, Hangzhou, 310018, Zhejiang, People's Republic of China
- Immunoinformatics and Vaccinomics Research Unit, RPG Interface Lab, Jashore, 7400, Bangladesh
| | - Maisha Farzana
- School of Medicine, Dentistry and Nursing, University of Glasgow, University Avenue, Glasgow, G12 8QQ, UK
| | - Iffat Ara Sharmeen
- Department of Mathematics & Natural Sciences, School of Data Sciences, BRAC University, Dhaka, 1212, Bangladesh
| | - Kaifi Sultana Kabbo
- Department of Biochemistry and Microbiology, North South University, Dhaka, 1229, Bangladesh
| | - Anika Jabin
- Department of Biochemistry and Microbiology, North South University, Dhaka, 1229, Bangladesh
- Immunoinformatics and Vaccinomics Research Unit, RPG Interface Lab, Jashore, 7400, Bangladesh
| | - Ashfaque Rahman
- Department of Biochemistry and Microbiology, North South University, Dhaka, 1229, Bangladesh
- Immunoinformatics and Vaccinomics Research Unit, RPG Interface Lab, Jashore, 7400, Bangladesh
| | - Farhan Jamil
- Department of Pharmacy, University of Asia Pacific, Farmgate, Dhaka, 1205, Bangladesh
| | | | - Fahmida Haque Riya
- School of Pharmacy, BRAC University, 66 Mohakhali, Dhaka, 1212, Bangladesh
| | - Towhid Khan
- Department of Medicine, Comilla Medical College, Kuchaitoli, Comilla, 3500, Bangladesh
| | - Rasel Ahmed
- School of Computing, Engineering and Digital Technologies, Teesside University, Middlesbrough, TS1 3BX, UK
| | - Nurunnahar
- Department of Mathematics, Mawlana Bhashani Science and Technology University, Tangail, 1902, Bangladesh
| | - Samiur Rahman
- Department of Biochemistry and Microbiology, North South University, Dhaka, 1229, Bangladesh
- Immunoinformatics and Vaccinomics Research Unit, RPG Interface Lab, Jashore, 7400, Bangladesh
| | - Mohammad Ferdousur Rahman Khan
- Molecular Microbiology and Vaccinology Lab, Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh
| | - Md Bahanur Rahman
- Molecular Microbiology and Vaccinology Lab, Department of Microbiology and Hygiene, Bangladesh Agricultural University, Mymensingh, 2202, Bangladesh.
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Potter RF, Zhang K, Reimler B, Marino J, Muenks CE, Alvarado K, Wallace MA, Westblade LF, McElvania E, Yarbrough ML, Hunstad DA, Dantas G, Burnham CAD. Uncharacterized and lineage-specific accessory genes within the Proteus mirabilis pan-genome landscape. mSystems 2023; 8:e0015923. [PMID: 37341494 PMCID: PMC10469602 DOI: 10.1128/msystems.00159-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2023] [Accepted: 05/07/2023] [Indexed: 06/22/2023] Open
Abstract
Proteus mirabilis is a Gram-negative bacterium recognized for its unique swarming motility and urease activity. A previous proteomic report on four strains hypothesized that, unlike other Gram-negative bacteria, P. mirabilis may not exhibit significant intraspecies variation in gene content. However, there has not been a comprehensive analysis of large numbers of P. mirabilis genomes from various sources to support or refute this hypothesis. We performed comparative genomic analysis on 2,060 Proteus genomes. We sequenced the genomes of 893 isolates recovered from clinical specimens from three large US academic medical centers, combined with 1,006 genomes from NCBI Assembly and 161 genomes assembled from Illumina reads in the public domain. We used average nucleotide identity (ANI) to delineate species and subspecies, core genome phylogenetic analysis to identify clusters of highly related P. mirabilis genomes, and pan-genome annotation to identify genes of interest not present in the model P. mirabilis strain HI4320. Within our cohort, Proteus is composed of 10 named species and 5 uncharacterized genomospecies. P. mirabilis can be subdivided into three subspecies; subspecies 1 represented 96.7% (1,822/1,883) of all genomes. The P. mirabilis pan-genome includes 15,399 genes outside of HI4320, and 34.3% (5,282/15,399) of these genes have no putative assigned function. Subspecies 1 is composed of several highly related clonal groups. Prophages and gene clusters encoding putatively extracellular-facing proteins are associated with clonal groups. Uncharacterized genes not present in the model strain P. mirabilis HI4320 but with homology to known virulence-associated operons can be identified within the pan-genome. IMPORTANCE Gram-negative bacteria use a variety of extracellular facing factors to interact with eukaryotic hosts. Due to intraspecies genetic variability, these factors may not be present in the model strain for a given organism, potentially providing incomplete understanding of host-microbial interactions. In contrast to previous reports on P. mirabilis, but similar to other Gram-negative bacteria, P. mirabilis has a mosaic genome with a linkage between phylogenetic position and accessory genome content. P. mirabilis encodes a variety of genes that may impact host-microbe dynamics beyond what is represented in the model strain HI4320. The diverse, whole-genome characterized strain bank from this work can be used in conjunction with reverse genetic and infection models to better understand the impact of accessory genome content on bacterial physiology and pathogenesis of infection.
