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Qian J, Jin P, Yang Y, Ma N, Yang Z, Zhang X. Protein function annotation and virulence factor identification of Klebsiella pneumoniae genome by multiple machine learning models. Microb Pathog 2024:106727. [PMID: 38851362 DOI: 10.1016/j.micpath.2024.106727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2023] [Revised: 05/27/2024] [Accepted: 06/03/2024] [Indexed: 06/10/2024]
Abstract
Klebsiella pneumoniae is a type of Gram-negative bacterium which can cause a range of infections in human. In recent years, an increasing number of strains of K. pneumoniae resistant to multiple antibiotics have emerged, posing a significant threat to public health. The protein function of this bacterium is not well known, thus a systematic investigation of K. pneumoniae proteome is in urgent need. In this study, the protein functions of this bacteria were re-annotated, and their function groups were analyzed. Moreover, three machine learning models were built to identify novel virulence factors. Results showed that the functions of 16 uncharacterized proteins were first annotated by sequence alignment. In addition, K. pneumoniae proteins share a high proportion of homology with Haemophilus influenzae and a low homology proportion with Chlamydia pneumoniae. By sequence analysis, 10 proteins were identified as potential drug targets for this bacterium. Our model achieved a high accuracy of 0.901 in the benchmark dataset. By applying our models to K. pneumoniae, we identified 39 virulence factors in this pathogen. Our findings could provide novel clues for the treatment of K. pneumoniae infection.
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Affiliation(s)
- Jinyang Qian
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, Zhejiang, China
| | - Pengfei Jin
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, Zhejiang, China
| | - Yueyue Yang
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, Zhejiang, China
| | - Nan Ma
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, Zhejiang, China
| | - Zhiyuan Yang
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, Zhejiang, China; School of Biomedical Sciences, The Chinese University of Hong Kong, Hong Kong, China.
| | - Xiaoli Zhang
- School of Artificial Intelligence, Hangzhou Dianzi University, Hangzhou, Zhejiang, China
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Kadkhoda H, Gholizadeh P, Ghotaslou R, Pirzadeh T, Ahangarzadeh Rezaee M, Nabizadeh E, Feizi H, Samadi Kafil H, Aghazadeh M. Prevalence of the CRISPR-cas system and its association with antibiotic resistance in clinical Klebsiella pneumoniae isolates. BMC Infect Dis 2024; 24:554. [PMID: 38831286 PMCID: PMC11149351 DOI: 10.1186/s12879-024-09451-5] [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: 02/04/2024] [Accepted: 05/30/2024] [Indexed: 06/05/2024] Open
Abstract
BACKGROUND AND OBJECTIVE(S) CRISPR-Cas is a prokaryotic adaptive immune system that protects bacteria and archaea against mobile genetic elements (MGEs) such as bacteriophages plasmids, and transposons. In this study, we aimed to assess the prevalence of the CRISPR-Cas systems and their association with antibiotic resistance in one of the most challenging bacterial pathogens, Klebsiella pneumoniae. MATERIALS AND METHODS A total of 105 K. pneumoniae isolates were collected from various clinical infections. Extended-spectrum β-lactamases (ESBLs) phenotypically were detected and the presence of ESBL, aminoglycoside-modifying enzymes (AME), and CRISPR-Cas system subtype genes were identified using PCR. Moreover, the diversity of the isolates was determined by enterobacterial repetitive intergenic consensus (ERIC)-PCR. RESULTS Phenotypically, 41.9% (44/105) of the isolates were found to be ESBL producers. A significant inverse correlation existed between the subtype I-E CRISPR-Cas system's presence and ESBL production in K. pneumoniae isolates. Additionally, the frequency of the ESBL genes blaCTX-M1 (3%), blaCTX-M9 (12.1%), blaSHV (51.5%), and blaTEM (33.3%), as well as some AME genes such as aac(3)-Iva (21.2%) and ant(2'')-Ia (3%) was significantly lower in the isolates with the subtype I-E CRISPR-Cas system in comparison to CRISPR-negative isolates. There was a significant inverse correlation between the presence of ESBL and some AME genes with subtype I-E CRISPR-Cas system. CONCLUSION The presence of the subtype I-E CRISPR-Cas system was correlated with the antibiotic-resistant gene (ARGs). The isolates with subtype I-E CRISPR-Cas system had a lower frequency of ESBL genes and some AME genes than CRISPR-negative isolates.
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Affiliation(s)
- Hiva Kadkhoda
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Pourya Gholizadeh
- Digestive Disease Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
- Zoonoses Research Center, Ardabil University of Medical Sciences, Ardabil, Iran
| | - Reza Ghotaslou
- Department of Medical Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Tahereh Pirzadeh
- Department of Medical Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
- Infectious and Tropical Diseases Research Center, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Edris Nabizadeh
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Microbiology, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hadi Feizi
- Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
- Department of Medical Microbiology, Aalinasab Hospital, Social Security Organization, Tabriz, Iran
| | - Hossein Samadi Kafil
- Drug Applied Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Mohammad Aghazadeh
- Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
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Tang F, Chen Z, Zhu H, Xi L, Li C, Luo W. Genetic relatedness, antibiotic resistance, and virulence of Klebsiella pneumoniae isolated from healthcare and food sources in Wuhan, China. Am J Infect Control 2024:S0196-6553(24)00504-2. [PMID: 38782211 DOI: 10.1016/j.ajic.2024.05.011] [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: 01/18/2024] [Revised: 05/06/2024] [Accepted: 05/16/2024] [Indexed: 05/25/2024]
Abstract
OBJECTIVE To investigate genetic relatedness and antibiotic resistance of Klebsiella pneumoniae from retail meat samples, clinical source samples, and hospital environmental samples in Wuhan, China. METHODS The hypermucoviscosity phenotypes and biofilm formation ability of K. pneumoniae were determined by string test and crystalline violet staining. The minimal inhibitory concentrations of 18 antimicrobial agents were determined by the broth microdilution test, and PCR assays were performed to detect 14 genes associated with antibiotic resistance. Pulsed-field gel electrophoresis (PFGE) analysis was used to assess the genetic relatedness and clonal dissemination. RESULTS Among the 5730 samples analyzed, 46 tested positive for K. pneumoniae, with higher rates observed in meat (23.4%, CI: 12.8-38.4%) than in clinical samples (0.6%, CI: 0.4-0.8%) and hospital environmental samples (8.0%, CI: 2.6-20.1%). Meat-derived isolates showed high resistance to tetracycline (36.4%, 4/11, CI: 12.4-68.4%), sulphonamide (27.3%, 3/11, CI: 7.3-60.7%), and gentamicin (27.3%, 3/11, CI: 7.3-60.7%), whereas clinical isolates exhibited significant resistance to ampicillin-sulbactam (32.3%, 10/31, CI: 17.3-51.5%). Multidrug resistance was observed in 17.4% (8/46, CI:8.3-32.0%) of the isolates, particularly in hospital environmental samples (3/4, CI: 21.9-98.7%). Biofilm production was observed in 88.1% (37/42, CI: 73.6-95.6%) of K. pneumoniae, with varying degrees of strength. PFGE analysis revealed patient-to-patient K. pneumoniae transmission, transmission between patients and hospital environment, as well as cross-contamination between markets. CONCLUSION The findings underscore the importance of comprehensive surveillance, infection control and judicious antibiotic use in mitigating the impact of K. pneumoniae on public health, especially in food chain and healthcare settings.
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Affiliation(s)
- Feng Tang
- Department of Laboratory Medicine, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430016, China
| | - Zhi Chen
- Microbiological Laboratory, Wuhan Center for Disease Control and Prevention, Wuhan 430024, People's Republic of China
| | - Hanjue Zhu
- Plastic Surgery, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430016, China
| | - Lei Xi
- Department of Laboratory Medicine, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430016, China.
| | - Changzhen Li
- Department of Laboratory Medicine, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430016, China.
| | - Wanjun Luo
- Hospital-Acquired Infection Control Department, Wuhan Children's Hospital (Wuhan Maternal and Child Healthcare Hospital), Tongji Medical College, Huazhong University of Science & Technology, Wuhan 430016, China.
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Nguyen Q, Nguyen YTP, Ha TT, Tran DTN, Voong PV, Chau V, Nguyen PLN, Le NTQ, Nguyen LPH, Nguyen TTN, Trinh TV, Carrique-Mas JJ, Baker S, Thwaites G, Rabaa MA, Choisy M, Chung HT, Pham DT. Genomic insights unveil the plasmid transfer mechanism and epidemiology of hypervirulent Klebsiella pneumoniae in Vietnam. Nat Commun 2024; 15:4187. [PMID: 38760381 PMCID: PMC11101633 DOI: 10.1038/s41467-024-48206-3] [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: 12/29/2023] [Accepted: 04/22/2024] [Indexed: 05/19/2024] Open
Abstract
Hypervirulent Klebsiella pneumoniae (hvKp) is a significant cause of severe invasive infections in Vietnam, yet data on its epidemiology, population structure and dynamics are scarce. We screened hvKp isolates from patients with bloodstream infections (BSIs) at a tertiary infectious diseases hospital in Vietnam and healthy individuals, followed by whole genome sequencing and plasmid analysis. Among 700 BSI-causing Kp strains, 100 (14.3%) were hvKp. Thirteen hvKp isolates were identified from 350 rectal swabs of healthy adults; none from 500 rectal swabs of healthy children. The hvKp isolates were genetically diverse, encompassing 17 sequence types (STs), predominantly ST23, ST86 and ST65. Among the 113 hvKp isolates, 14 (12.6%) carried at least one antimicrobial resistance (AMR) gene, largely mediated by IncFII, IncR, and IncA/C plasmids. Notably, the acquisition of AMR conjugative plasmids facilitated horizontal transfer of the non-conjugative virulence plasmid between K. pneumoniae strains. Phylogenetic analysis demonstrated hvKp isolates from BSIs and human carriage clustered together, suggesting a significant role of intestinal carriage in hvKp transmission. Enhanced surveillance is crucial to understand the factors driving intestinal carriage and hvKp transmission dynamics for informing preventive measures. Furthermore, we advocate the clinical use of our molecular assay for diagnosing hvKp infections to guide effective management.
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Affiliation(s)
- Quynh Nguyen
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Tuyen Thanh Ha
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | - Phat Vinh Voong
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Vinh Chau
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | | | | | | | | | - Tan Van Trinh
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Juan J Carrique-Mas
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Stephen Baker
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID) Department of Medicine, University of Cambridge, Cambridge, UK
| | - Guy Thwaites
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Maia A Rabaa
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Marc Choisy
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Hao The Chung
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam
| | - Duy Thanh Pham
- Oxford University Clinical Research Unit, Ho Chi Minh City, Vietnam.
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK.
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Farajzadeh Sheikh A, Abdi M, Farshadzadeh Z. Molecular detection of Class 1, 2, and 3 integrons in hypervirulent and classic Klebsiella pneumoniae isolates: A cross-sectional study. Health Sci Rep 2024; 7:e1962. [PMID: 38698788 PMCID: PMC11063457 DOI: 10.1002/hsr2.1962] [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: 06/28/2023] [Revised: 11/28/2023] [Accepted: 02/20/2024] [Indexed: 05/05/2024] Open
Abstract
Background and Aims The "hypervirulent" variant of Klebsiella pneumoniae (hvKp) is an emerging pathogen that cause life-threatening infection. The present study was conducted to identify the prevalence of hvKp and to investigate the presence class 1, 2, and 3 integrons in these isolates. Methods A cross-sectional study was conducted at three teaching hospitals, Ahvaz, South-west of Iran, from January 1, 2019 to December 31, 2020. Samples were collected from inpatients and included only the first samples collected from each patient. K. pneumoniae strains were isolated from different specimens using biochemical test and confirmed by targeting 16S-23S rDNA internal transcribed spacer. HvKp isolates were recovered using string test and were further characterized by detection virulence-associated genes (rmpA, iucA, and magA). Antibiotic susceptibility patterns of isolates were determined using the disc diffusion method. Isolates were screened for presence the integron genes (intI, intII, and intIII) and repetitive element sequence-based polymerase chain reaction (PCR) performed to determine strain relatedness. SPSS version 22 was used for the data analysis. Results Seventy-one (77%) of isolates showed multidrug-resistant (MDR) phenotype. HvKP accounted for 14% (13/92) of cKp isolated from blood (46%) and urinary tract infection (38%), and the great majority of them (61.5%; 8/13) exhibited MDR phenotype. Using the PCR assay, 29 of 92 isolates (31.5%) were found to have positive results for the presence of IntI. Three of the IntI-positive strains were hvKP. Class 2 integron was present in 8/92 cKp isolates. Integron Class 2 was found to coexist with Class 1 integron in 3/8 isolates. All integron-positive isolates (IntI and/or IntII) were resistant to at least three different classes of antibiotics and showed MDR phenotype. No Class 3 integrons were detected among the isolates. Conclusion The results of our study revealed that considering the role of integrons in facilitating the acquisition and dissemination of resistance genes among bacteria, monitoring the emergence of hvKp, emphasizing on the mechanism of antimicrobial resistance, can prevent from the spread of carbapenemase-producing hvKp strains.
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Affiliation(s)
- Ahmad Farajzadeh Sheikh
- Department of Microbiology, Infectious and Tropical Diseases Research Center, Health Research InstituteAhvaz Jundishapur University of Medical SciencesAhvazIran
- Department of Microbiology, School of MedicineAhvaz Jundishapur University of Medical SciencesAhvazIran
| | - Marjan Abdi
- Department of Microbiology, School of MedicineAhvaz Jundishapur University of Medical SciencesAhvazIran
| | - Zahra Farshadzadeh
- Department of Microbiology, Infectious and Tropical Diseases Research Center, Health Research InstituteAhvaz Jundishapur University of Medical SciencesAhvazIran
- Department of Microbiology, School of MedicineAhvaz Jundishapur University of Medical SciencesAhvazIran
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Castro J, Oliveira R, Fernandes L, Carvalho I, Oliveira H, Brinks E, Cho GS, Franz C, Almeida C, Silva S, Araújo D. Molecular characterization and virulence profile of Klebsiella pneumoniae and Klebsiella oxytoca isolated from ill cats and dogs in Portugal. Vet Microbiol 2024; 292:110056. [PMID: 38537400 DOI: 10.1016/j.vetmic.2024.110056] [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: 01/05/2024] [Revised: 03/11/2024] [Accepted: 03/15/2024] [Indexed: 04/10/2024]
Abstract
Klebsiella spp. are important pathogens of humans and companion animals such as cats and dogs, capable of causing severe life-threatening diseases. The aim of this study was to characterize the molecular and phenotypic properties of Klebsiella pneumoniae and Klebsiella oxytoca isolated from ill companion animals by whole genome sequencing, followed by in vitro assessment of biofilm formation and in vivo pathogenicity using the Galleria mellonella model. Two LPS O-types were identified for all the K. pneumoniae isolates tested (O3B and O1/O2v2) and only one for K. oxytoca isolates (OL104), and the most common STs found were ST11 and ST266. Furthermore, a high diversity of K-locus types was found for K. pneumoniae (KL102; KL105; KL31, and KL13). Within K. pneumoniae, one specific O/K/ST-types combination (i.e., KL105-ST11-O1/O2v2) showed results that were of concern, as it exhibited a high inflammatory response at 12 h post-infection in G. mellonella with 80% of the larvae dead at 72 h post-infection. This virulence potential, on the other hand, did not appear to be directly related to the biofilm-forming capacity. Also, virulence and resistance scores obtained for this set of strains did surpass score 1. The present study demonstrated that Klebsiella spp. isolated from companion animals belonging to STs that can cause human infections and present virulence on an invertebrate model. Thus, this study underscores the role of dogs and cats as reservoirs of resistant Klebsiella spp. that could potentially be transmitted to humans.
