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Yang Y, Zhou P, Tian D, Wang W, Zhou Y, Jiang X. CRISPR-Cas3 and type I restriction-modification team up against bla KPC-IncF plasmid transfer in Klebsiella pneumoniae. BMC Microbiol 2024; 24:240. [PMID: 38961341 PMCID: PMC11223367 DOI: 10.1186/s12866-024-03381-7] [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: 12/04/2023] [Accepted: 06/18/2024] [Indexed: 07/05/2024] Open
Abstract
OBJECTIVE We explored whether the Clustered regularly interspaced short palindromic repeat (CRISPR)-Cas and restriction-modification (R-M) systems are compatible and act together to resist plasmid attacks. METHODS 932 global whole-genome sequences from GenBank, and 459 K. pneumoniae isolates from six provinces of China, were collected to investigate the co-distribution of CRISPR-Cas, R-M systems, and blaKPC plasmid. Conjugation and transformation assays were applied to explore the anti-plasmid function of CRISPR and R-M systems. RESULTS We found a significant inverse correlation between the presence of CRISPR and R-M systems and blaKPC plasmids in K. pneumoniae, especially when both systems cohabited in one host. The multiple matched recognition sequences of both systems in blaKPC-IncF plasmids (97%) revealed that they were good targets for both systems. Furthermore, the results of conjugation assay demonstrated that CRISPR-Cas and R-M systems in K. pneumoniae could effectively hinder blaKPC plasmid invasion. Notably, CRISPR-Cas and R-M worked together to confer a 4-log reduction in the acquisition of blaKPC plasmid in conjugative events, exhibiting robust synergistic anti-plasmid immunity. CONCLUSIONS Our results indicate the synergistic role of CRISPR and R-M in regulating horizontal gene transfer in K. pneumoniae and rationalize the development of antimicrobial strategies that capitalize on the immunocompromised status of KPC-KP.
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Affiliation(s)
- Yang Yang
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai, China
- Key Laboratory of Clinical Pharmacology of Antibiotics, Ministry of Health, Shanghai, China
| | - Peiyao Zhou
- Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Dongxing Tian
- Department of Laboratory Medicine, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
| | - Weiwen Wang
- Department of Laboratory Medicine, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China
| | - Ying Zhou
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai, People's Republic of China.
| | - Xiaofei Jiang
- Department of Laboratory Medicine, Shanghai Medical College, Huashan Hospital, Fudan University, Shanghai, China.
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Talat A, Khan F, Khan AU. Genome analyses of colistin-resistant high-risk bla NDM-5 producing Klebsiella pneumoniae ST147 and Pseudomonas aeruginosa ST235 and ST357 in clinical settings. BMC Microbiol 2024; 24:174. [PMID: 38769479 PMCID: PMC11103832 DOI: 10.1186/s12866-024-03306-4] [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: 12/19/2023] [Accepted: 04/15/2024] [Indexed: 05/22/2024] Open
Abstract
BACKGROUND Colistin is a last-resort antibiotic used in extreme cases of multi-drug resistant (MDR) Gram-negative bacterial infections. Colistin resistance has increased in recent years and often goes undetected due to the inefficiency of predominantly used standard antibiotic susceptibility tests (AST). To address this challenge, we aimed to detect the prevalence of colistin resistance strains through both Vitek®2 and broth micro-dilution. We investigated 1748 blood, tracheal aspirate, and pleural fluid samples from the Intensive Care Unit (ICU), Neonatal Intensive Care Unit (NICU), and Tuberculosis and Respiratory Disease centre (TBRD) in an India hospital. Whole-genome sequencing (WGS) of extremely drug-resitant (XDR) and pan-drug resistant (PDR) strains revealed the resistance mechanisms through the Resistance Gene Identifier (RGI.v6.0.0) and Snippy.v4.6.0. Abricate.v1.0.1, PlasmidFinder.v2.1, MobileElementFinder.v1.0.3 etc. detected virulence factors, and mobile genetic elements associated to uncover the pathogenecity and the role of horizontal gene transfer (HGT). RESULTS This study reveals compelling insights into colistin resistance among global high-risk clinical isolates: Klebsiella pneumoniae ST147 (16/20), Pseudomonas aeruginosa ST235 (3/20), and ST357 (1/20). Vitek®2 found 6 colistin-resistant strains (minimum inhibitory concentrations, MIC = 4 μg/mL), while broth microdilution identified 48 (MIC = 32-128 μg/mL), adhering to CLSI guidelines. Despite the absence of mobile colistin resistance (mcr) genes, mechanisms underlying colistin resistance included mgrB deletion, phosphoethanolamine transferases arnT, eptB, ompA, and mutations in pmrB (T246A, R256G) and eptA (V50L, A135P, I138V, C27F) in K. pneumoniae. P. aeruginosa harbored phosphoethanolamine transferases basS/pmrb, basR, arnA, cprR, cprS, alongside pmrB (G362S), and parS (H398R) mutations. Both strains carried diverse clinically relevant antimicrobial resistance genes (ARGs), including plasmid-mediated blaNDM-5 (K. pneumoniae ST147) and chromosomally mediated blaNDM-1 (P. aeruginosa ST357). CONCLUSION The global surge in MDR, XDR and PDR bacteria necessitates last-resort antibiotics such as colistin. However, escalating resistance, particularly to colistin, presents a critical challenge. Inefficient colistin resistance detection methods, including Vitek2, alongside limited surveillance resources, accentuate the need for improved strategies. Whole-genome sequencing revealed alarming colistin resistance among K. pneumoniae and P. aeruginosa in an Indian hospital. The identification of XDR and PDR strains underscores urgency for enhanced surveillance and infection control. SNP analysis elucidated resistance mechanisms, highlighting the complexity of combatting resistance.
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Affiliation(s)
- Absar Talat
- Medical Microbiology and Molecular Biology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India
| | - Fatima Khan
- Microbiology Department, JNMC and Hospital, Aligarh Muslim University, Aligarh, 202002, India
| | - Asad U Khan
- Medical Microbiology and Molecular Biology Lab, Interdisciplinary Biotechnology Unit, Aligarh Muslim University, Aligarh, 202002, India.
