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Yuan H, Xu J, Wang Y, Shi L, Dong Y, Liu F, Long J, Duan G, Jin Y, Chen S, Zhu J, Yang H. The longitudinal trend and influential factors exploring of global antimicrobial resistance in Klebsiella pneumoniae. THE SCIENCE OF THE TOTAL ENVIRONMENT 2024; 950:175357. [PMID: 39127203 DOI: 10.1016/j.scitotenv.2024.175357] [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: 05/31/2024] [Revised: 08/01/2024] [Accepted: 08/05/2024] [Indexed: 08/12/2024]
Abstract
Klebsiella pneumoniae (Kp) is a human symbiotic opportunistic pathogen capable of causing severe hospital-based infections and community-acquired infections. The problem of antimicrobial resistance (AMR) has become increasing serious over time, posing a major threat to socio-economic and human development. In this study, we explored the global trend of AMR in 1786 strains of Kp isolated between 1982 and 2023. The number of antibiotic resistance genes (ARGs) in Kp increased significantly from 24.29 ± 5.44 to 32.42 ± 8.52 over time. Mobile genetic elements (MGEs) were responsible for the ARGs horizontal transfer of Kp strains. The results of structural equation modeling (SEM) indicated a strong association between the human development index and the increase of antibiotic consumption, which indirectly affected the occurrence and development of antibiotic resistance in Kp. The results of Generalized Linear Models (GLM) indicated that the influence of environmental factors such as temperature on the development of Kp resistance could not be ignored. Overall, this study monitored the longitudinal trend of antimicrobial resistance in Kp, explored the factors influencing antibiotic resistance, and provided insights for mitigating the threat of antimicrobial resistance.
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Affiliation(s)
- Haitao Yuan
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Jie Xu
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Ying Wang
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Liqin Shi
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Yuehan Dong
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Fang Liu
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Jinzhao Long
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Guangcai Duan
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Yuefei Jin
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Shuaiyin Chen
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Jingyuan Zhu
- Department of Environmental Health, School of Public Health, Zhengzhou University, Zhengzhou 450001, China
| | - Haiyan Yang
- Department of Epidemiology, School of Public Health, Zhengzhou University, Zhengzhou 450001, China.
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Bray AS, Zafar MA. Deciphering the gastrointestinal carriage of Klebsiella pneumoniae. Infect Immun 2024; 92: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] [MESH Headings] [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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Worku M, Belay S, Molla T, Aynalem M, Assefa M. Prevalence and antimicrobial susceptibility pattern of Klebsiella pneumoniae isolated from various clinical specimens at the University of Gondar Comprehensive Specialized Hospital, Northwest Ethiopia. BMC Infect Dis 2024; 24:917. [PMID: 39232652 PMCID: PMC11373452 DOI: 10.1186/s12879-024-09811-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2024] [Accepted: 08/26/2024] [Indexed: 09/06/2024] Open
Abstract
BACKGROUND K. pneumoniae become multidrug-resistant (MDR) and commonly poses a serious health threat to patients due to limited therapeutic options. As a result, determining the prevalence and antimicrobial susceptibility patterns of K. pneumoniae isolates from clinical specimens is substantial to patient diagnosis and treatment. METHODS AND MATERIALS A retrospective cross-sectional study was conducted from July 2021 to July 2022 at the University of Gondar Comprehensive Specialized Hospital, Northwest Ethiopia. Sociodemographic and laboratory data were collected from registered books using a data collection sheet. All types of samples were collected and processed using standard procedures. Identification of K. pneumoniae was done using Gram stain, colony characterization on culture media, anda series of biochemical tests. Antimicrobial susceptibility testing was done by the Kirby Bauer disc diffusion technique. The data were entered using Epi-info version 7 and exported to SPSS version 20 for analysis. RESULTS Among 2600 clinical specimens, 735 (28.3%) were positive for bacteria, and K. pneumoniae isolates accounted for 147 (20%). Most of them were isolated from neonates and mainly obtained from blood specimens (81.6%). These isolates were 100% resistant to Nalidixic acid, Cefotaxime, and Cefazolin. About 84% and 83.3% of the isolates were also resistant to Ceftriaxone and Tetracycline, respectively. However, they are sensitive to Nitrofurantoin (86.6%), Imipenem (85.7%), Meropenem (79%), and Amikacin (78.3%). The overall proportion of MDR K. pneumoniae isolates accounted for 57.1%. CONCLUSION The magnitude of MDR K. pneumoniae was very alarming. Therefore, strengthening antimicrobial stewardship programs and antimicrobial surveillance practices is strongly recommended in the study area.
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Affiliation(s)
- Minichil Worku
- University of Gondar Comprehensive Specialized Hospital, Gondar, Ethiopia
| | - Solomon Belay
- University of Gondar Comprehensive Specialized Hospital, Gondar, Ethiopia
| | - Tigist Molla
- University of Gondar Comprehensive Specialized Hospital, Gondar, Ethiopia
| | - Melak Aynalem
- Department of Hematology and Immunohematology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Science, University of Gondar, Gondar, Ethiopia
| | - Muluneh Assefa
- Department of Medical Microbiology, School of Biomedical and Laboratory Sciences, College of Medicine and Health Science, University of Gondar, Gondar, Ethiopia.
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Sheng Q, Wang X, Hou Z, Liu B, Jiang M, Ren M, Fu J, He M, Zhang J, Xiang Y, Zhang Q, Zhou L, Deng Y, Shen X. Novel functions of o-cymen-5-ol nanoemulsion in reversing colistin resistance in multidrug-resistant Klebsiella pneumoniae infections. Biochem Pharmacol 2024; 227:116384. [PMID: 38909787 DOI: 10.1016/j.bcp.2024.116384] [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: 02/21/2024] [Revised: 06/18/2024] [Accepted: 06/20/2024] [Indexed: 06/25/2024]
Abstract
Multidrug resistance (MDR) Klebsiella pneumoniae (K. pneumoniae) is a major emerging threat to human health, and leads to very high mortality rate. The effectiveness of colistin, the last resort against MDR Gram-negative bacteria, is significantly compromised due to the widespread presence of plasmid- or chromosome-mediated resistance genes. In this study, o-cymen-5-ol has been found to greatly restore colistin sensitivity in MDR K. pneumoniae. Importantly, this compound does not impact bacterial viability, induce resistance, or cause any noticeable cell toxicity. Various routes disclosed the potential mechanism of o-cymen-5-ol potentiating colistin activity against MDR K. pneumoniae. These include inhibiting the activity of plasmid-mediated mobile colistin resistance gene (mcr-1), accelerating lipopolysaccharide (LPS) - mediated membrane damage, and promoting the ATP-binding cassette (ABC) transporter pathway. To enhance the administration and bioavailability of o-cymen-5-ol, a nanoemulsion has been designed, which significantly improves the loading efficiency and solubility of o-cymen-5-ol, resulting in antimicrobial potentiation of colistin against K. pneumoniae infection. This study has revealed a new understanding of the o-cymen-5-ol nanoemulsion as a means to enhance the effectiveness of colistin against resistant factors. The finding also suggests that o-cymen-5-ol nanoemulsion could be a promising approach in the development of potential treatments for multidrug-resistant Gram-negative bacterial infections.
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Affiliation(s)
- Qiushuang Sheng
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Xiao Wang
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Zhaoyan Hou
- Changchun Center for Disease Control and Prevention, Changchun, China
| | - Bin Liu
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Mingquan Jiang
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Mingyue Ren
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Jingchao Fu
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Miao He
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Jingchen Zhang
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Yue Xiang
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Qingbo Zhang
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Lanying Zhou
- Department of Microbiology, Jilin Province Product Quality Supervision and Inspection Institute, Changchun 130103, China
| | - Yanhong Deng
- State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China.
| | - Xue Shen
- Department of Food Science, College of Food Science and Engineering, Jilin University, Changchun 130062, China; State Key Laboratory for Zoonotic Diseases, Key Laboratory for Zoonosis Research, Ministry of Education, Institute of Zoonosis, College of Veterinary Medicine, Jilin University, Changchun 130062, China.
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Zhang Z, Ren R, Peng C, Ji Y, Liu S, Wang F. Genomic characterisation of a multidrug-resistant Klebsiella pneumoniae co-harbouring bla NDM-1, bla KPC-2, and tet(A) isolated from the bloodstream infections of patients. Int J Antimicrob Agents 2024; 64:107290. [PMID: 39084573 DOI: 10.1016/j.ijantimicag.2024.107290] [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: 04/25/2024] [Revised: 07/11/2024] [Accepted: 07/22/2024] [Indexed: 08/02/2024]
Abstract
OBJECTIVES Carbapenem-resistant Klebsiella pneumoniae (CRKP), a superbug that can be difficult or impossible to treat, has become a worldwide problem. This study presents the first report of a CRKP strain carrying a plasmid co-harbouring blaNDM-1, blaKPC-2, and tet(A) and the subsequent analysis of its genomic features. METHODS Isolation and identification of bacteria, antimicrobial susceptibility test, whole genome sequencing, and conjugation experiments assay were conducted in clinical epidemiological investigations and plasmid genetic characterisation analysis. RESULTS A total of 116 strains of bacteria were isolated from patients with bloodstream infections (BSI) between 2018 and 2023. A total of 89.66% of the isolates were carbapenem-resistant Enterobacteriaceae (CRE), with the majority (75/116) being CRKP. Among these, a novel plasmid co-harbouring blaNDM-1, blaKPC-2, and tet(A) simultaneously was found in CRKP46, and the three genes mediated conjugation by IS26, ISAba125, and IS26, respectively. This plasmid conferred carbapenem resistance to E. coli J53 after conjugative transfer, which was 2 times greater than that of CRKP46. CONCLUSION The present study identified the occurrence of a rare plasmid co-harbouring blaNDM-1, blaKPC-2, and tet(A), and the spread of these genes was mediated by the corresponding mobile elements. The increased carbapenem resistance created by this novel plasmid challenges public health security and poses a potential threat to human health; therefore, it deserves attention.
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Affiliation(s)
- Zhijun Zhang
- Department of Clinical Laboratory, The Affiliated Tai'an City Central Hospital of Qingdao University, Tai'an City, Shandong, PR China
| | - Ren Ren
- Department of Intensive Care Medicine, The Affiliated Tai'an City Central Hospital of Qingdao University, Tai'an City, Shandong, PR China
| | - Chong Peng
- Department of Veterinary Public Health, College of Veterinary Medicine & Shandong Provincial Key Laboratory of Zoonoses, Shandong Agricultural University, Tai'an City, Shandong, PR China
| | - Yingying Ji
- Department of Clinical Laboratory, The Affiliated Tai'an City Central Hospital of Qingdao University, Tai'an City, Shandong, PR China
| | - Shuang Liu
- Department of Hematology, The Affiliated Tai'an City Central Hospital of Qingdao University, Tai'an City, Shandong, PR China.
| | - Fangkun Wang
- Department of Veterinary Public Health, College of Veterinary Medicine & Shandong Provincial Key Laboratory of Zoonoses, Shandong Agricultural University, Tai'an City, Shandong, PR China
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Ziller L, Blum PC, Buhl EM, Krüttgen A, Horz HP, Tagliaferri TL. Newly isolated Drexlerviridae phage LAPAZ is physically robust and fosters eradication of Klebsiella pneumoniae in combination with meropenem. Virus Res 2024; 347:199417. [PMID: 38880333 PMCID: PMC11245953 DOI: 10.1016/j.virusres.2024.199417] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Revised: 06/11/2024] [Accepted: 06/13/2024] [Indexed: 06/18/2024]
Abstract
Due to the spread of multidrug resistance there is a renewed interest in using bacteriophages (briefly: phages) for controlling bacterial pathogens. The objective of this study was the characterization of a newly isolated phage (i.e. phage LAPAZ, vB_KpnD-LAPAZ), its antimicrobial activity against multidrug resistant Klebsiella pneumoniae and potential synergistic interactions with antibiotics. LAPAZ belongs to the family Drexlerviridae (genus: Webervirus) and lysed 30 % of tested strains, whereby four distinct capsular types can be infected. The genome consists of 51,689 bp and encodes 84 ORFs. The latent period is 30 min with an average burst size of 27 PFU/cell. Long-term storage experiments show that LAPAZ is significantly more stable in wastewater compared to laboratory media. A phage titre of 90 % persists up to 30 min at 50 ˚C and entire phage loss was seen only at temperatures > 66 ˚C. Besides stability against UV-C, antibacterial activity in liquid culture medium was consistent at pH values ranging from 4 to 10. Unlike exposure to phage or antibiotic alone, synergistic interactions and a complete bacterial eradication was achieved when combining LAPAZ with meropenem. In addition, synergism with the co-presence of ciprofloxacin was observed and phage resistance emergence could be delayed. Without co-addition of the antibiotic, phage resistant mutants readily emerged and showed a mixed pattern of drug sensitivity alterations. Around 88 % became less sensitive towards ceftazidime, meropenem and gentamicin. Conversely, around 44 % showed decreased resistance levels against ciprofloxacin. Whole genome analysis of a phage-resistant mutant with a 16-fold increased sensitivity towards ciprofloxacin revealed one de novo frameshift mutation leading to a gene fusion affecting two transport proteins belonging to the major facilitator-superfamily (MFS). Apparently, this mutation compromises ciprofloxacin efflux efficiency and further studies are warranted to understand how the non-mutated protein might be involved in phage-host adsorption.
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Affiliation(s)
- Leonie Ziller
- Institute of Medical Microbiology, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | | | - Eva Miriam Buhl
- Electron Microscopy Facility, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Alex Krüttgen
- Laboratory Diagnostic Center, RWTH Aachen University Hospital, 52074 Aachen, Germany
| | - Hans-Peter Horz
- Institute of Medical Microbiology, RWTH Aachen University Hospital, 52074 Aachen, Germany.
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Gray J, Torres VVL, Goodall E, McKeand SA, Scales D, Collins C, Wetherall L, Lian ZJ, Bryant JA, Milner MT, Dunne KA, Icke C, Rooke JL, Schneiders T, Lund PA, Cunningham AF, Cole JA, Henderson IR. Transposon mutagenesis screen in Klebsiella pneumoniae identifies genetic determinants required for growth in human urine and serum. eLife 2024; 12:RP88971. [PMID: 39189918 PMCID: PMC11349299 DOI: 10.7554/elife.88971] [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] [Indexed: 08/28/2024] Open
Abstract
Klebsiella pneumoniae is a global public health concern due to the rising myriad of hypervirulent and multidrug-resistant clones both alarmingly associated with high mortality. The molecular mechanisms underpinning these recalcitrant K. pneumoniae infection, and how virulence is coupled with the emergence of lineages resistant to nearly all present-day clinically important antimicrobials, are unclear. In this study, we performed a genome-wide screen in K. pneumoniae ECL8, a member of the endemic K2-ST375 pathotype most often reported in Asia, to define genes essential for growth in a nutrient-rich laboratory medium (Luria-Bertani [LB] medium), human urine, and serum. Through transposon directed insertion-site sequencing (TraDIS), a total of 427 genes were identified as essential for growth on LB agar, whereas transposon insertions in 11 and 144 genes decreased fitness for growth in either urine or serum, respectively. These studies not only provide further knowledge on the genetics of this pathogen but also provide a strong impetus for discovering new antimicrobial targets to improve current therapeutic options for K. pneumoniae infections.