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Affiliation(s)
- Joana Castro
- INIAV, IP - National Institute for Agrarian and Veterinary Research, Rua dos Lagidos, Lugar da Madalena, Vairão 4485-655, Portugal; Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal
| | - Ricardo Oliveira
- INIAV, IP - National Institute for Agrarian and Veterinary Research, Rua dos Lagidos, Lugar da Madalena, Vairão 4485-655, Portugal; LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal; ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal
| | - Liliana Fernandes
- Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal; LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Isabel Carvalho
- Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal; LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Hugo Oliveira
- Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal; LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Erik Brinks
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Gyu-Sung Cho
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Charles Franz
- Department of Microbiology and Biotechnology, Max Rubner-Institut, Federal Research Institute of Nutrition and Food, Kiel, Germany
| | - Carina Almeida
- INIAV, IP - National Institute for Agrarian and Veterinary Research, Rua dos Lagidos, Lugar da Madalena, Vairão 4485-655, Portugal; Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal; LEPABE - Laboratory for Process Engineering, Environment, Biotechnology and Energy, Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal; ALiCE - Associate Laboratory in Chemical Engineering, Faculty of Engineering, University of Porto, 4200-465 Porto, Portugal
| | - Sónia Silva
- INIAV, IP - National Institute for Agrarian and Veterinary Research, Rua dos Lagidos, Lugar da Madalena, Vairão 4485-655, Portugal; Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal; LABBELS - Associate Laboratory, Braga/Guimarães, Portugal
| | - Daniela Araújo
- INIAV, IP - National Institute for Agrarian and Veterinary Research, Rua dos Lagidos, Lugar da Madalena, Vairão 4485-655, Portugal; Centre of Biological Engineering, University of Minho, 4710-057, Braga, Portugal; LABBELS - Associate Laboratory, Braga/Guimarães, Portugal.
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Bray AS, Zafar MA. Deciphering the gastrointestinal carriage of Klebsiella pneumoniae. Infect Immun 2024:e0048223. [PMID: 38597634 DOI: 10.1128/iai.00482-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024] Open
Abstract
Bacterial infections pose a significant global health threat, accounting for an estimated 7.7 million deaths. Hospital outbreaks driven by multi-drug-resistant pathogens, notably Klebsiella pneumoniae (K. pneumoniae), are of grave concern. This opportunistic pathogen causes pneumonia, urinary tract infections, and bacteremia, particularly in immunocompromised individuals. The rise of hypervirulent K. pneumoniae adds complexity, as it increasingly infects healthy individuals. Recent epidemiological data suggest that asymptomatic gastrointestinal carriage serves as a reservoir for infections in the same individual and allows for host-to-host transmission via the fecal-oral route. This review focuses on K. pneumoniae's gastrointestinal colonization, delving into epidemiological evidence, current animal models, molecular colonization mechanisms, and the protective role of the resident gut microbiota. Moreover, the review sheds light on in vivo high-throughput approaches that have been crucial for identifying K. pneumoniae factors in gut colonization. This comprehensive exploration aims to enhance our understanding of K. pneumoniae gut pathogenesis, guiding future intervention and prevention strategies.
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Affiliation(s)
- Andrew S Bray
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - M Ammar Zafar
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
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8
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Pustam A, Jayaraman J, Ramsubhag A. Whole genome sequencing reveals complex resistome features of Klebsiella pneumoniae isolated from patients at major hospitals in Trinidad, West Indies. J Glob Antimicrob Resist 2024; 37:141-149. [PMID: 38608934 DOI: 10.1016/j.jgar.2024.03.019] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2023] [Revised: 02/17/2024] [Accepted: 03/26/2024] [Indexed: 04/14/2024] Open
Abstract
OBJECTIVES Antibiotic-resistant Klebsiella pneumoniae is a human pathogen of major global concern due to its ability to cause multiple severe diseases that are often difficult to treat therapeutically. This study aimed to investigate the resistome of local clinical K. pneumoniae isolates. METHODS Herein, we used a whole genome sequencing approach and bioinformatics tools to reconstruct the resistome of 10 clinical K. pneumoniae isolates and one clinical isolate of the closely related Klebsiella quasipneumoniae obtained from patients from three major hospitals in Trinidad, West Indies. RESULTS The results of the study revealed the presence of a complex antibiotic-resistant armoury among the local isolates with multiple resistance mechanisms involving (i) inactivation of antibiotics, (ii) efflux pumps, (iii) antibiotic target alteration, protection, and replacement against antibiotics, and (iv) altered porin protein that reduced the permeability to antibiotics. Several resistance genes such as blaCTX-M-15, blaTEM-1B, blaSHV-28, blaKPC-2, oqxA, sul1, tetD, aac(6')-Ib-cr5, aph(6)-Id, and fosA6, which are known to confer resistance to antibiotics used to treat K. pneumoniae infections. In most cases, the resistance genes were flanked by mobile elements, including insertion sequences and transposons, which facilitate the spread of these genetic features among related organisms. CONCLUSION This is the first comprehensive study to thoroughly investigate the resistome of clinical K. pneumoniae isolates and K. quasipneumoniae from Trinidad, West Indies. These findings suggest that monitoring K. pneumoniae and its genome-wide antibiotic resistance features in clinical strains would be of critical importance for guiding antibiotic stewardship programs and improving regional disease management systems for this pathogen.
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Affiliation(s)
- Aarti Pustam
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Jayaraj Jayaraman
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Adesh Ramsubhag
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago.
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Kain MJW, Reece NL, Parry CM, Rajahram GS, Paterson DL, Woolley SD. The Rapid Emergence of Hypervirulent Klebsiella Species and Burkholderia pseudomallei as Major Health Threats in Southeast Asia: The Urgent Need for Recognition as Neglected Tropical Diseases. Trop Med Infect Dis 2024; 9:80. [PMID: 38668541 PMCID: PMC11054678 DOI: 10.3390/tropicalmed9040080] [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: 01/27/2024] [Revised: 03/29/2024] [Accepted: 04/05/2024] [Indexed: 04/29/2024] Open
Abstract
The World Health Organization (WHO)'s list of neglected tropical diseases (NTDs) highlights conditions that are responsible for devastating health, social and economic consequences, and yet, they are overlooked and poorly resourced. The NTD list does not include conditions caused by Gram-negative bacilli (GNB). Infections due to GNB cause significant morbidity and mortality and are prevalent worldwide. Southeast Asia is a WHO region of low- and middle-income countries carrying the largest burden of NTDs. Two significant health threats in Southeast Asia are Burkholderia pseudomallei (causing melioidosis) and hypervirulent Klebsiella pneumoniae (HvKp). Both diseases have high mortality and increasing prevalence, yet both suffer from a lack of awareness, significant under-resourcing, incomplete epidemiological data, limited diagnostics, and a lack of evidence-based treatment. Emerging evidence shows that both melioidosis and HvKp are spreading globally, including in high-income countries, highlighting the potential future global threat they pose. In this article, we review both conditions, identifying current trends and challenges in Southeast Asia and areas for future research. We also argue that melioidosis and HvKp merit inclusion as NTDs, and that mandatory global surveillance and reporting systems should be established, and we make an urgent call for research to better understand, detect, and treat these neglected diseases.
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Affiliation(s)
| | | | - Christopher M. Parry
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK;
- Centre for Tropical Medicine and Global Health, Nuffield Department of Clinical Medicine, University of Oxford, Oxford OX1 2JD, UK
| | - Giri Shan Rajahram
- Department of Medicine, Queen Elizabeth II Hospital, Kota Kinabalu 88300, Malaysia
- Infectious Diseases Society, Kota Kinabalu Sabah-Menzies School of Health Research, Clinical Research Unit, Kota Kinabalu 88994, Malaysia
| | - David L. Paterson
- ADVANCE-ID Network, Saw Swee Hock School of Public Health, National University of Singapore, Singapore 119077, Singapore
- Infectious Diseases Translational Research Programme, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 119077, Singapore
| | - Stephen D. Woolley
- Institute of Naval Medicine, Alverstoke, Hampshire PO12 2DL, UK
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool L3 5QA, UK;
- Tropical and Infectious Diseases Unit, Liverpool University Hospitals Foundation NHS Trust, Liverpool L7 8YE, UK
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Diab H, Rahy K, Jisr T, El Chaar M, Abboud E, Tokajian S. Phenotypic and molecular characterization of multi-drug resistant Klebsiella spp. isolates recovered from clinical settings. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2024; 119:105583. [PMID: 38484958 DOI: 10.1016/j.meegid.2024.105583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Revised: 03/08/2024] [Accepted: 03/10/2024] [Indexed: 03/18/2024]
Abstract
Klebsiella pneumoniae is a Gram-negative bacterium that colonizes the gastrointestinal tract and nasopharynx with many being linked to nosocomial infections. Extended-spectrum β-lactamases (ESBL)-producing and carbapenem-resistant K. pneumoniae is recognized by the World Health Organization (WHO) as a critical public health concern. In this study, whole-genome sequencing (WGS) - based analysis was performed to understand the molecular epidemiology of multi-drug resistant Klebsiella spp. clinical isolates. Genome comparison, multi-locus sequence typing (MLST), pulsed-field gel electrophoresis (PFGE), and whole-genome-SNP-based phylogenetic analysis (wg-SNP) were used for in-depth molecular characterization. in silico typing was used to determine the resistance genes, virulence factors, Inc. groups, and capsular types. All except one isolate were non-susceptible to meropenem and 89% were non-susceptible to ertapenem and imipenem. blaNDM, blaOXA-48, and blaKPC were the detected carbapenemases with blaNDM-1 found in half of the sequenced genomes. Resistance to colistin was detected in one isolate and was linked to several genetic alterations in crrB, pmrB, and pmrC genes. The most common plasmid type was IncFIB followed by IncR, and the Type 3 fimbriae, encoded by the mrkABCDF operon, was conserved among all isolates. The most common sequence- (ST) and K-type detected were ST147 and K64. The prevelance and the genomic relatedness of ST147 isolates, as shown by the data from SNP-based phylogenetic analysis, PFGE, and genomic clustering, may be an outbreak marker. However, this can only be validated through a more comprehensive study encompassing a wider sampling scheme and over an extended timeframe.
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Affiliation(s)
- Hassan Diab
- Department of Natural Sciences, Lebanese American University, P.O. Box 36, Byblos, Lebanon
| | - Kelven Rahy
- Department of Computer Science and Mathematics, Lebanese American University, P.O. Box 36, Byblos, Lebanon
| | - Tamima Jisr
- Clinical Laboratory Department, Makassed General Hospital, P.O.Box 11-6301, Beirut, Lebanon
| | - Mira El Chaar
- Faculty of Health Sciences, University of Balamand, P.O.Box: 55251, Beirut, Lebanon
| | - Edmond Abboud
- Middle East Institute of Health Hospital, Clinical Laboratory Department, P.O.Box 60-387, Bsalim, Lebanon
| | - Sima Tokajian
- Department of Natural Sciences, Lebanese American University, P.O. Box 36, Byblos, Lebanon.
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11
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Dangor Z, Benson N, Berkley JA, Bielicki J, Bijsma MW, Broad J, Buurman ET, Cross A, Duffy EM, Holt KE, Iroh Tam PY, Jit M, Karampatsas K, Katwere M, Kwatra G, Laxminarayan R, Le Doare K, Mboizi R, Micoli F, Moore CE, Nakabembe E, Naylor NR, O'Brien S, Olwagen C, Reddy D, Rodrigues C, Rosen DA, Sadarangani M, Srikantiah P, Tennant SM, Hasso-Agopsowicz M, Madhi SA. Vaccine value profile for Klebsiella pneumoniae. Vaccine 2024:S0264-410X(24)00248-2. [PMID: 38503661 DOI: 10.1016/j.vaccine.2024.02.072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/07/2024] [Accepted: 02/24/2024] [Indexed: 03/21/2024]
Abstract
Klebsiella pneumoniae causes community- and healthcare-associated infections in children and adults. Globally in 2019, an estimated 1.27 million (95% Uncertainty Interval [UI]: 0.91-1.71) and 4.95 million (95% UI: 3.62-6.57) deaths were attributed to and associated with bacterial antimicrobial resistance (AMR), respectively. K. pneumoniae was the second leading pathogen in deaths attributed to AMR resistant bacteria. Furthermore, the rise of antimicrobial resistance in both community- and hospital-acquired infections is a concern for neonates and infants who are at high risk for invasive bacterial disease. There is a limited antibiotic pipeline for new antibiotics to treat multidrug resistant infections, and vaccines targeted against K. pneumoniae are considered to be of priority by the World Health Organization. Vaccination of pregnant women against K. pneumoniae could reduce the risk of invasive K.pneumoniae disease in their young offspring. In addition, vulnerable children, adolescents and adult populations at risk of K. pneumoniae disease with underlying diseases such as immunosuppression from underlying hematologic malignancy, chemotherapy, patients undergoing abdominal and/or urinary surgical procedures, or prolonged intensive care management are also potential target groups for a K. pneumoniae vaccine. A 'Vaccine Value Profile' (VVP) for K.pneumoniae, which contemplates vaccination of pregnant women to protect their babies from birth through to at least three months of age and other high-risk populations, provides a high-level, holistic assessment of the available information to inform the potential public health, economic and societal value of a pipeline of K. pneumoniae vaccines and other preventatives and therapeutics. This VVP was developed by a working group of subject matter experts from academia, non-profit organizations, public-private partnerships, and multi-lateral organizations, and in collaboration with stakeholders from the WHO. All contributors have extensive expertise on various elements of the K.pneumoniae VVP and collectively aimed to identify current research and knowledge gaps. The VVP was developed using only existing and publicly available information.
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Affiliation(s)
- Ziyaad Dangor
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa.