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Moreira da Silva J, Menezes J, Fernandes L, Santos Costa S, Amaral A, Pomba C. Carbapenemase-producing Enterobacterales strains causing infections in companion animals-Portugal. Microbiol Spectr 2024; 12:e0341623. [PMID: 38446073 PMCID: PMC10986603 DOI: 10.1128/spectrum.03416-23] [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: 09/20/2023] [Accepted: 02/15/2024] [Indexed: 03/07/2024] Open
Abstract
An increase in Klebsiella pneumoniae carbapenem-resistant human nosocomial strains is occurring in Europe, namely with the blaOXA-48-like and blaKPC-like genes. We determined the prevalence of carbapenemase-producing Enterobacterales clinical strains in companion animals in Portugal and characterized their mobile genetic elements. Susceptibility data of a consecutive collection of 977 Enterobacterales clinical strains from a Portuguese private veterinary diagnostic laboratory were evaluated (January-December 2020). Additional phenotypical and genotypical assays were performed in a subset of 261 strains with a resistant phenotype. Whole-genome sequencing was performed for carbapenemase-producing strains. The frequency of carbapenemase-producing Enterobacterales clinical strains in companion animals in Portugal was 0.51% (n = 5/977). Thus, five strains were characterized: (i) one OXA-181-producing K. pneumoniae ST273, (ii) two KPC-3-producing K. pneumoniae ST147; (iii) one KPC-3-producing K. pneumoniae ST392; and (iv) one OXA-48-producing E. coli ST127. The blaKPC-3 gene was located on transposon Tn4401d on IncFIA type plasmid for the K. pneumoniae ST147 strains and on a IncN-type plasmid for the K. pneumoniae ST392 strain, while blaOXA-181 gene was located on an IncX3 plasmid. All de novo assembled plasmids and plasmid-encoded transposons harboring carbapenemase genes were homologous to those previously described in the human healthcare. No plasmid replicons were detected on the OXA-48-producing E. coli ST127. The dissemination of carbapenem resistance is occurring horizontally via plasmid spreading from the human high burden carbapenem resistance setting to the companion animal sector. Furthermore, companion animals may act as reservoirs of carbapenem resistance. Implementation of carbapenemase detection methods in routine clinical veterinary microbiology is urgently needed. IMPORTANCE This is the first study on the prevalence of carbapenemase-producing Enterobacterales (CPE) clinical strains from companion animals in Portugal. Despite the generally low prevalence of CPE in companion animals, it is imperative for veterinary diagnostic laboratories to employ diagnostic methods for carbapenemase detection. The resemblance found in the mobile genetic elements transporting carbapenemase genes between veterinary medicine and human medicine implies a potential circulation within a One Health framework.
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Affiliation(s)
- Joana Moreira da Silva
- CIISA—Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
- AL4AnimalS—Associate Laboratory for Animal and Veterinary Sciences, Vila Real, Portugal
| | - Juliana Menezes
- CIISA—Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
- AL4AnimalS—Associate Laboratory for Animal and Veterinary Sciences, Vila Real, Portugal
| | - Laura Fernandes
- CIISA—Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
- AL4AnimalS—Associate Laboratory for Animal and Veterinary Sciences, Vila Real, Portugal
| | - Sofia Santos Costa
- Global Health and Tropical Medicine, GHTM, Instituto de Higiene e Medicina Tropical, IHMT, Universidade Nova de Lisboa, UNL, Lisbon, Portugal
| | - Andreia Amaral
- CIISA—Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
- AL4AnimalS—Associate Laboratory for Animal and Veterinary Sciences, Vila Real, Portugal
| | - Constança Pomba
- CIISA—Centre for Interdisciplinary Research in Animal Health, Faculty of Veterinary Medicine, University of Lisbon, Lisbon, Portugal
- AL4AnimalS—Associate Laboratory for Animal and Veterinary Sciences, Vila Real, Portugal
- Genevet, Veterinary Molecular Diagnostic Laboratory, Carnaxide, Portugal
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Turton JF, Perry C, McGowan K, Turton JA, Hope R. Klebsiella pneumoniae sequence type 147: a high-risk clone increasingly associated with plasmids carrying both resistance and virulence elements. J Med Microbiol 2024; 73:001823. [PMID: 38629482 PMCID: PMC11084618 DOI: 10.1099/jmm.0.001823] [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: 12/22/2023] [Accepted: 03/18/2024] [Indexed: 04/19/2024] Open
Abstract
Introduction. The first hybrid resistance/virulence plasmid, combining elements from virulence plasmids described in hypervirulent types of Klebsiella pneumoniae with those from conjugative resistance plasmids, was described in an isolate of sequence type (ST) 147 from 2016. Subsequently, this type has been increasingly associated with these plasmids.Hypothesis or gap statement. The extent of carriage of hybrid virulence/resistance plasmids in nosocomial isolates of K. pneumoniae requires further investigation.Aim. To describe the occurrence of virulence/resistance plasmids among isolates of K. pneumoniae received by the UK reference laboratory, particularly among representatives of ST147, and to compare their sequences.Methodology. Isolates received by the laboratory during 2022 and the first half of 2023 (n=1278) were screened for virulence plasmids by PCR detection of rmpA/rmpA2 and typed by variable-number tandem repeat analysis. Twenty-nine representatives of ST147 (including a single-locus variant) from seven hospital laboratories were subjected to long-read nanopore sequencing using high-accuracy q20 chemistry to provide complete assemblies.Results. rmpA/rmpA2 were detected in 110 isolates, of which 59 belonged to hypervirulent K1-ST23, K2-ST86 and K2-ST65/375. Of the remainder, representatives of ST147 formed the largest group, with 22 rmpA/rmpA2-positive representatives (out of 47 isolates). Representatives were from 19 hospital laboratories, with rmpA/rmpA2-positive isolates from 10. Nanopore sequencing of 29 representatives of ST147 divided them into those with no virulence plasmid (n=12), those with non-New Delhi metallo-β-lactamase (NDM) virulence plasmids (n=6) and those carrying bla NDM-5 (n=9) or bla NDM-1 (n=2) virulence plasmids. These plasmids were of IncFIB(pNDM-Mar)/IncHI1B(pNDM-MAR) replicon types. Most of the non-NDM virulence plasmids were highly similar to the originally described KpvST147L_NDM plasmid. Those carrying bla NDM-5 were highly similar to one another and to previously described plasmids in ST383 and carried an extensive array of resistance genes. Comparison of the fully assembled chromosomes indicated multiple introductions of ST147 in UK hospitals.Conclusion. This study highlights the high proportion of representatives of ST147 that carry IncFIB(pNDM-Mar)/IncHI1B(pNDM-MAR) hybrid resistance virulence plasmids. It is important to be aware of the high probability that representatives of this type carry these plasmids combining resistance and virulence determinants and of the consequent increased risk to patients.