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Affiliation(s)
- Jessica Gray
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| | - Von Vergel L Torres
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| | - Emily Goodall
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| | - Samantha A McKeand
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Danielle Scales
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Christy Collins
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Laura Wetherall
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Zheng Jie Lian
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| | - Jack A Bryant
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Matthew T Milner
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Karl A Dunne
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Christopher Icke
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| | - Jessica L Rooke
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
| | - Thamarai Schneiders
- Division of Infection Medicine, University of EdinburghEdinburghUnited Kingdom
| | - Peter A Lund
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Adam F Cunningham
- Institute of Immunology and Immunotherapy, University of BirminghamBirminghamUnited Kingdom
| | - Jeff A Cole
- Institute of Microbiology and Infection, University of BirminghamBirminghamUnited Kingdom
| | - Ian R Henderson
- Institute for Molecular Bioscience, University of QueenslandBrisbaneAustralia
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Song S, Yang S, Zheng R, Yin D, Cao Y, Wang Y, Qiao L, Bai R, Wang S, Yin W, Dong Y, Bai L, Yang H, Shen J, Wu C, Hu F, Wang Y. Adaptive evolution of carbapenem-resistant hypervirulent Klebsiella pneumoniae in the urinary tract of a single patient. Proc Natl Acad Sci U S A 2024; 121:e2400446121. [PMID: 39150777 PMCID: PMC11363291 DOI: 10.1073/pnas.2400446121] [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: 01/15/2024] [Accepted: 06/26/2024] [Indexed: 08/18/2024] Open
Abstract
The emergence of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp) is a growing concern due to its high mortality and limited treatment options. Although hypermucoviscosity is crucial for CR-hvKp infection, the role of changes in bacterial mucoviscosity in the host colonization and persistence of CR-hvKp is not clearly defined. Herein, we observed a phenotypic switch of CR-hvKp from a hypermucoviscous to a hypomucoviscous state in a patient with scrotal abscess and urinary tract infection (UTI). This switch was attributed to decreased expression of rmpADC, the regulator of mucoid phenotype, caused by deletion of the upstream insertion sequence ISKpn26. Postswitching, the hypomucoid variant showed a 9.0-fold decrease in mice sepsis mortality, a >170.0-fold reduction in the ability to evade macrophage phagocytosis in vitro, and an 11.2- to 40.9-fold drop in growth rate in normal mouse serum. Conversely, it exhibited an increased residence time in the mouse urinary tract (21 vs. 6 d), as well as a 216.4-fold boost in adhesion to bladder epithelial cells and a 48.7% enhancement in biofilm production. Notably, the CR-hvKp mucoid switch was reproduced in an antibiotic-free mouse UTI model. The in vivo generation of hypomucoid variants was primarily associated with defective or low expression of rmpADC or capsule synthesis gene wcaJ, mediated by ISKpn26 insertion/deletion or base-pair insertion. The spontaneous hypomucoid variants also outcompeted hypermucoid bacteria in the mouse urinary tract. Collectively, the ISKpn26-associated mucoid switch in CR-hvKp signifies the antibiotic-independent host adaptive evolution, providing insights into the role of mucoid switch in the persistence of CR-hvKp.
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Affiliation(s)
- Shikai Song
- National Key Laboratory of Veterinary Public Health and Safety, Department of Basic Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing100193, China
- Poultry Research Institute, Shandong Academy of Agricultural Science, Jinan250100, Shandong, China
| | - Shixin Yang
- National Key Laboratory of Veterinary Public Health and Safety, Department of Basic Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing100193, China
| | - Ruicheng Zheng
- National Key Laboratory of Veterinary Public Health and Safety, Department of Basic Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing100193, China
| | - Dandan Yin
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai200433, China
| | - Yue Cao
- National Key Laboratory of Veterinary Public Health and Safety, Department of Basic Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing100193, China
| | - Yao Wang
- Shandong Animal Disease Prevention and Control Center, Jinan250100, Shandong, China
| | - Lu Qiao
- National Key Laboratory of Veterinary Public Health and Safety, Department of Basic Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing100193, China
| | - Rina Bai
- National Key Laboratory of Veterinary Public Health and Safety, Department of Basic Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing100193, China
| | - Shuge Wang
- National Key Laboratory of Veterinary Public Health and Safety, Department of Basic Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing100193, China
| | - Wenjuan Yin
- Department of Microbiology and Immunology, College of Basic Medical Science, Key Laboratory of Pathogenesis Mechanism and Control of Inflammatory-Autoimmune Diseases of Hebei Province, Hebei University, Baoding071002, China
| | - Yanjun Dong
- National Key Laboratory of Veterinary Public Health and Safety, Department of Basic Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing100193, China
| | - Li Bai
- National Center for Food Safety Risk Assessment, Beijing100022, China
| | - Hui Yang
- National Center for Food Safety Risk Assessment, Beijing100022, China
| | - Jianzhong Shen
- National Key Laboratory of Veterinary Public Health and Safety, Department of Basic Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing100193, China
| | - Congming Wu
- National Key Laboratory of Veterinary Public Health and Safety, Department of Basic Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing100193, China
| | - Fupin Hu
- Institute of Antibiotics, Huashan Hospital, Fudan University, Shanghai200433, China
| | - Yang Wang
- National Key Laboratory of Veterinary Public Health and Safety, Department of Basic Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing100193, China
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9
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Khan MM, Mushtaq MA, Abbas N, Fatima F, Gibbon MJ, Schierack P, Mohsin M. Occurrence, antimicrobial resistance and genomic features of Klebsiella pneumoniae from broiler chicken in Faisalabad, Pakistan. Front Vet Sci 2024; 11:1433124. [PMID: 39224453 PMCID: PMC11366712 DOI: 10.3389/fvets.2024.1433124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2024] [Accepted: 08/05/2024] [Indexed: 09/04/2024] Open
Abstract
Introduction The dissemination of antimicrobial resistance (AMR) in critical priority pathogens is a significant threat. Non-clinical reservoirs of AMR, such as agriculture and food production facilities, may contribute to the transmission of clinically relevant pathogens such as multidrug-resistant (MDR) Klebsiella pneumoniae. There is currently very limited knowledge regarding the population structure and genomic diversity of K. pneumoniae in poultry production in Pakistan. Methods We explored healthy broilers in a commercial farm from Faisalabad, Pakistan, and identified six K. pneumoniae strains from 100 broiler birds. We characterized the strains, determining clonality, virulence and antimicrobial resistance genes using next generation sequencing. Results The evaluation of antimicrobial susceptibility revealed that all the strains were MDR. Genomic analysis showed that 3/6 strains belonged to ST152, harbouring acquired resistance aminoglycosides [aadA2, aph(4')-Ia], β-lactams (blaSHV-187 , blaLAP2 ), fosfomycin (fosA6), tetracycline (tetA), trimethoprim (dfrA12), quinolone (qnrS1), sulphonamides (sul2) and phenicol (floR). All the strains harboured the efflux pump genes oqxA, oqxB, emrR, kpnG, kpnH, kpnF, baeR, mtdB and mtdC. All six strains encoded identical virulence profiles possessing six genes, i.e., ureA, iutA, entB, allS, fimH and mrkD. Phylogenomic analysis of the dominant sequence type (ST152) present in our dataset with publicly available genomes showed that the isolates clustered to strains mainly from human sources and could pose a potential threat to food safety and public health. Discussion The combination of these findings with antimicrobial use data would allow a better understanding of the selective pressures that may be driving the spread of AMR. This is the first report of MDR K. pneumoniae isolated from broiler hens in Pakistan, and the finding suggests that routine surveillance of WHO critical priority pathogens in such settings would be beneficial to the development of effective control strategies to reduce AMR.
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Affiliation(s)
- Muhammad Moman Khan
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Muhammad Ahmed Mushtaq
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Nayyar Abbas
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | - Fariha Fatima
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
| | - Marjorie J. Gibbon
- Department of Life Sciences, The Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Peter Schierack
- Institute of Biotechnology, Brandenburg University of Technology Cottbus-Senftenberg, Senftenberg, Germany
| | - Mashkoor Mohsin
- Institute of Microbiology, University of Agriculture, Faisalabad, Pakistan
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Ikhimiukor OO, Zac Soligno NI, Akintayo IJ, Marcovici MM, Souza SSR, Workman A, Martin IW, Andam CP. Clonal background and routes of plasmid transmission underlie antimicrobial resistance features of bloodstream Klebsiella pneumoniae. Nat Commun 2024; 15:6969. [PMID: 39138200 PMCID: PMC11322185 DOI: 10.1038/s41467-024-51374-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2024] [Accepted: 08/07/2024] [Indexed: 08/15/2024] Open
Abstract
Bloodstream infections caused by the opportunistic pathogen Klebsiella pneumoniae are associated with adverse health complications and high mortality rates. Antimicrobial resistance (AMR) limits available treatment options, thus exacerbating its public health and clinical burden. Here, we aim to elucidate the population structure of K. pneumoniae in bloodstream infections from a single medical center and the drivers that facilitate the dissemination of AMR. Analysis of 136 short-read genome sequences complemented with 12 long-read sequences shows the population consisting of 94 sequence types (STs) and 99 clonal groups, including globally distributed multidrug resistant and hypervirulent clones. In vitro antimicrobial susceptibility testing and in silico identification of AMR determinants reveal high concordance (90.44-100%) for aminoglycosides, beta-lactams, carbapenems, cephalosporins, quinolones, and sulfonamides. IncF plasmids mediate the clonal (within the same lineage) and horizontal (between lineages) transmission of the extended-spectrum beta-lactamase gene blaCTX-M-15. Nearly identical plasmids are recovered from isolates over a span of two years indicating long-term persistence. The genetic determinants for hypervirulence are carried on plasmids exhibiting genomic rearrangement, loss, and/or truncation. Our findings highlight the importance of considering both the genetic background of host strains and the routes of plasmid transmission in understanding the spread of AMR in bloodstream infections.
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Affiliation(s)
- Odion O Ikhimiukor
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA.
| | - Nicole I Zac Soligno
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, 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, State University of New York at Albany, Albany, NY, USA
| | - Stephanie S R Souza
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA
| | - Adrienne Workman
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Isabella W Martin
- Department of Pathology and Laboratory Medicine, Dartmouth-Hitchcock Medical Center, Lebanon, NH, USA
| | - Cheryl P Andam
- Department of Biological Sciences, State University of New York at Albany, Albany, NY, USA.
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11
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Jia X, Zhu Y, Jia P, Li C, Chu X, Sun T, Liu X, Yu W, Chen F, Xu Y, Yang Q. The key role of iroBCDN-lacking pLVPK-like plasmid in the evolution of the most prevalent hypervirulent carbapenem-resistant ST11-KL64 Klebsiella pneumoniae in China. Drug Resist Updat 2024; 77:101137. [PMID: 39178714 DOI: 10.1016/j.drup.2024.101137] [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: 03/20/2024] [Revised: 07/31/2024] [Accepted: 08/11/2024] [Indexed: 08/26/2024]
Abstract
AIMS Hypervirulent carbapenem-resistant Klebsiella pneumoniae (hv-CRKP), coharboring hypervirulence and carbapenem-resistance genes mediated by plasmids, causes infections with extremely high mortality and seriously impacts public health. Exploring the transfer mechanisms of virulence/carbapenem-resistance plasmids, as well as the formation and evolution pathway of hv-CRKP is of great significance to the control of hv-CRKP infections. METHODS In this study, we identified the predominant clone of hv-CRKP in China and elucidated its genomic characteristics and formation route based on 239 multicenter clinical K. pneumoniae isolates and 1014 GenBank genomes by using comparative genomic analysis. Further, we revealed the factors affecting the transfer of virulence plasmids, and explained the genetic foundation for the prevalence of Chinese predominant hv-CRKP clone. RESULTS ST11-KL64 is the predominant clone of hv-CRKP in China and primarily evolved from ST11-KL64 CRKP by acquiring the pLVPK-like virulence plasmid from hvKP. Significantly, the virulence gene cluster iroBCDN was lost in the virulence plasmid of ST11-KL64 hv-CRKP but existed in that of hvKP. Moreover, the absence of iroBCDN didn't decrease the virulence of hv-CRKP, which was proved by bacterial test, cell-interaction test and mice infection model. On the contrary, loss of iroBCDN was observed to regulate virulence/carbapenem-resistance plasmid transfer and oxidative stress-related genes in strains and thus promoted the mobilization of nonconjugative virulence plasmid from hvKP into ST11-KL64 CRKP, forming hv-CRKP which finally had elevated antioxidant capacity and enhanced survival capacity in macrophages. The loss of iroBCDN increased the survival ability of hv-CRKP without decreasing its virulence, endowing it with an evolutionary advantage. CONCLUSIONS Our work provides new insights into the key role of iroBCDN loss in convergence of CRKP and hvKP, and the genetic and biological foundation for the widespread prevalence of ST11-KL64 hv-CRKP in China.
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Affiliation(s)
- Xinmiao Jia
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Center for bioinformatics, National Infrastructures for Translational Medicine, Institute of Clinical Medicine & Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Ying Zhu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Peiyao Jia
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Cuidan Li
- China National Center for Bioinformation, Beijing, China; Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Xiaobing Chu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Tianshu Sun
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Clinical Biobank, Center for Biomedical Technology, National Science and Technology Key Infrastructure on Translational Medicine, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Xiaoyu Liu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Wei Yu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Fei Chen
- China National Center for Bioinformation, Beijing, China; Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yingchun Xu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Qiwen Yang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China; Key Laboratory of Pathogen Infection Prevention and Control (Peking Union Medical College), Ministry of Education, Beijing, China.
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12
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Jiang C, Yu C, Sun S, Lin J, Cai M, Wei Z, Feng L, Li J, Zhang Y, Dong K, Guo X, Qin J, Zhang Y. A new anti-CRISPR gene promotes the spread of drug-resistance plasmids in Klebsiella pneumoniae. Nucleic Acids Res 2024; 52:8370-8384. [PMID: 38888121 DOI: 10.1093/nar/gkae516] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2024] [Revised: 05/25/2024] [Accepted: 06/07/2024] [Indexed: 06/20/2024] Open
Abstract
The Klebsiella pneumoniae (K. pneumoniae, Kp) populations carrying both resistance-encoding and virulence-encoding mobile genetic elements (MGEs) significantly threaten global health. In this study, we identified a new anti-CRISPR gene (acrIE10) on a conjugative plasmid with self-target sequence in K. pneumoniae with type I-E* CRISPR-Cas system. AcrIE10 interacts with the Cas7* subunit of K. pneumoniae I-E* CRISPR-Cas system. The crystal structure of the AcrIE10-KpCas7* complex suggests that AcrIE10 suppresses the I-E* CRISPR-Cas by binding directly to Cas7 to prevent its hexamerization, thereby preventing the surveillance complex assembly and crRNA loading. Bioinformatic and functional analyses revealed that AcrIE10 is functionally widespread across diverse species. Our study reports a novel anti-CRISPR and highlights its potential role in spreading resistance and virulence among pathogens.