| | - Nicole Benson
- Global Health Division, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - James A Berkley
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya; Centre for Tropical Medicine & Global Health, University of Oxford, UK
| | - Julia Bielicki
- Centre for Neonatal and Paediatric Infection, St George's, University of London, UK; Paediatric Research Centre (PRC), University of Basel Children's Hospital, Basel, Switzerland
| | - Merijn W Bijsma
- Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscience, Meibergdreef, Amsterdam, the Netherlands; Amsterdam UMC, University of Amsterdam, Department of Pediatrics, Amsterdam Neuroscience, Meibergdreef, Amsterdam, the Netherlands
| | | | - Ed T Buurman
- CARB-X, Boston University, Boston, MA 02215, USA
| | - Alan Cross
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Erin M Duffy
- CARB-X, Boston University, Boston, MA 02215, USA
| | - Kathryn E Holt
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
| | - Pui-Ying Iroh Tam
- Paediatrics and Child Health Research Group, Malawi-Liverpool Wellcome Programme, Blantyre, Malawi
| | - Mark Jit
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | | | - Michael Katwere
- Makerere University-Johns Hopkins University Research Collaboration, Kampala, Uganda
| | - Gaurav Kwatra
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa; Division of Infectious Diseases, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, OH, USA; Department of Clinical Microbiology, Christian Medical College, Vellore, India
| | | | - Kirsty Le Doare
- Centre for Neonatal and Paediatric Infection, St George's, University of London, UK; UK Health Security Agency, Porton Down, UK; World Health Organization, Geneva, Switzerland
| | - Robert Mboizi
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | | | - Catrin E Moore
- Centre for Neonatal and Paediatric Infection, St George's, University of London, UK
| | - Eve Nakabembe
- Department of Obstetrics and Gynaecology, School of Medicine, Makerere University College of Health Sciences, Upper Mulago Hill Road, P.O. Box 7072 Kampala, Uganda
| | - Nichola R Naylor
- UK Health Security Agency, Porton Down, UK; Department of Health Services Research and Policy, London School of Hygiene & Tropical Medicine, London, UK
| | - Seamus O'Brien
- Global Antibiotic Research & Development Partnership (GARDP), Geneva, Switzerland
| | - Courtney Olwagen
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Denasha Reddy
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Charlene Rodrigues
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK; Dept of Paediatrics, Imperial College Healthcare NHS Trust, London, UK; Pathogen Genomics Programme, UK Health Security Agency, London, UK
| | - David A Rosen
- Department of Pediatrics and Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Manish Sadarangani
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Padmini Srikantiah
- Global Health Division, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Sharon M Tennant
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mateusz Hasso-Agopsowicz
- Department of Immunization, Vaccines & Biologicals, World Health Organization, Geneva, Switzerland
| | - Shabir A Madhi
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
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12
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Rodríguez-Medina N, Rodríguez-Santiago J, Alvarado-Delgado A, Sagal-Prado A, Silva-Sánchez J, De la Cruz MA, Ares MA, Sánchez-Arias M, Morfín-Otero R, Hernández-Castro R, Cornejo-Juárez P, Jiménez-Villanueva E, Sánchez-Francia D, Garza-Ramos U. Comprehensive study reveals phenotypic heterogeneity in Klebsiella pneumoniae species complex isolates. Sci Rep 2024; 14:5876. [PMID: 38467675 PMCID: PMC10928225 DOI: 10.1038/s41598-024-55546-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Accepted: 02/25/2024] [Indexed: 03/13/2024] Open
Abstract
Here, we conducted a comprehensive analysis of 356 Klebsiella pneumoniae species complex (KpSC) isolates that were classified as classical (cl), presumptive hypervirulent (p-hv) and hypermucoviscous-like (hmv-like). Overall, K. pneumoniae (82.3%), K. variicola (2.5%) and K. quasipneumoniae (2.5%) were identified. These isolates comprised 321 cl-KpSC, 7 p-hv-KpSC and 18 hmv-like-KpSC. A large proportion of cl-KpSC isolates were extended-spectrum-β-lactamases (ESBLs)-producers (64.4%) and 3.4% of isolates were colistin-resistant carrying carbapenemase and ESBL genes. All p-hv-KpSC showed an antibiotic susceptible phenotype and hmv-like isolates were found to be ESBL-producers (8/18). Assays for capsule production and capsule-dependent virulence phenotypes and whole-genome sequencing (WGS) were performed in a subset of isolates. Capsule amount differed in all p-hv strains and hmv-like produced higher capsule amounts than cl strains; these variations had important implications in phagocytosis and virulence. Murine sepsis model showed that most cl strains were nonlethal and the hmv-like caused 100% mortality with 3 × 108 CFUs. Unexpectedly, 3/7 (42.9%) of p-hv strains required 108 CFUs to cause 100% mortality (atypical hypervirulent), and 4/7 (57.1%) strains were considered truly hypervirulent (hv). Genomic analyses confirmed the diverse population, including isolates belonging to hv clonal groups (CG) CG23, CG86, CG380 and CG25 (this corresponded to the ST3999 a novel hv clone) and MDR clones such as CG258 and CG147 (ST392) among others. We noted that the hmv-like and hv-ST3999 isolates showed a close phylogenetic relationship with cl-MDR K. pneumoniae. The information collected here is important to understand the evolution of clinically important phenotypes such as hypervirulent and ESBL-producing-hypermucoviscous-like amongst the KpSC in Mexican healthcare settings. Likewise, this study shows that mgrB inactivation is the main mechanism of colistin resistance in K. pneumoniae isolates from Mexico.
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Affiliation(s)
- Nadia Rodríguez-Medina
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Santa María Ahuacatitlán, C.P. 62100, Cuernavaca, Morelos, Mexico
| | - Jonathan Rodríguez-Santiago
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Santa María Ahuacatitlán, C.P. 62100, Cuernavaca, Morelos, Mexico
| | - Alejandro Alvarado-Delgado
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Santa María Ahuacatitlán, C.P. 62100, Cuernavaca, Morelos, Mexico
| | - Alan Sagal-Prado
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Santa María Ahuacatitlán, C.P. 62100, Cuernavaca, Morelos, Mexico
| | - Jesús Silva-Sánchez
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Santa María Ahuacatitlán, C.P. 62100, Cuernavaca, Morelos, Mexico
| | - Miguel A De la Cruz
- Facultad de Medicina, Benemérita Universidad Autónoma de Puebla, Puebla, Mexico
| | - Miguel Angel Ares
- Unidad de Investigación Médica en Enfermedades Infecciosas y Parasitarias, Hospital de Pediatría, Centro Médico Nacional Siglo XXI, Instituto Mexicano del Seguro Social, Mexico City, Mexico
| | - Margarita Sánchez-Arias
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Santa María Ahuacatitlán, C.P. 62100, Cuernavaca, Morelos, Mexico
| | - Rayo Morfín-Otero
- Hospital Civil de Guadalajara "Fray Antonio Alcalde", Instituto de Patología Infecciosa y Experimental, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | | | | | | | | | - Ulises Garza-Ramos
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Santa María Ahuacatitlán, C.P. 62100, Cuernavaca, Morelos, Mexico.
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13
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Duwor S, Brites D, Mäser P. Phylogenetic Analysis of Pyruvate-Ferredoxin Oxidoreductase, a Redox Enzyme Involved in the Pharmacological Activation of Nitro-Based Prodrugs in Bacteria and Protozoa. BIOLOGY 2024; 13:178. [PMID: 38534448 DOI: 10.3390/biology13030178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 02/29/2024] [Accepted: 03/06/2024] [Indexed: 03/28/2024]
Abstract
The present frontrunners in the chemotherapy of infections caused by protozoa are nitro-based prodrugs that are selectively activated by PFOR-mediated redox reactions. This study seeks to analyze the distribution of PFOR in selected protozoa and bacteria by applying comparative genomics to test the hypothesis that PFOR in eukaryotes was acquired through horizontal gene transfer (HGT) from bacteria. Furthermore, to identify other putatively acquired genes, proteome-wide and gene enrichment analyses were used. A plausible explanation for the patchy occurrence of PFOR in protozoa is based on the hypothesis that bacteria are potential sources of genes that enhance the adaptation of protozoa in hostile environments. Comparative genomics of Entamoeba histolytica and the putative gene donor, Desulfovibrio vulgaris, identified eleven candidate genes for HGT involved in intermediary metabolism. If these results can be reproduced in other PFOR-possessing protozoa, it would provide more validated evidence to support the horizontal transfer of pfor from bacteria.
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Affiliation(s)
- Seth Duwor
- Swiss Tropical and Public Health Institute, 4123 Allschwil, Switzerland
- Faculty of Science, University of Basel, 4001 Basel, Switzerland
- Department of Clinical Pharmacology and Toxicology, University Hospital Zurich, University of Zurich, 8091 Zurich, Switzerland
| | - Daniela Brites
- Swiss Tropical and Public Health Institute, 4123 Allschwil, Switzerland
- Faculty of Science, University of Basel, 4001 Basel, Switzerland
| | - Pascal Mäser
- Swiss Tropical and Public Health Institute, 4123 Allschwil, Switzerland
- Faculty of Science, University of Basel, 4001 Basel, Switzerland
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14
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Haudiquet M, Le Bris J, Nucci A, Bonnin RA, Domingo-Calap P, Rocha EPC, Rendueles O. Capsules and their traits shape phage susceptibility and plasmid conjugation efficiency. Nat Commun 2024; 15:2032. [PMID: 38448399 PMCID: PMC10918111 DOI: 10.1038/s41467-024-46147-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Accepted: 02/14/2024] [Indexed: 03/08/2024] Open
Abstract
Bacterial evolution is affected by mobile genetic elements like phages and conjugative plasmids, offering new adaptive traits while incurring fitness costs. Their infection is affected by the bacterial capsule. Yet, its importance has been difficult to quantify because of the high diversity of confounding mechanisms in bacterial genomes such as anti-viral systems and surface receptor modifications. Swapping capsule loci between Klebsiella pneumoniae strains allowed us to quantify their impact on plasmid and phage infection independently of genetic background. Capsule swaps systematically invert phage susceptibility, revealing serotypes as key determinants of phage infection. Capsule types also influence conjugation efficiency in both donor and recipient cells, a mechanism shaped by capsule volume and conjugative pilus structure. Comparative genomics confirmed that more permissive serotypes in the lab correspond to the strains acquiring more conjugative plasmids in nature. The least capsule-sensitive pili (F-like) are the most frequent in the species' plasmids, and are the only ones associated with both antibiotic resistance and virulence factors, driving the convergence between virulence and antibiotics resistance in the population. These results show how traits of cellular envelopes define slow and fast lanes of infection by mobile genetic elements, with implications for population dynamics and horizontal gene transfer.
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Affiliation(s)
- Matthieu Haudiquet
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France.
- Ecole Doctoral FIRE-Programme Bettencourt, CRI, Paris, France.
| | - Julie Le Bris
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France
- Sorbonne Université, Collège Doctoral, Ecole Doctorale Complexité du Vivant, 75005, Paris, France
| | - Amandine Nucci
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France
| | - Rémy A Bonnin
- Team Resist UMR1184 Université Paris Saclay, CEA, Inserm, Le Kremlin-Bicêtre, Paris, France
- Service de bactériologie, Hôpital Bicêtre, Université Paris Saclay, AP-HP, Le Kremlin-Bicêtre, Paris, France
- Centre National de Référence Associé de la Résistance aux Antibiotiques, Le Kremlin-Bicêtre, Paris, France
| | - Pilar Domingo-Calap
- Instituto de Biología Integrativa de Sistemas, Universitat de València-CSIC, 46980, Paterna, Spain
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France.
| | - Olaya Rendueles
- Institut Pasteur, Université Paris Cité, CNRS UMR3525, Microbial Evolutionary Genomics, Paris, 75015, France.
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15
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Yang X, Man MY, Heng H, Chan BKW, Hu Q, Chan EWC, Shum HP, Chen S. Molecular epidemiology and clinical impact of Klebsiella spp. causing bloodstream infections in Hong Kong. EBioMedicine 2024; 101:104998. [PMID: 38340556 PMCID: PMC10869758 DOI: 10.1016/j.ebiom.2024.104998] [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: 11/03/2023] [Revised: 01/23/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
BACKGROUND The epidemiological features of the Klebsiella pneumoniae causing bloodstream infections in Hong Kong and their potential threats to human health remained unknown. METHODS K. pneumoniae strains collected from four hospitals in Hong Kong during the period of 2009-2018 were subjected to molecular typing, string test, antimicrobial susceptibility testing, whole genome sequencing and analysis. Clinical data of patients from whom these strains were isolated were analyzed retrospectively using univariate and multivariate logistic regression approaches. FINDINGS The 240 Klebsiella spp. strains belonged to 123 different STs and 63 different capsule loci (KLs), with KL1 and KL2 being the major type. 86 out of 212 BSI-KP (40.6%) carried at least one of the virulence genes iuc, iro, rmpA or rmpA2. Virulence plasmid correlated well with the string test positive result, yet 8 strains without rmp genes were also hypermucoviscous, which was due to wzc mutation. The mortality rate of bloodstream infection patients was 43.0%. Univariant analysis showed that factors including renal replacement therapy (FDR adjusted p = 0.0007), mechanical ventilation (FDR adjusted p < 0.0001) and respiratory sepsis (FDR adjusted p < 0.0001) were found to pose the highest risk of death upon infection by Klebsiella spp. INTERPRETATION This study revealed the high mortality rate and risk factors associated with bloodstream infections caused by K. pneumoniae in Hong Kong, which warrants immediate action to develop effective solution to tackle this problem. FUNDING Theme Based Research Scheme (T11-104/22-R), Research Impact Fund (R5011-18 F) and Postdoctoral Fellowship (PDFS2223-1S09).
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Affiliation(s)
- Xuemei Yang
- State Key Lab of Chemical Biology and Drug Discovery and the Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, China; Shenzhen Key Lab for Food Biological Safety Control, The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, China
| | - Man-Yee Man
- Department of Intensive Care, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong SAR, China
| | - Heng Heng
- State Key Lab of Chemical Biology and Drug Discovery and the Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, China; Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Bill Kwan-Wai Chan
- State Key Lab of Chemical Biology and Drug Discovery and the Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, China; Shenzhen Key Lab for Food Biological Safety Control, The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, China
| | - Qiao Hu
- State Key Lab of Chemical Biology and Drug Discovery and the Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, China; Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon Tong, Hong Kong SAR, China
| | - Edward Wai-Chi Chan
- State Key Lab of Chemical Biology and Drug Discovery and the Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, China
| | - Hoi-Ping Shum
- Department of Intensive Care, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong SAR, China.
| | - Sheng Chen
- State Key Lab of Chemical Biology and Drug Discovery and the Department of Food Science and Nutrition, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, China; Shenzhen Key Lab for Food Biological Safety Control, The Hong Kong Polytechnic University Shenzhen Research Institute, Shenzhen, China.
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16
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Lahij HF, Almeani SAL. Multidrug-resistant clinical K. pneumoniae ST16, ST218, and ST283 and emergence of pandrug-resistant KPC-positive ST6434/K2 lineage in Iraq. Braz J Microbiol 2024; 55:375-382. [PMID: 38091237 PMCID: PMC10920612 DOI: 10.1007/s42770-023-01205-w] [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: 08/07/2023] [Accepted: 11/28/2023] [Indexed: 03/09/2024] Open
Abstract
BACKGROUND AND AIM The increasing incidence of Klebsiella pneumoniae infections, both in the community and in hospitals, is a huge health problem. This is due to the increasing resistance of the bacteria to antibiotics and biofilm formation, as well as the presence of a capsule. This study focuses on two main objectives: to survey the most common capsular types in local isolates for the first time in Anbar, Iraq, on molecular level and to distinguish between infectious pathogen strains using multilocus sequence typing (MLST) for more efficient epidemiological and surveillance analysis, in order to determine the source of these strains (invasive or purebred). METHODOLOGY Multidrug-resistant (MDR) isolates adapted to genomic extraction and molecular screening of capsular type and MLST, and then to data processing by Pasteur Institut. RESULTS For the first time, one isolate was registered as a new strain in the world with ST 6434; the other strains demonstrated as preregistered with ST16, ST218, and ST283. 33% of MDR isolates belonged to the capsular K2 type. CONCLUSION The study's findings were not aligned with the global knowledge base about the distribution of capsular type in Asia. To prevent the spread of highly resistant strains, careful monitoring of virulence determinants is necessary in addition to the observation of antibiotic resistance.
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Affiliation(s)
- Hasan Falah Lahij
- Department of Biology, Collage of Sciences, University of Anbar, Ramadi, Anbar, Iraq.
- Medical Laboratory Technology, Almaarif University College, Ramadi, 31001, Iraq.
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17
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Teo TH, Ayuni NN, Yin M, Liew JH, Chen JQ, Kurepina N, Rajarethinam R, Kreiswirth BN, Chen L, Bifani P. Differential mucosal tropism and dissemination of classical and hypervirulent Klebsiella pneumoniae infection. iScience 2024; 27:108875. [PMID: 38313058 PMCID: PMC10835444 DOI: 10.1016/j.isci.2024.108875] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Revised: 09/28/2023] [Accepted: 01/08/2024] [Indexed: 02/06/2024] Open
Abstract
Klebsiella pneumoniae (Kp) infection is an important healthcare concern. The ST258 classical (c)Kp strain is dominant in hospital-acquired infections in North America and Europe, while ST23 hypervirulent (hv)Kp prevails in community-acquired infections in Asia. This study aimed to develop symptomatic mucosal infection models in mice that mirror natural infections in humans to gain a deeper understanding of Kp mucosal pathogenesis. We showed that cKp replicates in the nasal cavity instead of the lungs, and this early infection event is crucial for the establishment of chronic colonization in the cecum and colon. In contrast, hvKp replicates directly in the lungs to lethal bacterial load, and early infection of esophagus supported downstream transient colonization in the ileum and cecum. Here, we have developed an in vivo model that illuminates how differences in Kp tropism are responsible for virulence and disease phenotype in cKp and hvKp, providing the basis for further mechanistic study.