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Affiliation(s)
- Jane F. Turton
- HealthCare Associated Infections, Fungal, Antimicrobial Resistance, Antimicrobial Use and Sepsis Division, UK Health Security Agency, 61, Colindale Avenue, London NW9 5HT, UK
| | - Claire Perry
- Public Health Microbiology, UK Health Security Agency, 61, Colindale Avenue, London NW9 5HT, UK
| | - Kim McGowan
- Public Health Microbiology, UK Health Security Agency, 61, Colindale Avenue, London NW9 5HT, UK
| | - Jack A. Turton
- HealthCare Associated Infections, Fungal, Antimicrobial Resistance, Antimicrobial Use and Sepsis Division, UK Health Security Agency, 61, Colindale Avenue, London NW9 5HT, UK
| | - Russell Hope
- HealthCare Associated Infections, Fungal, Antimicrobial Resistance, Antimicrobial Use and Sepsis Division, UK Health Security Agency, 61, Colindale Avenue, London NW9 5HT, UK
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Singh D, Pal S, Subramanian S, Manickam N. Comparative genomics of an extensively drug resistant strain Klebsiella pneumoniae IITR008 with international high-risk clonal lineage ST147 isolated from river water. Antonie Van Leeuwenhoek 2024; 117:57. [PMID: 38491220 DOI: 10.1007/s10482-024-01955-z] [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: 08/14/2023] [Accepted: 02/26/2024] [Indexed: 03/18/2024]
Abstract
Carbapenem resistant Klebsiella pneumoniae causing severe infection resulting in morbidity and mortality have become a global health concern. K. pneumoniae with sequence type ST147 is an international high-risk clonal lineage, genomic studies have been done on K. pneumoniae ST147 isolated from clinical origin but genomic data for environmental K. pneumoniae ST147 is very scarce. Herein, K. pneumoniae IITR008, an extensively drug resistant and potentially hypervirulent bacterium, was isolated from Triveni Sangam, the confluence of three rivers where religious congregations are organized. Phenotypic, genomic and comparative genomic analysis of strain IITR008 was performed. Antibiotic susceptibility profiling revealed resistance to 9 different classes of antibiotics including ß-lactams, ß-lactam combination agents, carbapenem, aminoglycoside, macrolide, quinolones, cephams, phenicol, and folate pathway antagonists and was found to be susceptible to only tetracycline. The strain IITR008 possesses hypervirulence genes namely, iutA and iroN in addition to numerous virulence factors coding for adherence, regulation, iron uptake, secretion system and toxin. Both the IITR008 chromosome and plasmid pIITR008_75 possess a plethora of clinically relevant antibiotic-resistant genes (ARGs) including blaCTX-M-15, blaTEM-1, and blaSHV-11, corroborating the phenotypic resistance. Comparative genomic analysis with other ST147 K. pneumoniae provided insights on the phylogenetic clustering of IITR008 with a clinical strain isolated from a patient in Czech with recent travel history in India and other clinical strains isolated from India and Pakistan. According to the 'One Health' perspective, surveillance of antibiotic resistance in the environment is crucial to impede its accelerated development in diverse ecological niches.
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Affiliation(s)
- Deeksha Singh
- Environmental Biotechnology Laboratory, Environmental Toxicology Group, FEST Division, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, 226001, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Shilpee Pal
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
| | - Srikrishna Subramanian
- Bioinformatics Centre, CSIR-Institute of Microbial Technology, Sector 39A, Chandigarh, 160036, India
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India
| | - Natesan Manickam
- Environmental Biotechnology Laboratory, Environmental Toxicology Group, FEST Division, CSIR-Indian Institute of Toxicology Research, Vishvigyan Bhawan, 31 Mahatma Gandhi Marg, Lucknow, Uttar Pradesh, 226001, India.
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, Uttar Pradesh, 201002, India.
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Addis E, Unali I, Bertoncelli A, Ventura A, Cecchetto R, Mazzariol A. Different OXA-Carbapenemases in Genetically Unrelated Klebsiella pneumoniae Strains Isolated in a North Italian Hospital During Multidrug Resistance Screening. Microb Drug Resist 2024; 30:127-133. [PMID: 38165645 DOI: 10.1089/mdr.2023.0134] [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] [Indexed: 01/04/2024] Open
Abstract
Klebsiella pneumoniae is one of the main opportunistic pathogens that cause a broad spectrum of diseases with increasingly frequent acquisition of resistance to antibiotics, namely carbapenems. This study focused on the characterization of 23 OXA-48-like carbapenemase-producing K. pneumoniae isolates using phenotypic and molecular tests. Phenotypic determination of the presence of β-lactamases was performed using the extended-spectrum beta-lactamase (ESBL) NP test, and phenotypic determination of the presence of carbapenemase was based on the Carba NP test. Antimicrobial susceptibility tests were performed to assess the resistance against carbapenems. Molecular characterization of ESBL genes and carbapenemase genes (blaOXA-48, blaKPC, blaVIM, and blaNDM) was performed using polymerase chain reaction (PCR) techniques. In addition, K. pneumoniae strains were analyzed for their relatedness using multilocus sequence typing PCR analysis based on the Institut Pasteur protocol, which produces allelic profiles that contain their evolutionary and geographic pattern. Following further Sanger sequencing of the blaOXA-48 genes, no genetic mutations were found. Some OXA-48-producing K. pneumoniae isolates coharbored blaKPC, blaNDM, and blaVIM genes, which encode other carbapenemases that can hydrolyze carbapenem antibiotics. The final part of the study focused on the characterization of the plasmid profiles of all isolates to better understand the spreading of the IncL/M blaOXA-48 plasmid gene. The plasmid profile also revealed other incompatibility groups, suggesting that other plasmid genes are spreading in K. pneumoniae isolates, which can coharbor and spread different carbapenemases simultaneously.
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Affiliation(s)
- Elena Addis
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Ilaria Unali
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Anna Bertoncelli
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Anna Ventura
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Riccardo Cecchetto
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
| | - Annarita Mazzariol
- Department of Diagnostics and Public Health, University of Verona, Verona, Italy
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Novais Â, Gonçalves AB, Ribeiro TG, Freitas AR, Méndez G, Mancera L, Read A, Alves V, López-Cerero L, Rodríguez-Baño J, Pascual Á, Peixe L. Development and validation of a quick, automated, and reproducible ATR FT-IR spectroscopy machine-learning model for Klebsiella pneumoniae typing. J Clin Microbiol 2024; 62:e0121123. [PMID: 38284762 PMCID: PMC10865814 DOI: 10.1128/jcm.01211-23] [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: 09/18/2023] [Accepted: 12/18/2023] [Indexed: 01/30/2024] Open
Abstract
The reliability of Fourier-transform infrared (FT-IR) spectroscopy for Klebsiella pneumoniae typing and outbreak control has been previously assessed, but issues remain in standardization and reproducibility. We developed and validated a reproducible FT-IR with attenuated total reflectance (ATR) workflow for the identification of K. pneumoniae lineages. We used 293 isolates representing multidrug-resistant K. pneumoniae lineages causing outbreaks worldwide (2002-2021) to train a random forest classification (RF) model based on capsular (KL)-type discrimination. This model was validated with 280 contemporaneous isolates (2021-2022), using wzi sequencing and whole-genome sequencing as references. Repeatability and reproducibility were tested in different culture media and instruments throughout time. Our RF model allowed the classification of 33 capsular (KL)-types and up to 36 clinically relevant K. pneumoniae lineages based on the discrimination of specific KL- and O-type combinations. We obtained high rates of accuracy (89%), sensitivity (88%), and specificity (92%), including from cultures obtained directly from the clinical sample, allowing to obtain typing information the same day bacteria are identified. The workflow was reproducible in different instruments throughout time (>98% correct predictions). Direct colony application, spectral acquisition, and automated KL prediction through Clover MS Data analysis software allow a short time-to-result (5 min/isolate). We demonstrated that FT-IR ATR spectroscopy provides meaningful, reproducible, and accurate information at a very early stage (as soon as bacterial identification) to support infection control and public health surveillance. The high robustness together with automated and flexible workflows for data analysis provide opportunities to consolidate real-time applications at a global level. IMPORTANCE We created and validated an automated and simple workflow for the identification of clinically relevant Klebsiella pneumoniae lineages by FT-IR spectroscopy and machine-learning, a method that can be extremely useful to provide quick and reliable typing information to support real-time decisions of outbreak management and infection control. This method and workflow is of interest to support clinical microbiology diagnostics and to aid public health surveillance.