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Affiliation(s)
- Chunyu Jiang
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Chengzhi Yu
- Key Laboratory of Synthetic Biology, State Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shuyi Sun
- Key Laboratory of Synthetic Biology, State Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiajia Lin
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Mufeng Cai
- Shanghai Immune Therapy Institute, Renji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Zhenquan Wei
- Core Facility of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Lingling Feng
- Core Facility of Basic Medical Sciences, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jianhui Li
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
| | - Yan Zhang
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Ke Dong
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Xiaokui Guo
- School of Global Health, Chinese Center for Tropical Diseases Research, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Jinhong Qin
- Department of Microbiology and Immunology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Shanghai Institute of Phage, Shanghai Public Health Clinical Center, Fudan University, Shanghai 201508, China
- NHC Key Laboratory of Parasite and Vector Biology (National Institute of Parasitic Diseases, Chinese Center for Disease Control and Prevention), Shanghai 200025, China
| | - Yu Zhang
- Key Laboratory of Synthetic Biology, State Key Laboratory of Plant Design, CAS Center for Excellence in Molecular Plant Sciences, Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai 200032, China
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13
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Lei TY, Liao BB, Yang LR, Wang Y, Chen XB. Hypervirulent and carbapenem-resistant Klebsiella pneumoniae: A global public health threat. Microbiol Res 2024; 288:127839. [PMID: 39141971 DOI: 10.1016/j.micres.2024.127839] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2024] [Revised: 07/08/2024] [Accepted: 07/13/2024] [Indexed: 08/16/2024]
Abstract
The evolution of hypervirulent and carbapenem-resistant Klebsiella pneumoniae can be categorized into three main patterns: the evolution of KL1/KL2-hvKp strains into CR-hvKp, the evolution of carbapenem-resistant K. pneumoniae (CRKp) strains into hv-CRKp, and the acquisition of hybrid plasmids carrying carbapenem resistance and virulence genes by classical K. pneumoniae (cKp). These strains are characterized by multi-drug resistance, high virulence, and high infectivity. Currently, there are no effective methods for treating and surveillance this pathogen. In addition, the continuous horizontal transfer and clonal spread of these bacteria under the pressure of hospital antibiotics have led to the emergence of more drug-resistant strains. This review discusses the evolution and distribution characteristics of hypervirulent and carbapenem-resistant K. pneumoniae, the mechanisms of carbapenem resistance and hypervirulence, risk factors for susceptibility, infection syndromes, treatment regimens, real-time surveillance and preventive control measures. It also outlines the resistance mechanisms of antimicrobial drugs used to treat this pathogen, providing insights for developing new drugs, combination therapies, and a "One Health" approach. Narrowing the scope of surveillance but intensifying implementation efforts is a viable solution. Monitoring of strains can be focused primarily on hospitals and urban wastewater treatment plants.
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Affiliation(s)
- Ting-Yu Lei
- College of Pharmaceutical Science, Dali University, Dali 671000, China.
| | - Bin-Bin Liao
- College of Pharmaceutical Science, Dali University, Dali 671000, China.
| | - Liang-Rui Yang
- First Affiliated Hospital of Dali University, Yunnan 671000, China.
| | - Ying Wang
- College of Pharmaceutical Science, Dali University, Dali 671000, China.
| | - Xu-Bing Chen
- College of Pharmaceutical Science, Dali University, Dali 671000, China.
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14
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Crestani C, Forde TL, Bell J, Lycett SJ, Oliveira LMA, Pinto TCA, Cobo-Ángel CG, Ceballos-Márquez A, Phuoc NN, Sirimanapong W, Chen SL, Jamrozy D, Bentley SD, Fontaine M, Zadoks RN. Genomic and functional determinants of host spectrum in Group B Streptococcus. PLoS Pathog 2024; 20:e1012400. [PMID: 39133742 PMCID: PMC11341095 DOI: 10.1371/journal.ppat.1012400] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 08/22/2024] [Accepted: 07/08/2024] [Indexed: 08/24/2024] Open
Abstract
Group B Streptococcus (GBS) is a major human and animal pathogen that threatens public health and food security. Spill-over and spill-back between host species is possible due to adaptation and amplification of GBS in new niches but the evolutionary and functional mechanisms underpinning those phenomena are poorly known. Based on analysis of 1,254 curated genomes from all major GBS host species and six continents, we found that the global GBS population comprises host-generalist, host-adapted and host-restricted sublineages, which are found across host groups, preferentially within one host group, or exclusively within one host group, respectively, and show distinct levels of recombination. Strikingly, the association of GBS genomes with the three major host groups (humans, cattle, fish) is driven by a single accessory gene cluster per host, regardless of sublineage or the breadth of host spectrum. Moreover, those gene clusters are shared with other streptococcal species occupying the same niche and are functionally relevant for host tropism. Our findings demonstrate (1) the heterogeneity of genome plasticity within a bacterial species of public health importance, enabling the identification of high-risk clones; (2) the contribution of inter-species gene transmission to the evolution of GBS; and (3) the importance of considering the role of animal hosts, and the accessory gene pool associated with their microbiota, in the evolution of multi-host bacterial pathogens. Collectively, these phenomena may explain the adaptation and clonal expansion of GBS in animal reservoirs and the risk of spill-over and spill-back between animals and humans.
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Affiliation(s)
- Chiara Crestani
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - Taya L. Forde
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, Scotland, United Kingdom
| | - John Bell
- Moredun Research Institute, Penicuik, Scotland, United Kingdom
| | - Samantha J. Lycett
- The Roslin Institute, University of Edinburgh, Midlothian, Scotland, United Kingdom
| | - Laura M. A. Oliveira
- Instituto de Microbiologia Paulo de Goes, Federal University of Rio de Janeiro, Rio de Janeiro, State of Rio de Janeiro, Brazil
| | - Tatiana C. A. Pinto
- Instituto de Microbiologia Paulo de Goes, Federal University of Rio de Janeiro, Rio de Janeiro, State of Rio de Janeiro, Brazil
| | | | | | - Nguyen N. Phuoc
- Faculty of Fisheries, University of Agriculture and Forestry, Hue University, Hue, Vietnam
| | - Wanna Sirimanapong
- Faculty of Veterinary Science, Mahidol University, Nakhon Pathom, Thailand
| | - Swaine L. Chen
- Infectious Diseases Translational Research Programme, Department of Medicine, Division of Infectious Diseases, Yong Loo Lin School of Medicine, National University of Singapore, Singapore
- Laboratory of Bacterial Genomics, Genome Institute of Singapore, Singapore
| | - Dorota Jamrozy
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, England, United Kingdom
| | - Stephen D. Bentley
- Parasites and Microbes Programme, Wellcome Sanger Institute, Hinxton, England, United Kingdom
| | | | - Ruth N. Zadoks
- Institute of Biodiversity, Animal Health & Comparative Medicine, University of Glasgow, Glasgow, Scotland, United Kingdom
- Moredun Research Institute, Penicuik, Scotland, United Kingdom
- Sydney School of Veterinary Science, Faculty of Science, University of Sydney, Camden, NSW, Australia
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15
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Allami M, Mohammed EJ, Alnaji Z, A Jassim S. Antibiotic resistance and its correlation with biofilm formation and virulence genes in Klebsiella pneumoniae isolated from wounds. J Appl Genet 2024:10.1007/s13353-024-00893-w. [PMID: 39031267 DOI: 10.1007/s13353-024-00893-w] [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: 12/16/2023] [Revised: 05/29/2024] [Accepted: 07/12/2024] [Indexed: 07/22/2024]
Abstract
Klebsiella pneumoniae is the most important species of the Klebsiella genus and often causes hospital infections. These bacteria have a high resistance to most of the available drugs, which has caused concern all over the world. In this study, we investigated the antibiotic resistance profile and the ability to produce extended-spectrum beta-lactamase (ESBL) among K. pneumoniae isolates, and then we investigated the relationship between these two factors with biofilm formation and the prevalence of different virulence genes. In this study, 130 isolates of K. pneumoniae isolated from wounds were investigated. The antibiotic resistance of the isolates was evaluated by the disk diffusion method. The microtiter plate method was used to measure biofilm formation. The prevalence of virulence genes was detected by multiplex PCR. Among the examined isolates, 85.3% showed multidrug resistance. 87.6% of the isolates were ESBL-positive. Imipenem, meropenem, and fosfomycin were the most effective drugs. The ability of the isolates to produce biofilm was strong (80%), moderate (12.3%), and weak (7.6%), respectively. fimH, mrKD, entB, and tolC virulence genes were observed in all isolates. High prevalence of antibiotic resistance (especially multidrug resistance), high prevalence of ESBL-producing isolates, the ability of all isolates to biofilm formation, and the presence of fimH, mrKD, entB, and tolC virulence genes in all isolates show the importance of these factors in the pathogenesis of K. pneumoniae isolates in Iraq.
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Affiliation(s)
- Mohammed Allami
- Department of Dentistry, Al-Manara College for Medical Sciences, Misan, Iraq.
- Department of Biology, Faculty of Science, Ferdowsi University of Mashhad, Mashhad, Iran.
- Microbiology Laboratory, Qal'at Saleh General Hospital, Misan Health Department, Misan, Iraq.
| | - Eman Jassim Mohammed
- Department of Microbiology, College of Science, Mustansiriyah University, Baghdad, Iraq
| | - Zainab Alnaji
- College of Pharmacy, University of Misan, Misan, Iraq
| | - Salsabil A Jassim
- Department of Biology, College of Science, Mustansiriyah University, Baghdad, Iraq
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16
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O’Brien B, Yushchenko A, Suh J, Jung D, Cai Z, Nguyen NS, Semret M, Dufour S, Ronholm J. Draft genome sequences of 148 Klebsiella pneumoniae species complex members from bovine and human hosts. Microbiol Resour Announc 2024; 13:e0013224. [PMID: 38864639 PMCID: PMC11256802 DOI: 10.1128/mra.00132-24] [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: 02/13/2024] [Accepted: 05/21/2024] [Indexed: 06/13/2024] Open
Abstract
Klebsiella pneumoniae species complex members, particularly K. pnemoniae sensu stricto, are common bovine clinical mastitis pathogens and often the cause of hospital- and community-acquired infections in humans. Here, we present 148 draft genome assemblies and annotations of K. pneumoniae species complex members from bovine and human hosts in Canada.
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Affiliation(s)
- Bridget O’Brien
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montréal, Québec, Canada
| | - Alla Yushchenko
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montréal, Québec, Canada
| | - Jinha Suh
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montréal, Québec, Canada
| | - Dongyun Jung
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montréal, Québec, Canada
- Mastitis Network, Saint-Hyacinthe, Québec, Canada
- Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Québec, Canada
| | - Zhangbin Cai
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montréal, Québec, Canada
| | - Ngoc Sang Nguyen
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montréal, Québec, Canada
| | - Makeda Semret
- McGill University Health Centre (Infectious Diseases and Medical Microbiology), Montréal, Québec, Canada
| | - Simon Dufour
- Mastitis Network, Saint-Hyacinthe, Québec, Canada
- Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Québec, Canada
- Faculté de Médecine Vétérinaire, Université de Montréal, Saint-Hyacinthe, Québec, Canada
| | - Jennifer Ronholm
- Faculty of Agricultural and Environmental Sciences, Macdonald Campus, McGill University, Montréal, Québec, Canada
- Mastitis Network, Saint-Hyacinthe, Québec, Canada
- Regroupement FRQNT Op+Lait, Saint-Hyacinthe, Québec, Canada
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17
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Elgayar FA, Gouda MK, Badran AA, El Halfawy NM. Pathogenomics analysis of high-risk clone ST147 multidrug-resistant Klebsiella pneumoniae isolated from a patient in Egypt. BMC Microbiol 2024; 24:256. [PMID: 38987681 PMCID: PMC11234735 DOI: 10.1186/s12866-024-03389-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Accepted: 06/19/2024] [Indexed: 07/12/2024] Open
Abstract
BACKGROUND The emergence of multi-drug-resistant Klebsiella pneumoniae (MDR-KP) represents a serious clinical health concern. Antibiotic resistance and virulence interactions play a significant role in the pathogenesis of K. pneumoniae infections. Therefore, tracking the clinical resistome and virulome through monitoring antibiotic resistance genes (ARG) and virulence factors in the bacterial genome using computational analysis tools is critical for predicting the next epidemic. METHODS In the current study, one hundred extended spectrum β-lactamase (ESBL)-producing clinical isolates were collected from Mansoura University Hospital, Egypt, in a six-month period from January to June 2022. One isolate was selected due to the high resistance phenotype, and the genetic features of MDR-KP recovered from hospitalized patient were investigated. Otherwise, the susceptibility to 25 antimicrobials was determined using the DL Antimicrobial Susceptibility Testing (AST) system. Whole genome sequencing (WGS) using Illumina NovaSeq 6000 was employed to provide genomic insights into K. pneumoniae WSF99 clinical isolate. RESULTS The isolate K. pneumoniae WSF99 was phenotypically resistant to the antibiotics under investigation via antibiotic susceptibility testing. WGS analysis revealed that WSF99 total genome length was 5.7 Mb with an estimated 5,718 protein-coding genes and a G + C content of 56.98 mol%. Additionally, the allelic profile of the WSF99 isolate was allocated to the high-risk clone ST147. Furthermore, diverse antibiotic resistance genes were determined in the genome that explain the high-level resistance phenotypes. Several β-lactamase genes, including blaCTX-M-15, blaTEM-1, blaTEM-12, blaSHV-11, blaSHV-67, and blaOXA-9, were detected in the WSF99 isolate. Moreover, a single carbapenemase gene, blaNDM-5, was predicted in the genome, positioned within a mobile cassette. In addition, other resistance genes were predicted in the genome including, aac(6')-Ib, aph(3')-VI, sul1, sul2, fosA, aadA, arr-2, qnrS1, tetA and tetC. Four plasmid replicons CoIRNAI, IncFIB(K), IncFIB(pQil), and IncR were predicted in the genome. The draft genome analysis revealed the occurrence of genetic mobile elements positioned around the ARGs, suggesting the ease of dissemination via horizontal gene transfer. CONCLUSIONS This study reports a comprehensive pathogenomic analysis of MDR-KP isolated from a hospitalized patient. These findings could be relevant for future studies investigating the diversity of antimicrobial resistance and virulence in Egypt.
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Affiliation(s)
- Fatma A Elgayar
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Moharram Bek 21511, Alexandria, Egypt
| | - Mona K Gouda
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Moharram Bek 21511, Alexandria, Egypt
| | - Alaa Aboelnour Badran
- Department of Clinical Pathology, Faculty of Medicine, Mansoura University, Mansoura, Egypt
| | - Nancy M El Halfawy
- Department of Botany and Microbiology, Faculty of Science, Alexandria University, Moharram Bek 21511, Alexandria, Egypt.
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18
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Sundaresan AK, Gangwar J, Murugavel A, Malli Mohan GB, Ramakrishnan J. Complete genome sequence, phenotypic correlation and pangenome analysis of uropathogenic Klebsiella spp. AMB Express 2024; 14:78. [PMID: 38965152 PMCID: PMC11224175 DOI: 10.1186/s13568-024-01737-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2024] [Accepted: 06/25/2024] [Indexed: 07/06/2024] Open
Abstract
Urinary tract infections (UTI) by antibiotic resistant and virulent K. pneumoniae are a growing concern. Understanding the genome and validating the genomic profile along with pangenome analysis will facilitate surveillance of high-risk clones of K. pneumoniae to underpin management strategies toward early detection. The present study aims to correlate resistome with phenotypic antimicrobial resistance and virulome with pathogenicity in Klebsiella spp. The present study aimed to perform complete genome sequences of Klebsiella spp. and to analyse the correlation of resistome with phenotypic antimicrobial resistance and virulome with pathogenicity. To understand the resistome, pangenome and virulome in the Klebsiella spp, the ResFinder, CARD, IS Finder, PlasmidFinder, PHASTER, Roary, VFDB were used. The phenotypic susceptibility profiling identified the uropathogenic kp3 to exhibit multi drug resistance. The resistome and in vitro antimicrobial profiling showed concordance with all the tested antibiotics against the study strains. Hypermucoviscosity was not observed for any of the test isolates; this phenotypic character matches perfectly with the absence of rmpA and magA genes. To the best of our knowledge, this is the first report on the presence of ste, stf, stc and sti major fimbrial operons of Salmonella enterica serotype Typhimurium in K. pneumoniae genome. The study identifies the discordance of virulome and virulence in Klebsiella spp. The complete genome analysis and phenotypic correlation identify uropathogenic K. pneumoniae kp3 as a carbapenem-resistant and virulent pathogen. The Pangenome of K. pneumoniae was open suggesting high genetic diversity. Diverse K serotypes were observed. Sequence typing reveals the prevalence of K. pneumoniae high-risk clones in UTI catheterised patients. The study also highlights the concordance of resistome and in vitro susceptibility tests. Importantly, the study identifies the necessity of virulome and phenotypic virulence markers for timely diagnosis and immediate treatment for the management of high-risk K. pneumoniae clones.