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Affiliation(s)
- Teck-Hui Teo
- Agency for Science, Technology and Research (A∗STAR), Infectious Diseases (ID) Labs, Singapore 429621, Singapore
| | - Nurul N. Ayuni
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Michelle Yin
- Agency for Science, Technology and Research (A∗STAR), Infectious Diseases (ID) Labs, Singapore 429621, Singapore
| | - Jun Hao Liew
- Agency for Science, Technology and Research (A∗STAR), Infectious Diseases (ID) Labs, Singapore 429621, Singapore
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
| | - Jason Q. Chen
- Agency for Science, Technology and Research (A∗STAR), Infectious Diseases (ID) Labs, Singapore 429621, Singapore
| | - Natalia Kurepina
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA
| | - Ravisankar Rajarethinam
- Institute of Molecular and Cell Biology, Agency for Science, Technology and Research (A∗STAR), Singapore 138673, Singapore
| | - Barry N. Kreiswirth
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA
| | - Liang Chen
- Hackensack Meridian Health Center for Discovery and Innovation, Nutley, NJ 07110, USA
| | - Pablo Bifani
- Agency for Science, Technology and Research (A∗STAR), Infectious Diseases (ID) Labs, Singapore 429621, Singapore
- Infectious Diseases Translational Research Programme, Department of Microbiology and Immunology, Yong Loo Lin School of Medicine, National University of Singapore, Singapore 117545, Singapore
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London WC1E7HT, UK
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18
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Yang P, Liu C, Du P, Yi J, Wu Z, Zheng J, Shen N, Cui L, Lu M. ST218 Klebsiella pneumoniae became a high-risk clone for multidrug resistance and hypervirulence. BMC Microbiol 2024; 24:56. [PMID: 38347440 PMCID: PMC10860259 DOI: 10.1186/s12866-024-03205-8] [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: 11/06/2023] [Accepted: 01/28/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND The occurrence of multidrug-resistant and hypervirulent Klebsiella pneumoniae (MDR-hvKp) worldwide poses a great challenge for public health. Few studies have focused on ST218 MDR-hvKp. METHODS Retrospective genomic surveillance was conducted at the Peking University Third Hospital from 2017 and clinical information was obtained. To understand genomic and microbiological characteristics, antimicrobial susceptibility testing, plasmid conjugation and stability, biofilm formation, serum killing, growth curves and whole-genome sequencing were performed. We also assessed the clinical and microbiological characteristics of ST218 compared with ST23. RESULTS A total of eleven ST218 Kp isolates were included. The most common infection type was lower respiratory tract infection (72.7%, 8/11) in our hospital, whereas ST23 hvKp (72.7%, 8/11) was closely associated with bloodstream infection. Notably, nosocomial infections caused by ST218 (54.5%, 6/11) was slightly higher than ST23 (36.4%, 4/11). All of the ST218 and ST23 strains presented with the virulence genes combination of iucA + iroB + peg344 + rmpA + rmpA2. Interestingly, the virulence score of ST218 was lower than ST23, whereas one ST218 strain (pPEKP3107) exhibited resistance to carbapenems, cephalosporins, β-lactamase/inhibitors and quinolones and harbored an ~ 59-kb IncN type MDR plasmid carrying resistance genes including blaNDM-1, dfrA14 and qnrS1. Importantly, blaNDM-1 and qnrS1 were flanked with IS26 located within the plasmid that could successfully transfer into E. coli J53. Additionally, PEKP2044 harbored an ~ 41-kb resistance plasmid located within tetA indicating resistance to doxycycline. CONCLUSION The emergence of blaNDM-1 revealed that there is great potential for ST218 Kp to become a high-risk clone for MDR-hvKp, indicating the urgent need for enhanced genomic surveillance.
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Affiliation(s)
- Ping Yang
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, China
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Chao Liu
- Department of Infectious Diseases, Peking University Third Hospital, Beijing, China
- Center of Infectious Disease, Peking University Third Hospital, Beijing, China
| | | | - Juan Yi
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Zhenchao Wu
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, China
| | - Jiajia Zheng
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Ning Shen
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, China
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
- Department of Infectious Diseases, Peking University Third Hospital, Beijing, China
- Center of Infectious Disease, Peking University Third Hospital, Beijing, China
| | - Liyan Cui
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China.
| | - Ming Lu
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, China.
- Department of Infectious Diseases, Peking University Third Hospital, Beijing, China.
- Center of Infectious Disease, Peking University Third Hospital, Beijing, China.
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19
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Hamed SM, Mohamed HO, Ashour HM, Fahmy LI. Comparative genomic analysis of strong biofilm-forming Klebsiella pneumoniae isolates uncovers novel IS Ecp1-mediated chromosomal integration of a full plasmid-like sequence. Infect Dis (Lond) 2024; 56:91-109. [PMID: 37897710 DOI: 10.1080/23744235.2023.2272624] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Accepted: 10/12/2023] [Indexed: 10/30/2023] Open
Abstract
BACKGROUND The goal of the current study was to elucidate the genomic background of biofilm formation in Klebsiella pneumoniae. METHODS Clinical isolates were screened for biofilm formation using the crystal violet assay. Antimicrobial resistance (AMR) profiles were assessed by disk diffusion and broth microdilution tests. Biofilm formation was correlated to virulence and resistance genes screened by PCR. Draft genomes of three isolates that form strong biofilm were generated by Illumina sequencing. RESULTS Only the siderophore-coding gene iutA was significantly associated with more pronounced biofilm formation. ST1399-KL43-O1/O2v1 and ST11-KL15-O4 were assigned to the multidrug-resistant strain K21 and the extensively drug-resistant strain K237, respectively. ST1999-KL38-O12 was assigned to K57. Correlated with CRISPR/Cas distribution, more plasmid replicons and prophage sequences were identified in K21 and K237 compared to K57. The acquired AMR genes (blaOXA-48, rmtF, aac(6')-Ib and qnrB) and (blaNDM-1, blaCTX-M, aph(3')-VI, qnrS, and aac(6')-Ib-cr) were found in K237 and K21, respectively. The latter showed a novel ISEcp1-mediated chromosomal integration of replicon type IncM1 plasmid-like structure harboring blaCTX-M-14 and aph(3')-VI that uniquely interrupted rcsC. The plasmid-mediated heavy metal resistance genes merACDEPRT and arsABCDR were spotted in K21, which also exclusively carried the acquired virulence genes mrkABCDF and the hypervirulence-associated genes iucABCD-iutA, and rmpA/A2. Pangenome analysis revealed NTUH-K2044 accessory genes most frequently shared with K21. CONCLUSIONS While less virulent to Galleria mellonella than ST1999 (K57), the strong biofilm former, multidrug-resistant, NDM-producer K. pneumoniae K21 (ST1399-KL43-O1/O2v1) carries a novel chromosomally integrated plasmid-like structure and hypervirulence-associated genes and represents a serious threat to countries in the area.
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Affiliation(s)
- Samira M Hamed
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza, Egypt
| | - Hend O Mohamed
- Department of Biological Control Research, Plant Protection Research Institute, Agricultural Research Center, Giza, Egypt
| | - Hossam M Ashour
- Department of Integrative Biology, College of Arts and Sciences, University of South Florida, St. Petersburg, FL, USA
| | - Lamiaa I Fahmy
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), Giza, Egypt
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20
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Wan S, Zhou A, Chen R, Fang S, Lu J, Lv N, Wang C, Gao J, Li J, Wu W. Metagenomics next-generation sequencing (mNGS) reveals emerging infection induced by Klebsiella pneumoniaeniae. Int J Antimicrob Agents 2024; 63:107056. [PMID: 38081548 DOI: 10.1016/j.ijantimicag.2023.107056] [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: 08/12/2023] [Revised: 11/27/2023] [Accepted: 12/05/2023] [Indexed: 01/11/2024]
Abstract
OBJECTIVES The increasing emergence of hypervirulent Klebsiella pneumoniae (hv-Kp) and carbapenem-resistant K. pneumoniae (CR-Kp) is a serious and substantial public health problem. The use of the last resort antimicrobials, tigecycline and polymyxin to combat infections is complicated by the expanding repertoire of newly-identified CR-hvKp. The transmission and co-occurrence of the corresponding antimicrobial resistance and virulence determinants are largely unknown. The aim of this study was to investigate the dissemination and dynamics of CR-Kp and its antibiotic resistance in a hospitalised patient. METHODS Metagenomic next-generation sequencing (mNGS) was conducted for different specimens collected from an elderly male hospitalised patient. CR-Kp strains were examined using antibiotic susceptibility and string testing. Antimicrobial and virulence genes were annotated using whole-genome sequencing (WGS). RESULTS A clinical case of a patient infected with a variety of CR-Kp isolates was reported. The co-occurrence of KPC-2 and NDM-1 in the patient was revealed. The CR-Kp isolates, such as BALF2, and Sputum T1 and T3, were classified into ST11 and ST147, respectively. The genetic signature (iuc operon) of hypervirulence was identified in strain T1, although string testing indicated its intermediate virulence. CONCLUSIONS In this study, multiple infections of CR-Kp isolates were revealed by mNGS, and their dissemination was attributed to plasmid variations, mgrB inactivation and integrative conjugative elements (ICEs). Furthermore, the finding indicated one likely convergence to form CR-hvKp, different from acquisition of carbapenem-resistance determinants in hvKp. A combination of mNGS and WGS is beneficial for clinical diagnosis and anti-infection therapy, and facilitates a better understanding of genetic variants conferring antimicrobial and virulence properties.
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Affiliation(s)
- Shuang Wan
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200123, China; College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Aiping Zhou
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200123, China; Shanghai East Hospital Ji'an Hospital, Ji'an, 343000, China
| | - Rongrong Chen
- College of Bioscience and Bioengineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Shiqi Fang
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Jinfeng Lu
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Na Lv
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China
| | - Chu Wang
- Genskey Medical Technology Co., Ltd., Beijing, 102206, China
| | - Jianpeng Gao
- Genskey Medical Technology Co., Ltd., Beijing, 102206, China
| | - Jun Li
- College of Food Science and Engineering, Jiangxi Agricultural University, Nanchang, 330045, China.
| | - Wenjuan Wu
- Department of Laboratory Medicine, Shanghai East Hospital, Tongji University School of Medicine, Shanghai, 200123, China.
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21
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Abbas R, Chakkour M, Zein El Dine H, Obaseki EF, Obeid ST, Jezzini A, Ghssein G, Ezzeddine Z. General Overview of Klebsiella pneumonia: Epidemiology and the Role of Siderophores in Its Pathogenicity. BIOLOGY 2024; 13:78. [PMID: 38392297 PMCID: PMC10886558 DOI: 10.3390/biology13020078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Revised: 01/23/2024] [Accepted: 01/24/2024] [Indexed: 02/24/2024]
Abstract
The opportunistic pathogen Klebsiella pneumoniae (K. pneumoniae) can colonize mucosal surfaces and spread from mucosae to other tissues, causing fatal infections. Medical equipment and the healthcare setting can become colonized by Klebsiella species, which are widely distributed in nature and can be found in water, soil, and animals. Moreover, a substantial number of community-acquired illnesses are also caused by this organism worldwide. These infections are characterized by a high rate of morbidity and mortality as well as the capacity to spread metastatically. Hypervirulent Klebsiella strains are thought to be connected to these infections. Four components are critical to this bacterium's pathogenicity-the capsule, lipopolysaccharide, fimbriae, and siderophores. Siderophores are secondary metabolites that allow iron to sequester from the surrounding medium and transport it to the intracellular compartment of the bacteria. A number of variables may lead to K. pneumoniae colonization in a specific area. Risk factors for infection include local healthcare practices, antibiotic use and misuse, infection control procedures, nutrition, gender, and age.
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Affiliation(s)
- Rim Abbas
- Faculty of Health Sciences, Beirut Arab University, Beirut P.O. Box 11-5020, Lebanon
| | - Mohamed Chakkour
- Department of Biological Sciences, Wayne State University, Detroit, MI 48202, USA
| | - Hiba Zein El Dine
- Department of Cell Physiology and Metabolism, Faculty of Medicine, University of Geneva, 1205 Geneva, Switzerland
| | | | - Soumaya T Obeid
- Laboratory Sciences Department, Faculty of Public Health, Islamic University of Lebanon (IUL), Khalde P.O. Box 30014, Lebanon
| | - Aya Jezzini
- Laboratory Sciences Department, Faculty of Public Health, Islamic University of Lebanon (IUL), Khalde P.O. Box 30014, Lebanon
| | - Ghassan Ghssein
- Laboratory Sciences Department, Faculty of Public Health, Islamic University of Lebanon (IUL), Khalde P.O. Box 30014, Lebanon
| | - Zeinab Ezzeddine
- Laboratory Sciences Department, Faculty of Public Health, Islamic University of Lebanon (IUL), Khalde P.O. Box 30014, Lebanon
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22
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Yang S, Chen J, Fu J, Huang J, Li T, Yao Z, Ye X. Disease-Associated Streptococcus pneumoniae Genetic Variation. Emerg Infect Dis 2024; 30:39-49. [PMID: 38146979 PMCID: PMC10756394 DOI: 10.3201/eid3001.221927] [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: 12/27/2023] Open
Abstract
Streptococcus pneumoniae is an opportunistic pathogen that causes substantial illness and death among children worldwide. The genetic backgrounds of pneumococci that cause infection versus asymptomatic carriage vary substantially. To determine the evolutionary mechanisms of opportunistic pathogenicity, we conducted a genomic surveillance study in China. We collected 783 S. pneumoniae isolates from infected and asymptomatic children. By using a 2-stage genomewide association study process, we compared genomic differences between infection and carriage isolates to address genomic variation associated with pathogenicity. We identified 8 consensus k-mers associated with adherence, antimicrobial resistance, and immune modulation, which were unevenly distributed in the infection isolates. Classification accuracy of the best k-mer predictor for S. pneumoniae infection was good, giving a simple target for predicting pathogenic isolates. Our findings suggest that S. pneumoniae pathogenicity is complex and multifactorial, and we provide genetic evidence for precise targeted interventions.
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23
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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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24
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Tian D, Zhao M, Zheng S, Jiang X, Zhang B. Involvement of Tn3 transposon in formation and transmission of hypervirulent and carbapenem-resistant Klebsiella pneumoniae. Microbiol Spectr 2023; 11:e0303823. [PMID: 37982629 PMCID: PMC10714771 DOI: 10.1128/spectrum.03038-23] [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: 08/07/2023] [Accepted: 10/14/2023] [Indexed: 11/21/2023] Open
Abstract
IMPORTANCE Carbapenem-resistant Klebsiella pneumoniae (CRKP) is resistant to most common antibiotics, becoming the most important and prevalent nosocomial opportunity pathogen. Besides, K. pneumoniae can also cause severe community-acquired infections, such as primary liver abscess and endophthalmitis. These pathogens are commonly referred to as hvKp. CRKP and hvKp have evolved separately, each occupying its own clonal lineage and exhibiting a variety of properties. Our study provides important insights into the evolutionary events related to the arousal of virulence and drug resistance in K. pneumoniae through plasmid transmission, mediated by Tn3 transposon. Our study also provides evidence that multiple mechanisms contribute to the successful transfer of non-conjugative virulence plasmid, and the involvement of transposons enhances the efficiency. A good knowledge of its transmission mechanisms is fundamental to finding effective strategies to combat these threatening pathogens. Transposons are widely present in bacteria, spreading resistance and virulence genes between the environment and humans. Therefore, emerging transposon-mediated hypervirulent and carbapenem-resistant pathogens should be highly valued.