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Affiliation(s)
- Robert F. Potter
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Pathology & Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Kailun Zhang
- Department of Pathology & Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Ben Reimler
- Department of Pathology & Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Jamie Marino
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Carol E. Muenks
- Department of Pathology & Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Kelly Alvarado
- Department of Pathology & Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Meghan A. Wallace
- Department of Pathology & Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Lars F. Westblade
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, New York, USA
| | - Erin McElvania
- Department of Pathology and Laboratory Medicine, NorthShore University Health System, Evanston, Illinois, USA
| | - Melanie L. Yarbrough
- Department of Pathology & Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - David A. Hunstad
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
| | - Gautam Dantas
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Pathology & Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- The Edison Family Center for Genome Sciences & Systems Biology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Carey-Ann D. Burnham
- Department of Pediatrics, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Pathology & Immunology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Molecular Microbiology, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
- Department of Medicine, Washington University School of Medicine in St. Louis, St. Louis, Missouri, USA
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Mourão J, Ribeiro-Almeida M, Novais C, Magalhães M, Rebelo A, Ribeiro S, Peixe L, Novais Â, Antunes P. From Farm to Fork: Persistence of Clinically Relevant Multidrug-Resistant and Copper-Tolerant Klebsiella pneumoniae Long after Colistin Withdrawal in Poultry Production. Microbiol Spectr 2023; 11:e0138623. [PMID: 37428073 PMCID: PMC10434174 DOI: 10.1128/spectrum.01386-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/13/2023] [Indexed: 07/11/2023] Open
Abstract
Concerns about colistin-resistant bacteria in animal food-environmental-human ecosystems prompted the poultry sector to implement colistin restrictions and explore alternative trace metals/copper feed supplementation. The impact of these strategies on the selection and persistence of colistin-resistant Klebsiella pneumoniae in the whole poultry production chain needs clarification. We assessed colistin-resistant and copper-tolerant K. pneumoniae occurrence in chickens raised with inorganic and organic copper formulas from 1-day-old chicks to meat (7 farms from 2019 to 2020), after long-term colistin withdrawal (>2 years). Clonal diversity and K. pneumoniae adaptive features were characterized by cultural, molecular, and whole-genome-sequencing (WGS) approaches. Most chicken flocks (75%) carried K. pneumoniae at early and preslaughter stages, with a significant decrease (P < 0.05) in meat batches (17%) and sporadic water/feed contamination. High rates (>50%) of colistin-resistant/mcr-negative K. pneumoniae were observed among fecal samples, independently of feed. Most samples carried multidrug-resistant (90%) and copper-tolerant (81%; silA and pcoD positive and with a MICCuSO4 of ≥16 mM) isolates. WGS revealed accumulation of colistin resistance-associated mutations and F type multireplicon plasmids carrying antibiotic resistance and metal/copper tolerance genes. The K. pneumoniae population was polyclonal, with various lineages dispersed throughout poultry production. ST15-KL19, ST15-KL146, and ST392-KL27 and IncF plasmids were similar to those from global human clinical isolates, suggesting chicken production as a reservoir/source of clinically relevant K. pneumoniae lineages and genes with potential risk to humans through food and/or environmental exposure. Despite the limited mcr spread due to the long-term colistin ban, this action was ineffective in controlling colistin-resistant/mcr-negative K. pneumoniae, regardless of feed. This study provides crucial insights into the persistence of clinically relevant K. pneumoniae in the poultry production chain and highlights the need for continued surveillance and proactive food safety actions within a One Health perspective. IMPORTANCE The spread of bacteria resistant to last-resort antibiotics such as colistin throughout the food chain is a serious concern for public health. The poultry sector has responded by restricting colistin use and exploring alternative trace metals/copper feed supplements. However, it is unclear how and to which extent these changes impact the selection and persistence of clinically relevant Klebsiella pneumoniae throughout the poultry chain. We found a high occurrence of copper-tolerant and colistin-resistant/mcr-negative K. pneumoniae in chicken flocks, regardless of inorganic and organic copper formulas use and a long-term colistin ban. Despite the high K. pneumoniae isolate diversity, the occurrence of identical lineages and plasmids across samples and/or clinical isolates suggests poultry as a potential source of human K. pneumoniae exposure. This study highlights the need for continued surveillance and proactive farm-to-fork actions to mitigate the risks to public health, relevant for stakeholders involved in the food industry and policymakers tasked with regulating food safety.
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Affiliation(s)
- Joana Mourão
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal
| | - Marisa Ribeiro-Almeida
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
| | - Carla Novais
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Mafalda Magalhães
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
| | - Andreia Rebelo
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
- ESS, Polytechnic of Porto, Porto, Portugal
| | - Sofia Ribeiro
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ângela Novais
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Patrícia Antunes
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
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Jati AP, Sola-Campoy PJ, Bosch T, Schouls LM, Hendrickx APA, Bautista V, Lara N, Raangs E, Aracil B, Rossen JWA, Friedrich AW, Navarro Riaza AM, Cañada-García JE, Ramírez de Arellano E, Oteo-Iglesias J, Pérez-Vázquez M, García-Cobos S. Widespread Detection of Yersiniabactin Gene Cluster and Its Encoding Integrative Conjugative Elements (ICE Kp) among Nonoutbreak OXA-48-Producing Klebsiella pneumoniae Clinical Isolates from Spain and the Netherlands. Microbiol Spectr 2023; 11:e0471622. [PMID: 37310221 PMCID: PMC10434048 DOI: 10.1128/spectrum.04716-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Accepted: 05/22/2023] [Indexed: 06/14/2023] Open