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Affiliation(s)
- Abhirami Krishnamoorthy Sundaresan
- Actinomycetes Bioprospecting Lab, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Tirumalaisamudram, Thanjavur, 613401, Tamil Nadu, India
| | - Jaya Gangwar
- Actinomycetes Bioprospecting Lab, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Tirumalaisamudram, Thanjavur, 613401, Tamil Nadu, India
| | - Aravind Murugavel
- Actinomycetes Bioprospecting Lab, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Tirumalaisamudram, Thanjavur, 613401, Tamil Nadu, India
| | - Ganesh Babu Malli Mohan
- Microbial Omics Lab, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Tirumalaisamudram, Thanjavur, 613401, Tamil Nadu, India
- Center for Tropical and Emerging Global Diseases (CTEGD), University of Georgia, Georgia, Athens, United States of America
| | - Jayapradha Ramakrishnan
- Actinomycetes Bioprospecting Lab, Centre for Research in Infectious Diseases (CRID), School of Chemical and Biotechnology (SCBT), SASTRA Deemed University, Tirumalaisamudram, Thanjavur, 613401, Tamil Nadu, India.
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19
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Kim N, Ma J, Kim W, Kim J, Belenky P, Lee I. Genome-resolved metagenomics: a game changer for microbiome medicine. Exp Mol Med 2024; 56:1501-1512. [PMID: 38945961 PMCID: PMC11297344 DOI: 10.1038/s12276-024-01262-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 03/06/2024] [Accepted: 03/25/2024] [Indexed: 07/02/2024] Open
Abstract
Recent substantial evidence implicating commensal bacteria in human diseases has given rise to a new domain in biomedical research: microbiome medicine. This emerging field aims to understand and leverage the human microbiota and derivative molecules for disease prevention and treatment. Despite the complex and hierarchical organization of this ecosystem, most research over the years has relied on 16S amplicon sequencing, a legacy of bacterial phylogeny and taxonomy. Although advanced sequencing technologies have enabled cost-effective analysis of entire microbiota, translating the relatively short nucleotide information into the functional and taxonomic organization of the microbiome has posed challenges until recently. In the last decade, genome-resolved metagenomics, which aims to reconstruct microbial genomes directly from whole-metagenome sequencing data, has made significant strides and continues to unveil the mysteries of various human-associated microbial communities. There has been a rapid increase in the volume of whole metagenome sequencing data and in the compilation of novel metagenome-assembled genomes and protein sequences in public depositories. This review provides an overview of the capabilities and methods of genome-resolved metagenomics for studying the human microbiome, with a focus on investigating the prokaryotic microbiota of the human gut. Just as decoding the human genome and its variations marked the beginning of the genomic medicine era, unraveling the genomes of commensal microbes and their sequence variations is ushering us into the era of microbiome medicine. Genome-resolved metagenomics stands as a pivotal tool in this transition and can accelerate our journey toward achieving these scientific and medical milestones.
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Affiliation(s)
- Nayeon Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Junyeong Ma
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Wonjong Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Jungyeon Kim
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea
| | - Peter Belenky
- Department of Molecular Microbiology and Immunology, Brown University, Providence, RI, 02912, USA.
| | - Insuk Lee
- Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, 03722, Republic of Korea.
- POSTECH Biotech Center, Pohang University of Science and Technology (POSTECH), Pohang, 37673, Republic of Korea.
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20
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Rahmat Ullah S, Jamal M, Rahman A, Andleeb S. Comprehensive insights into Klebsiella pneumoniae: unravelling clinical impact, epidemiological trends and antibiotic-resistance challenges. J Antimicrob Chemother 2024; 79:1484-1492. [PMID: 38832539 DOI: 10.1093/jac/dkae184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 05/08/2024] [Indexed: 06/05/2024] Open
Abstract
Klebsiella pneumoniae, a challenging opportunistic bacterium, became a notable global health concern owing to its clinical impact, widespread epidemiology and escalating antibiotic resistance. This comprehensive review delves into the multifaceted dimensions of K. pneumoniae, with a focus on its clinical implications, epidemiological patterns and the critical issue of antibiotic resistance. The review also emphasizes the implications of K. pneumoniae in the context of antimicrobial stewardship and infection control. Epidemiological aspects are scrutinized, shedding light on the global distribution and prevalence of K. pneumoniae. Factors influencing its transmission and persistence in healthcare facilities and communities are examined, with patient demographics, healthcare practices and geographical variations. The review centres on antibiotic resistance, a critical issue in the era of bacteria displaying resistance to multiple drugs. The mechanisms of resistance used by K. pneumoniae against various classes of antibiotics are elucidated, along with the alarming rise of carbapenem-resistant strains. It also highlights ongoing research efforts and innovative strategies aimed at addressing this critical public health issue. This comprehensive review offers a holistic understanding of K. pneumoniae, emphasizing its clinical significance, global epidemiology and the immediate necessity for effective strategies to combat antibiotic resistance. It serves as a valuable resource for healthcare practitioners, researchers and policymakers seeking to manage better and mitigate the impact of this pathogen on public health.
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Affiliation(s)
- Sidra Rahmat Ullah
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan
| | - Muhsin Jamal
- Department of Microbiology, Abdul Wali Khan University, Mardan, 23200 Mardan, Pakistan
| | - Abdur Rahman
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan
| | - Saadia Andleeb
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan
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Shamanna V, Srinivas S, Couto N, Nagaraj G, Sajankila SP, Krishnappa HG, Kumar KA, Aanensen DM, Lingegowda RK. Geographical distribution, disease association and diversity of Klebsiella pneumoniae K/L and O antigens in India: roadmap for vaccine development. Microb Genom 2024; 10:001271. [PMID: 39037209 PMCID: PMC11316559 DOI: 10.1099/mgen.0.001271] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Accepted: 06/25/2024] [Indexed: 07/23/2024] Open
Abstract
Klebsiella pneumoniae poses a significant healthcare challenge due to its multidrug resistance and diverse serotype landscape. This study aimed to explore the serotype diversity of 1072 K. pneumoniae and its association with geographical distribution, disease severity and antimicrobial/virulence patterns in India. Whole-genome sequencing was performed on the Illumina platform, and genomic analysis was carried out using the Kleborate tool. The analysis revealed a total of 78 different KL types, among which KL64 (n=274/1072, 26 %), KL51 (n=249/1072, 24 %), and KL2 (n=88/1072, 8 %) were the most prevalent. In contrast, only 13 distinct O types were identified, with O1/O2v1 (n=471/1072, 44 %), O1/O2v2 (n=353/1072, 33 %), and OL101 (n=66/1072, 6 %) being the predominant serotypes. The study identified 114 different sequence types (STs) with varying serotypes, with ST231 being the most predominant. O serotypes were strongly linked with STs, with O1/O2v1 predominantly associated with ST231. Simpson's diversity index and Fisher's exact test revealed higher serotype diversity in the north and east regions, along with intriguing associations between specific serotypes and resistance profiles. No significant association between KL or O types and disease severity was observed. Furthermore, we found the specific association of virulence factors yersiniabactin and aerobactin (P<0.05) with KL types but no association with O antigen types (P>0.05). Conventionally described hypervirulent clones (i.e. KL1 and KL2) in India lacked typical virulent markers (i.e. aerobactin), contrasting with other regional serotypes (KL51). The cumulative distribution of KL and O serotypes suggests that future vaccines may have to include either ~20 KL or four O types to cover >85 % of the carbapenemase-producing Indian K. pneumoniae population. The results highlight the necessity for comprehensive strategies to manage the diverse landscape of K. pneumoniae strains across different regions in India. Understanding regional serotype dynamics is pivotal for targeted surveillance, interventions, and tailored vaccine strategies to tackle the diverse landscape of K. pneumoniae infections across India. This article contains data hosted by Microreact.
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Affiliation(s)
- Varun Shamanna
- Central Research Laboratory, KIMS, Bengaluru, India
- Department of Biotechnology, NMAM Institute of Technology, Nitte, Udupi, India
| | | | - Natacha Couto
- Centre for Genomic Pathogen Surveillance, Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | | | | | | | | | - David M. Aanensen
- Centre for Genomic Pathogen Surveillance, Pandemic Sciences Institute, University of Oxford, Oxford, UK
| | | | - NIHR Global Health Research Unit on genomic surveillance - India consortium
- Central Research Laboratory, KIMS, Bengaluru, India
- Department of Biotechnology, NMAM Institute of Technology, Nitte, Udupi, India
- Centre for Genomic Pathogen Surveillance, Pandemic Sciences Institute, University of Oxford, Oxford, UK
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22
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Mills RO, Dadzie I, Le-Viet T, Baker DJ, Addy HPK, Akwetey SA, Donkoh IE, Quansah E, Semanshia PS, Morgan J, Mensah A, Adade NE, Ampah EO, Owusu E, Mwintige P, Amoako EO, Spadar A, Holt KE, Foster-Nyarko E. Genomic diversity and antimicrobial resistance in clinical Klebsiella pneumoniae isolates from tertiary hospitals in Southern Ghana. J Antimicrob Chemother 2024; 79:1529-1539. [PMID: 38751093 PMCID: PMC11215549 DOI: 10.1093/jac/dkae123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2024] [Accepted: 04/09/2024] [Indexed: 07/02/2024] Open
Abstract
OBJECTIVES Comprehensive data on the genomic epidemiology of hospital-associated Klebsiella pneumoniae in Ghana are scarce. This study investigated the genomic diversity, antimicrobial resistance patterns, and clonal relationships of 103 clinical K. pneumoniae isolates from five tertiary hospitals in Southern Ghana-predominantly from paediatric patients aged under 5 years (67/103; 65%), with the majority collected from urine (32/103; 31%) and blood (25/103; 24%) cultures. METHODS We generated hybrid Nanopore-Illumina assemblies and employed Pathogenwatch for genotyping via Kaptive [capsular (K) locus and lipopolysaccharide (O) antigens] and Kleborate (antimicrobial resistance and hypervirulence) and determined clonal relationships using core-genome MLST (cgMLST). RESULTS Of 44 distinct STs detected, ST133 was the most common, comprising 23% of isolates (n = 23/103). KL116 (28/103; 27%) and O1 (66/103; 64%) were the most prevalent K-locus and O-antigen types. Single-linkage clustering highlighted the global spread of MDR clones such as ST15, ST307, ST17, ST11, ST101 and ST48, with minimal allele differences (1-5) from publicly available genomes worldwide. Conversely, 17 isolates constituted novel clonal groups and lacked close relatives among publicly available genomes, displaying unique genetic diversity within our study population. A significant proportion of isolates (88/103; 85%) carried resistance genes for ≥3 antibiotic classes, with the blaCTX-M-15 gene present in 78% (n = 80/103). Carbapenem resistance, predominantly due to blaOXA-181 and blaNDM-1 genes, was found in 10% (n = 10/103) of the isolates. CONCLUSIONS Our findings reveal a complex genomic landscape of K. pneumoniae in Southern Ghana, underscoring the critical need for ongoing genomic surveillance to manage the substantial burden of antimicrobial resistance.
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Affiliation(s)
- Richael O Mills
- Department of Biomedical Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Isaac Dadzie
- Department of Medical Laboratory Technology, University of Cape Coast, Cape Coast, Ghana
| | - Thanh Le-Viet
- Quadram Institute Biosciences, Norwich Research Park, Norwich NR4 7UQ, UK
| | - David J Baker
- Quadram Institute Biosciences, Norwich Research Park, Norwich NR4 7UQ, UK
| | - Humphrey P K Addy
- Department of Biomedical Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Samuel A Akwetey
- Department of Clinical Microbiology, University of Development Studies, Tamale, Ghana
| | - Irene E Donkoh
- Department of Medical Laboratory Technology, University of Cape Coast, Cape Coast, Ghana
| | - Elvis Quansah
- Department of Biomedical Sciences, University of Cape Coast, Cape Coast, Ghana
- Anhui Provincial Laboratory of Microbiology and Parasitology, Anhui Key Laboratory of Zoonoses, Department of Microbiology and Parasitology, School of Basic Medical Sciences, Anhui Medical University, Hefei, China
| | - Prince S Semanshia
- Department of Biomedical Sciences, University of Cape Coast, Cape Coast, Ghana
| | - Jennifer Morgan
- Department of Medical Laboratory Technology, University of Cape Coast, Cape Coast, Ghana
| | - Abraham Mensah
- Department of Microbiology and Immunology, University of Cape Coast, Cape Coast, Ghana
| | - Nana E Adade
- West African Centre for Cell Biology of Infectious Pathogens, College of Basic and Applied Sciences, University of Ghana, Accra, Ghana
- Department of Microbiology, Korle-Bu Teaching Hospital, Accra, Ghana
| | - Emmanuel O Ampah
- Microbiology Department, Greater Accra Regional Hospital, Ridge, Accra, Ghana
| | - Emmanuel Owusu
- Microbiology Department, Greater Accra Regional Hospital, Ridge, Accra, Ghana
| | - Philimon Mwintige
- Microbiology Laboratory, Cape Coast Teaching Hospital, Cape Coast, Ghana
| | - Eric O Amoako
- Public Health Laboratory, Effia Nkwanta Regional Hospital, Sekondi-Takoradi, Ghana
| | - Anton Spadar
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, Keppel Street, London, UK
| | - Kathryn E Holt
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, Keppel Street, London, UK
| | - Ebenezer Foster-Nyarko
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, Keppel Street, London, UK
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23
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Lee GY, Song J. Single missense mutations in Vi capsule synthesis genes confer hypervirulence to Salmonella Typhi. Nat Commun 2024; 15:5258. [PMID: 38898034 PMCID: PMC11187135 DOI: 10.1038/s41467-024-49590-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2024] [Accepted: 06/07/2024] [Indexed: 06/21/2024] Open
Abstract
Many bacterial pathogens, including the human exclusive pathogen Salmonella Typhi, express capsular polysaccharides as a crucial virulence factor. Here, through S. Typhi whole genome sequence analyses and functional studies, we found a list of single point mutations that make S. Typhi hypervirulent. We discovered a single point mutation in the Vi biosynthesis enzymes that control Vi polymerization or acetylation is enough to result in different capsule variants of S. Typhi. All variant strains are pathogenic, but the hyper Vi capsule variants are particularly hypervirulent, as demonstrated by the high morbidity and mortality rates observed in infected mice. The hypo Vi capsule variants have primarily been identified in Africa, whereas the hyper Vi capsule variants are distributed worldwide. Collectively, these studies increase awareness about the existence of different capsule variants of S. Typhi, establish a solid foundation for numerous future studies on S. Typhi capsule variants, and offer valuable insights into strategies to combat capsulated bacteria.
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Affiliation(s)
- Gi Young Lee
- Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA
| | - Jeongmin Song
- Department of Microbiology and Immunology, Cornell University College of Veterinary Medicine, Ithaca, NY, 14853, USA.