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Affiliation(s)
- Dongxing Tian
- Department of Clinical Laboratory, Affiliated Hospital of Jining Medical University, Jining, Shandong Province, China
- Postdoctoral Mobile Station of Shandong University of Traditional Chinese Medicine, Jinan, Shandong Province, China
| | - Mingqi Zhao
- Affiliated Hospital of Jining Medical University, Jining, Shandong Province, China
| | - Sasa Zheng
- Department of Oncology, Affiliated Hospital of Jining Medical University, Jining, Shandong Province, China
| | - Xiaofei Jiang
- Department of Clinical Laboratory, Huashan Hospital, Fudan University, Shanghai, China
| | - Bin Zhang
- Department of Clinical Laboratory, Affiliated Hospital of Jining Medical University, Jining, Shandong Province, China
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25
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Bina XR, Weng Y, Budnick J, Van Allen ME, Bina JE. Klebsiella pneumoniae TolC contributes to antimicrobial resistance, exopolysaccharide production, and virulence. Infect Immun 2023; 91:e0030323. [PMID: 37982617 PMCID: PMC10715176 DOI: 10.1128/iai.00303-23] [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: 08/04/2023] [Accepted: 10/26/2023] [Indexed: 11/21/2023] Open
Abstract
Klebsiella pneumoniae is a Gram-negative bacterium that causes a variety of human diseases, ranging from pneumonia to urinary tract infections and invasive diseases. The emergence of K. pneumoniae strains that are resistant to multiple antibiotics has made treatment more complex and led to K. pneumoniae becoming a global health threat. Addressing this threat necessitates the development of new therapeutic strategies to combat this pathogen, including strategies to overcome antimicrobial resistance and therapeutics for novel targets such as antivirulence. Here, we investigated the function of TolC, an outer membrane protein essential for the function of tripartite transporters, in K. pneumoniae. Mutation of tolC rendered K. pneumoniae hypersensitive to multiple antibiotics. Moreover, the tolC mutation impaired capsule production and affected the expression of key capsule biosynthetic genes, indicating a regulatory role for TolC in capsule biosynthesis. Additionally, TolC was essential for growth under iron-limiting conditions, suggesting its involvement in iron acquisition. The tolC mutant exhibited increased adherence to human enterocytes and enhanced serum sensitivity. In the Galleria mellonella infection model, the tolC mutant displayed reduced virulence compared to the wild type. Our findings highlight the pleiotropic role of TolC in K. pneumoniae pathobiology, influencing antimicrobial resistance, capsule production, iron homeostasis, adherence to host cells, and virulence. Understanding the multifaceted role of TolC in K. pneumoniae may guide the development of new therapeutic strategies against this pathogen. .
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Affiliation(s)
- X. Renee Bina
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Yuding Weng
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - James Budnick
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Mia E. Van Allen
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - James E. Bina
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
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26
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Kochan TJ, Nozick SH, Valdes A, Mitra SD, Cheung BH, Lebrun-Corbin M, Medernach RL, Vessely MB, Mills JO, Axline CMR, Nelson JA, VanGosen EM, Ward TJ, Ozer EA, van Duin D, Chen L, Kreiswirth BN, Long SW, Musser JM, Bulman ZP, Wunderink RG, Hauser AR. Klebsiella pneumoniae clinical isolates with features of both multidrug-resistance and hypervirulence have unexpectedly low virulence. Nat Commun 2023; 14:7962. [PMID: 38042959 PMCID: PMC10693551 DOI: 10.1038/s41467-023-43802-1] [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: 07/07/2023] [Accepted: 11/21/2023] [Indexed: 12/04/2023] Open
Abstract
Klebsiella pneumoniae has been classified into two types, classical K. pneumoniae (cKP) and hypervirulent K. pneumoniae (hvKP). cKP isolates are highly diverse and important causes of nosocomial infections; they include globally disseminated antibiotic-resistant clones. hvKP isolates are sensitive to most antibiotics but are highly virulent, causing community-acquired infections in healthy individuals. The virulence phenotype of hvKP is associated with pathogenicity loci responsible for siderophore and hypermucoid capsule production. Recently, convergent strains of K. pneumoniae, which possess features of both cKP and hvKP, have emerged and are cause of much concern. Here, we screen the genomes of 2,608 multidrug-resistant K. pneumoniae isolates from the United States and identify 47 convergent isolates. We perform phenotypic and genomic characterization of 12 representative isolates. These 12 convergent isolates contain a variety of antimicrobial resistance plasmids and virulence plasmids. Most convergent isolates contain aerobactin biosynthesis genes and produce more siderophores than cKP isolates but not more capsule. Unexpectedly, only 1 of the 12 tested convergent isolates has a level of virulence consistent with hvKP isolates in a murine pneumonia model. These findings suggest that additional studies should be performed to clarify whether convergent strains are indeed more virulent than cKP in mouse and human infections.
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Affiliation(s)
- Travis J Kochan
- Laboratory of Respiratory and Special Pathogens, Division of Bacterial, Parasitic, and Allergenic Products, Office of Vaccines Research and Review, Center for Biologics Evaluation and Research, Food and Drug Administration, Silver Spring, MD, USA.
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA.
| | - Sophia H Nozick
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Aliki Valdes
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Sumitra D Mitra
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Bettina H Cheung
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Marine Lebrun-Corbin
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Rachel L Medernach
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Madeleine B Vessely
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Jori O Mills
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Christopher M R Axline
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Julia A Nelson
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Ethan M VanGosen
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Timothy J Ward
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Egon A Ozer
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - David van Duin
- Division of Infectious Diseases, University of North Carolina, Chapel Hill, NC, USA
| | - Liang Chen
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - Barry N Kreiswirth
- Center for Discovery and Innovation, Hackensack Meridian Health, Nutley, NJ, USA
| | - S Wesley Long
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital Research Institute, Houston, TX, USA
| | - James M Musser
- Department of Pathology and Genomic Medicine, Houston Methodist Hospital Research Institute, Houston, TX, USA
| | - Zackery P Bulman
- College of Pharmacy, University of Illinois at Chicago, Chicago, IL, USA
| | - Richard G Wunderink
- Division of Pulmonary and Critical Care Medicine, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Simpson Querrey Institute for Epigenetics, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
| | - Alan R Hauser
- Department of Microbiology-Immunology, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
- Division of Infectious Diseases, Department of Medicine, Feinberg School of Medicine, Northwestern University, Chicago, IL, USA
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27
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Mendes G, Santos ML, Ramalho JF, Duarte A, Caneiras C. Virulence factors in carbapenem-resistant hypervirulent Klebsiella pneumoniae. Front Microbiol 2023; 14:1325077. [PMID: 38098668 PMCID: PMC10720631 DOI: 10.3389/fmicb.2023.1325077] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Accepted: 11/16/2023] [Indexed: 12/17/2023] Open
Abstract
Hypervirulence and carbapenem-resistant have emerged as two distinct evolutionary pathotypes of Klebsiella pneumoniae, with both reaching their epidemic success and posing a great threat to public health. However, as the boundaries separating these two pathotypes fade, we assist a worrisome convergence in certain high-risk clones, causing hospital outbreaks and challenging every therapeutic option available. To better understand the basic biology of these pathogens, this review aimed to describe the virulence factors and their distribution worldwide among carbapenem-resistant highly virulent or hypervirulent K. pneumoniae strains, as well as to understand the interplay of these virulence strains with the carbapenemase produced and the sequence type of such strains. As we witness a shift in healthcare settings where carbapenem-resistant highly virulent or hypervirulent K. pneumoniae are beginning to emerge and replace classical K. pneumoniae strains, a better understanding of these strains is urgently needed for immediate and appropriate response.
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Affiliation(s)
- Gabriel Mendes
- Microbiology Research Laboratory on Environmental Health, Institute of Environmental Health (ISAMB), Associate Laboratory TERRA, Faculty of Medicine, Universidade de Lisboa, Lisbon, Portugal
| | - Maria Leonor Santos
- Microbiology Research Laboratory on Environmental Health, Institute of Environmental Health (ISAMB), Associate Laboratory TERRA, Faculty of Medicine, Universidade de Lisboa, Lisbon, Portugal
| | - João F. Ramalho
- Microbiology Research Laboratory on Environmental Health, Institute of Environmental Health (ISAMB), Associate Laboratory TERRA, Faculty of Medicine, Universidade de Lisboa, Lisbon, Portugal
| | - Aida Duarte
- Faculty of Pharmacy, Universidade de Lisboa, Lisbon, Portugal
- Egas Moniz Center for Interdisciplinary Research, Egas Moniz School of Health and Science, Almada, Portugal
| | - Cátia Caneiras
- Microbiology Research Laboratory on Environmental Health, Institute of Environmental Health (ISAMB), Associate Laboratory TERRA, Faculty of Medicine, Universidade de Lisboa, Lisbon, Portugal
- Egas Moniz Center for Interdisciplinary Research, Egas Moniz School of Health and Science, Almada, Portugal
- Institute of Preventive Medicine and Public Health, Faculty of Medicine, Universidade de Lisboa, Lisbon, Portugal
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Zhou C, Zhang H, Xu M, Liu Y, Yuan B, Lin Y, Shen F. Within-Host Resistance and Virulence Evolution of a Hypervirulent Carbapenem-Resistant Klebsiella pneumoniae ST11 Under Antibiotic Pressure. Infect Drug Resist 2023; 16:7255-7270. [PMID: 38023413 PMCID: PMC10658960 DOI: 10.2147/idr.s436128] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 11/07/2023] [Indexed: 12/01/2023] Open
Abstract
Background Hypervirulent carbapenem-resistant Klebsiella pneumoniae (hv-CRKP) has recently aroused an extremely severe health challenge and public concern. However, the underlying mechanisms of fitness costs that accompany antibiotic resistance acquisition remain largely unexplored. Here, we report a hv-CRKP-associated fatal infection and reveal a reduction in virulence due to the acquisition of aminoglycoside resistance. Methods The bacterial identification, antimicrobial susceptibility, hypermucoviscosity, virulence factors, MLST and serotypes were profiled.The clonal homology and plasmid acquisition among hv-CRKP strains were detected by XbaI and S1-PFGE. The virulence potential of the strains was evaluated using Galleria mellonella larvae infection model, serum resistance assay, capsular polysaccharide quantification, and biofilm formation assay. Genomic variations were identified using whole-genome sequencing (WGS). Results Four K. pneumoniae carbapenemase (KPC)-producing CRKP strains were consecutively isolated from an 86-year-old patient with severe pneumonia. Whole-genome sequencing (WGS) showed that all four hv-CRKP strains belonged to the ST11-KL64 clone. PFGE analysis revealed that the four ST11-KL64 hv-CRKP strains could be grouped into the same PFGE type. Under the pressure of antibiotics, the antimicrobial resistance of the strains increased and the virulence potential decreased. Further sequencing, using the Nanopore platform, was performed on three representative isolates (WYKP586, WYKP589, and WYKP594). Genomic analysis showed that the plasmids of these three strains underwent a large number of breaks and recombination events under antibiotic pressure. We found that as aminoglycoside resistance emerged via acquisition of the rmtB gene, the hypermucoviscosity and virulence of the strains decreased because of internal mutations in the rmpA and rmpA2 genes. Conclusion This study shows that ST11-KL64 hv-CRKP can further evolve to acquire aminoglycoside resistance accompanied by decreased virulence to adapt to antibiotic pressure in the host.
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Affiliation(s)
- Cong Zhou
- Department of Clinical Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, People’s Republic of China
| | - Hui Zhang
- Department of Clinical Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, People’s Republic of China
| | - Maosuo Xu
- Department of Clinical Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, People’s Republic of China
| | - Yajuan Liu
- Department of Clinical Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, People’s Republic of China
| | - Baoyu Yuan
- Department of Clinical Laboratory, Shanghai Children’s Hospital, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yong Lin
- Department of Clinical Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, People’s Republic of China
| | - Fang Shen
- Department of Clinical Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, People’s Republic of China
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Pu D, Zhao J, Chang K, Zhuo X, Cao B. "Superbugs" with hypervirulence and carbapenem resistance in Klebsiella pneumoniae: the rise of such emerging nosocomial pathogens in China. Sci Bull (Beijing) 2023; 68:2658-2670. [PMID: 37821268 DOI: 10.1016/j.scib.2023.09.040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Revised: 08/19/2023] [Accepted: 09/26/2023] [Indexed: 10/13/2023]
Abstract
Although hypervirulent Klebsiella pneumoniae (hvKP) can produce community-acquired infections that are fatal in young and adult hosts, such as pyogenic liver abscess, endophthalmitis, and meningitis, it has historically been susceptible to antibiotics. Carbapenem-resistant K. pneumoniae (CRKP) is usually associated with urinary tract infections acquired in hospitals, pneumonia, septicemias, and soft tissue infections. Outbreaks and quick spread of CRKP in hospitals have become a major challenge in public health due to the lack of effective antibacterial treatments. In the early stages of K. pneumoniae development, HvKP and CRKP first appear as distinct routes. However, the lines dividing the two pathotypes are vanishing currently, and the advent of carbapenem-resistant hypervirulent K. pneumoniae (CR-hvKP) is devastating as it is simultaneously multidrug-resistant, hypervirulent, and highly transmissible. Most CR-hvKP cases have been reported in Asian clinical settings, particularly in China. Typically, CR-hvKP develops when hvKP or CRKP acquires plasmids that carry either the carbapenem-resistance gene or the virulence gene. Alternatively, classic K. pneumoniae (cKP) may acquire a hybrid plasmid carrying both genes. In this review, we provide an overview of the key antimicrobial resistance mechanisms, virulence factors, clinical presentations, and outcomes associated with CR-hvKP infection. Additionally, we discuss the possible evolutionary processes and prevalence of CR-hvKP in China. Given the wide occurrence of CR-hvKP, continued surveillance and control measures of such organisms should be assigned a higher priority.
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Affiliation(s)
- Danni Pu
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100730, China; Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing 100029, China; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing 100029, China
| | - Jiankang Zhao
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing 100029, China; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing 100029, China
| | - Kang Chang
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing 100029, China; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing 100029, China
| | - Xianxia Zhuo
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing 100029, China; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing 100029, China; Department of Pulmonary and Critical Care Medicine, Capital Medical University, Beijing 100069, China
| | - Bin Cao
- Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing 100730, China; Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing 100029, China; Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing 100029, China; Department of Pulmonary and Critical Care Medicine, Capital Medical University, Beijing 100069, China; Tsinghua University-Peking University Joint Center for Life Sciences, Beijing 100084, China.
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Byarugaba DK, Erima B, Wokorach G, Alafi S, Kibuuka H, Mworozi E, Najjuka F, Kiyengo J, Musinguzi AK, Wabwire-Mangen F. Genome Analysis of Klebsiella pneumoniae Reveals International High-Risk Pandemic MDR Clones Emerging in Tertiary Healthcare Settings in Uganda. Pathogens 2023; 12:1334. [PMID: 38003798 PMCID: PMC10674604 DOI: 10.3390/pathogens12111334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Revised: 10/14/2023] [Accepted: 10/26/2023] [Indexed: 11/26/2023] Open
Abstract
Klebsiella pneumoniae is a threat to public health due to its continued evolution. In this study, we investigated the evolution, convergence, and transmission of hypervirulent and multi-drug resistant (MDR) clones of K. pneumoniae within healthcare facilities in Uganda. There was high resistance to piperacillin (90.91%), cefuroxime (86.96%), ceftazidime (84.62%), cefotaxime (84.00%), amoxicillin/clavulanate (75%), nalidixic acid (73.68%), and nitrofurantoin (71.43%) antibiotics among K. pneumoniae isolates. The isolates were genetically diverse, consisting of 20 different sequence types (STs) and 34 K-serotype groups. Chromosomal fosA (for fosfomycin) and oqxAB efflux pump genes were detected in all isolates. Two carbapenem resistance genes, blaNDM-5 and blaOXA-181 plus extended-spectrum beta-lactamase (blaCTX-M-15) gene (68.12%), quinolone-resistant genes qnrS1 (28.99%), qnrB1 (13.04%), and qnrB6 (13.04%) and others were found. All, except three of the isolates, harbored plasmids. While the isolates carried a repertoire of virulence genes, only two isolates carried hypervirulent genes demonstrating a low prevalence (2.90%) of hypervirulent strains. Our study demonstrated genetically diverse populations of K. pneumoniae, low levels of carbapenem resistance among the isolates, and no convergence of MDR and hypervirulence. Emerging high-risk international pandemic clones (ST11, ST14, ST147, ST 86 and ST307) were detected in these healthcare settings which are difficult to treat.
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Affiliation(s)
- Denis K. Byarugaba
- Makerere University Walter Reed Project, Kampala P.O. Box 16524, Uganda; (B.E.); (G.W.); (S.A.); (H.K.); (E.M.); (F.W.-M.)
- College of Veterinary Medicine, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Bernard Erima
- Makerere University Walter Reed Project, Kampala P.O. Box 16524, Uganda; (B.E.); (G.W.); (S.A.); (H.K.); (E.M.); (F.W.-M.)
| | - Godfrey Wokorach
- Makerere University Walter Reed Project, Kampala P.O. Box 16524, Uganda; (B.E.); (G.W.); (S.A.); (H.K.); (E.M.); (F.W.-M.)