Abstract
In this study, we determined the presence of virulence factors in nonoutbreak, high-risk clones and other isolates belonging to less common sequence types associated with the spread of OXA-48-producing Klebsiella pneumoniae clinical isolates from The Netherlands (n = 61) and Spain (n = 53). Most isolates shared a chromosomally encoded core of virulence factors, including the enterobactin gene cluster, fimbrial fim and mrk gene clusters, and urea metabolism genes (ureAD). We observed a high diversity of K-Locus and K/O loci combinations, KL17 and KL24 (both 16%), and the O1/O2v1 locus (51%) being the most prevalent in our study. The most prevalent accessory virulence factor was the yersiniabactin gene cluster (66.7%). We found seven yersiniabactin lineages-ybt 9, ybt 10, ybt 13, ybt 14, ybt 16, ybt 17, and ybt 27-which were chromosomally embedded in seven integrative conjugative elements (ICEKp): ICEKp3, ICEKp4, ICEKp2, ICEKp5, ICEKp12, ICEKp10, and ICEKp22, respectively. Multidrug-resistant lineages-ST11, ST101, and ST405-were associated with ybt 10/ICEKp4, ybt 9/ICEKp3, and ybt 27/ICEKp22, respectively. The fimbrial adhesin kpi operon (kpiABCDEFG) was predominant among ST14, ST15, and ST405 isolates, as well as the ferric uptake system kfuABC, which was also predominant among ST101 isolates. No convergence of hypervirulence and resistance was observed in this collection of OXA-48-producing K. pneumoniae clinical isolates. Nevertheless, two isolates, ST133 and ST792, were positive for the genotoxin colibactin gene cluster (ICEKp10). In this study, the integrative conjugative element, ICEKp, was the major vehicle for yersiniabactin and colibactin gene clusters spreading. IMPORTANCE Convergence of multidrug resistance and hypervirulence in Klebsiella pneumoniae isolates has been reported mostly related to sporadic cases or small outbreaks. Nevertheless, little is known about the real prevalence of carbapenem-resistant hypervirulent K. pneumoniae since these two phenomena are often separately studied. In this study, we gathered information on the virulent content of nonoutbreak, high-risk clones (i.e., ST11, ST15, and ST405) and other less common STs associated with the spread of OXA-48-producing K. pneumoniae clinical isolates. The study of virulence content in nonoutbreak isolates can help us to expand information on the genomic landscape of virulence factors in K. pneumoniae population by identifying virulence markers and their mechanisms of spread. Surveillance should focus not only on antimicrobial resistance but also on virulence characteristics to avoid the spread of multidrug and (hyper)virulent K. pneumoniae that may cause untreatable and more severe infections.
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Affiliation(s)
- Afif P. Jati
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
- Indonesian Society of Bioinformatics and Biodiversity, Indonesia
| | - Pedro J. Sola-Campoy
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Thijs Bosch
- Infectious Diseases Research, Diagnostics and Laboratory Surveillance, Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Leo M. Schouls
- Infectious Diseases Research, Diagnostics and Laboratory Surveillance, Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Antoni P. A. Hendrickx
- Infectious Diseases Research, Diagnostics and Laboratory Surveillance, Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Verónica Bautista
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Noelia Lara
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Erwin Raangs
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
| | - Belén Aracil
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- CIBER de Enfermedades Infecciosas, Spanish Network for Research in Infectious Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - John W. A. Rossen
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
- Laboratory of Medical Microbiology and Infectious Diseases, Isala Hospital, Zwolle, The Netherlands
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
| | - Alex W. Friedrich
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
- University Hospital Münster, Institute of European Prevention Networks in Infection Control, Münster, Germany
| | - Ana M. Navarro Riaza
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Javier E. Cañada-García
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - Eva Ramírez de Arellano
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- CIBER de Enfermedades Infecciosas, Spanish Network for Research in Infectious Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Jesús Oteo-Iglesias
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- CIBER de Enfermedades Infecciosas, Spanish Network for Research in Infectious Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - María Pérez-Vázquez
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- CIBER de Enfermedades Infecciosas, Spanish Network for Research in Infectious Diseases, Instituto de Salud Carlos III, Madrid, Spain
| | - Silvia García-Cobos
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
| | - The Dutch and Spanish Collaborative Working Groups on Surveillance on Carbapenemase-Producing Enterobacterales
- University of Groningen, University Medical Center Groningen, Department of Medical Microbiology and Infection Prevention, Groningen, The Netherlands
- Indonesian Society of Bioinformatics and Biodiversity, Indonesia
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain
- Infectious Diseases Research, Diagnostics and Laboratory Surveillance, Centre for Infectious Disease Control Netherlands, National Institute for Public Health and the Environment, Bilthoven, The Netherlands
- CIBER de Enfermedades Infecciosas, Spanish Network for Research in Infectious Diseases, Instituto de Salud Carlos III, Madrid, Spain
- Laboratory of Medical Microbiology and Infectious Diseases, Isala Hospital, Zwolle, The Netherlands
- Department of Pathology, University of Utah School of Medicine, Salt Lake City, Utah, USA
- University Hospital Münster, Institute of European Prevention Networks in Infection Control, Münster, Germany
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Rodrigues C, Lanza VF, Peixe L, Coque TM, Novais Â. Phylogenomics of Globally Spread Clonal Groups 14 and 15 of Klebsiella pneumoniae. Microbiol Spectr 2023; 11:e0339522. [PMID: 37098951 PMCID: PMC10269502 DOI: 10.1128/spectrum.03395-22] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 03/26/2023] [Indexed: 04/27/2023] Open