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Affiliation(s)
- Ângela Novais
- UCIBIO, Applied Molecular Biosciences Unit, 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
| | - Ana Beatriz Gonçalves
- UCIBIO, Applied Molecular Biosciences Unit, 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
| | - Teresa G. Ribeiro
- UCIBIO, Applied Molecular Biosciences Unit, 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
- CCP, Culture Collection of Porto, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ana R. Freitas
- UCIBIO, Applied Molecular Biosciences Unit, 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
- 1H-TOXRUN, One Health Toxicology Research Unit, University Institute of Health Sciences, CESPU, CRL, Gandra, Portugal
| | - Gema Méndez
- CLOVER Bioanalytical Software, Granada, Spain
| | | | - Antónia Read
- Clinical Microbiology Laboratory, Local Healthcare Unit, Matosinhos, Portugal
| | - Valquíria Alves
- Clinical Microbiology Laboratory, Local Healthcare Unit, Matosinhos, Portugal
| | - Lorena López-Cerero
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Vírgen Macarena, Instituto de Biomedicina de Sevilla (IBIS; CSIC/Hospital Virgen Macarena/Universidad de Sevilla), Sevilla, Spain
- Departamentos de Microbiología y Medicina, Universidad de Sevilla, Sevilla, Spain
| | - Jesús Rodríguez-Baño
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Vírgen Macarena, Instituto de Biomedicina de Sevilla (IBIS; CSIC/Hospital Virgen Macarena/Universidad de Sevilla), Sevilla, Spain
- Departamentos de Microbiología y Medicina, Universidad de Sevilla, Sevilla, Spain
| | - Álvaro Pascual
- Unidad Clínica de Enfermedades Infecciosas y Microbiología, Hospital Universitario Vírgen Macarena, Instituto de Biomedicina de Sevilla (IBIS; CSIC/Hospital Virgen Macarena/Universidad de Sevilla), Sevilla, Spain
- Departamentos de Microbiología y Medicina, Universidad de Sevilla, Sevilla, Spain
| | - Luísa Peixe
- UCIBIO, Applied Molecular Biosciences Unit, 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
- CCP, Culture Collection of Porto, Faculty of Pharmacy, University of Porto, Porto, Portugal
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Di Pilato V, Pollini S, Miriagou V, Rossolini GM, D'Andrea MM. Carbapenem-resistant Klebsiella pneumoniae: the role of plasmids in emergence, dissemination, and evolution of a major clinical challenge. Expert Rev Anti Infect Ther 2024; 22:25-43. [PMID: 38236906 DOI: 10.1080/14787210.2024.2305854] [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: 11/13/2023] [Accepted: 01/11/2024] [Indexed: 01/31/2024]
Abstract
INTRODUCTION Klebsiella pneumoniae is a major agent of healthcare-associated infections and a cause of some community-acquired infections, including severe bacteremic infections associated with metastatic abscesses in liver and other organs. Clinical relevance is compounded by its outstanding propensity to evolve antibiotic resistance. In particular, the emergence and dissemination of carbapenem resistance in K. pneumoniae has posed a major challenge due to the few residual treatment options, which have only recently been expanded by some new agents. The epidemiological success of carbapenem-resistant K. pneumoniae (CR-Kp) is mainly linked with clonal lineages that produce carbapenem-hydrolyzing enzymes (carbapenemases) encoded by plasmids. AREAS COVERED Here, we provide an updated overview on the mechanisms underlying the emergence and dissemination of CR-Kp, focusing on the role that plasmids have played in this phenomenon and in the co-evolution of resistance and virulence in K. pneumoniae. EXPERT OPINION CR-Kp have disseminated on a global scale, representing one of the most important contemporary public health issues. These strains are almost invariably associated with complex multi-drug resistance (MDR) phenotypes, which can also include recently approved antibiotics. The heterogeneity of the molecular bases responsible for these phenotypes poses significant hurdles for therapeutic and diagnostic purposes.
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Affiliation(s)
- Vincenzo Di Pilato
- Department of Surgical Sciences and Integrated Diagnostics (DISC), University of Genoa, Genoa, Italy
| | - Simona Pollini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
| | - Vivi Miriagou
- Laboratory of Bacteriology, Hellenic Pasteur Institute, Athens, Greece
| | - Gian Maria Rossolini
- Department of Experimental and Clinical Medicine, University of Florence, Florence, Italy
- Microbiology and Virology Unit, Careggi University Hospital, Florence, Italy
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Wu Y, Jiang T, He X, Shao J, Wu C, Mao W, Jia H, He F, Kong Y, Wu J, Sun Q, Sun L, Draz MS, Xie X, Zhang J, Ruan Z. Global Phylogeography and Genomic Epidemiology of Carbapenem-Resistant bla OXA-232-Carrying Klebsiella pneumoniae Sequence Type 15 Lineage. Emerg Infect Dis 2023; 29:2246-2256. [PMID: 37877525 PMCID: PMC10617323 DOI: 10.3201/eid2911.230463] [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] [Indexed: 10/26/2023] Open
Abstract
Prevalence of carbapenem-resistant Klebsiella pneumoniae (CRKP) has compromised antimicrobial efficacy against severe infections worldwide. To monitor global spread, we conducted a comprehensive genomic epidemiologic study comparing sequences from 21 blaOXA-232-carrying CRKP isolates from China with K. pneumoniae sequence type (ST) 15 strains from 68 countries available in GenBank. Phylogenetic and phylogeographic analyses revealed all blaOXA-232-carrying CRKP isolates belonged to ST15 lineage and exhibited multidrug resistance. Analysis grouped 330 global blaOXA-232-carrying ST15 CRKP strains into 5 clades, indicating clonal transmission with small genetic distances among multiple strains. The lineage originated in the United States, then spread to Europe, Asia, Oceania, and Africa. Most recent common ancestor was traced back to 2000; mutations averaged ≈1.7 per year per genome. Our research helps identify key forces driving global spread of blaOXA-232-carrying CRKP ST15 lineage and emphasizes the importance of ongoing surveillance of epidemic CRKP.