- Multifunctional Research Laboratories, Gulu University, Gulu P.O. Box 166, Uganda
| | - Stephen Alafi
- Makerere University Walter Reed Project, Kampala P.O. Box 16524, Uganda; (B.E.); (G.W.); (S.A.); (H.K.); (E.M.); (F.W.-M.)
| | - Hannah Kibuuka
- Makerere University Walter Reed Project, Kampala P.O. Box 16524, Uganda; (B.E.); (G.W.); (S.A.); (H.K.); (E.M.); (F.W.-M.)
- College of Veterinary Medicine, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Edison Mworozi
- Makerere University Walter Reed Project, Kampala P.O. Box 16524, Uganda; (B.E.); (G.W.); (S.A.); (H.K.); (E.M.); (F.W.-M.)
- College of Health Sciences, Makerere University, Kampala P.O. Box 7062, Uganda;
| | - Florence Najjuka
- College of Health Sciences, Makerere University, Kampala P.O. Box 7062, Uganda;
| | - James Kiyengo
- Uganda Peoples’ Defence Forces, Ministry of Defence, Kampala P.O. Box 3798, Uganda; (J.K.); (A.K.M.)
| | - Ambrose K. Musinguzi
- Uganda Peoples’ Defence Forces, Ministry of Defence, Kampala P.O. Box 3798, Uganda; (J.K.); (A.K.M.)
| | - Fred Wabwire-Mangen
- Makerere University Walter Reed Project, Kampala P.O. Box 16524, Uganda; (B.E.); (G.W.); (S.A.); (H.K.); (E.M.); (F.W.-M.)
- College of Health Sciences, Makerere University, Kampala P.O. Box 7062, Uganda;
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Haddadi MH, Khoshnood S, Koupaei M, Heidary M, Moradi M, Jamshidi A, Behrouj H, Movahedpour A, Maleki MH, Ghanavati R. Evaluating the incidence of ampC-β-lactamase genes, biofilm formation, and antibiotic resistance among hypervirulent and classical Klebsiella pneumoniae strains. J Appl Microbiol 2023; 134:lxad241. [PMID: 37881066 DOI: 10.1093/jambio/lxad241] [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: 07/07/2023] [Revised: 09/18/2023] [Accepted: 10/21/2023] [Indexed: 10/27/2023]
Abstract
AIM Both immunocompetent and healthy individuals can become life-threateningly ill when exposed to the hypervirulent (hvKp) strains of Klebsiella pneumoniae (Kp). The main objectives of this study were to evaluate the presence of ampC-lactamase genes, biofilm formation, and antibiotic resistance in clinical strains of hvKp and cKp (classical K. pneumoniae). MATERIALS AND METHODS Kp strains were collected from patients referred to Shahidzadeh Hospital in Behbahan City, Khuzestan Province, Iran. Several techniques were used to identify hvKp. The hypermucoviscosity phenotype was determined using the string test. Isolates that developed dark colonies on tellurite agar were assumed to be hvKp strains. If any of the iucA, iutA, or peg-344 genes were detected, the isolates were classified as hvKp. Phenotypic and genotypic detection of AmpC β-lactamases of hvKp strains was performed by the combined disk method and polymerase chain reaction, respectively. In addition, crystal violet staining was used to determine the biofilm formation of these isolates. RESULTS For this study, 76 non-duplicative isolates of Kp were collected. Overall, 22 (28.94%) strains had positive string test results, and 31 (40.78%) isolates were grown in tellurite-containing medium. The genes iucA and iutA or peg-344 were found in 23.68% of all Kp strains and in 50% of tellurite-resistant isolates, respectively. The most effective antibiotics against hvKp isolates were tetracycline (85.52%) and chloramphenicol (63.15%). Using the cefoxitin disc diffusion method, we observed that 56.57% (43/76) of the strains were AmpC producer. A total of 30.26% (n = 23/76) of the isolates tested positive for at least one ampC gene, including blaDHA (52.63%, n = 40), blaCIT (40.78%, n = 31), blaACC (19.76%, n = 15), blaMOX (25%, n = 19), and blaFOX (43.42%, n = 33). Biofilm formation analysis revealed that most hvKp isolates were weak (n = 6, 40%) and moderate (n = 5, 33.33%) biofilm producers. CONCLUSION Healthcare practitioners should consider the possibility of the existence and acquisition of hvKp everywhere. The exact mechanisms of bacterial acquisition are also unknown, and it is unclear whether the occurrence of infections is related to healthcare or not. Thus, there are still many questions about hvKp that need to be investigated.
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Affiliation(s)
| | - Saeed Khoshnood
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam 69316, Iran
| | - Maryam Koupaei
- Department of Microbiology and Immunology, School of Medicine, Kashan University of Medical Sciences, Kashan 8759187131, Iran
| | - Mohsen Heidary
- Department of Laboratory Sciences, School of Paramedical Sciences, Sabzevar University of Medical Sciences, Sabzevar 6971938668 , Iran
| | - Melika Moradi
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz 6136763316, Iran
| | - Ali Jamshidi
- Behbahan Faculty of Medical Sciences, Behbahan 6361796819, Iran
| | - Hamid Behrouj
- Behbahan Faculty of Medical Sciences, Behbahan 6361796819, Iran
| | | | - Mohammad Hassan Maleki
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam 69316, Iran
| | - Roya Ghanavati
- School of Paramedical Sciences, Behbahan Faculty of Medical Sciences, Behbahan 63617, Iran
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Ikhimiukor OO, Souza SSR, Akintayo IJ, Marcovici MM, Workman A, Martin IW, Andam CP. Phylogenetic lineages and antimicrobial resistance determinants of clinical Klebsiella oxytoca spanning local to global scales. Microbiol Spectr 2023; 11:e0054923. [PMID: 37676032 PMCID: PMC10581156 DOI: 10.1128/spectrum.00549-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 07/19/2023] [Indexed: 09/08/2023] Open
Abstract
Klebsiella oxytoca is an opportunistic pathogen causing serious nosocomial infections. Knowledge about the population structure and diversity of healthcare-associated K. oxytoca from a genomic standpoint remains limited. Here, we characterized the phylogenetic relationships and genomic characteristics of 20 K. oxytoca sensu stricto isolates recovered from bloodstream infections at the Dartmouth-Hitchcock Medical Center, New Hampshire, USA from 2017 to 2021. Results revealed a diverse population consisting of 15 sequence types (STs) that together harbored 10 variants of the intrinsic beta-lactamase gene bla OXY-2, conferring resistance to penicillins. Similar sets of antimicrobial resistance (AMR) determinants reside in multiple distinct lineages, with no one lineage dominating the local population. To place the New Hampshire K. oxytoca in a broader context, we compared them to 304 publicly available genomes of clinical isolates from 18 countries. This global clinical K. oxytoca sensu stricto population is represented by over 65 STs that together harbored resistance genes against 14 antimicrobial classes, including eight bla OXY-2 variants. Three dominant STs in the global population (ST2, ST176, ST199) circulate across multiple countries and were also present in the New Hampshire population. The global K. oxytoca population is genetically diverse, but there is evidence for broad dissemination of a few lineages carrying distinct set of AMR determinants. Our findings reveal the clinical diversity of K. oxytoca sensu stricto and its importance in surveillance efforts aimed at monitoring the evolution of this drug-resistant nosocomial pathogen. IMPORTANCE The opportunistic pathogen Klebsiella oxytoca has been increasingly implicated in patient morbidity and mortality worldwide, including several outbreaks in healthcare settings. The emergence and spread of antimicrobial resistant strains exacerbate the disease burden caused by this species. Our study showed that clinical K. oxytoca sensu stricto is phylogenetically diverse, harboring various antimicrobial resistance determinants and bla OXY-2 variants. Understanding the genomic and population structure of K. oxytoca is important for international initiatives and local epidemiological efforts for surveillance and control of drug-resistant K. oxytoca.
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Affiliation(s)
- Odion O. Ikhimiukor
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Stephanie S. R. Souza
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Ifeoluwa J. Akintayo
- Institute for Infection Prevention and Hospital Epidemiology, Medical Centre, University of Freiburg, Freiburg, Germany
| | - Michael M. Marcovici
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
| | - Adrienne Workman
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Isabella W. Martin
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, New Hampshire, USA
| | - Cheryl P. Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, New York, USA
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Hazen TH, Adediran T, Hitchcock S, O’Hara LM, Pineles L, Michalski JM, Johnson JK, Nguyen MH, Calfee DP, Miller LG, Harris AD, Rasko DA. Clinical and Bacterial Characteristics Associated with Glove and Gown Contamination by Carbapenem-Resistant Klebsiella pneumoniae in the Health Care Setting. Microbiol Spectr 2023; 11:e0177523. [PMID: 37289087 PMCID: PMC10434059 DOI: 10.1128/spectrum.01775-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 05/17/2023] [Indexed: 06/09/2023] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKp) is a pathogen of significant concern to public health, as it has become increasingly associated with difficult-to-treat community-acquired and hospital-associated infections. Transmission of K. pneumoniae between patients through interactions with shared health care personnel (HCP) has been described as a source of infection in health care settings. However, it is not known whether specific lineages or isolates of K. pneumoniae are associated with increased transmission. Thus, we used whole-genome sequencing to analyze the genetic diversity of 166 carbapenem-resistant K. pneumoniae isolates from five U.S. hospitals in four states as part of a multicenter study examining risk factors for glove and gown contamination by carbapenem-resistant Enterobacterales (CRE). The CRKp isolates exhibited considerable genomic diversity with 58 multilocus sequence types (STs), including four newly designated STs. ST258 was the most prevalent ST, representing 31% (52/166) of the CRKp isolates, but was similarly prevalent among patients who had high, intermediate, and low CRKp transmission. Increased transmission was associated with clinical characteristics including a nasogastric (NG) tube or an endotracheal tube or tracheostomy (ETT/Trach). Overall, our findings provide important insight into the diversity of CRKp associated with transmission from patients to the gloves and gowns of HCP. These findings suggest that certain clinical characteristics and the presence of CRKp in the respiratory tract, rather than specific lineages or genetic content, are more often associated with increased transmission of CRKp from patients to HCP. IMPORTANCE Carbapenem-resistant Klebsiella pneumoniae (CRKp) is a significant public health concern that has contributed to the spread of carbapenem resistance and has been linked to high morbidity and mortality. Transmission of K. pneumoniae among patients through interactions with shared health care personnel (HCP) has been described as a source of infection in health care settings; however, it remains unknown whether particular bacterial characteristics are associated with increased CRKp transmission. Using comparative genomics, we demonstrate that CRKp isolates associated with high or intermediate transmission exhibit considerable genomic diversity, and there were no K. pneumoniae lineages or genes that were universally predictive of increased transmission. Our findings suggest that certain clinical characteristics and the presence of CRKp, rather than specific lineages or genetic content of CRKp, are more often associated with increased transmission of CRKp from patients to HCP.
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Affiliation(s)
- Tracy H. Hazen
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Timileyin Adediran
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Stephanie Hitchcock
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Lyndsay M. O’Hara
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Lisa Pineles
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - Jane M. Michalski
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - J. Kristie Johnson
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - M. Hong Nguyen
- Department of Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania, USA
| | - David P. Calfee
- Division of Infectious Diseases, Weill Cornell Medicine, New York, New York, USA
| | - Loren G. Miller
- Lundquist Institute at Harbor-UCLA Medical Center, Torrance, California, USA
| | - Anthony D. Harris
- Department of Epidemiology and Public Health, University of Maryland School of Medicine, Baltimore, Maryland, USA
| | - David A. Rasko
- Institute for Genome Sciences, University of Maryland School of Medicine, Baltimore, Maryland, USA
- Department of Microbiology and Immunology, University of Maryland School of Medicine, Baltimore, Maryland, USA
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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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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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Alkompoz AK, Hamed SM, Zaid ASA, Almangour TA, Al-Agamy MH, Aboshanab KM. Correlation of CRISPR/Cas and Antimicrobial Resistance in Klebsiella pneumoniae Clinical Isolates Recovered from Patients in Egypt Compared to Global Strains. Microorganisms 2023; 11:1948. [PMID: 37630508 PMCID: PMC10459600 DOI: 10.3390/microorganisms11081948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023] Open
Abstract
The CRISPR/Cas system has been long known to interfere with the acquisition of foreign genetic elements and was recommended as a tool for fighting antimicrobial resistance. The current study aimed to explore the prevalence of the CRISPR/Cas system in Klebsiella pneumoniae isolates recovered from patients in Egypt in comparison to global strains and correlate the CRISPR/Cas to susceptibility to antimicrobial agents. A total of 181 clinical isolates were PCR-screened for cas and selected antimicrobial resistance genes (ARGs). In parallel, 888 complete genome sequences were retrieved from the NCBI database for in silico analysis. CRISPR/Cas was found in 46 (25.4%) isolates, comprising 18.8% type I-E and 6.6% type I-E*. Multidrug resistance (MDR) and extensive drug resistance (XDR) were found in 73.5% and 25.4% of the isolates, respectively. More than 95% of the CRISPR/Cas-bearing isolates were MDR (65.2%) or XDR (32.6%). No significant difference was found in the susceptibility to the tested antimicrobial agents among the CRISPR/Cas-positive and -negative isolates. The same finding was obtained for the majority of the screened ARGs. Among the published genomes, 23.2% carried CRISPR/Cas, with a higher share of I-E* (12.8%). They were confined to specific sequence types (STs), most commonly ST147, ST23, ST15, and ST14. More plasmids and ARGs were carried by the CRISPR/Cas-negative group than others, but their distribution in the two groups was not significantly different. The prevalence of some ARGs, such as blaKPC, blaTEM, and rmtB, was significantly higher among the genomes of the CRISPR/Cas-negative strains. A weak, nonsignificant positive correlation was found between the number of spacers and the number of resistance plasmids and ARGs. In conclusion, the correlation between CRISPR/Cas and susceptibility to antimicrobial agents or bearing resistance plasmids and ARGs was found to be nonsignificant. Plasmid-targeting spacers might not be naturally captured by CRISPR/Cas. Spacer match analysis is recommended to provide a clearer image of the exact behavior of CRISPR/Cas towards resistance plasmids.
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Affiliation(s)
| | - Samira M. Hamed
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), 6th of October, Giza 12451, Egypt;
| | - Ahmed S. Abu Zaid
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt;
| | - Thamer A. Almangour
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Mohamed H. Al-Agamy
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Cairo 11651, Egypt
| | - Khaled M. Aboshanab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt;
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Tsui CKM, Ben Abid F, Al Ismail K, McElheny CL, Al Maslamani M, Omrani AS, Doi Y. Genomic Epidemiology of Carbapenem-Resistant Klebsiella in Qatar: Emergence and Dissemination of Hypervirulent Klebsiella pneumoniae Sequence Type 383 Strains. Antimicrob Agents Chemother 2023; 67:e0003023. [PMID: 37310284 PMCID: PMC10353355 DOI: 10.1128/aac.00030-23] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2023] [Accepted: 05/23/2023] [Indexed: 06/14/2023] Open
Abstract
The emergence of carbapenem-resistant, hypervirulent Klebsiella pneumoniae is a new threat to health care. We studied the molecular epidemiology of carbapenem-resistant Klebsiella pneumoniae isolates in Qatar using whole-genome sequence data. We also characterized the prevalence and genetic basis of hypervirulent phenotypes and established the virulence potential using a Galleria mellonella model. Of 100 Klebsiella isolates studied, NDM and OXA-48 were the most common carbapenemases. Core genome single-nucleotide polymorphism (SNP) analysis indicated the presence of diverse sequence types and clonal lineages; isolates belonging to Klebsiella quasipneumoniae subsp. quasipneumoniae sequence type 196 (ST196) and ST1416 may be disseminated among several health care centers. Ten K. pneumoniae isolates carried rmpA and/or truncated rmpA2, and 2 isolates belonged to KL2, indicating low prevalence of classical hypervirulent isolates. Isolates carrying both carbapenem resistance and hypervirulence genes were confined mainly to ST231 and ST383 isolates. One ST383 isolate was further investigated by MinION sequencing, and the assembled genome indicated that blaNDM was located on an IncHI1B-type plasmid (pFQ61_ST383_NDM-5) which coharbored several virulence factors, including the regulator of the mucoid phenotype (rmpA), the regulator of mucoid phenotype 2 (rmpA2), and aerobactin (iucABCD and iutA), likely resulting from recombination events. Comparative genomics indicated that this hybrid plasmid may be present in two additional Qatari ST383 isolates. Carbapenem-resistant, hypervirulent K. pneumoniae ST383 isolates pose an emerging threat to global health due to their simultaneous hypervirulence and multidrug resistance.