Abstract
Klebsiella pneumoniae sequence type 14 (ST14) and ST15 caused outbreaks of CTX-M-15 and/or carbapenemase producers worldwide, but their phylogeny and global dynamics remain unclear. We clarified the evolution of K. pneumoniae clonal group 14 (CG14) and CG15 by analyzing the capsular locus (KL), resistome, virulome, and plasmidome of public genomes (n = 481) and de novo sequences (n = 9) representing main sublineages circulating in Portugal. CG14 and CG15 evolved independently within 6 main subclades defined according to the KL and the accessory genome. The CG14 (n = 65) clade was structured in two large monophyletic subclades, CG14-I (KL2, 86%) and CG14-II (KL16, 14%), whose emergences were dated to 1932 and 1911, respectively. Genes encoding extended-spectrum β-lactamase (ESBL), AmpC, and/or carbapenemases were mostly observed in CG14-I (71% versus 22%). CG15 clade (n = 170) was segregated into subclades CG15-IA (KL19/KL106, 9%), CG15-IB (variable KL types, 6%), CG15-IIA (KL24, 43%) and CG15-IIB (KL112, 37%). Most CG15 genomes carried specific GyrA and ParC mutations and emerged from a common ancestor in 1989. CTX-M-15 was especially prevalent in CG15 (68% CG15 versus 38% CG14) and in CG15-IIB (92%). Plasmidome analysis revealed 27 predominant plasmid groups (PG), including particularly pervasive and recombinant F-type (n = 10), Col (n = 10), and new plasmid types. While blaCTX-M-15 was acquired multiple times by a high diversity of F-type mosaic plasmids, other antibiotic resistance genes (ARGs) were dispersed by IncL (blaOXA-48) or IncC (blaCMY/TEM-24) plasmids. We first demonstrate an independent evolutionary trajectory for CG15 and CG14 and how the acquisition of specific KL, quinolone-resistance determining region (QRDR) mutations (CG15), and ARGs in highly recombinant plasmids could have shaped the expansion and diversification of particular subclades (CG14-I and CG15-IIA/IIB). IMPORTANCE Klebsiella pneumoniae represents a major threat in the burden of antibiotic resistance (ABR). Available studies to explain the origin, the diversity, and the evolution of certain ABR K. pneumoniae populations have mainly been focused on a few clonal groups (CGs) using phylogenetic analysis of the core genome, the accessory genome being overlooked. Here, we provide unique insights into the phylogenetic evolution of CG14 and CG15, two poorly characterized CGs which have contributed to the global dissemination of genes responsible for resistance to first-line antibiotics such as β-lactams. Our results point out an independent evolution of these two CGs and highlight the existence of different subclades structured by the capsular type and the accessory genome. Moreover, the contribution of a turbulent flux of plasmids (especially multireplicon F type and Col) and adaptive traits (antibiotic resistance and metal tolerance genes) to the pangenome reflect the exposure and adaptation of K. pneumoniae under different selective pressures.
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Affiliation(s)
- Carla Rodrigues
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Val F. Lanza
- Unidad de Genómica Traslacional Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
| | - Luísa Peixe
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Teresa M. Coque
- CIBER en Enfermedades Infecciosas (CIBERINFEC), Madrid, Spain
- Servicio de Microbiología, Hospital Universitario Ramón y Cajal (IRYCIS), Madrid, Spain
| | - Ângela Novais
- UCIBIO, Applied Molecular Biosciences Unit, Department of Biological Sciences, Laboratory of Microbiology, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
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9
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Álvarez VE, Quiroga MP, Centrón D. Identification of a Specific Biomarker of Acinetobacter baumannii Global Clone 1 by Machine Learning and PCR Related to Metabolic Fitness of ESKAPE Pathogens. mSystems 2023:e0073422. [PMID: 37184409 DOI: 10.1128/msystems.00734-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023] Open
Abstract
Since the emergence of high-risk clones worldwide, constant investigations have been undertaken to comprehend the molecular basis that led to their prevalent dissemination in nosocomial settings over time. So far, the complex and multifactorial genetic traits of this type of epidemic clones have allowed only the identification of biomarkers with low specificity. A machine learning algorithm was able to recognize unequivocally a biomarker for early and accurate detection of Acinetobacter baumannii global clone 1 (GC1), one of the most disseminated high-risk clones. A support vector machine model identified the U1 sequence with a length of 367 nucleotides that matched a fragment of the moaCB gene, which encodes the molybdenum cofactor biosynthesis C and B proteins. U1 differentiates specifically between A. baumannii GC1 and non-GC1 strains, becoming a suitable biomarker capable of being translated into clinical settings as a molecular typing method for early diagnosis based on PCR as shown here. Since the metabolic pathways of Mo enzymes have been recognized as putative therapeutic targets for ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens, our findings highlight that machine learning can also be useful in knowledge gaps of high-risk clones and provides noteworthy support to the literature to identify relevant nosocomial biomarkers for other multidrug-resistant high-risk clones. IMPORTANCE A. baumannii GC1 is an important high-risk clone that rapidly develops extreme drug resistance in the nosocomial niche. Furthermore, several strains have been identified worldwide in environmental samples, exacerbating the risk of human interactions. Early diagnosis is mandatory to limit its dissemination and to outline appropriate antibiotic stewardship schedules. A region with a length of 367 bp (U1) within the moaCB gene that is not subjected to lateral genetic transfer or to antibiotic pressures was successfully found by a support vector machine model that predicts A. baumannii GC1 strains. At the same time, research on the group of Mo enzymes proposed this metabolic pathway related to the superbug's metabolism as a potential future drug target site for ESKAPE pathogens due to its central role in bacterial fitness during infection. These findings confirm that machine learning used for the identification of biomarkers of high-risk lineages can also serve to identify putative novel therapeutic target sites.