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24
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Cismaru IM, Văcăroiu MC, Soium E, Holban T, Radu AM, Melinte V, Gheorghiță V. Synergistic Combination of Aztreonam and Ceftazidime-Avibactam-A Promising Defense Strategy against OXA-48 + NDM Klebsiella pneumoniae in Romania. Antibiotics (Basel) 2024; 13:550. [PMID: 38927216 PMCID: PMC11201077 DOI: 10.3390/antibiotics13060550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2024] [Revised: 06/03/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
With the increasing burden of carbapenem-resistant Klebsiella pneumoniae (CR-Kp), including high rates of healthcare-associated infections, treatment failure, and mortality, a good therapeutic strategy for attacking this multi-resistant pathogen is one of the main goals in current medical practice and necessitates the use of novel antibiotics or new drug combinations. OBJECTIVES We reviewed the clinical and microbiological outcomes of seven patients treated at the "Agrippa Ionescu" Clinical Emergency Hospital between October 2023 and January 2024, aiming to demonstrate the synergistic activity of the ceftazidime-avibactam (C/A) plus aztreonam (ATM) combination against the co-producers of blaNDM + blaOXA-48-like CR-Kp. MATERIAL AND METHODS Seven CR-Kp with blaNDM and blaOXA-48 as resistance mechanisms were tested. Seven patients treated with C/A + ATM were included. The synergistic activity of C/A + ATM was proven through double-disk diffusion in all seven isolates. Resistance mechanisms like KPC, VIM, OXA-48, NDM, IMP, and CTX-M were assessed through immunochromatography. RESULTS With a mean of nine days of treatment with the synergistic combination C/A + ATM, all patients achieved clinical recovery, and five achieved microbiological recovery. CONCLUSIONS With the emerging co-occurrence of blaOXA-48 and blaNDM among Kp in Romania, the combination of C/A and ATM could be a promising therapeutic option.
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Affiliation(s)
- Ioana Miriana Cismaru
- Agrippa Ionescu Clinical Emergency Hospital, 011356 Bucharest, Romania; (I.M.C.); (E.S.); (T.H.); (A.M.R.); (V.M.); (V.G.)
| | - Maria Cristina Văcăroiu
- Agrippa Ionescu Clinical Emergency Hospital, 011356 Bucharest, Romania; (I.M.C.); (E.S.); (T.H.); (A.M.R.); (V.M.); (V.G.)
| | - Elif Soium
- Agrippa Ionescu Clinical Emergency Hospital, 011356 Bucharest, Romania; (I.M.C.); (E.S.); (T.H.); (A.M.R.); (V.M.); (V.G.)
| | - Tiberiu Holban
- Agrippa Ionescu Clinical Emergency Hospital, 011356 Bucharest, Romania; (I.M.C.); (E.S.); (T.H.); (A.M.R.); (V.M.); (V.G.)
| | - Adelina Maria Radu
- Agrippa Ionescu Clinical Emergency Hospital, 011356 Bucharest, Romania; (I.M.C.); (E.S.); (T.H.); (A.M.R.); (V.M.); (V.G.)
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Violeta Melinte
- Agrippa Ionescu Clinical Emergency Hospital, 011356 Bucharest, Romania; (I.M.C.); (E.S.); (T.H.); (A.M.R.); (V.M.); (V.G.)
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
| | - Valeriu Gheorghiță
- Agrippa Ionescu Clinical Emergency Hospital, 011356 Bucharest, Romania; (I.M.C.); (E.S.); (T.H.); (A.M.R.); (V.M.); (V.G.)
- Faculty of Medicine, Carol Davila University of Medicine and Pharmacy, 020021 Bucharest, Romania
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25
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Silva JTP, Santos FF, Valiatti TB, Valêncio A, Ribeiro ÁCDS, Oliveira LFV, Cayô R, Pignatari ACC, Gales AC. Unravelling the genomic characteristics of a Klebsiella quasipneumoniae clinical isolate carrying bla NDM-1. J Glob Antimicrob Resist 2024; 38:302-305. [PMID: 38852850 DOI: 10.1016/j.jgar.2024.05.022] [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: 10/05/2023] [Revised: 05/23/2024] [Accepted: 05/29/2024] [Indexed: 06/11/2024] Open
Abstract
OBJECTIVE Despite the increasing reports of blaNDM in Enterobacterales in Brazil, comprehensive whole genome sequencing (WGS) data remain scarce. To address this knowledge gap, our study focuses on the characterization of the genome of an New Delhi Metallo-β-lactamase (NDM)-1-producing Klebsiella quasipneumoniae subsp. quasipneumoniae (KQPN) clinical strain isolated in Brazil. METHODS The antimicrobial susceptibility profile of the A-73.113 strain was performed by agar dilution or broth microdilution following the Brazilian Antimicrobial Susceptibility Testing Committee/European Committee on Antimicrobial Susceptibility Testing recommendations. WGS was performed using the Illumina® NextSeq platform and the generated reads were assembled using the SPAdes software. The sequences obtained were submitted to the bioinformatics pipelines to determine the sequence type, resistome, plasmidome, and virulome. RESULTS The A-73.113 strain was identified as KQPN and was susceptible to polymyxins (MICs, ≤0.25 µg/mL), tigecycline (MIC, 0.5 µg/mL), ciprofloxacin (MIC, 0.5 µg/mL), and levofloxacin (MIC, 1 µg/mL). WGS analysis revealed the presence of genes conferring resistance to β-lactams (blaNDM-1, blaCTX-M-15, blaOXA-9, blaOKP-A-5, blaTEM-1), aminoglycosides [aph(3')-VI, aadA1, aac(6')-Ib], and fluoroquinolones (oqxAB, qnrS1, aac(6')-Ib-cr]. Additionally, the presence of the plasmid replicons Col(pHAD28), IncFIA(HI1), IncFIB(K) (pCAV1099-114), IncFIB(pQil), and IncFII(K), as well as virulence-encoding genes fimABCDEFGHIK (type 1 fimbria), pilW (type IV pili), iutA (aerobactin), entABCDEFS/fepABCDG/fes (Ent siderophores), iroE (salmochelin), and allABCDRS (allantoin utilization) was verified. Furthermore, we found that the A-73.113 strain belongs to ST1040. CONCLUSIONS Here we report the genomic characteristics of an NDM-1-producing KQPN ST1040 strain isolated from blood cultures in Brazil. These data will enhance our comprehension of how this species contributes to the acquisition and dissemination of blaNDM-1 in Brazilian nosocomial settings.
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Affiliation(s)
- Juliana Thalita P Silva
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil
| | - Fernanda F Santos
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil.
| | - Tiago B Valiatti
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil
| | - André Valêncio
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil
| | - Ághata Cardoso da Silva Ribeiro
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil
| | | | - Rodrigo Cayô
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil; Universidade Federal de São Paulo (UNIFESP), Laboratório de Bacteriologia e Imunologia (LIB), Setor de Biologia Molecular, Microbiologia e Imunologia, Departamento de Ciências Biológicas (DCB), Instituto de Ciências Ambientais, Químicas e Farmacêuticas (ICAQF), Diadema SP, Brazil
| | - Antônio Carlos C Pignatari
- Universidade Federal de São Paulo (UNIFESP), Laboratório Especial de Microbiologia Clínica (LEMC), Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil
| | - Ana Cristina Gales
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil; Universidade Federal de São Paulo (UNIFESP), Laboratório Especial de Microbiologia Clínica (LEMC), Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil
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Wu Y, Yu W, Chu X, Zhang J, Jia P, Liu X, Zhu Y, Xu Y, Yang Q. Effect of ceftazidime-avibactam combined with different antimicrobials against carbapenem-resistant Klebsiella pneumoniae. Microbiol Spectr 2024; 12:e0010724. [PMID: 38712934 PMCID: PMC11237391 DOI: 10.1128/spectrum.00107-24] [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: 01/13/2024] [Accepted: 04/05/2024] [Indexed: 05/08/2024] Open
Abstract
This study aimed to assess the in vitro efficacy of ceftazidime-avibactam (CZA) in combination with various antimicrobial agents against carbapenem-resistant Klebsiella pneumoniae (CRKP). We selected 59 clinical CRKP isolates containing distinct drug resistance mechanisms. The minimum inhibitory concentrations (MICs) of meropenem (MEM), colistin (COL), eravacycline (ERA), amikacin (AK), fosfomycin (FOS), and aztreonam (ATM), both individually and in combination with CZA, were tested using the checkerboard method. The interactions of antimicrobial agent combinations were assessed by fractional inhibitory concentration index (FICI) and susceptible breakpoint index (SBPI). The time-kill curve assay was employed to dynamically evaluate the effects of these drugs alone and in combination format. In the checkerboard assay, the combination of CZA+MEM showed the highest level of synergistic effect against both KPC-producing and carbapenemase-non-producing isolates, with synergy rates of 91.3% and 100%, respectively. Following closely was the combination of FOS+CZA . For metallo-beta-lactamases (MBLs) producing strains, ATM+CZA displayed complete synergy, while the combination of MEM+CZA showed a synergy rate of only 57.14% for NDM-producing strains and 91.67% for IMP-producing strains. In the time-kill assay, MEM+CZA also demonstrated significant synergistic effects against the two KPC-2-producing isolates (Y070 and L70), the two carbapenemase-non-producing isolates (Y083 and L093), and the NDM-1-producing strain L13, with reductions in log10 CFU/mL exceeding 10 compared to the control. Against the IMP-producing strain Y047, ATM+CZA exhibited the highest synergistic effect, resulting in a log10 CFU/mL reduction of 10.43 compared to the control. The combination of CZA and MEM exhibited good synergistic effects against KPC-producing and non-enzyme-producing strains, followed by the FOS+CZA combination. Among MBL-producing strains, ATM+CZA demonstrated the most pronounced synergistic effect. However, the combinations of CZA with ERA, AK, and COL show irrelevant effects against the tested clinical isolates. IMPORTANCE Our study confirmed the efficacy of the combination CZA+MEM against KPC-producing and non-carbapenemase-producing strains. For metalloenzyme-producing strains, CZA+ATM demonstrated the most significant synergy. Additionally, CZA exhibited a notable synergy effect when combined with FOS. These combination therapies present promising new options for the treatment of CRKP infection.
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Affiliation(s)
- Yun Wu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Beijing, China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Wei Yu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Beijing, China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xiaobing Chu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Beijing, China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Jingjia Zhang
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Beijing, China
| | - Peiyao Jia
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Beijing, China
| | - XiaoYu Liu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Beijing, China
| | - Ying Zhu
- Department of Clinical Laboratory, State Key Laboratory of Complex Severe and Rare Diseases, Peking Union Medical College Hospital, Beijing, China
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - YingChun Xu
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Qiwen Yang
- Graduate School, Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
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Miller WR, Arias CA. ESKAPE pathogens: antimicrobial resistance, epidemiology, clinical impact and therapeutics. Nat Rev Microbiol 2024:10.1038/s41579-024-01054-w. [PMID: 38831030 DOI: 10.1038/s41579-024-01054-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2024] [Indexed: 06/05/2024]
Abstract
The rise of antibiotic resistance and a dwindling antimicrobial pipeline have been recognized as emerging threats to public health. The ESKAPE pathogens - Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp. - were initially identified as critical multidrug-resistant bacteria for which effective therapies were rapidly needed. Now, entering the third decade of the twenty-first century, and despite the introduction of several new antibiotics and antibiotic adjuvants, such as novel β-lactamase inhibitors, these organisms continue to represent major therapeutic challenges. These bacteria share several key biological features, including adaptations for survival in the modern health-care setting, diverse methods for acquiring resistance determinants and the dissemination of successful high-risk clones around the world. With the advent of next-generation sequencing, novel tools to track and combat the spread of these organisms have rapidly evolved, as well as renewed interest in non-traditional antibiotic approaches. In this Review, we explore the current epidemiology and clinical impact of this important group of bacterial pathogens and discuss relevant mechanisms of resistance to recently introduced antibiotics that affect their use in clinical settings. Furthermore, we discuss emerging therapeutic strategies needed for effective patient care in the era of widespread antimicrobial resistance.
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Affiliation(s)
- William R Miller
- Department of Internal Medicine, Division of Infectious Diseases, Houston Methodist Hospital, Houston, TX, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Cesar A Arias
- Department of Internal Medicine, Division of Infectious Diseases, Houston Methodist Hospital, Houston, TX, USA.
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX, USA.
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
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Monteiro ADSS, Cordeiro SM, Reis JN. Virulence Factors in Klebsiella pneumoniae: A Literature Review. Indian J Microbiol 2024; 64:389-401. [PMID: 39011017 PMCID: PMC11246375 DOI: 10.1007/s12088-024-01247-0] [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: 01/09/2024] [Accepted: 02/28/2024] [Indexed: 07/17/2024] Open
Abstract
Klebsiella pneumoniae, a member of the autochthonous human gut microbiota, utilizes a variety of virulence factors for survival and pathogenesis. Consequently, it is responsible for several human infections, including urinary tract infections, respiratory tract infections, liver abscess, meningitis, bloodstream infections, and medical device-associated infections. The main studied virulence factors in K. pneumoniae are capsule-associated, fimbriae, siderophores, Klebsiella ferric iron uptake, and the ability to metabolize allantoin. They are crucial for virulence and were associated with specific infections in the mice infection model. Notably, these factors are also prevalent in strains from the same infections in humans. However, the type and quantity of virulence factors may vary between strains, which defines the degree of pathogenicity. In this review, we summarize the main virulence factors investigated in K. pneumoniae from different human infections. We also cover the specific identification genes and their prevalence in K. pneumoniae, especially in hypervirulent strains.
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Affiliation(s)
- Adriano de Souza Santos Monteiro
- Laboratory of Pathology and Molecular Biology (LPBM), Gonçalo Moniz Research Institute, Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia Brazil
| | | | - Joice Neves Reis
- Laboratory of Pathology and Molecular Biology (LPBM), Gonçalo Moniz Research Institute, Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Bahia Brazil
- Faculty of Pharmacy, Federal University of Bahia, Salvador, Bahia Brazil
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Dwi Fatmawati NN, Aviana F, Maharianto R, Ngurah Rsi Suwardana G, Adi Tarini NM, Nengah Sujaya I. Antibiotyping, RAPD- and ERIC-PCR fingerprinting of Klebsiella pneumoniae clinical isolates at a tertiary reference hospital in Denpasar, Bali, Indonesia. IRANIAN JOURNAL OF MICROBIOLOGY 2024; 16:306-313. [PMID: 39005601 PMCID: PMC11245350 DOI: 10.18502/ijm.v16i3.15761] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 07/16/2024]
Abstract
Background and Objectives Klebsiella pneumoniae is a healthcare-associated infections agent and could be an extended spectrum β-lactamase (ESBL) producer. Understanding the transmission of this bacterium in a hospital setting needs accurate typing methods. An antibiogram is used to detect the resistance pattern of the isolates. Random Amplified Polymorphic DNA (RAPD) and Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR are rapid, technically simple, and easy-to-interpret DNA typing methods. This study aimed to evaluate the use of antibiotyping, RAPD-, and ERIC-PCR to investigate the heterogeneity of K. pneumoniae isolated from clinical specimens. Materials and Methods The antibiograms of 46 K. pneumoniae clinical isolates were determined by Vitek® 2 Compact. All isolates underwent RAPD-PCR using AP4 primer and ERIC-PCR using ERIC-2 primer. The dendrogram was generated using the GelJ software and analyzed to determine its similarity. The analysis of antibiogram and the molecular typing diversity index was calculated using the formula of the Simpson's diversity index. Results About 71.7% of the isolates were ESBL-producers, and more than 80% of isolates were susceptible to amikacin, ertapenem, and meropenem. The antibiotyping produced 32 diverse types with DI = 0.964. In addition, the RAPD-PCR produced 47 different types with DI = 1, while ERIC-PCR was 46 (DI=0.999). Conclusion Antibiotyping, RAPD- and ERIC-PCR showed powerful discrimination power among the isolates, supported the diversity of K. pneumoniae isolates in current study. These combination could be promising tools for clonal relationship determination, including in tracking the transmission of the outbreak's agent in hospital setting.