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Affiliation(s)
- Clement Kin-Ming Tsui
- Infectious Diseases Research Laboratory, National Centre for Infectious Diseases, Tan Tock Seng Hospital, Singapore, Singapore
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore, Singapore
- Division of Infectious Diseases, Faculty of Medicine, University of British Columbia, Vancouver, Canada
- Weill Cornell Medicine—Qatar, Doha, Qatar
| | - Fatma Ben Abid
- Weill Cornell Medicine—Qatar, Doha, Qatar
- Communicable Diseases Center, Hamad Medical Corporation, Doha, Qatar
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Khalil Al Ismail
- Communicable Diseases Center, Hamad Medical Corporation, Doha, Qatar
| | - Christi Lee McElheny
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Muna Al Maslamani
- Communicable Diseases Center, Hamad Medical Corporation, Doha, Qatar
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha, Qatar
| | - Ali S. Omrani
- Communicable Diseases Center, Hamad Medical Corporation, Doha, Qatar
- Division of Infectious Diseases, Department of Medicine, Hamad Medical Corporation, Doha, Qatar
- College of Medicine, Qatar University, Doha, Qatar
| | - Yohei Doi
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Japan
- Department of Infectious Diseases, Fujita Health University School of Medicine, Toyoake, Japan
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38
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Crippa C, Pasquali F, Rodrigues C, De Cesare A, Lucchi A, Gambi L, Manfreda G, Brisse S, Palma F. Genomic features of Klebsiella isolates from artisanal ready-to-eat food production facilities. Sci Rep 2023; 13:10957. [PMID: 37414963 PMCID: PMC10326032 DOI: 10.1038/s41598-023-37821-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/27/2023] [Indexed: 07/08/2023] Open
Abstract
Increasing reports on K. pneumoniae strains with antimicrobial resistance and virulence traits from food and farm animals are raising concerns about the potential role of Klebsiella spp. as a foodborne pathogen. This study aimed to report and characterize Klebsiella spp. isolates from two artisanal ready-to-eat food (soft cheese and salami) producing facilities, and to track similar genotypes in different ecological niches. Over 1170 samples were collected during the whole production chain of different food batches. The overall Klebsiella prevalence was 6%. Strains were classified into the three Klebsiella species complexes: K. pneumoniae (KpSC, n = 17), K. oxytoca (KoSC, n = 38) and K. planticola (KplaSC, n = 18). Despite high genetic diversity we found in terms of known and new sequence types (STs), core genome phylogeny revealed clonal strains persisting in the same processing setting for over 14 months, isolated from the environment, raw materials and end-products. Strains showed a natural antimicrobial resistance phenotype-genotype. K. pneumoniae strains showed the highest virulence potential, with sequence types ST4242 and ST107 strains carrying yersiniabactin ybt16 and aerobactin iuc3. The latter was detected in all K. pneumoniae from salami and was located on a large conjugative plasmid highly similar (97% identity) to iuc3+ plasmids from human and pig strains circulating in nearby regions of Italy. While identical genotypes may persist along the whole food production process, different genotypes from distinct sources in the same facility shared an iuc3-plasmid. Surveillance in the food chain will be crucial to obtain a more comprehensive picture of the circulation of Klebsiella strains with pathogenic potential.
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Affiliation(s)
- Cecilia Crippa
- Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, Ozzano dell'Emilia, 40064, Bologna, Italy.
| | - Frédérique Pasquali
- Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Carla Rodrigues
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Alessandra De Cesare
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Ozzano Dell'Emilia, 40064, Bologna, Italy
| | - Alex Lucchi
- Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Lucia Gambi
- Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Gerardo Manfreda
- Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Sylvain Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Université Paris Cité, 75015, Paris, France
- Biological Resource Center of Institut Pasteur, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Federica Palma
- Biological Resource Center of Institut Pasteur, Institut Pasteur, Université Paris Cité, 75015, Paris, France
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Prince A, Wong Fok Lung T. Immunometabolic control by Klebsiella pneumoniae. IMMUNOMETABOLISM (COBHAM, SURREY) 2023; 5:e00028. [PMID: 37492184 PMCID: PMC10364963 DOI: 10.1097/in9.0000000000000028] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/14/2023] [Accepted: 06/27/2023] [Indexed: 07/27/2023]
Abstract
Klebsiella pneumoniae is a common Gram-negative pathogen associated with community-acquired and healthcare-associated infections. Its ability to acquire genetic elements resulted in its rapid development of resistance to virtually all antimicrobial agents. Once infection is established, K. pneumoniae is able to evade the host immune response and perhaps more importantly, undergo metabolic rewiring to optimize its ability to maintain infection. K. pneumoniae lipopolysaccharide and capsular polysaccharide are central factors in the induction and evasion of immune clearance. Less well understood is the importance of immunometabolism, the intersection between cellular metabolism and immune function, in the host response to K. pneumoniae infection. Bacterial metabolism itself is perceived as a metabolic stress to the host, altering the microenvironment at the site of infection. In this review, we will discuss the metabolic responses induced by K. pneumoniae, particularly in response to stimulation with the metabolically active bacteria versus pathogen-associated molecular patterns alone, and their implications in shaping the nature of the immune response and the infection outcome. A better understanding of the immunometabolic response to K. pneumoniae may help identify new targets for therapeutic intervention in the treatment of multidrug-resistant bacterial infections.
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Affiliation(s)
- Alice Prince
- Department of Pediatrics, Columbia University, New York, NY, USA
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40
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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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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: 16] [Impact Index Per Article: 16.0] [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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Yin L, Yan G, Lu L, He L, Wu N, Cao Y, Lu G, Zhai X, Wang C. Molecular characteristics and virulence factors of carbapenem-resistant Klebsiella pneumoniae among pediatric patients in Shanghai, China. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2023; 112:105451. [PMID: 37230160 DOI: 10.1016/j.meegid.2023.105451] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/09/2023] [Revised: 05/09/2023] [Accepted: 05/22/2023] [Indexed: 05/27/2023]
Abstract
We retrospectively investigated CRKP isolates among 92 pediatric patients (32 neonates and 60 non‑neonates) in 2019 and 2020 (59 and 33 isolates, respectively) to investigate the molecular characteristics and virulence factors of carbapenem-resistant Klebsiella pneumoniae (CRKP) isolated from pediatric patients,. All the CRKP isolates were subjected to antimicrobial susceptibility testing, string testing, molecular typing of virulence and carbapenemase genes, and multilocus sequence typing. Hypervirulent K. pneumoniae (Hvkp) was defined based on the detection of the regulator of mucoid phenotype A (rmpA).Sequence type 11 (ST11) accounted for the majority of infections in both neonates (37.5%) and non‑neonates (43.3%) (P > 0.05), whereas it increased from 30.5% (18/59) in 2019 to 60.6% (20/33) in 2020 (P < 0.05). Carbapenemase gene KPC-2 was predominant in both neonates and non‑neonates (46.9% vs. 51.7%, respectively), followed by New Delhi metallo-beta-lactamase 1 (NDM-1) (34.4% vs. 28.3%, respectively) (all P > 0.05). Compared to 2019, the proportion of blaNDM-1 decreased (44.1% vs. 6.1%) (P < 0.001), while that of blaKPC-2 increased (40.7% vs. 66.7%) (P = 0.017) in 2020. ybtS and iutA had a higher positivity rate in KPC-2 and ST11 producers (all P < 0.05); the KPC-2-, ybtS-, and iutA-positive isolates showed relatively higher resistance to fluoroquinolones and aminoglycosides, nitrofurantoin, and piperacillin/tazobactam, respectively. Furthermore, the combined expression (95.7%, 88/92) of carbapenemase and virulence-associated genes was detected, with the carbapenemase genes blaKPC-2 and blaTEM-1 combined with virulence-associated genes entB, mrkD, and ybtS accounting for the highest percentage (20.7%).Carbapenemase gene mutations in the CRKP strain from 2019 to 2020 highlight the importance of dynamic monitoring. The spread of hypervirulence-associated genes in CRKP strains and the high positivity rates of ybtS and iutA in KPC-2- and ST11-producing ones signify their high virulence potential in pediatric patients.
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Affiliation(s)
- Lijun Yin
- Department of Nosocomial Infection Control, Children's Hospital of Fudan University, Shanghai, China
| | - Gangfeng Yan
- Department of Pediatric Intensive Care Unit, Children's Hospital of Fudan University, Shanghai, China
| | - Lu Lu
- Department of Nosocomial Infection Control, Children's Hospital of Fudan University, Shanghai, China
| | - Leiyan He
- The Clinical Microbiology Laboratory, Children's Hospital of Fudan University, Shanghai, China
| | - Nana Wu
- Department of Nosocomial Infection Control, Children's Hospital of Fudan University, Shanghai, China
| | - Yun Cao
- Department of neonatal intensive care unit, Children's Hospital of Fudan University, Shanghai, China
| | - Guoping Lu
- Department of Pediatric Intensive Care Unit, Children's Hospital of Fudan University, Shanghai, China.
| | - Xiaowen Zhai
- Department of Hematology, Children's Hospital of Fudan University, Shanghai, China.
| | - Chuanqing Wang
- Department of Nosocomial Infection Control and the Clinical Microbiology Laboratory, Children's Hospital of Fudan University, Shanghai, China.
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Shelenkov A, Mikhaylova Y, Voskanyan S, Egorova A, Akimkin V. Whole-Genome Sequencing Revealed the Fusion Plasmids Capable of Transmission and Acquisition of Both Antimicrobial Resistance and Hypervirulence Determinants in Multidrug-Resistant Klebsiella pneumoniae Isolates. Microorganisms 2023; 11:1314. [PMID: 37317293 DOI: 10.3390/microorganisms11051314] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2023] [Revised: 05/11/2023] [Accepted: 05/15/2023] [Indexed: 06/16/2023] Open
Abstract
Klebsiella pneumoniae, a member of the Enterobacteriaceae family, has become a dangerous pathogen accountable for a large fraction of the various infectious diseases in both clinical and community settings. In general, the K. pneumoniae population has been divided into the so-called classical (cKp) and hypervirulent (hvKp) lineages. The former, usually developing in hospitals, can rapidly acquire resistance to a wide spectrum of antimicrobial drugs, while the latter is associated with more aggressive but less resistant infections, mostly in healthy humans. However, a growing number of reports in the last decade have confirmed the convergence of these two distinct lineages into superpathogen clones possessing the properties of both, and thus imposing a significant threat to public health worldwide. This process is associated with horizontal gene transfer, in which plasmid conjugation plays a very important role. Therefore, the investigation of plasmid structures and the ways plasmids spread within and between bacterial species will provide benefits in developing prevention measures against these powerful pathogens. In this work, we investigated clinical multidrug-resistant K. pneumoniae isolates using long- and short-read whole-genome sequencing, which allowed us to reveal fusion IncHI1B/IncFIB plasmids in ST512 isolates capable of simultaneously carrying hypervirulence (iucABCD, iutA, prmpA, peg-344) and resistance determinants (armA, blaNDM-1 and others), and to obtain insights into their formation and transmission mechanisms. Comprehensive phenotypic, genotypic and phylogenetic analysis of the isolates, as well as of their plasmid repertoire, was performed. The data obtained will facilitate epidemiological surveillance of high-risk K. pneumoniae clones and the development of prevention strategies against them.
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Affiliation(s)
- Andrey Shelenkov
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia
| | - Yulia Mikhaylova
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia
| | - Shushanik Voskanyan
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia
| | - Anna Egorova
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia
| | - Vasiliy Akimkin
- Central Research Institute of Epidemiology, Novogireevskaya Str., 3a, 111123 Moscow, Russia
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Ikhimiukor OO, Souza SSR, Marcovici MM, Nye GJ, Gibson R, Andam CP. Leaky barriers to gene sharing between locally co-existing coagulase-negative Staphylococcus species. Commun Biol 2023; 6:482. [PMID: 37137974 PMCID: PMC10156822 DOI: 10.1038/s42003-023-04877-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Accepted: 04/26/2023] [Indexed: 05/05/2023] Open
Abstract
Coagulase-negative Staphylococcus (CoNS) are opportunistic pathogens implicated in many human and animal infections. The evolutionary history of CoNS remains obscure because of the historical lack of recognition for their clinical importance and poor taxonomic sampling. Here, we sequenced the genomes of 191 CoNS isolates representing 15 species sampled from diseased animals diagnosed in a veterinary diagnostic laboratory. We found that CoNS are important reservoirs of diverse phages, plasmids and mobilizable genes encoding antimicrobial resistance, heavy metal resistance, and virulence. Frequent exchange of DNA between certain donor-recipient partners suggests that specific lineages act as hubs of gene sharing. We also detected frequent recombination between CoNS regardless of their animal host species, indicating that ecological barriers to horizontal gene transfer can be surmounted in co-circulating lineages. Our findings reveal frequent but structured patterns of transfer that exist within and between CoNS species, which are driven by their overlapping ecology and geographical proximity.
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Affiliation(s)
- Odion O Ikhimiukor
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA.
| | - Stephanie S R Souza
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA
| | - Michael M Marcovici
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA
| | - Griffin J Nye
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
- The Jackson Laboratory, 600 Main Street, Bar Harbor, ME, USA
| | - Robert Gibson
- Department of Molecular, Cellular and Biomedical Sciences, University of New Hampshire, Durham, NH, USA
- New Hampshire Veterinary Diagnostic Laboratory, Durham, NH, USA
| | - Cheryl P Andam
- Department of Biological Sciences, University at Albany, State University of New York, Albany, NY, USA.
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45
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Martin MJ, Stribling W, Ong AC, Maybank R, Kwak YI, Rosado-Mendez JA, Preston LN, Lane KF, Julius M, Jones AR, Hinkle M, Waterman PE, Lesho EP, Lebreton F, Bennett JW, Mc Gann PT. A panel of diverse Klebsiella pneumoniae clinical isolates for research and development. Microb Genom 2023; 9. [PMID: 37141116 DOI: 10.1099/mgen.0.000967] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
Klebsiella pneumoniae are a leading cause of healthcare-associated infections worldwide. In particular, strains expressing extended-spectrum β-lactamases (ESBLs) and carbapenemases pose serious treatment challenges, leading the World Health Organization (WHO) to designate ESBL and carbapenem-resistant Enterobacteriaceae as 'critical' threats to human health. Research efforts to combat these pathogens can be supported by accessibility to diverse and clinically relevant isolates for testing novel therapeutics. Here, we describe a panel of 100 diverse K. pneumoniae isolates that are publicly available to assist the research community in this endeavour. Whole-genome sequencing (WGS) was performed on 3878 K. pneumoniae clinical isolates housed at the Multidrug-Resistant Organism Repository and Surveillance Network. The isolates were cultured from 63 facilities in 19 countries between 2001 and 2020. Core-genome multilocus sequence typing and high-resolution single-nucleotide polymorphism-based phylogenetic analyses captured the genetic diversity of the collection and were used to select the final panel of 100 isolates. In addition to known multidrug-resistant (MDR) pandemic lineages, the final panel includes hypervirulent lineages and isolates with specific and diverse resistance genes and virulence biomarkers. A broad range of antibiotic susceptibilities, ranging from pan-sensitive to extensively drug-resistant isolates, are described. The panel collection, and all associated metadata and genome sequences, are available at no additional cost and will be an important resource for the research community and for the design and development of novel antimicrobial agents and diagnostics against this important pathogen.