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Affiliation(s)
- Verónica Elizabeth Álvarez
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos (LIMRA), Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - María Paula Quiroga
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos (LIMRA), Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, Argentina
- Nodo de Bioinformática. Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, Argentina
| | - Daniela Centrón
- Laboratorio de Investigaciones en Mecanismos de Resistencia a Antibióticos (LIMRA), Instituto de Investigaciones en Microbiología y Parasitología Médica, Facultad de Medicina, Universidad de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Tecnológicas (IMPaM, UBA-CONICET), Ciudad Autónoma de Buenos Aires, Argentina
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10
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Li Y, Shi X, Zuo Y, Li T, Liu L, Shen Z, Shen J, Zhang R, Wang S. Multiplexed Target Enrichment Enables Efficient and In-Depth Analysis of Antimicrobial Resistome in Metagenomes. Microbiol Spectr 2022; 10:e0229722. [PMID: 36287061 PMCID: PMC9769626 DOI: 10.1128/spectrum.02297-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Accepted: 10/04/2022] [Indexed: 01/06/2023] Open
Abstract
Antibiotic resistance genes (ARGs) pose a serious threat to public health and ecological security in the 21st century. However, the resistome only accounts for a tiny fraction of metagenomic content, which makes it difficult to investigate low-abundance ARGs in various environmental settings. Thus, a highly sensitive, accurate, and comprehensive method is needed to describe ARG profiles in complex metagenomic samples. In this study, we established a high-throughput sequencing method based on targeted amplification, which could simultaneously detect ARGs (n = 251), mobile genetic element genes (n = 8), and metal resistance genes (n = 19) in metagenomes. The performance of amplicon sequencing was compared with traditional metagenomic shotgun sequencing (MetaSeq). A total of 1421 primer pairs were designed, achieving extremely high coverage of target genes. The amplicon sequencing significantly improved the recovery of target ARGs (~9 × 104-fold), with higher sensitivity and diversity, less cost, and computation burden. Furthermore, targeted enrichment allows deep scanning of single nucleotide polymorphisms (SNPs), and elevated SNPs detection was shown in this study. We further performed this approach for 48 environmental samples (37 feces, 20 soils, and 7 sewage) and 16 clinical samples. All samples tested in this study showed high diversity and recovery of targeted genes. Our results demonstrated that the approach could be applied to various metagenomic samples and served as an efficient tool in the surveillance and evolution assessment of ARGs. Access to the resistome using the enrichment method validated in this study enabled the capture of low-abundance resistomes while being less costly and time-consuming, which can greatly advance our understanding of local and global resistome dynamics. IMPORTANCE ARGs, an increasing global threat to human health, can be transferred into health-related microorganisms in the environment by horizontal gene transfer, posing a serious threat to public health. Advancing profiling methods are needed for monitoring and predicting the potential risks of ARGs in metagenomes. Our study described a customized amplicon sequencing assay that could enable a high-throughput, targeted, in-depth analysis of ARGs and detect a low-abundance portion of resistomes. This method could serve as an efficient tool to assess the variation and evolution of specific ARGs in the clinical and natural environment.
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Affiliation(s)
- Yiming Li
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Xiaomin Shi
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Yang Zuo
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Tian Li
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Lu Liu
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Zhangqi Shen
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Jianzhong Shen
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
| | - Rong Zhang
- The Second Affiliated Hospital of Zhejiang University, Zhejiang University, Hangzhou, China
| | - Shaolin Wang
- Beijing Key Laboratory of Detection Technology for Animal-Derived Food Safety, College of Veterinary Medicine, China Agricultural University, Beijing, China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, China
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Ribeiro ÁCDS, Santos FF, Moses IB, Minarini LADR, Gales AC. Sequencing of fosA: A Rapid and Inexpensive Method for Discriminating Klebsiella pneumoniae CC258 from Other Clones. Microb Drug Resist 2022; 28:1037-1042. [DOI: 10.1089/mdr.2022.0081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Ághata Cardoso da Silva Ribeiro
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo (UNIFESP), São Paulo, São Paulo, Brazil
| | - Fernanda Fernandes Santos
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo (UNIFESP), São Paulo, São Paulo, Brazil
| | - Ikechukwu Benjamin Moses
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo (UNIFESP), São Paulo, São Paulo, Brazil
- Department of Applied Microbiology, Faculty of Science, Ebonyi State University, Abakaliki, Nigeria
| | - Luciene Andrade da Rocha Minarini
- Laboratório Multidisciplinar em Saúde e Meio Ambiente, Departamento de Ciências Farmacêuticas, Instituto de Ciências Ambientais, Químicas e Farmacêuticas, Universidade Federal de São Paulo (UNIFESP), Diadema, São Paulo, Brazil
| | - Ana Cristina Gales
- Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina/Universidade Federal de São Paulo (UNIFESP), São Paulo, São Paulo, Brazil
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12
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Pandemic Clones of CTX-M-15 Producing Klebsiella pneumoniae ST15, ST147, and ST307 in Companion Parrots. Microorganisms 2022; 10:microorganisms10071412. [PMID: 35889131 PMCID: PMC9320316 DOI: 10.3390/microorganisms10071412] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 12/22/2022] Open
Abstract
Psittacine birds are commonly kept as companion birds and the maintenance of these birds in captivity may represent a zoonotic risk and contribute to the propagation of multidrug-resistant and β-lactamase extended-spectrum (ESBLs)-producing pathogens. This study aimed to identify and characterize strains of the Klebsiella pneumoniae complex isolated from diseased psittacine birds, determining virulence and resistance profiles. K. pneumoniae strains were isolated from 16 birds (16/46). All strains carried more than three virulence genes, with a high frequency of fimH and kpn (93.75%), uge (87.52%), and irp-2 (81.25%) genes. The antimicrobial susceptibility revealed that 3/16 strains were ESBL producers. Genomic analysis revealed that CTX-M-15-positive strains belonged to sequence types (STs) ST15, ST147, and ST307, characterized as international clones associated with outbreaks of healthcare-associated infections (HAIs) worldwide.