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Affiliation(s)
- Ni Nengah Dwi Fatmawati
- Department of Clinical Microbiology, Faculty of Medicine, Udayana University, Denpasar, Bali, Indonesia
| | - Felicia Aviana
- Department of Clinical Microbiology, Faculty of Medicine, Udayana University, Denpasar, Bali, Indonesia
| | - Ronny Maharianto
- Department of Clinical Microbiology, Faculty of Medicine, Udayana University, Denpasar, Bali, Indonesia
| | - Gede Ngurah Rsi Suwardana
- Department of Clinical Microbiology, Faculty of Medicine, Udayana University, Denpasar, Bali, Indonesia
| | - Ni Made Adi Tarini
- Department of Clinical Microbiology, Faculty of Medicine, Udayana University, Denpasar, Bali, Indonesia
| | - I Nengah Sujaya
- Department of Public Health and Preventive Medicine, Faculty of Medicine, Udayana University, Denpasar, Bali, Indonesia
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30
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Ding H, Chen XC, Wan L, Zhang YY, Rui XH, He T, Liu J, Shang ZB. Klebsiella pneumoniae alters zebrafish circadian rhythm via inflammatory pathways and is dependent on light cues. Heliyon 2024; 10:e30829. [PMID: 38770281 PMCID: PMC11103479 DOI: 10.1016/j.heliyon.2024.e30829] [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: 11/09/2023] [Revised: 05/02/2024] [Accepted: 05/06/2024] [Indexed: 05/22/2024] Open
Abstract
Klebsiella pneumoniae is an opportunistic pathogen causing severe infections. The circadian rhythm is the internal rhythm mechanism of an organism and plays an important role in coping with changes in the 24-h circadian rhythm. Disruption of the circadian rhythm can lead to immune, behavioral, mental, and other related disorders. Whether K. pneumoniae can disrupt the circadian rhythm after infection remains unclear. Here, we examined the effects of K. pneumoniae NTUH-K2044 infection on biological rhythm and inflammation in zebrafish using behavioral assays, quantitative real-time reverse transcription PCR, neutrophil and macrophage transgenic fish, and drug treatment. The results showed that K. pneumoniae infection decreased the motor activity of zebrafish and reduced the circadian rhythm amplitude, phase, and period. The expression of core circadian rhythm-associated genes increased under light-dark conditions, whereas they were downregulated under continuous darkness. Analysis of Klebsiella pneumoniae-mediated inflammation using Tg(mpx:EGFP) and Tg(mpeg:EGFP) transgenic zebrafish, expressing fluorescent neutrophils and macrophages, respectively, showed increased induction of inflammatory cells, upregulated expression of inflammatory factor genes, and stronger inflammatory responses under light-dark conditions. These effects were reversed by the anti-inflammatory drug G6PDi-1, and the expression of clock genes following K. pneumoniae treatment was disrupted. We determined the relationship among K. pneumoniae, inflammation, and the circadian rhythm, providing a theoretical reference for studying circadian rhythm disorders caused by inflammation.
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Affiliation(s)
- Hui Ding
- Department of Laboratory Medicine, Affiliated Wuxi Fifth Hospital of Jiangnan University, Wuxi, 214005, China
| | - Xiao-chun Chen
- Department of Laboratory Medicine, Taizhou Second People's Hospital, Taizhou, 225411, China
| | - Lin Wan
- Department of Laboratory Medicine, Jiangnan University Medical Center, Wuxi, 214000, China
| | - Ying-ying Zhang
- Department of Laboratory Medicine, Affiliated Wuxi Fifth Hospital of Jiangnan University, Wuxi, 214005, China
| | - Xiao-hong Rui
- Department of Laboratory Medicine, Affiliated Wuxi Fifth Hospital of Jiangnan University, Wuxi, 214005, China
| | - Tian He
- Department of Laboratory Medicine, Affiliated Wuxi Fifth Hospital of Jiangnan University, Wuxi, 214005, China
| | - Jun Liu
- Department of Laboratory Medicine, Affiliated Wuxi Fifth Hospital of Jiangnan University, Wuxi, 214005, China
| | - Zhong-bo Shang
- Department of Laboratory Medicine, Wuxi Huishan District People's Hospital, Wuxi, 214000, China
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Rivera-Galindo MA, Aguirre-Garrido F, Garza-Ramos U, Villavicencio-Pulido JG, Fernández Perrino FJ, López-Pérez M. Relevance of the Adjuvant Effect between Cellular Homeostasis and Resistance to Antibiotics in Gram-Negative Bacteria with Pathogenic Capacity: A Study of Klebsiella pneumoniae. Antibiotics (Basel) 2024; 13:490. [PMID: 38927157 PMCID: PMC11200652 DOI: 10.3390/antibiotics13060490] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Revised: 05/17/2024] [Accepted: 05/23/2024] [Indexed: 06/28/2024] Open
Abstract
Antibiotic resistance has become a global issue. The most significant risk is the acquisition of these mechanisms by pathogenic bacteria, which can have a severe clinical impact and pose a public health risk. This problem assumes that bacterial fitness is a constant phenomenon and should be approached from an evolutionary perspective to develop the most appropriate and effective strategies to contain the emergence of strains with pathogenic potential. Resistance mechanisms can be understood as adaptive processes to stressful conditions. This review examines the relevance of homeostatic regulatory mechanisms in antimicrobial resistance mechanisms. We focus on the interactions in the cellular physiology of pathogenic bacteria, particularly Gram-negative bacteria, and specifically Klebsiella pneumoniae. From a clinical research perspective, understanding these interactions is crucial for comprehensively understanding the phenomenon of resistance and developing more effective drugs and treatments to limit or attenuate bacterial sepsis, since the most conserved adjuvant phenomena in bacterial physiology has turned out to be more optimized and, therefore, more susceptible to alterations due to pharmacological action.
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Affiliation(s)
- Mildred Azucena Rivera-Galindo
- Doctorado en Ciencias Biológicas y de la Salud Universidad Autónoma Metropolitana, Ciudad de México, México Universidad Autónoma Metropolitana-Unidad Xochimilco Calz, del Hueso 1100, Coapa, Villa Quietud, Coyoacán CP 04960, Mexico;
| | - Félix Aguirre-Garrido
- Environmental Sciences Department, Division of Biological and Health Sciences, Autonomous Metropolitan University (Lerma Unit), Av. de las Garzas N◦ 10, Col. El Panteón, Lerma de Villada CP 52005, Mexico; (F.A.-G.); (J.G.V.-P.)
| | - Ulises Garza-Ramos
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca CP 62100, Mexico;
| | - José Geiser Villavicencio-Pulido
- Environmental Sciences Department, Division of Biological and Health Sciences, Autonomous Metropolitan University (Lerma Unit), Av. de las Garzas N◦ 10, Col. El Panteón, Lerma de Villada CP 52005, Mexico; (F.A.-G.); (J.G.V.-P.)
| | - Francisco José Fernández Perrino
- Department of Biotechnology, Division of Biological and Health Sciences, Universidad Autónoma Metropolitana-Unidad Iztapalapa, Av. San Rafael Atlixco 186, Leyes de Reforma, México City CP 09340, Mexico;
| | - Marcos López-Pérez
- Environmental Sciences Department, Division of Biological and Health Sciences, Autonomous Metropolitan University (Lerma Unit), Av. de las Garzas N◦ 10, Col. El Panteón, Lerma de Villada CP 52005, Mexico; (F.A.-G.); (J.G.V.-P.)
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Le HH, Nguyen AV, Vu LH, Nguyen VTH, Pham HQ, Le HV, Nguyen ST, Le HT, Dinh HV, Le NV, Le TD, Le MN, Nguyen VH, Hoang KT, Le HHL. Antimicrobial Resistance Patterns of Common Gram-Negative Microorganisms Isolated from Patients with Lower Respiratory Tract Infections in a Teaching Hospital in Vietnam. Jpn J Infect Dis 2024; 77:144-154. [PMID: 38296537 DOI: 10.7883/yoken.jjid.2023.260] [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: 05/24/2024]
Abstract
This cross-sectional study investigated the antimicrobial resistance (AMR) patterns of gram-negative pathogens isolated from 4,789 hospitalized patients with lower respiratory tract infections (LRTIs). Of the collected specimens, 1,325 (27.7%) tested positive for gram-negative bacteria. Acinetobacter baumannii (38.6%), Pseudomonas aeruginosa (33.5%), Klebsiella pneumoniae (18.7%), Escherichia coli (5.6%), and Klebsiella aerogenes (3.5%) were the most prevalent isolates. AMR analysis revealed high resistance rates (79.9%-100%) of A. baumannii isolates to multiple classes of antibiotics except amikacin, trimethoprim/sulfamethoxazole, and colistin. P. aeruginosa displayed low resistance to colistin (< 10%) but high resistance to other antibiotics. K. pneumoniae displayed high resistance rates of 90.0%-100.0% to most penicillins, whereas resistance rates were notably lower for colistin (7.1%) and amikacin (16.7%). K. aerogenes exhibited high resistance to various antibiotics and sensitivity to amikacin (95.1%), ampicillin (100.0%), and colistin (100.0%). E. coli isolates exhibited resistance to ampicillin (96.9%) and maximum sensitivity to several antibiotics. Our study identified significant AMR trends and highlighted the prevalence of multidrug-resistant strains (93.6% for K. aerogenes and 69.1%-92.4% for other isolates). These findings emphasize the urgent need for appropriate antibiotic management practices to combat AMR in gram-negative pathogens associated with LRTIs.
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Affiliation(s)
- Hoang Huy Le
- Department of Bacteriology, National Institute of Hygiene and Epidemiology, Vietnam
| | - An Van Nguyen
- Department of Microbiology, Military Hospital 103, Vietnam Military Medical University, Vietnam
| | - Luong Huy Vu
- Department of Laser and Skin Care, National Hospital of Dermatology and Venereology, Vietnam
- Department of Dermatology and Venereology, Hanoi Medical University, Vietnam
| | - Vinh Thi Ha Nguyen
- Department of Dermatology and Venereology, Hanoi Medical University, Vietnam
- Department of General Planning, National Hospital of Dermatology and Venereology, Vietnam
| | - Hoa Quynh Pham
- Department of Microbiology, Mycology and Parasitology, National Hospital of Dermatology and Venereology, Vietnam
| | - Hung Van Le
- Department of Dermatology and Venereology, Hanoi Medical University, Vietnam
- Department of Microbiology, Mycology and Parasitology, National Hospital of Dermatology and Venereology, Vietnam
| | - Son Thai Nguyen
- Department of Microbiology, Military Hospital 103, Vietnam Military Medical University, Vietnam
| | - Hong Thu Le
- Department of Microbiology, Military Hospital 103, Vietnam Military Medical University, Vietnam
| | - Hung Viet Dinh
- Department of Psychiatry, Military Hospital 103, Vietnam Military Medical University, Vietnam
| | - Nam Van Le
- Department of Infectious Diseases, Military Hospital 103, Vietnam Military Medical University, Vietnam
| | - Tuan Dinh Le
- Department of Rheumatology and Endocrinology, Military Hospital 103, Vietnam Military Medical University, Vietnam
| | - Minh Nhat Le
- Tay Nguyen Institute of Scientific Research, Vietnam Academy of Science and Technology, Vietnam
| | - Viet Hoang Nguyen
- Molecular Pathology Department, Faculty of Medical Technology, Hanoi Medical University, Vietnam
| | - Kien Trung Hoang
- Department of Immunology, Vietnam Military Medical University, Vietnam
| | - Hai Ha Long Le
- Department of Clinical Microbiology and Parasitology, Faculty of Medical Technology, Hanoi Medical University, Vietnam
- Department of Biochemistry, Haematology and Immunology, National Hospital of Dermatology and Venereology, Vietnam
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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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Denissen J, Havenga B, Reyneke B, Khan S, Khan W. Comparing antibiotic resistance and virulence profiles of Enterococcus faecium, Klebsiella pneumoniae, and Pseudomonas aeruginosa from environmental and clinical settings. Heliyon 2024; 10:e30215. [PMID: 38720709 PMCID: PMC11076977 DOI: 10.1016/j.heliyon.2024.e30215] [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: 08/17/2023] [Revised: 04/19/2024] [Accepted: 04/22/2024] [Indexed: 05/12/2024] Open
Abstract
Antibiotic resistance and virulence profiles of Enterococcus faecium, Klebsiella pneumoniae, and Pseudomonas aeruginosa, isolated from water sources collected in informal settlements, were compared to clinical counterparts. Cluster analysis using repetitive extragenic palindromic sequence-based polymerase chain reaction (REP-PCR) indicated that, for each respective species, low genetic relatedness was observed between most of the clinical and environmental isolates, with only one clinical P. aeruginosa (PAO1) and one clinical K. pneumoniae (P2) exhibiting high genetic similarity to the environmental strains. Based on the antibiograms, the clinical E. faecium Ef CD1 was extensively drug resistant (XDR); all K. pneumoniae isolates (n = 12) (except K. pneumoniae ATCC 13883) were multidrug resistant (MDR), while the P. aeruginosa (n = 16) isolates exhibited higher susceptibility profiles. The tetM gene (tetracycline resistance) was identified in 47.4 % (n = 6 environmental; n = 3 clinical) of the E. faecium isolates, while the blaKPC gene (carbapenem resistance) was detected in 52.6 % (n = 7 environmental; n = 3 clinical) and 15.4 % (n = 2 environmental) of the E. faecium and K. pneumoniae isolates, respectively. The E. faecium isolates were predominantly poor biofilm formers, the K. pneumoniae isolates were moderate biofilm formers, while the P. aeruginosa isolates were strong biofilm formers. All E. faecium and K. pneumoniae isolates were gamma (γ)-haemolytic, non-gelatinase producing (E. faecium only), and non-hypermucoviscous (K. pneumoniae only), while the P. aeruginosa isolates exhibited beta (β)-haemolysis and produced gelatinase. The fimH (type 1 fimbriae adhesion) and ugE (uridine diphosphate galacturonate 4-epimerase synthesis) virulence genes were detected in the K. pneumoniae isolates, while the P. aeruginosa isolates possessed the phzM (phenazine production) and algD (alginate biosynthesis) genes. Similarities in antibiotic resistance and virulence profiles of environmental and clinical E. faecium, K. pneumoniae, and P. aeruginosa, thus highlights the potential health risks posed by using environmental water sources for daily water needs in low-and-middle-income countries.