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Affiliation(s)
- Melissa J Martin
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - William Stribling
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Ana C Ong
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Rosslyn Maybank
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Yoon I Kwak
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Joshua A Rosado-Mendez
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Lan N Preston
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Katharine F Lane
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Michael Julius
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Anthony R Jones
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Mary Hinkle
- Infectious Diseases Unit, Rochester General Hospital, Rochester, New York, USA
| | - Paige E Waterman
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Emil P Lesho
- Infectious Diseases Unit, Rochester General Hospital, Rochester, New York, USA
| | - Francois Lebreton
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Jason W Bennett
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Patrick T Mc Gann
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
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Zhou K, Xue CX, Xu T, Shen P, Wei S, Wyres KL, Lam MMC, Liu J, Lin H, Chen Y, Holt KE, Xiao Y. A point mutation in recC associated with subclonal replacement of carbapenem-resistant Klebsiella pneumoniae ST11 in China. Nat Commun 2023; 14:2464. [PMID: 37117217 PMCID: PMC10147710 DOI: 10.1038/s41467-023-38061-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Accepted: 04/13/2023] [Indexed: 04/30/2023] Open
Abstract
Adaptation to selective pressures is crucial for clinically important pathogens to establish epidemics, but the underlying evolutionary drivers remain poorly understood. The current epidemic of carbapenem-resistant Klebsiella pneumoniae (CRKP) poses a significant threat to public health. In this study we analyzed the genome sequences of 794 CRKP bloodstream isolates collected in 40 hospitals in China between 2014 and 2019. We uncovered a subclonal replacement in the predominant clone ST11, where the previously prevalent subclone OL101:KL47 was replaced by O2v1:KL64 over time in a stepwise manner. O2v1:KL64 carried a higher load of mobile genetic elements, and a point mutation exclusively detected in the recC of O2v1:KL64 significantly promotes recombination proficiency. The epidemic success of O2v1:KL64 was further associated with a hypervirulent sublineage with enhanced resistance to phagocytosis, sulfamethoxazole-trimethoprim, and tetracycline. The phenotypic alterations were linked to the overrepresentation of hypervirulence determinants and antibiotic genes conferred by the acquisition of an rmpA-positive pLVPK-like virulence plasmid and an IncFII-type multidrug-resistant plasmid, respectively. The dissemination of the sublineage was further promoted by more frequent inter-hospital transmission. The results collectively demonstrate that the expansion of O2v1:KL64 is correlated to a repertoire of genomic alterations convergent in a subpopulation with evolutionary advantages.
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Affiliation(s)
- Kai Zhou
- Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, China.
| | - Chun-Xu Xue
- Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, China
| | - Tingting Xu
- Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, China
| | - Ping Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Sha Wei
- Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, China
| | - Kelly L Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Margaret M C Lam
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
| | - Jinquan Liu
- Shenzhen Institute of Respiratory Diseases, Shenzhen People's Hospital (Second Clinical Medical College, Jinan University; The First Affiliated Hospital, Southern University of Science and Technology), Shenzhen, 518020, China
| | - Haoyun Lin
- Department of Clinical Laboratory, Shenzhen People's Hospital, Shenzhen, China
| | - Yunbo Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Yonghong Xiao
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, 310003, China.
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47
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Zhou Y, Wu C, Wang B, Xu Y, Zhao H, Guo Y, Wu X, Yu J, Rao L, Wang X, Yu F. Characterization difference of typical KL1, KL2 and ST11-KL64 hypervirulent and carbapenem-resistant Klebsiella pneumoniae. Drug Resist Updat 2023; 67:100918. [PMID: 36610180 DOI: 10.1016/j.drup.2023.100918] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 12/31/2022] [Accepted: 01/02/2023] [Indexed: 01/05/2023]
Abstract
Almost all the formation of hypervirulent and carbapenem-resistant Klebsiella pneumoniae follow two major patterns: KL1/KL2 hvKP strains acquire carbapenem-resistance plasmids (CR-hvKP), and carbapenem-resistant Klebsiella pneumoniae (CRKP) strains obtain virulence plasmids (hv-CRKP). These two patterns may pose different phenotypes. In this study, three typical resistance and hypervirulent K. pneumoniae (KL1, KL2, and ST11-KL64), isolating from poor prognosis patients, were selected. Compared with ST11-KL64 hv-CRKP, KL1/KL2 hypervirulent lineages harbor significantly fewer resistance determinants and exhibited lower-level resistance to antibiotics. Notably, though the blaKPC gene could be detected in all these isolates, KL1/KL2 hvKP strain did not exhibit corresponding high-level carbapenem resistance. Unlike the resistance features, we did not observe significant virulence differences between the three strains. The ST11-KL64 hv-CRKP (1403) in this study, showed similar mucoviscosity, siderophores production, and biofilm production compared with KL1 and KL2 hvKP. Moreover, the hypervirulent of ST11-KL64 hvKP also verified with the human lung epithelial cells infection and G. mellonella infection models. Moreover, we found the pLVPK-like virulence plasmid and IncF blaKPC-2 plasmid was crucial for the formation of hypervirulent and carbapenem-resistant K. pneumoniae. The conservation of origin of transfer site (oriT) in these virulence and blaKPC-2 plasmids, indicated the virulence plasmids could transfer to CRKP with the help of blaKPC-2 plasmids. The co-existence of virulence plasmid and blaKPC-2 plasmid facilitate the formation of ST11-KL64 hv-CPKP, which then become nosocomial epidemic under the antibiotic stress. The ST11-KL64 hv-CPKP may poses a substantial threat to healthcare networks, urgent measures were needed to prevent further dissemination in nosocomial settings.
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Affiliation(s)
- Ying Zhou
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, People's Republic of China
| | - Chunyang Wu
- Department of Respiratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou 325000, People's Republic of China
| | - Bingjie Wang
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, People's Republic of China
| | - YanLei Xu
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, People's Republic of China
| | - Huilin Zhao
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, People's Republic of China
| | - Yinjuan Guo
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, People's Republic of China
| | - Xiaocui Wu
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, People's Republic of China
| | - Jingyi Yu
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, People's Republic of China
| | - Lulin Rao
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, People's Republic of China
| | - Xinyi Wang
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, People's Republic of China
| | - Fangyou Yu
- Department of Clinical Laboratory Medicine, Shanghai Pulmonary Hospital, Tongji University School of Medicine, Shanghai 200082, People's Republic of China; Department of Laboratory Medicine, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, People's Republic of China.
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48
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Beamud B, García-González N, Gómez-Ortega M, González-Candelas F, Domingo-Calap P, Sanjuan R. Genetic determinants of host tropism in Klebsiella phages. Cell Rep 2023; 42:112048. [PMID: 36753420 PMCID: PMC9989827 DOI: 10.1016/j.celrep.2023.112048] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2022] [Revised: 11/25/2022] [Accepted: 01/13/2023] [Indexed: 02/08/2023] Open
Abstract
Bacteriophages play key roles in bacterial ecology and evolution and are potential antimicrobials. However, the determinants of phage-host specificity remain elusive. Here, we isolate 46 phages to challenge 138 representative clinical isolates of Klebsiella pneumoniae, a widespread opportunistic pathogen. Spot tests show a narrow host range for most phages, with <2% of 6,319 phage-host combinations tested yielding detectable interactions. Bacterial capsule diversity is the main factor restricting phage host range. Consequently, phage-encoded depolymerases are key determinants of host tropism, and depolymerase sequence types are associated with the ability to infect specific capsular types across phage families. However, all phages with a broader host range found do not encode canonical depolymerases, suggesting alternative modes of entry. These findings expand our knowledge of the complex interactions between bacteria and their viruses and point out the feasibility of predicting the first steps of phage infection using bacterial and phage genome sequences.
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Affiliation(s)
- Beatriz Beamud
- Joint Research Unit Infection and Public Health, FISABIO-Universitat de València, 46020 València, Spain; Institute for Integrative Systems Biology (I(2)SysBio), Universitat de València-CSIC, 46980 Paterna, Spain
| | - Neris García-González
- Joint Research Unit Infection and Public Health, FISABIO-Universitat de València, 46020 València, Spain; Institute for Integrative Systems Biology (I(2)SysBio), Universitat de València-CSIC, 46980 Paterna, Spain
| | - Mar Gómez-Ortega
- Joint Research Unit Infection and Public Health, FISABIO-Universitat de València, 46020 València, Spain
| | - Fernando González-Candelas
- Joint Research Unit Infection and Public Health, FISABIO-Universitat de València, 46020 València, Spain; Institute for Integrative Systems Biology (I(2)SysBio), Universitat de València-CSIC, 46980 Paterna, Spain.
| | - Pilar Domingo-Calap
- Institute for Integrative Systems Biology (I(2)SysBio), Universitat de València-CSIC, 46980 Paterna, Spain.
| | - Rafael Sanjuan
- Institute for Integrative Systems Biology (I(2)SysBio), Universitat de València-CSIC, 46980 Paterna, Spain.
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49
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Gorodnichev RB, Kornienko MA, Malakhova MV, Bespiatykh DA, Manuvera VA, Selezneva OV, Veselovsky VA, Bagrov DV, Zaychikova MV, Osnach VA, Shabalina AV, Goloshchapov OV, Bespyatykh JA, Dolgova AS, Shitikov EA. Isolation and Characterization of the First Zobellviridae Family Bacteriophage Infecting Klebsiella pneumoniae. Int J Mol Sci 2023; 24:ijms24044038. [PMID: 36835449 PMCID: PMC9960094 DOI: 10.3390/ijms24044038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2022] [Revised: 02/13/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
In order to address the upcoming crisis in the treatment of Klebsiella pneumoniae infections, caused by an increasing proportion of resistant isolates, new approaches to antimicrobial therapy must be developed. One approach would be to use (bacterio)phages and/or phage derivatives for therapy. In this study, we present a description of the first K. pneumoniae phage from the Zobellviridae family. The vB_KpnP_Klyazma podovirus, which forms translucent halos around the plaques, was isolated from river water. The phage genome is composed of 82 open reading frames, which are divided into two clusters located on opposite strands. Phylogenetic analysis revealed that the phage belongs to the Zobellviridae family, although its identity with the closest member of this family was not higher than 5%. The bacteriophage demonstrated lytic activity against all (n = 11) K. pneumoniae strains with the KL20 capsule type, but only the host strain was lysed effectively. The receptor-binding protein of the phage was identified as a polysaccharide depolymerase with a pectate lyase domain. The recombinant depolymerase protein showed concentration-dependent activity against all strains with the KL20 capsule type. The ability of a recombinant depolymerase to cleave bacterial capsular polysaccharides regardless of a phage's ability to successfully infect a particular strain holds promise for the possibility of using depolymerases in antimicrobial therapy, even though they only make bacteria sensitive to environmental factors, rather than killing them directly.
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Affiliation(s)
- Roman B. Gorodnichev
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
- Correspondence:
| | - Maria A. Kornienko
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Maja V. Malakhova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Dmitry A. Bespiatykh
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Valentin A. Manuvera
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Oksana V. Selezneva
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Vladimir A. Veselovsky
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Dmitry V. Bagrov
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
- Department of Bioengineering, Faculty of Biology, Lomonosov Moscow State University, 119234 Moscow, Russia
| | - Marina V. Zaychikova
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Veronika A. Osnach
- Saint Petersburg Pasteur Institute, Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, 197101 St. Petersburg, Russia
| | - Anna V. Shabalina
- Saint Petersburg Pasteur Institute, Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, 197101 St. Petersburg, Russia
| | - Oleg V. Goloshchapov
- R.M. Gorbacheva Memorial Institute of Oncology, Hematology and Transplantation, Pavlov First Saint Petersburg State Medical University, 197022 St. Petersburg, Russia
| | - Julia A. Bespyatykh
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
| | - Anna S. Dolgova
- Saint Petersburg Pasteur Institute, Federal Service on Consumer Rights Protection and Human Well-Being Surveillance, 197101 St. Petersburg, Russia
| | - Egor A. Shitikov
- Lopukhin Federal Research and Clinical Center of Physical-Chemical Medicine of Federal Medical Biological Agency, 119435 Moscow, Russia
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Qian C, Zhang S, Xu M, Zeng W, Chen L, Zhao Y, Zhou C, Zhang Y, Cao J, Zhou T. Genetic and Phenotypic Characterization of Multidrug-Resistant Klebsiella pneumoniae from Liver Abscess. Microbiol Spectr 2023; 11:e0224022. [PMID: 36598251 PMCID: PMC9927449 DOI: 10.1128/spectrum.02240-22] [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: 06/16/2022] [Accepted: 12/05/2022] [Indexed: 01/05/2023] Open
Abstract
Cooccurrence of multidrug resistant (MDR) and hypervirulence phenotypes in liver abscess-causing Klebsiella pneumoniae (LAKp) would pose a major threat to public health. However, relatively little information is available on the genomic and phenotypic characteristics of this pathogen. This study aimed to investigate the virulence and resistance phenotype and genotype of MDR LAKp strains from 2016 to 2020. We collected 18 MDR LAKp strains from 395 liver abscess samples and characterized these strains using antimicrobial susceptibility test, string test, mucoviscosity assay, biofilm formation assay, Galleria mellonella killing assay, and whole-genome sequencing. Besides, phylogenetic and comparative genomic analyses were performed on these MDR LAKp, along with 94 LAKp genomes from global sources. Most of these MDR LAKp strains exhibited resistance to cephalosporins, quinolones, and chloramphenicol. Virulence assays revealed that only half of MDR LAKp strains exhibited higher virulence than classical MDR strain K. pneumoniae MGH78578. Importantly, we identified three ST11 KL64 hypervirulence carbapenem-resistant strains carrying blaKPC-2 and one colistin-resistant strain carrying mcr-1. Phylogenetic analysis revealed that 112 LAKp genomes were divided into two clades, and most of MDR LAKp strains in this study belonged to clade 1 (83.33%, 15/18). We also detected the loss of mucoviscosity mediated by mutations and ISKpn14 insertion in rmpA, and the latter representing a novel mechanism by which bacteria regulate RmpA system. This study provides novel insights into MDR LAKp and highlights the necessity for measures to prevent further spread of such organisms in hospital settings and the community. IMPORTANCE Pyogenic liver abscess is a potentially life-threatening suppurative infection of hepatic parenchyma. K. pneumoniae has emerged as a predominant pathogen of pyogenic liver abscess. Liver abscess-causing K. pneumoniae is generally considered hypervirulent K. pneumoniae and is susceptible to most antibiotics. Recently, convergence of multidrug resistant and hypervirulence phenotypes in liver abscess-causing K. pneumoniae was emerging and poses a major threat to public health. However, relatively little information is available on liver abscess-causing multidrug-resistant hypervirulent K. pneumoniae. In this study, we characterized phenotype and genotype of virulence and resistance of 18 multidrug-resistant hypervirulent liver abscess-causing K. pneumoniae strains collected from 395 pyogenic liver abscess cases in a tertiary teaching hospital over a 5-year period to enable in-depth understanding of this pathogen.
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Affiliation(s)
- Changrui Qian
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang Province, People’s Republic of China
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, People’s Republic of China
| | - Siqin Zhang
- Department of Clinical Laboratory, Hangzhou Hospital of Traditional Chinese Medicine, Hangzhou, Zhejiang Province, People’s Republic of China
| | - Mengxin Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang Province, People’s Republic of China
| | - Weiliang Zeng
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang Province, People’s Republic of China
| | - Lijiang Chen
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang Province, People’s Republic of China
| | - Yining Zhao
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang Province, People’s Republic of China
| | - Cui Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang Province, People’s Republic of China
| | - Ying Zhang
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang Province, People’s Republic of China
| | - Jianming Cao
- School of Basic Medical Sciences, Wenzhou Medical University, Wenzhou, Zhejiang Province, People’s Republic of China
| | - Tieli Zhou
- Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Wenzhou, Zhejiang Province, People’s Republic of China
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