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13
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Lu J, Wang Y, Liu C, Sun Q, Zeng Y, Cai C, Shen Z, Zhang R. Prevalence, genomic characterization and pathogenic capability of kpi-positive Klebsiella pneumoniae in China. J Glob Antimicrob Resist 2022; 30:259-261. [DOI: 10.1016/j.jgar.2022.06.031] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Revised: 06/27/2022] [Accepted: 06/28/2022] [Indexed: 11/29/2022] Open
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A New Live Auxotrophic Vaccine Induces Cross-Protection against Klebsiella pneumoniae Infections in Mice. Vaccines (Basel) 2022; 10:vaccines10060953. [PMID: 35746561 PMCID: PMC9227041 DOI: 10.3390/vaccines10060953] [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] [Received: 05/30/2022] [Revised: 06/13/2022] [Accepted: 06/14/2022] [Indexed: 02/04/2023] Open
Abstract
The development of a whole-cell vaccine from bacteria auxotrophic for D-amino acids present in the bacterial cell wall is considered a promising strategy for providing protection against bacterial infections. Here, we constructed a prototype vaccine, consisting of a glutamate racemase-deficient mutant, for preventing Klebsiella pneumoniae infections. The deletion mutant lacks the murI gene and requires exogenous addition of D-glutamate for growth. The results showed that the K. pneumoniae ΔmurI strain is attenuated and includes a favourable combination of antigens for inducing a robust immune response and conferring an adequate level of cross-protection against systemic infections caused by K. pneumoniae strains, including some hypervirulent serotypes with elevated production of capsule polysaccharide as well as multiresistant K. pneumoniae strains. The auxotroph also induced specific production of IL-17A and IFN-γ. The rapid elimination of the strain from the blood of mice without causing disease suggests a high level of safety for administration as a vaccine.
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Wu X, Liu J, Feng J, Shabbir MAB, Feng Y, Guo R, Zhou M, Hou S, Wang G, Hao H, Cheng G, Wang Y. Epidemiology, Environmental Risks, Virulence, and Resistance Determinants of Klebsiella pneumoniae From Dairy Cows in Hubei, China. Front Microbiol 2022; 13:858799. [PMID: 35602033 PMCID: PMC9117759 DOI: 10.3389/fmicb.2022.858799] [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: 01/20/2022] [Accepted: 04/08/2022] [Indexed: 11/21/2022] Open
Abstract
Klebsiella pneumoniae (K. pneumoniae) is an opportunistic pathogen, which causes serious infections in humans and animals. To investigate the antimicrobial resistance pattern and virulence profile of K. pneumoniae, a total of 887 samples were collected from both the healthy and mastitis cows and the bedding, feed, feces, air, drinking water, spraying water, washing water, and milk cup swabs from five dairy farms in Hubei, China, during 2019 and 2020. K. pneumoniae was isolated and identified using PCR of the khe and 16S rDNA sequencing. A genotypic characterization was performed for K. pneumoniae isolates using wzi typing and multilocus sequence typing (MLST). Antimicrobial resistances were confirmed using broth microdilution against 17 antimicrobial agents and resistance and virulence genes were determined by PCR. The prevalence of K. pneumoniae was 26.94% (239/887) distributed in 101 wzi allele types (199/239, 83.26%) and 100 sequence types (STs) (209/239, 87.45%), including 5 new wzi allele type and 25 new STs. Phylogenetic analysis showed that K. pneumoniae isolated from milk, nipple swab, feed, and feces is classified in the same clone complex. By comparing with the PubMLST database, at least 67 STs have the risk of spreading in different species and regions. Interestingly, 60 STs have been isolated from humans. The isolates were highly sensitive to meropenem and colistin, but resistant to ampicillin (100%), sulfisoxazole (94.56%), cephalothin (47.28%), streptomycin (30.13%), and so on. Noteworthy, multidrug-resistant (MDR) rate was found to be 43.93% in this study. By PCR, 30 of 68 antimicrobial resistance (AMR) genes were identified; the prevalence rate of blaTEM, blaSHV, strA, strB, aadA1, and aac(6′)-Ib-cr was more than 50%. Eleven CTX-M-producing K. pneumoniae were found. The detection rate of fimH, mrkD, uge, wabG, entB, iutA, iroN, and ureA was over 85%. This study reinforces the epidemiological importance of K. pneumoniae in food-producing animals in Hubei. The emergence and spread of environmental MDR K. pneumoniae may pose a potential threat to food safety and public health.