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Affiliation(s)
- Julia Denissen
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Benjamin Havenga
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Brandon Reyneke
- Faculty of Health Sciences, University of Johannesburg, PO Box 17011, Doornfontein, 2028, South Africa
| | - Sehaam Khan
- Faculty of Health Sciences, University of Johannesburg, PO Box 17011, Doornfontein, 2028, South Africa
| | - Wesaal Khan
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
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Li L, Zhang Y, Wang W, Chen Y, He F, Yu Y. Global Emergence and Genomic Epidemiology of blaNDM-Carrying Klebsiella variicola. Infect Drug Resist 2024; 17:1893-1901. [PMID: 38766676 PMCID: PMC11102106 DOI: 10.2147/idr.s460569] [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: 02/26/2024] [Accepted: 05/01/2024] [Indexed: 05/22/2024] Open
Abstract
Purpose Klebsiella variicola has emerged as a human pathogen in the past decade. Here, we present findings related to a K. variicola strain carrying the blaNDM-1 gene, which was isolated from a urinary tract infection in China. Global transmission dynamics and genomic epidemiology of blaNDM-carrying K. variicola were further investigated. Material and Methods The complete genome sequence of the strain was determined using the Illumina NovaSeq 6000 and Nanopore MinION sequencer. Genomic features and resistance mechanisms were analyzed through diverse bioinformatics approaches. Additionally, genome sequences of K. variicola strains carrying blaNDM were retrieved from the NCBI database, and a comprehensive analysis of the global dissemination trends of these strains was conducted. Results K. variicola strain 353 demonstrated resistance to multiple antimicrobials, including carbapenems. Within its genome, we identified fourteen antimicrobial resistance genes associated with β-lactam, aminoglycoside, fosfomycin, quinolone, trimethoprim, rifamycin, and sulfonamide resistance. The carbapenem-resistant gene blaNDM-1 was located on an IncU-type plasmid spanning 294,608 bp and flanked by ISCR1 and IS26. Downstream of blaNDM-1, we identified an Intl1 element housing numerous antibiotic resistance genes. A comprehensive search of the NCBI database revealed 72 K. variicola strains carrying blaNDM from twelve different countries, predominantly from clinical sources, with the highest prevalence observed in the USA and China. A total of 28 distinct sequence types (STs) were identified, with ST115 being the most prevalent, followed by ST60. Conclusion In summary, this study presents the genomic characterization of a K. variicola strain carrying blaNDM-1 on an IncU-type plasmid. The research highlights the global dissemination of blaNDM-carrying K. variicola, observed in both healthcare settings and natural environments. Our data have revealed a diverse array of antimicrobial resistance determinants in K. variicola, providing valuable insights that could aid in the development of strategies for the prevention, diagnosis, and treatment of K. variicola infections.
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Affiliation(s)
- Lirong Li
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
| | - Yawen Zhang
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
| | - Weizhong Wang
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
| | - Yanmin Chen
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
| | - Fang He
- Laboratory Medicine Center, Department of Clinical Laboratory, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
| | - Yan Yu
- Center for Rehabilitation Medicine, Department of Ophthalmology, Zhejiang Provincial People’s Hospital (Affiliated People’s Hospital), Hangzhou Medical College, Hangzhou, Zhejiang, People’s Republic of China
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Gaetano AS, Semeraro S, Greco S, Greco E, Cain A, Perrone MG, Pallavicini A, Licen S, Fornasaro S, Barbieri P. Bioaerosol Sampling Devices and Pretreatment for Bacterial Characterization: Theoretical Differences and a Field Experience in a Wastewater Treatment Plant. Microorganisms 2024; 12:965. [PMID: 38792794 PMCID: PMC11124041 DOI: 10.3390/microorganisms12050965] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Revised: 05/06/2024] [Accepted: 05/08/2024] [Indexed: 05/26/2024] Open
Abstract
Studies on bioaerosol bacterial biodiversity have relevance in both ecological and health contexts, and molecular methods, such as 16S rRNA gene-based barcoded sequencing, provide efficient tools for the analysis of airborne bacterial communities. Standardized methods for sampling and analysis of bioaerosol DNA are lacking, thus hampering the comparison of results from studies implementing different devices and procedures. Three samplers that use gelatin filtration, swirling aerosol collection, and condensation growth tubes for collecting bioaerosol at an aeration tank of a wastewater treatment plant in Trieste (Italy) were used to determine the bacterial biodiversity. Wastewater samples were collected directly from the untreated sewage to obtain a true representation of the microbiological community present in the plant. Different samplers and collection media provide an indication of the different grades of biodiversity, with condensation growth tubes and DNA/RNA shieldTM capturing the richer bacterial genera. Overall, in terms of relative abundance, the air samples have a lower number of bacterial genera (64 OTUs) than the wastewater ones (75 OTUs). Using the metabarcoding approach to aerosol samples, we provide the first preliminary step toward the understanding of a significant diversity between different air sampling systems, enabling the scientific community to orient research towards the most informative sampling strategy.
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Affiliation(s)
- Anastasia Serena Gaetano
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri, 1, 34127 Trieste, Italy; (A.S.G.); (S.S.); (E.G.); (S.L.); (S.F.)
- INSTM National Interuniversity Consortium of Materials Science and Technology, Via G. Giusti, 9, 50121 Firenze, Italy
| | - Sabrina Semeraro
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri, 1, 34127 Trieste, Italy; (A.S.G.); (S.S.); (E.G.); (S.L.); (S.F.)
- INSTM National Interuniversity Consortium of Materials Science and Technology, Via G. Giusti, 9, 50121 Firenze, Italy
| | - Samuele Greco
- Department of Life Sciences, University of Trieste, Via L. Giorgieri, 5, 34127 Trieste, Italy;
| | - Enrico Greco
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri, 1, 34127 Trieste, Italy; (A.S.G.); (S.S.); (E.G.); (S.L.); (S.F.)
- INSTM National Interuniversity Consortium of Materials Science and Technology, Via G. Giusti, 9, 50121 Firenze, Italy
| | - Andrea Cain
- ACEGAS APS AMGA S.p.a., Via degli Alti Forni, 11, 34121 Trieste, Italy;
| | | | - Alberto Pallavicini
- Department of Life Sciences, University of Trieste, Via L. Giorgieri, 5, 34127 Trieste, Italy;
| | - Sabina Licen
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri, 1, 34127 Trieste, Italy; (A.S.G.); (S.S.); (E.G.); (S.L.); (S.F.)
| | - Stefano Fornasaro
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri, 1, 34127 Trieste, Italy; (A.S.G.); (S.S.); (E.G.); (S.L.); (S.F.)
| | - Pierluigi Barbieri
- Department of Chemical and Pharmaceutical Sciences, University of Trieste, Via L. Giorgieri, 1, 34127 Trieste, Italy; (A.S.G.); (S.S.); (E.G.); (S.L.); (S.F.)
- INSTM National Interuniversity Consortium of Materials Science and Technology, Via G. Giusti, 9, 50121 Firenze, Italy
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Yang J, Xiong Y, Barkema HW, Tong X, Lin Y, Deng Z, Kastelic JP, Nobrega DB, Wang Y, Han B, Gao J. Comparative genomic analyses of Klebsiella pneumoniae K57 capsule serotypes isolated from bovine mastitis in China. J Dairy Sci 2024; 107:3114-3126. [PMID: 37944808 DOI: 10.3168/jds.2023-23721] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2023] [Accepted: 09/21/2023] [Indexed: 11/12/2023]
Abstract
Klebsiella pneumoniae can cause severe clinical mastitis in dairy cows, with K. pneumoniae type K57 (K57-KP) being the most common capsular serotype. To identify virulence factors and antimicrobial-resistance (AMR) genes of K57-KP with varying virulence, Galleria mellonella (greater wax moth) larvae were infected as a screening model to characterize virulence of 90 K57-KP strains, with 10 and 11 strains defined as virulent or attenuated, respectively, based on larval survival rates. Next, virulence of these 21 isolates was subsequently confirmed in adhesion and lactate dehydrogenase release assays, using bovine mammary epithelial cells cultured in vitro. Finally, genes associated with virulence and AMR were characterize with whole-genome sequencing. These 21 K57-KP strains were designated into 16 sequence types based on multi-locus sequence typing and allocated in phylogenetic analysis based on single nucleotide polymorphisms. We found great genetic diversity among isolates. In addition, adhesion-associated genes (e.g., fimA, sfaA, and focA) aminoglycoside-resistance genes (aph(6)-Id, strAB) were associated with virulence. This study provided new knowledge regarding virulence of K57-KP associated with bovine mastitis, which may inform development of novel diagnostic tools and prevention strategies for bovine mastitis.
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Affiliation(s)
- Jingyue Yang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Yindi Xiong
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Herman W Barkema
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Xiaofang Tong
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Yushan Lin
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Zhaoju Deng
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - John P Kastelic
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Diego B Nobrega
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, T2N 4N1, Canada
| | - Yue Wang
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China
| | - Bo Han
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
| | - Jian Gao
- Department of Clinical Veterinary Medicine, College of Veterinary Medicine, China Agricultural University, Beijing 100193, China.
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Rahmat Ullah S, Irum S, Mahnoor I, Ismatullah H, Mumtaz M, Andleeb S, Rahman A, Jamal M. Exploring the resistome, virulome, and mobilome of multidrug-resistant Klebsiella pneumoniae isolates: deciphering the molecular basis of carbapenem resistance. BMC Genomics 2024; 25:408. [PMID: 38664636 PMCID: PMC11044325 DOI: 10.1186/s12864-024-10139-y] [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: 06/04/2023] [Accepted: 02/19/2024] [Indexed: 04/29/2024] Open
Abstract
BACKGROUND Klebsiella pneumoniae, a notorious pathogen for causing nosocomial infections has become a major cause of neonatal septicemia, leading to high morbidity and mortality worldwide. This opportunistic bacterium has become highly resistant to antibiotics due to the widespread acquisition of genes encoding a variety of enzymes such as extended-spectrum beta-lactamases (ESBLs) and carbapenemases. We collected Klebsiella pneumoniae isolates from a local tertiary care hospital from February 2019-February 2021. To gain molecular insight into the resistome, virulome, and genetic environment of significant genes of multidrug-resistant K. pneumoniae isolates, we performed the short-read whole-genome sequencing of 10 K. pneumoniae isolates recovered from adult patients, neonates, and hospital tap water samples. RESULTS The draft genomes of the isolates varied in size, ranging from 5.48 to 5.96 Mbp suggesting the genome plasticity of this pathogen. Various genes conferring resistance to different classes of antibiotics e.g., aminoglycosides, quinolones, sulfonamides, tetracycline, and trimethoprim were identified in all sequenced isolates. The highest resistance was observed towards carbapenems, which has been putatively linked to the presence of both class B and class D carbapenemases, blaNDM, and blaOXA, respectively. Moreover, the biocide resistance gene qacEdelta1 was found in 6/10 of the sequenced strains. The sequenced isolates exhibited a broad range of sequence types and capsular types. The significant antibiotic resistance genes (ARGs) were bracketed by a variety of mobile genetic elements (MGEs). Various spontaneous mutations in genes other than the acquired antibiotic-resistance genes were observed, which play an indirect role in making these bugs resistant to antibiotics. Loss or deficiency of outer membrane porins, combined with ESBL production, played a significant role in carbapenem resistance in our sequenced isolates. Phylogenetic analysis revealed that the study isolates exhibited evolutionary relationships with strains from China, India, and the USA suggesting a shared evolutionary history and potential dissemination of similar genes amongst the isolates of different origins. CONCLUSIONS This study provides valuable insight into the presence of multiple mechanisms of carbapenem resistance in K. pneumoniae strains including the acquisition of multiple antibiotic-resistance genes through mobile genetic elements. Identification of rich mobilome yielded insightful information regarding the crucial role of insertion sequences, transposons, and integrons in shaping the genome of bacteria for the transmission of various resistance-associated genes. Multi-drug resistant isolates that had the fewest resistance genes exhibited a significant number of mutations. K. pneumoniae isolate from water source displayed comparable antibiotic resistance determinants to clinical isolates and the highest number of virulence-associated genes suggesting the possible interplay of ARGs amongst bacteria from different sources.
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Affiliation(s)
- Sidra Rahmat Ullah
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan
| | - Sidra Irum
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan
| | - Iqra Mahnoor
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan
| | - Humaira Ismatullah
- Research Centre for Modelling & Simulation (RCMS), National University of Sciences and Technology, Islamabad, Pakistan
| | - Mariam Mumtaz
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan
| | - Saadia Andleeb
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan.
| | - Abdur Rahman
- Atta-ur-Rahman School of Applied Biosciences (ASAB), National University of Sciences and Technology, Islamabad, Pakistan
| | - Muhsin Jamal
- Department of Microbiology, Abdul Wali Khan University, Mardan, Pakistan
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Nery Garcia BL, Dantas STA, da Silva Barbosa K, Mendes Mitsunaga T, Butters A, Camargo CH, Nobrega DB. Extended-Spectrum Beta-Lactamase-Producing Escherichia coli and Other Antimicrobial-Resistant Gram-Negative Pathogens Isolated from Bovine Mastitis: A One Health Perspective. Antibiotics (Basel) 2024; 13:391. [PMID: 38786120 PMCID: PMC11117280 DOI: 10.3390/antibiotics13050391] [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: 03/31/2024] [Revised: 04/17/2024] [Accepted: 04/19/2024] [Indexed: 05/25/2024] Open
Abstract
Antimicrobial resistance (AMR) poses an imminent threat to global public health, driven in part by the widespread use of antimicrobials in both humans and animals. Within the dairy cattle industry, Gram-negative coliforms such as Escherichia coli and Klebsiella pneumoniae stand out as major causative agents of clinical mastitis. These same bacterial species are frequently associated with severe infections in humans, including bloodstream and urinary tract infections, and contribute significantly to the alarming surge in antimicrobial-resistant bacterial infections worldwide. Additionally, mastitis-causing coliforms often carry AMR genes akin to those found in hospital-acquired strains, notably the extended-spectrum beta-lactamase genes. This raises concerns regarding the potential transmission of resistant bacteria and AMR from mastitis cases in dairy cattle to humans. In this narrative review, we explore the distinctive characteristics of antimicrobial-resistant E. coli and Klebsiella spp. strains implicated in clinical mastitis and human infections. We focus on the molecular mechanisms underlying AMR in these bacterial populations and critically evaluate the potential for interspecies transmission. Despite some degree of similarity observed in sequence types and mobile genetic elements between strains found in humans and cows, the existing literature does not provide conclusive evidence to assert that coliforms responsible for mastitis in cows pose a direct threat to human health. Finally, we also scrutinize the existing literature, identifying gaps and limitations, and propose avenues for future research to address these pressing challenges comprehensively.
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Affiliation(s)
- Breno Luis Nery Garcia
- Department of Animal Nutrition and Production, School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga 13635-900, SP, Brazil; (B.L.N.G.); (S.T.A.D.); (K.d.S.B.); (T.M.M.)