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Emeraud C, Mahamat A, Jousset AB, Bernabeu S, Goncalves T, Pommier C, Girlich D, Birer A, Rodriguez C, Pawlotsky JM, Naas T, Bonnin RA, Dortet L. Emergence and rapid dissemination of highly resistant NDM-14-producing Klebsiella pneumoniae ST147, France, 2022. Euro Surveill 2023; 28:2300095. [PMID: 37855905 PMCID: PMC10588306 DOI: 10.2807/1560-7917.es.2023.28.42.2300095] [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: 02/06/2023] [Accepted: 06/26/2023] [Indexed: 10/20/2023] Open
Abstract
BackgroundSince 2021, an emergence of New Delhi metallo-β-lactamase (NDM)-14-producing Klebsiella pneumoniae has been identified in France. This variant with increased carbapenemase activity was not previously detected in Enterobacterales.AimWe investigated the rapid dissemination of NDM-14 producers among patients in hospitals in France.MethodsAll NDM-14-producing non-duplicate clinical isolates identified in France until June 2022 (n = 37) were analysed by whole genome sequencing. The phylogeny of NDM-14-producers among all K. pneumoniae sequence type (ST) 147 reported in France since 2014 (n = 431) was performed. Antimicrobial susceptibility testing, conjugation experiments, clonal relationship and molecular clock analysis were performed.ResultsThe 37 NDM-14 producers recovered in France until 2022 belonged to K. pneumoniae ST147. The dissemination of NDM-14-producing K. pneumoniae was linked to a single clone, likely imported from Morocco and responsible for several outbreaks in France. The gene bla NDM-14 was harboured on a 54 kilobase non-conjugative IncFIB plasmid that shared high homology with a known bla NDM-1-carrying plasmid. Using Bayesian analysis, we estimated that the NDM-14-producing K. pneumoniae ST147 clone appeared in 2020. The evolutionary rate of this clone was estimated to 5.61 single nucleotide polymorphisms per genome per year. The NDM-14 producers were highly resistant to all antimicrobials tested except to colistin, cefiderocol (minimum inhibitory concentration 2 mg/L) and the combination of aztreonam/avibactam.ConclusionHighly resistant NDM-14 producing K. pneumoniae can rapidly spread in healthcare settings. Surveillance and thorough investigations of hospital outbreaks are critical to evaluate and limit the dissemination of this clone.
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Affiliation(s)
- Cécile Emeraud
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- UMR-1184, INSERM, University Paris-Saclay, CEA, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Aba Mahamat
- Corsica Centre for Healthcare-Associated Infections Control and Prevention, Hôpital Eugénie, Ajaccio, France
| | - Agnès B Jousset
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- UMR-1184, INSERM, University Paris-Saclay, CEA, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Sandrine Bernabeu
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- UMR-1184, INSERM, University Paris-Saclay, CEA, Faculty of Medicine, Le Kremlin-Bicêtre, France
| | - Tania Goncalves
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
| | - Camille Pommier
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
| | - Delphine Girlich
- UMR-1184, INSERM, University Paris-Saclay, CEA, Faculty of Medicine, Le Kremlin-Bicêtre, France
| | - Aurélien Birer
- Centre National de Référence de la Résistance aux antibiotiques, Service de Bactériologie, CHU Gabriel-Montpied, Clermont-Ferrand, France
| | - Christophe Rodriguez
- Université Paris-Est-Créteil (UPEC), Créteil, France
- Department of Virology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France
- INSERM U955, Team Viruses, Hepatology, Cancer, Créteil, France
| | - Jean-Michel Pawlotsky
- Université Paris-Est-Créteil (UPEC), Créteil, France
- Department of Virology, Hôpitaux Universitaires Henri Mondor, Assistance Publique-Hôpitaux de Paris, Créteil, France
- INSERM U955, Team Viruses, Hepatology, Cancer, Créteil, France
| | - Thierry Naas
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- UMR-1184, INSERM, University Paris-Saclay, CEA, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Rémy A Bonnin
- UMR-1184, INSERM, University Paris-Saclay, CEA, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
| | - Laurent Dortet
- Department of Bacteriology-Hygiene, Bicêtre Hospital, Assistance Publique - Hôpitaux de Paris, Le Kremlin-Bicêtre, France
- UMR-1184, INSERM, University Paris-Saclay, CEA, Faculty of Medicine, Le Kremlin-Bicêtre, France
- French National Reference Center for Antibiotic Resistance, Le Kremlin-Bicêtre, France
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11
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Pajand O, Rahimi H, Badmasti F, Gholami F, Alipour T, Darabi N, Aarestrup FM, Leekitcharoenphon P. Various arrangements of mobile genetic elements among CC147 subpopulations of Klebsiella pneumoniae harboring bla NDM-1: a comparative genomic analysis of carbapenem resistant strains. J Biomed Sci 2023; 30:73. [PMID: 37626377 PMCID: PMC10464136 DOI: 10.1186/s12929-023-00960-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 07/31/2023] [Indexed: 08/27/2023] Open
Abstract
BACKGROUND Certain clonal complexes (CCs) of Klebsiella pneumoniae such as CC147 (ST147 and ST392) are major drivers of blaNDM dissemination across the world. ST147 has repeatedly reported from our geographical region, but its population dynamics and evolutionary trajectories need to be further studied. METHODS Comparative genomic analysis of 51 carbapenem-nonsusceptible strains as well as three hypervirulent K. pneumoniae (hvKp) recovered during 16-months of surveillance was performed using various bioinformatics tools. We investigated the genetic proximity of our ST147 strains with publicly available corresponding genomes deposited globally and from neighbor countries in our geographic region. RESULTS While IncL/M plasmid harboring blaOXA-48 was distributed among divergent clones, blaNDM-1 was circulated by twenty of the 25 CC147 dominant clone and were mostly recovered from the ICU. The NDM-1 core structure was bracketed by a single isoform of mobile genetic elements (MGEs) [ΔISKpn26-NDM-TnAs3-ΔIS3000-Tn5403] and was located on Col440I plasmid in 68.7% of ST392. However, various arrangements of MGEs including MITESen1/MITESen1 composite transposon or combination of MITESen1/ISSen4/IS903B/IS5/ISEhe3 on IncFIb (pB171) were identified in ST147. It seems that ST392 circulated blaNDM-1 in 2018 before being gradually replaced by ST147 from the middle to the end of sample collection in 2019. ST147 strains possessed the highest number of resistance markers and showed high genetic similarity with four public genomes that harbored blaNDM-1 on the same replicon type. Mainly, there was a convergence between clusters and isolated neighboring countries in the minimum-spanning tree. A conserved arrangement of resistance markers/MGEs was linked to methyltransferase armA which was embedded in class 1 integron in 8 isolates of ST147/ST48 high-risk clones. CONCLUSION Our findings highlight the dynamic nature of blaNDM-1 transmission among K. pneumoniae in Iran that occurs both clonally and horizontally via various combinations of MGEs. This is the first analysis of Iranian ST147/NDM + clone in the global context.