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Affiliation(s)
- Xiangyun Wu
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
| | - Jiayi Liu
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
| | - Jiawei Feng
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
| | | | - Yali Feng
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
| | - Rui Guo
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
| | - Meifang Zhou
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
| | - Sulin Hou
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China
| | - Guiqiang Wang
- Hubei Livestock and Poultry Breeding Centre, Wuhan, China
| | - Haihong Hao
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China.,National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, China
| | - Guyue Cheng
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China.,National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, China
| | - Yulian Wang
- MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, China.,National Reference Laboratory of Veterinary Drug Residues (HZAU) and MOA Key Laboratory for Detection of Veterinary Drug Residues, Huazhong Agricultural University, Wuhan, China
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Liu Y, Bai J, Kang J, Song Y, Yin D, Wang J, Li H, Duan J. Three Novel Sequence Types Carbapenem-Resistant Klebsiella pneumoniae Strains ST5365, ST5587, ST5647 Isolated from Two Tertiary Teaching General Hospitals in Shanxi Province, in North China: Molecular Characteristics, Resistance and Virulence Factors. Infect Drug Resist 2022; 15:2551-2563. [PMID: 35614966 PMCID: PMC9124815 DOI: 10.2147/idr.s366480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 05/12/2022] [Indexed: 11/29/2022] Open
Abstract
Background Carbapenem-resistant Klebsiella pneumoniae (CRKP) represents a significant threat to public health and has already drawn worldwide attention. Hence, we aim to comprehensively analyze the case condition, as well as molecular epidemiology, resistance and virulence of three CRKP isolates with new sequence types (STs). Methods Three CRKP were collected from November 2019 to April 2021. The three patients’ clinical characteristics were analyzed through His system. In order to screen phenotype of metallo-carbapenemase, the modified Carbapenem Inactivation Method (mCIM) and EDTA-modified Carbapenem Inactivation Method (eCIM) were conducted. Three isolates were subjected to antimicrobial susceptibility testing (AST) using the agar dilution method or minimal broth dilution method. The string test, the sedimentation assay, biofilm formation and the serum resistance assay were performed as phenotypic experiments to assist in evaluating virulence. The presence of resistance and virulence genes were detected by Whole-Genome Sequencing (WGS). Serotypes and new STs were compared and determined by multi-locus sequence typing (MLST). Results Overall, all Klebsiella pneumoniae isolates were multi-resistant, but sensitive to tigecycline and colistin. Among them, all formed biofilms, strain 1 and strain 2 were classified as moderate-producers, while strain 3 as weak-producer. The results of the serum resistance assay indicated that only strain 2 was resistant. From WGS analysis, it showed that all isolates co-harbored multiple resistance genes, such as carbapenemase genes, sulfonamides, fluoroquinolones, aminoglycosides, and tetracyclines. Meanwhile, several virulence genes were also contained, including siderophores, fimbriae, capsule and lipopolysaccharides-associated genes. The serotypes of strain 1 and strain 2 manifested K35 and KL47, respectively. Conclusion Three novel ST5365, ST5587, ST5647 were first discovered in North China. Our study suggested that we should pay more attention to their resistance. And the results will help treat CRKP infections caused by these novel STs.
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Affiliation(s)
- Yujie Liu
- Department of Pharmacy, School of Pharmacy, Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
| | - Jing Bai
- Department of Pharmacy, School of Pharmacy, Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
| | - Jianbang Kang
- Department of Pharmacy, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
| | - Yan Song
- Department of Pharmacy, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
| | - Donghong Yin
- Department of Pharmacy, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
| | - Jing Wang
- Department of Pharmacy, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
| | - Hao Li
- Department of Clinical Laboratory, First Hospital of Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
- Correspondence: Hao Li, Department of Clinical Laboratory, First Hospital of Shanxi Medical University, No. 85, Jiefang South Road, Taiyuan, Shanxi, People’s Republic of China, Tel +86 15340705830, Email
| | - Jinju Duan
- Department of Pharmacy, Second Hospital of Shanxi Medical University, Taiyuan, Shanxi, People’s Republic of China
- Jinju Duan, Department of Pharmacy, Second Hospital of Shanxi Medical University, No. 382, Wuyi Road, Xinghualing District, Taiyuan, Shanxi, People’s Republic of China, Tel +86 351 3365713, Email
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17
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Muhsin EA, Sajid Al-Jubori S, Abdulhemid Said L. Prevalence of Efflux Pump and Porin-Related Antimicrobial Resistance in Clinical Klebsiella pneumoniae in Baghdad, Iraq. ARCHIVES OF RAZI INSTITUTE 2022; 77:785-798. [PMID: 36284955 PMCID: PMC9548288 DOI: 10.22092/ari.2022.356976.1952] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Accepted: 01/16/2022] [Indexed: 05/24/2023]
Abstract
Klebsiella pneumoniae is an opportunistic bacterium that causes many infections, including septicemia, pneumonia, urinary tract infection, and liver abscesses. There are many mechanisms for antibiotic resistance and K. pneumonia is considered a multidrug-resistant pathogen. This study aimed to find the correlation between the susceptibility of K. pneumonia to certain antibiotics with the porin-related resistance and pumps mechanisms. In total, two genes that are responsible for porin formation were considered in the current study OmpK-35gene and OmpK-36 gene, in addition to other four genes (CfiaS, CfiaL, MFS, and MdtK genes) related to an efflux pump mechanism of antibiotic resistance. The bacterial resistance was investigated towards five cephalosporins (Cefazolin, Cefoxitin, Ceftazidime, Ceftriaxone, and Cefepime) and two carbapenems (imipenem and ertapenem). Clinical samples, including blood, swabs, and urine, consisting of 20 specimens for each group, were collected from patients who attended three hospitals in Baghdad. The VITEK-2 system and genetic tests (polymerase chain reaction and sequencing) of bacterial isolates were applied to confirm the diagnosis of K. pneumoniae and detect the antibiotic sensitivity profile. The results showed that 51 (85%) and 15 (25%) of the total 60 isolates had positive results for OmpK-35 and Omp-K36 genes, respectively. The MFS and MdtK genes were observed (70-88.3%) in cephalosporin-resistant isolates of K. pneumoniae. There were no significant variations of bacterial resistance genes of antibiotics within the specimen groups. It was concluded that the bacterial resistance of the selected antibiotics was elevated markedly with the loss of the OmpK-36 gene with a high expression of MFS and MdtK genes and a slight minimal occurrence in the new generation of carbapenems. The best antimicrobial agent was ertapenem with a percentage of 0% of resistance in all bacterial isolates.