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Affiliation(s)
- Omid Pajand
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby, Denmark
- Clinical Research Development Unit, Kowsar Educational, Research and Therapeutic Hospital, Semnan University of Medical Sciences, Semnan, Iran
- Abnormal Uterine Bleeding Research Center, Semnan University of Medical Sciences, Semnan, Iran
| | - Hamzeh Rahimi
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Farzad Badmasti
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Faeze Gholami
- Social Determinants of Health Research Center, Semnan University of Medical Sciences, Semnan, Iran
| | - Tahereh Alipour
- Microbiology Department, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Narges Darabi
- Microbiology Department, Faculty of Medicine, Semnan University of Medical Sciences, Semnan, Iran
| | - Frank M Aarestrup
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby, Denmark.
| | - Pimlapas Leekitcharoenphon
- Research Group for Genomic Epidemiology, National Food Institute, Technical University of Denmark, Lyngby, Denmark
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12
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Lourenço M, Osbelt L, Passet V, Gravey F, Megrian D, Strowig T, Rodrigues C, Brisse S. Phages against Noncapsulated Klebsiella pneumoniae: Broader Host range, Slower Resistance. Microbiol Spectr 2023; 11:e0481222. [PMID: 37338376 PMCID: PMC10433977 DOI: 10.1128/spectrum.04812-22] [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: 11/22/2022] [Accepted: 05/23/2023] [Indexed: 06/21/2023] Open
Abstract
Klebsiella pneumoniae (Kp), a human gut colonizer and opportunistic pathogen, is a major contributor to the global burden of antimicrobial resistance. Virulent bacteriophages represent promising agents for decolonization and therapy. However, the majority of anti-Kp phages that have been isolated thus far are highly specific to unique capsular types (anti-K phages), which is a major limitation to phage therapy prospects due to the highly polymorphic capsule of Kp. Here, we report on an original anti-Kp phage isolation strategy, using capsule-deficient Kp mutants as hosts (anti-Kd phages). We show that anti-Kd phages have a broad host range, as the majority are able to infect noncapsulated mutants of multiple genetic sublineages and O-types. Additionally, anti-Kd phages induce a lower rate of resistance emergence in vitro and provide increased killing efficiency when in combination with anti-K phages. In vivo, anti-Kd phages are able to replicate in mouse guts colonized with a capsulated Kp strain, suggesting the presence of noncapsulated Kp subpopulations. The original strategy proposed here represents a promising avenue that circumvents the Kp capsule host restriction barrier, offering promise for therapeutic development. IMPORTANCE Klebsiella pneumoniae (Kp) is an ecologically generalist bacterium as well as an opportunistic pathogen that is responsible for hospital-acquired infections and a major contributor to the global burden of antimicrobial resistance. In the last decades, limited advances have been made in the use of virulent phages as alternatives or complements to antibiotics that are used to treat Kp infections. This work demonstrates the potential value of an anti-Klebsiella phage isolation strategy that addresses the issue of the narrow host range of anti-K phages. Anti-Kd phages may be active in infection sites in which capsule expression is intermittent or repressed or in combination with anti-K phages, which often induce the loss of capsule in escape mutants.
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Affiliation(s)
- Marta Lourenço
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Lisa Osbelt
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Virginie Passet
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - François Gravey
- Dynamycure Inserm UM1311 Normandie Univ, UNICAEN, UNIROUEN, Caen, France
| | - Daniela Megrian
- Unité de Microbiologie Structurale, Institut Pasteur, CNRS UMR 3528, Université Paris Cité, Paris, France
| | - Till Strowig
- Department of Microbial Immune Regulation, Helmholtz Center for Infection Research, Braunschweig, Germany
- German Center for Infection Research (DZIF), partner site Hannover-Braunschweig, Braunschweig, Germany
| | - Carla Rodrigues
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
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13
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Afolayan AO, Rigatou A, Grundmann H, Pantazatou A, Daikos G, Reuter S. Three Klebsiella pneumoniae lineages causing bloodstream infections variably dominated within a Greek hospital over a 15 year period. Microb Genom 2023; 9:mgen001082. [PMID: 37642647 PMCID: PMC10483420 DOI: 10.1099/mgen.0.001082] [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: 02/16/2023] [Accepted: 07/18/2023] [Indexed: 08/31/2023] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) has emerged as a major clinical and public health threat. The rapid dissemination of this pathogen is driven by several successful clones worldwide. We aimed to investigate the CRKP clonal lineages, their antibiotic resistance determinants and their potential transmissions in a tertiary care hospital located in Athens, Greece. Between 2003 and 2018, 392 CRKP isolates from bloodstream infections were recovered from hospitalized patients. Whole genome sequencing (WGS) was performed on the Illumina platform to characterize 209 of these isolates. In total, 74 % (n=155) of 209 isolates belonged to three major clonal lineages: ST258 (n=108), ST147 (n=29) and ST11 (n=18). Acquired carbapenemase genes were the mechanisms of resistance in 205 isolates (bla KPC, n=123; bla VIM, n=56; bla NDM, n=20; bla OXA-48, n=6). Strong associations (P=0.0004) were observed between carbapenemase genes and clonal lineages. We first isolated bla VIM-1-carrying ST147 strains during the early sampling period in 2003, followed by the emergence of bla KPC-2-carrying ST258 in 2006 and bla NDM-1-carrying ST11 in 2013. Analysis of genetic distances between the isolates revealed six potential transmission events. When contextualizing the current collection with published data, ST147 reflected the global diversity, ST258 clustered with isolates representing the first introduction into Europe and ST11 formed a distinct geographically restricted lineage indicative of local spread. This study demonstrates the changing profile of bloodstream CRKP in a tertiary care hospital over a 15 year period and underlines the need for continued genomic surveys to develop strategies to contain further dissemination. This article contains data hosted by Microreact.
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Affiliation(s)
- Ayorinde O. Afolayan
- Institute for Infection Prevention and Control, Medical Center - University of Freiburg, Freiburg, Germany
| | | | - Hajo Grundmann
- Institute for Infection Prevention and Control, Medical Center - University of Freiburg, Freiburg, Germany
| | | | - George Daikos
- First Department of Medicine, Laiko General Hospital, National and Kapodistrian University of Athens, Athens, Greece
| | - Sandra Reuter
- Institute for Infection Prevention and Control, Medical Center - University of Freiburg, Freiburg, Germany
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14
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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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15
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Arcari G, Carattoli A. Global spread and evolutionary convergence of multidrug-resistant and hypervirulent Klebsiella pneumoniae high-risk clones. Pathog Glob Health 2023; 117:328-341. [PMID: 36089853 PMCID: PMC10177687 DOI: 10.1080/20477724.2022.2121362] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Abstract
For people living in developed countries life span is growing at a faster pace than ever. One of the main reasons for such success is attributable to the introduction and extensive use in the clinical practice of antibiotics over the course of the last seven decades. In hospital settings, Klebsiella pneumoniae represents a well-known and commonly described opportunistic pathogen, typically characterized by resistance to several antibiotic classes. On the other hand, the broad wedge of population living in Low and/or Middle Income Countries is increasing rapidly, allowing the spread of several commensal bacteria which are transmitted via human contact. Community transmission has been the original milieu of K. pneumoniae isolates characterized by an outstanding virulence (hypervirulent). These two characteristics, also defined as "pathotypes", originally emerged as different pathways in the evolutionary history of K. pneumoniae. For a long time, the Sequence Type (ST), which is defined by the combination of alleles of the 7 housekeeping genes of the Multi-Locus Sequence Typing, has been a reliable marker of the pathotype: multidrug-resistant clones (e.g. ST258, ST147, ST101) in the Western world and hypervirulent clones (e.g. ST23, ST65, ST86) in the Eastern. Currently, the boundaries separating the two pathotypes are fading away due to several factors, and we are witnessing a worrisome convergence in certain high-risk clones. Here we review the evidence available on confluence of multidrug-resistance and hypervirulence in specific K. pneumoniae clones.
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Affiliation(s)
- Gabriele Arcari
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
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16
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Liu C, Du P, Yang P, Lu M, Shen N. Fusion plasmid enhanced the endemic extensively drug resistant Klebsiella pneumoniae clone ST147 harbored bla OXA-48 to acquire the hypervirulence and cause fatal infection. Ann Clin Microbiol Antimicrob 2023; 22:11. [PMID: 36788555 PMCID: PMC9927049 DOI: 10.1186/s12941-022-00551-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Accepted: 12/20/2022] [Indexed: 02/16/2023] Open
Abstract
BACKGROUND Klebsiella Pneumoniae (Kp) sequence type (ST) 147 has emerged globally and spread rapidly, particularly the extensively drug resistant (XDR) isolates. However, the infections caused by this subtype is rare reported in China for now. The clinical, microbiological and genomic characteristics are unclear. METHODS A systemic retrospective study was conducted in a Chinese tertiary hospital. Clinical information of the infection cases was collected, and whole-genome sequencing and phenotypic experiments were performed on the ST147 isolates. The resistance and virulence genes were identified, and the plasmids harboring these genes were further studied. RESULTS Six ST147 isolates from six patients among 720 available clincial Kp isolates were detected. Notably, two isolates, PEKP4035 and PEKP4265, represented both XDR and hypervirulence by acquiring blaOXA-48, blaCTX-M-15 and key virulence genes, iucA + rmpA2, representing no fitness cost and resulting fatal infection. Four of the six ST147 isolates presented with more nucleotide differences, whereas the PEKP4035 and PEKP4265 both isolated from the intensive care unit possessed 20 single nucleotide polymorphisms among one year, indicating the prolonged survive and transmission. Interestingly, the two isolates harbored the same fused plasmid composed of sul2 and iucA + rmpA2, which might be generated by recombination of a plasmid like KpvST101_OXA-48 with the pLVPK plasmid via IS26. Besides, two ~ 70 kb plasmids conferring multiple-drug resistance were also identified among the two isolates, which presented resistance genes including blaOXA-48, blaCTX-M-16, strA and strB. Interestingly, we reported that blaCTX-M-15, a common resistance gene within ST147, has successfully transferred into the chromosome by ISEcp1. CONCLUSIONS XDR hypervirulent ST147 Kp is emerging, suggesting enhanced surveillance is essential.
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Affiliation(s)
- Chao Liu
- grid.411642.40000 0004 0605 3760Department of Infectious Disease, Peking University Third Hospital, Beijing, China ,grid.411642.40000 0004 0605 3760Center of Infectious Disease, Peking University Third Hospital, Beijing, China
| | | | - Ping Yang
- grid.411642.40000 0004 0605 3760Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, China ,grid.11135.370000 0001 2256 9319Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Ming Lu
- Department of Infectious Disease, Peking University Third Hospital, Beijing, China. .,Center of Infectious Disease, Peking University Third Hospital, Beijing, China. .,Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, China.
| | - Ning Shen
- Department of Infectious Disease, Peking University Third Hospital, Beijing, China. .,Center of Infectious Disease, Peking University Third Hospital, Beijing, China. .,Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, China. .,Institute of Medical Technology, Peking University Health Science Center, Beijing, China.
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17
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Shaidullina ER, Schwabe M, Rohde T, Shapovalova VV, Dyachkova MS, Matsvay AD, Savochkina YA, Shelenkov AA, Mikhaylova YV, Sydow K, Lebreton F, Idelevich EA, Heiden SE, Becker K, Kozlov RS, Shipulin GA, Akimkin VG, Lalk M, Guenther S, Zautner AE, Bohnert JA, Mardanova AM, Bouganim R, Marchaim D, Hoff KJ, Schaufler K, Edelstein MV. Genomic analysis of the international high-risk clonal lineage Klebsiella pneumoniae sequence type 395. Genome Med 2023; 15:9. [PMID: 36782220 PMCID: PMC9926764 DOI: 10.1186/s13073-023-01159-6] [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: 06/23/2022] [Accepted: 01/20/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND Klebsiella pneumoniae, which is frequently associated with hospital- and community-acquired infections, contains multidrug-resistant (MDR), hypervirulent (hv), non-MDR/non-hv as well as convergent representatives. It is known that mostly international high-risk clonal lineages including sequence types (ST) 11, 147, 258, and 307 drive their global spread. ST395, which was first reported in the context of a carbapenemase-associated outbreak in France in 2010, is a less well-characterized, yet emerging clonal lineage. METHODS We computationally analyzed a large collection of K. pneumoniae ST395 genomes (n = 297) both sequenced in this study and reported previously. By applying multiple bioinformatics tools, we investigated the core-genome phylogeny and evolution of ST395 as well as distribution of accessory genome elements associated with antibiotic resistance and virulence features. RESULTS Clustering of the core-SNP alignment revealed four major clades with eight smaller subclades. The subclades likely evolved through large chromosomal recombination, which involved different K. pneumoniae donors and affected, inter alia, capsule and lipopolysaccharide antigen biosynthesis regions. Most genomes contained acquired resistance genes to extended-spectrum cephalosporins, carbapenems, and other antibiotic classes carried by multiple plasmid types, and many were positive for hypervirulence markers, including the siderophore aerobactin. The detection of "hybrid" resistance and virulence plasmids suggests the occurrence of the convergent ST395 pathotype. CONCLUSIONS To the best of our knowledge, this is the first study that investigated a large international collection of K. pneumoniae ST395 genomes and elucidated phylogenetics and detailed genomic characteristics of this emerging high-risk clonal lineage.