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Affiliation(s)
| | - S Sajid Al-Jubori
- Biology Department, College of Science, Mustansiriyah University, Baghdad, Iraq
| | - L Abdulhemid Said
- Biology Department, College of Science, Mustansiriyah University, Baghdad, Iraq
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18
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Cardoso B, Esposito F, Fontana H, Fuga B, Moura Q, Sano E, Sato MIZ, Brandão CJ, Oliveira FA, Levy CE, Lincopan N. Genomic analysis of a Kpi (pilus system)-positive and CTX-M-15-producing Klebsiella pneumoniae belonging to the high-risk clone ST15 isolated from an impacted river in Brazil. Genomics 2021; 114:378-383. [PMID: 34923088 DOI: 10.1016/j.ygeno.2021.12.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 08/27/2021] [Accepted: 12/14/2021] [Indexed: 11/04/2022]
Abstract
Convergence of resistance and virulence in Klebsiella pneumoniae is a critical public health issue worldwide. A multidrug-resistant CTX-M-15-producing K. pneumoniae (TIES-4900 strain) was isolated from a highly impacted urban river, in Brazil. The genome was sequenced by MiSeq Illumina platform and de novo assembled using Unicycler. In silico prediction was accomplished by bioinformatics tools. The size of the genome is 5.4 Mb with 5145 protein-coding genes. TIES-4900 strain belonged to the sequence type ST15, yersiniabactin sequence type YbST10, ICEKp4, KL24 (wzi-24) and O1v1 locus. Phylogenomics confirmed genomic relatedness with ST15 clones from human and animal hosts. Convergence of broad resistome (antibiotics, heavy-metals and biocides) and virulome, including the Kpi pilus system involved in host-pathogen interaction and persistence of ST15 clone to hospital environments, were predicted. Virulent behavior was confirmed in the Galleria mellonella infection model. This study may give genomic insights on the spread of critical-priority WHO pathogens beyond hospital settings.
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Affiliation(s)
- Brenda Cardoso
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), Brazil
| | - Fernanda Esposito
- One Health Brazilian Resistance Project (OneBR), Brazil; Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Herrison Fontana
- One Health Brazilian Resistance Project (OneBR), Brazil; Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Bruna Fuga
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), Brazil; Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil
| | - Quézia Moura
- Faculty of Health Sciences, Federal University of Grande Dourados, Mato Grosso do Sul, Brazil
| | - Elder Sano
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), Brazil
| | - Maria I Z Sato
- Environmental Company of São Paulo State (CETESB), São Paulo, Brazil
| | - Carlos J Brandão
- Environmental Company of São Paulo State (CETESB), São Paulo, Brazil
| | | | - Carlos E Levy
- Hospital de Clínicas, Universidade Estadual de Campinas, Brazil
| | - Nilton Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, University of São Paulo, São Paulo, Brazil; One Health Brazilian Resistance Project (OneBR), Brazil; Department of Clinical Analysis, School of Pharmacy, University of São Paulo, São Paulo, Brazil.
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19
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Gato E, Rosalowska A, Martínez-Guitián M, Lores M, Bou G, Pérez A. Anti-adhesive activity of a Vaccinium corymbosum polyphenolic extract targeting intestinal colonization by Klebsiella pneumoniae. Biomed Pharmacother 2020; 132:110885. [PMID: 33113420 DOI: 10.1016/j.biopha.2020.110885] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Revised: 10/09/2020] [Accepted: 10/12/2020] [Indexed: 11/26/2022] Open
Abstract
The therapeutic effect of Vaccinium polyphenols against uropathogens has been widely studied. Most attention has focused on the antimicrobial activity against P-fimbriated Escherichia coli strains. The present study investigated the anti-adhesive and anti-biofilm activity of a saline extract of blueberry (Vaccinium corymbosum) targeting intestinal colonization by a highly adherent Klebsiella pneumoniae strain. This strain, responsible for a large outbreak of infection in Spain, was selected on the basis of its remarkable capacity to colonize the gastrointestinal tract of patients. The blueberry extract was obtained using a medium scale ambient temperature system (MSAT) in a novel approach based on the use of an aqueous solvent and addition of mineral salts. The polyphenolic content was determined by liquid chromatography coupled to tandem mass-spectrometry (LC-MS/MS). The findings confirmed that the blueberry extract is a rich source of phenolic compounds, including the most polar polyphenols (mostly non-flavonoids), intermediate polarity compounds (flavan-3-ols and most procyanidins) and low polarity compounds (flavonols and anthocyanins). The extract significantly inhibited biofilm formation and bacterial adhesion to HT-29 colorectal cells by a highly adherent multidrug-resistant K. pneumoniae. Although some individual anthocyanidins (malvidin, delphinidin and cyanidin) and one hydroxycinnamic acid (caffeic acid) proved capable of reducing bacterial adhesion, the unfractionated extract was more active than any of the individual polyphenolic compounds. In addition, the extract displayed considerable potential as an intestinal decolonization treatment in a murine model. The study findings demonstrate the potential value of the V. corymbosum extract as an alternative treatment for K. pneumoniae infections.
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Affiliation(s)
- Eva Gato
- Departamento de Microbiología, Complejo Hospitalario Universitario A Coruña (HUAC), Instituto de Investigación Biomédica A Coruña (INIBIC), Universidad de A Coruña (UDC), A Coruña, Spain
| | - Alicja Rosalowska
- Departamento de Química Analítica, Nutrición y Bromatología, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - Marta Martínez-Guitián
- Departamento de Microbiología, Complejo Hospitalario Universitario A Coruña (HUAC), Instituto de Investigación Biomédica A Coruña (INIBIC), Universidad de A Coruña (UDC), A Coruña, Spain
| | - Marta Lores
- Departamento de Química Analítica, Nutrición y Bromatología, Universidad de Santiago de Compostela, Santiago de Compostela, Spain
| | - German Bou
- Departamento de Microbiología, Complejo Hospitalario Universitario A Coruña (HUAC), Instituto de Investigación Biomédica A Coruña (INIBIC), Universidad de A Coruña (UDC), A Coruña, Spain
| | - Astrid Pérez
- Departamento de Microbiología, Complejo Hospitalario Universitario A Coruña (HUAC), Instituto de Investigación Biomédica A Coruña (INIBIC), Universidad de A Coruña (UDC), A Coruña, Spain.
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