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Affiliation(s)
- Elvira R. Shaidullina
- grid.446122.70000 0004 0620 2113Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia
| | - Michael Schwabe
- grid.5603.0Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Thomas Rohde
- grid.5603.0Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Valeria V. Shapovalova
- grid.513078.8Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, Russia
| | - Marina S. Dyachkova
- grid.513078.8Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, Russia
| | - Alina D. Matsvay
- grid.513078.8Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, Russia
| | - Yuliya A. Savochkina
- grid.513078.8Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, Russia
| | | | | | - Katharina Sydow
- grid.5603.0Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - François Lebreton
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, USA
| | - Evgeny A. Idelevich
- grid.5603.0Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany ,grid.16149.3b0000 0004 0551 4246Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Stefan E. Heiden
- grid.5603.0Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Karsten Becker
- grid.5603.0Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Roman S. Kozlov
- grid.446122.70000 0004 0620 2113Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia
| | - German A. Shipulin
- grid.513078.8Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, Russia
| | | | - Michael Lalk
- grid.5603.0Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Sebastian Guenther
- grid.5603.0Pharmaceutical Biology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Andreas E. Zautner
- grid.5807.a0000 0001 1018 4307Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Otto-Von-Guericke University Magdeburg, Magdeburg, Germany
| | - Jürgen A. Bohnert
- grid.5603.0Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Ayslu M. Mardanova
- grid.77268.3c0000 0004 0543 9688Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Ruth Bouganim
- grid.413990.60000 0004 1772 817XDepartment of Internal Medicine A, Shamir (Assaf Harofeh) Medical Center, Zerifin, Israel
| | - Dror Marchaim
- grid.12136.370000 0004 1937 0546Infection Control Unit, Shamir (Assaf Harofeh) Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Katharina J. Hoff
- grid.5603.0Institute of Mathematics and Computer Science, University of Greifswald, Greifswald, Germany
| | - Katharina Schaufler
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany. .,Institute of Infection Medicine, Christian-Albrecht University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany.
| | - Mikhail V. Edelstein
- grid.446122.70000 0004 0620 2113Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia
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18
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Osman EA, Yokoyama M, Altayb HN, Cantillon D, Wille J, Seifert H, Higgins PG, Al-Hassan L. Klebsiella pneumonia in Sudan: Multidrug Resistance, Polyclonal Dissemination, and Virulence. Antibiotics (Basel) 2023; 12:antibiotics12020233. [PMID: 36830144 PMCID: PMC9952582 DOI: 10.3390/antibiotics12020233] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/13/2023] [Accepted: 01/18/2023] [Indexed: 01/26/2023] Open
Abstract
The emergence and global expansion of hyper-virulent and multidrug resistant (MDR) Klebsiella pneumoniae is an increasing healthcare threat worldwide. The epidemiology of MDR K. pneumoniae is under-characterized in many parts of the world, particularly Africa. In this study, K. pneumoniae isolates from hospitals in Khartoum, Sudan, have been whole-genome sequenced to investigate their molecular epidemiology, virulence, and resistome profiles. Eighty-six K. pneumoniae were recovered from patients in five hospitals in Khartoum between 2016 and 2020. Antimicrobial susceptibility was performed by disk-diffusion and broth microdilution. All isolates underwent whole genome sequencing using Illumina MiSeq; cgMLST was determined using Ridom SeqSphere+, and 7-loci MLST virulence genes and resistomes were identified. MDR was observed at 80%, with 35 isolates (41%) confirmed carbapenem-resistant. Thirty-seven sequence types were identified, and 14 transmission clusters (TC). Five of these TCs involved more than one hospital. Ybt9 was the most common virulence gene detected, in addition to some isolates harbouring iuc and rmp1. There is a diverse population of K. pneumoniae in Khartoum hospitals, harbouring multiple resistance genes, including genes coding for ESBLs, carbapenemases, and aminoglycoside-modifying enzymes, across multiple ST's. The majority of isolates were singletons and transmissions were rare.
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Affiliation(s)
- Einas A. Osman
- Bioscience Research Institute, Ibn Sina University, Khartoum 11111, Sudan
| | - Maho Yokoyama
- Department of Global Health and Infection, Brighton & Sussex Medical School, Brighton BN1 9PX, UK
| | - Hisham N. Altayb
- Department of Biochemistry, Faculty of Sciences, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Daire Cantillon
- Department of Tropical Disease Biology, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK
| | - Julia Wille
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50935 Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50935 Cologne, Germany
| | - Harald Seifert
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50935 Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50935 Cologne, Germany
| | - Paul G. Higgins
- Institute for Medical Microbiology, Immunology and Hygiene, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50935 Cologne, Germany
- German Center for Infection Research (DZIF), Partner Site Bonn-Cologne, 50935 Cologne, Germany
- Center for Molecular Medicine Cologne, Faculty of Medicine and University Hospital Cologne, University of Cologne, 50931 Cologne, Germany
| | - Leena Al-Hassan
- Department of Global Health and Infection, Brighton & Sussex Medical School, Brighton BN1 9PX, UK
- Correspondence: ; Tel.: +44-(0)-1278877817
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19
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Ge H, Qiao J, Xu H, Liu R, Chen R, Li C, Hu X, Zhou J, Guo X, Zheng B. First report of Klebsiella pneumoniae co-producing OXA-181, CTX-M-55, and MCR-8 isolated from the patient with bacteremia. Front Microbiol 2022; 13:1020500. [PMID: 36312943 PMCID: PMC9614159 DOI: 10.3389/fmicb.2022.1020500] [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: 08/16/2022] [Accepted: 09/30/2022] [Indexed: 11/13/2022] Open
Abstract
The worldwide spread of carbapenem-resistant Enterobacteriaceae (CRE) has led to a major challenge to human health. In this case, colistin is often used to treat the infection caused by CRE. However, the coexistence of genes conferring resistance to carbapenem and colistin is of great concern. In this work, we reported the coexistence of blaOXA-181, blaCTX-M-55, and mcr-8 in an ST273 Klebsiella pneumoniae isolate for the first time. The species identification was performed using MALDI-TOF MS, and the presence of various antimicrobial resistance genes (ARGs) and virulence genes were detected by PCR and whole-genome sequencing. Antimicrobial susceptibility testing showed that K. pneumoniae 5589 was resistant to aztreonam, imipenem, meropenem, ceftriaxone, cefotaxime, ceftazidime, levofloxacin, ciprofloxacin, gentamicin, piperacillin-tazobactam, cefepime, and polymyxin B, but sensitive to amikacin. S1-pulsed-field gel electrophoresis (PFGE) and Southern blotting revealed the mcr-8 gene was carried on a ~ 138 kb plasmid with a conserved structure (IS903B-ymoA-inhA-mcr-8-copR-baeS-dgkA-ampC). In addition, blaOXA-181 was found on another ~51 kb plasmid with a composite transposon flanked by insertion sequence IS26. The in vitro conjugation experiments and plasmid sequence probe indicated that the plasmid p5589-OXA-181 and the p5589-mcr-8 were conjugative, which may contribute to the propagation of ARGs. Relevant detection and investigation measures should be taken to control the prevalence of pathogens coharboring blaOXA-181, blaCTX-M-55 and mcr-8.
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Affiliation(s)
- Haoyu Ge
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jie Qiao
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Hao Xu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ruishan Liu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ruyan Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Chenyu Li
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xinjun Hu
- Department of Infectious Diseases, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, China
| | - Jiawei Zhou
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Xiaobing Guo
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
- Xiaobing Guo,
| | - Beiwen Zheng
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Department of Structure and Morphology, Jinan Microecological Biomedicine Shandong Laboratory, Jinan, Shandong, China
- Research Units of Infectious Diseases and Microecology, Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Beiwen Zheng,
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