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada;
| | - Stéfani Thais Alves Dantas
- Department of Animal Nutrition and Production, School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga 13635-900, SP, Brazil; (B.L.N.G.); (S.T.A.D.); (K.d.S.B.); (T.M.M.)
| | - Kristian da Silva Barbosa
- Department of Animal Nutrition and Production, School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga 13635-900, SP, Brazil; (B.L.N.G.); (S.T.A.D.); (K.d.S.B.); (T.M.M.)
| | - Thatiane Mendes Mitsunaga
- Department of Animal Nutrition and Production, School of Veterinary Medicine and Animal Science, University of São Paulo, Pirassununga 13635-900, SP, Brazil; (B.L.N.G.); (S.T.A.D.); (K.d.S.B.); (T.M.M.)
| | - Alyssa Butters
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada;
| | | | - Diego Borin Nobrega
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada;
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Xie J, Ma R, Li M, Li B, Xiong L. [Effect of intestinal nitrate on growth of Klebsiella pneumoniae and its regulatory mechanism]. NAN FANG YI KE DA XUE XUE BAO = JOURNAL OF SOUTHERN MEDICAL UNIVERSITY 2024; 44:757-764. [PMID: 38708510 DOI: 10.12122/j.issn.1673-4254.2024.04.18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 05/07/2024]
Abstract
OBJECTIVE To explore the effect of intestinal nitrates on the growth of Klebsiella pneumoniae and its regulatory mechanisms. METHODS K. pneumoniae strains with nitrate reductase narG and narZ single or double gene knockout or with NarXL gene knockout were constructed and observed for both aerobic and anaerobic growth in the presence of KNO3 using an automated bacterial growth analyzer and a spectrophotometer, respectively. The mRNA expressions of narG and narZ in K. pneumoniae in anaerobic cultures in the presence of KNO3 and the effect of the binary regulatory system NarXL on their expresisons were detected using qRT-PCR. Electrophoretic mobility shift assays (EMSA) and MST analysis were performed to explore the specific regulatory mechanisms of NarXL in sensing and utilizing nitrates. Competitive experiments were conducted to examine anaerobic growth advantages of narG and narZ gene knockout strains of K. pneumoniae in the presence of KNO3. RESULTS The presence of KNO3 in anaerobic conditions, but not in aerobic conditions, promoted bacterial growth more effectively in the wild-type K. pneumoniae strain than in the narXL gene knockout strain. In anaerobic conditions, the narXL gene knockout strain showed significantly lowered mRNA expressions of narG and narZ (P < 0.0001). EMSA and MST experiments demonstrated that the NarXL regulator could directly bind to narG and narZ promoter regions. The wild-type K. pneumoniae strain in anaerobic cultures showed significantly increased expressions of narG and narZ mRNAs in the presence of KNO3 (P < 0.01), and narG gene knockout resulted in significantly attenuated anaerobic growth and competitive growth abilities of K. pneumoniae in the presence of KNO3 (P < 0.01). CONCLUSION The binary regulatory system NarXL of K. pneumoniae can sense changes in intestinal nitrate concentration and directly regulate the expression of nitrate reductase genes narG and narZ to promote bacterial growth.
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Affiliation(s)
- J Xie
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, China
| | - R Ma
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, China
| | - M Li
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, China
| | - B Li
- School of Basic Medical Sciences, Hubei University of Medicine, Shiyan 442000, China
| | - L Xiong
- Department of Gastroenterology, Liyuan Hospital Affiliated to Tongji Medical College of Huazhong University of Science and Technology, Wuhan 430077, China
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Hala S, Malaikah M, Huang J, Bahitham W, Fallatah O, Zakri S, Antony CP, Alshehri M, Ghazzali RN, Ben-Rached F, Alsahafi A, Alsaedi A, AlAhmadi G, Kaaki M, Alazmi M, AlhajHussein B, Yaseen M, Zowawi HM, Alghoribi MF, Althaqafi AO, Al-Amri A, Moradigaravand D, Pain A. The emergence of highly resistant and hypervirulent Klebsiella pneumoniae CC14 clone in a tertiary hospital over 8 years. Genome Med 2024; 16:58. [PMID: 38637822 PMCID: PMC11025284 DOI: 10.1186/s13073-024-01332-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 04/08/2024] [Indexed: 04/20/2024] Open
Abstract
BACKGROUND Klebsiella pneumoniae is a major bacterial and opportunistic human pathogen, increasingly recognized as a healthcare burden globally. The convergence of resistance and virulence in K. pneumoniae strains has led to the formation of hypervirulent and multidrug-resistant strains with dual risk, limiting treatment options. K. pneumoniae clones are known to emerge locally and spread globally. Therefore, an understanding of the dynamics and evolution of the emerging strains in hospitals is warranted to prevent future outbreaks. METHODS In this study, we conducted an in-depth genomic analysis on a large-scale collection of 328 multidrug-resistant (MDR) K. pneumoniae strains recovered from 239 patients from a single major hospital in the western coastal city of Jeddah in Saudi Arabia from 2014 through 2022. We employed a broad range of phylogenetic and phylodynamic methods to understand the evolution of the predominant clones on epidemiological time scales, virulence and resistance determinants, and their dynamics. We also integrated the genomic data with detailed electronic health record (EHR) data for the patients to understand the clinical implications of the resistance and virulence of different strains. RESULTS We discovered a diverse population underlying the infections, with most strains belonging to Clonal Complex 14 (CC14) exhibiting dominance. Specifically, we observed the emergence and continuous expansion of strains belonging to the dominant ST2096 in the CC14 clade across hospital wards in recent years. These strains acquired resistance mutations against colistin and extended spectrum β-lactamase (ESBL) and carbapenemase genes, namely blaOXA-48 and blaOXA-232, located on three distinct plasmids, on epidemiological time scales. Strains of ST2096 exhibited a high virulence level with the presence of the siderophore aerobactin (iuc) locus situated on the same mosaic plasmid as the ESBL gene. Integration of ST2096 with EHR data confirmed the significant link between colonization by ST2096 and the diagnosis of sepsis and elevated in-hospital mortality (p-value < 0.05). CONCLUSIONS Overall, these results demonstrate the clinical significance of ST2096 clones and illustrate the rapid evolution of an emerging hypervirulent and MDR K. pneumoniae in a clinical setting.
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Affiliation(s)
- Sharif Hala
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, 23955-6900, Jeddah, Makkah, Saudi Arabia
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Jeddah, Saudi Arabia
- Ministry of National Guard Health Affairs, Riyadh, Western Region, Saudi Arabia
| | - Mohammed Malaikah
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, 23955-6900, Jeddah, Makkah, Saudi Arabia
- Laboratory of Infectious Disease Epidemiology, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Jiayi Huang
- Laboratory of Infectious Disease Epidemiology, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- KAUST Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
| | - Wesam Bahitham
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Jeddah, Saudi Arabia
- Ministry of National Guard Health Affairs, Riyadh, Western Region, Saudi Arabia
| | - Omniya Fallatah
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Jeddah, Saudi Arabia
- Ministry of National Guard Health Affairs, Riyadh, Western Region, Saudi Arabia
| | - Samer Zakri
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Jeddah, Saudi Arabia
- Ministry of National Guard Health Affairs, Riyadh, Western Region, Saudi Arabia
| | - Chakkiath Paul Antony
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, 23955-6900, Jeddah, Makkah, Saudi Arabia
- International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan
| | - Mohammed Alshehri
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Jeddah, Saudi Arabia
- Ministry of National Guard Health Affairs, Riyadh, Western Region, Saudi Arabia
| | - Raeece Naeem Ghazzali
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, 23955-6900, Jeddah, Makkah, Saudi Arabia
| | - Fathia Ben-Rached
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, 23955-6900, Jeddah, Makkah, Saudi Arabia
| | - Abdullah Alsahafi
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Jeddah, Saudi Arabia
- Ministry of National Guard Health Affairs, Riyadh, Western Region, Saudi Arabia
| | - Asim Alsaedi
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Jeddah, Saudi Arabia
- Ministry of National Guard Health Affairs, Riyadh, Western Region, Saudi Arabia
| | - Ghadeer AlAhmadi
- King Faisal Specialist Hospital and Research Centre, Jeddah, Saudi Arabia
| | - Mai Kaaki
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Jeddah, Saudi Arabia
- Ministry of National Guard Health Affairs, Riyadh, Western Region, Saudi Arabia
| | - Meshari Alazmi
- KAUST Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia
- College of Computer Science and Engineering, University of Hail, Hail, Saudi Arabia
| | - Baraa AlhajHussein
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Jeddah, Saudi Arabia
- Ministry of National Guard Health Affairs, Riyadh, Western Region, Saudi Arabia
| | - Muhammad Yaseen
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Jeddah, Saudi Arabia
- Ministry of National Guard Health Affairs, Riyadh, Western Region, Saudi Arabia
| | - Hosam M Zowawi
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Jeddah, Saudi Arabia
- Ministry of National Guard Health Affairs, Riyadh, Western Region, Saudi Arabia
- The University of Queensland, UQ Centre for Clinical Research, Herston, QLD, Australia
| | - Majed F Alghoribi
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Jeddah, Saudi Arabia
- Ministry of National Guard Health Affairs, Riyadh, Western Region, Saudi Arabia
| | - Abdulhakeem O Althaqafi
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Jeddah, Saudi Arabia
- Ministry of National Guard Health Affairs, Riyadh, Western Region, Saudi Arabia
| | - Abdulfattah Al-Amri
- King Saud Bin Abdulaziz University for Health Sciences, Riyadh, Saudi Arabia
- Infectious Disease Research Department, King Abdullah International Medical Research Centre, Jeddah, Saudi Arabia
- Ministry of National Guard Health Affairs, Riyadh, Western Region, Saudi Arabia
| | - Danesh Moradigaravand
- Laboratory of Infectious Disease Epidemiology, Biological and Environmental Science and Engineering (BESE) Division, King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
- KAUST Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology (KAUST), Thuwal, Saudi Arabia.
| | - Arnab Pain
- Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, 23955-6900, Jeddah, Makkah, Saudi Arabia.
- The University of Queensland, UQ Centre for Clinical Research, Herston, QLD, Australia.
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Das S, Pandey AK, Morris DE, Anderson R, Lim V, Wie CC, Yap IKS, Alattraqchi AG, Simin H, Abdullah R, Yeo CC, Clarke SC, Cleary DW. Respiratory carriage of hypervirulent Klebsiella pneumoniae by indigenous populations of Malaysia. BMC Genomics 2024; 25:381. [PMID: 38632538 PMCID: PMC11025145 DOI: 10.1186/s12864-024-10276-4] [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: 10/03/2023] [Accepted: 04/01/2024] [Indexed: 04/19/2024] Open
Abstract
Klebsiella pneumoniae is a Gram-negative Enterobacteriaceae that is classified by the World Health Organisation (WHO) as a Priority One ESKAPE pathogen. South and Southeast Asian countries are regions where both healthcare associated infections (HAI) and community acquired infections (CAI) due to extended-spectrum β-lactamase (ESBL)-producing and carbapenem-resistant K. pneumoniae (CRKp) are of concern. As K. pneumoniae can also exist as a harmless commensal, the spread of resistance genotypes requires epidemiological vigilance. However there has been no significant study of carriage isolates from healthy individuals, particularly in Southeast Asia, and specially Malaysia. Here we describe the genomic analysis of respiratory isolates of K. pneumoniae obtained from Orang Ulu and Orang Asli communities in Malaysian Borneo and Peninsular Malaysia respectively. The majority of isolates were K. pneumoniae species complex (KpSC) 1 K. pneumoniae (n = 53, 89.8%). Four Klebsiella variicola subsp. variicola (KpSC3) and two Klebsiella quasipneumoniae subsp. similipneumoniae (KpSC4) were also found. It was discovered that 30.2% (n = 16) of the KpSC1 isolates were ST23, 11.3% (n = 6) were of ST65, 7.5% (n = 4) were ST13, and 13.2% (n = 7) were ST86. Only eight of the KpSC1 isolates encoded ESBL, but importantly not carbapenemase. Thirteen of the KpSC1 isolates carried yersiniabactin, colibactin and aerobactin, all of which harboured the rmpADC locus and are therefore characterised as hypervirulent. Co-carriage of multiple strains was minimal. In conclusion, most isolates were KpSC1, ST23, one of the most common sequence types and previously found in cases of K. pneumoniae infection. A proportion were hypervirulent (hvKp) however antibiotic resistance was low.
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Affiliation(s)
- Souradeep Das
- Faculty of Medicine, Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Anish K Pandey
- Faculty of Medicine, Institute for Life Sciences, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust, Southampton, UK
| | - Denise E Morris
- Faculty of Medicine, Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Rebecca Anderson
- Faculty of Medicine, Institute for Life Sciences, University of Southampton, Southampton, UK
| | - Victor Lim
- School of Medicine, International Medical University, Kuala Lumpur, Malaysia
| | - Chong Chun Wie
- Institute for Research, Development and Innovation, International Medical University, Kuala Lumpur, Malaysia
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - Ivan Kok Seng Yap
- School of Pharmacy, Monash University Malaysia, Bandar Sunway, Selangor, Malaysia
| | - Ahmed Ghazi Alattraqchi
- Centre for Research in Infectious Diseases and Biotechnology (CeRIDB), Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Hafis Simin
- Faculty of Applied Social Sciences, Universiti Sultan Zainal Abidin, Gong Badak Campus, 21300, Kuala Nerus, Terengganu, Malaysia
| | - Ramle Abdullah
- Centre of Excellence in National Indigenous Pedagogy, Institute of Teacher Education Tengku, Ampuan Afzan Campus, Pahang, Malaysia
| | - Chew Chieng Yeo
- Centre for Research in Infectious Diseases and Biotechnology (CeRIDB), Faculty of Medicine, Universiti Sultan Zainal Abidin, Medical Campus, 20400, Kuala Terengganu, Terengganu, Malaysia
| | - Stuart C Clarke
- Faculty of Medicine, Institute for Life Sciences, University of Southampton, Southampton, UK
- NIHR Southampton Biomedical Research Centre, University Hospital Southampton Foundation NHS Trust, Southampton, UK
- Institute for Research, Development and Innovation, International Medical University, Kuala Lumpur, Malaysia
- Global Health Research Institute, University of Southampton, Southampton, UK
| | - David W Cleary
- Institute of Microbiology and Infection, College of Medical and Dental Sciences, University of Birmingham, University of Birmingham, UK.
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Hyun M, Lee JY, Kim HA. Clinical and Microbiologic Analysis of Klebsiella pneumoniae Infection: Hypermucoviscosity, Virulence Factor, Genotype, and Antimicrobial Susceptibility. Diagnostics (Basel) 2024; 14:792. [PMID: 38667438 PMCID: PMC11048833 DOI: 10.3390/diagnostics14080792] [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: 02/24/2024] [Revised: 03/29/2024] [Accepted: 04/08/2024] [Indexed: 04/28/2024] Open
Abstract
Hypervirulent Klebsiella pneumoniae (KP) is defined according to hypermucoviscosity or various virulence factors and is clinically associated with community-acquired liver abscess (CLA). In this study, we investigated the clinical and microbiological characteristics of KP and significant factors associated with hypervirulence. The clinical characteristics, antimicrobial susceptibility, hypermucoviscosity, serotypes, hypervirulence-related genes, and biofilm formation of 414 KP isolates collected from the Keimyung University Dongsan Hospital between December 2013 and November 2015 were analyzed according to CLA. Significant risk factors for hypervirulent KP (HvKP) associated with CLA were investigated using logistic regression analysis. Notably, 155 (37.4%) isolates were hypermucoviscous, and 170 (41.1%) harbored aerobactin. CLA was present in 34 cases (8.2%). Epidemiology and treatment outcomes did not differ significantly between the CLA and non-CLA groups. The CLA group had significantly higher antibiotic susceptibility, K1/K2, rmpA, magA, allS, kfu, iutA, string test-positive result, and biofilm mass. Multivariate logistic regression revealed rmpA (OR, 5.67; 95% CI, 2.09-15.33; p = 0.001), magA (OR, 2.34; 95% CI, 1.01-5.40; p = 0.047), and biofilm mass >0.80 (OR, 2.13; 95% CI, 1.00-4.56; p = 0.050) as significant risk factors for CLA. rmpA was identified as the most significant risk factor for CLA among KP strains, implying that it is an important factor associated with HvKP.
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Affiliation(s)
| | | | - Hyun Ah Kim
- Department of Infectious Diseases, Keimyung University Dongsan Hospital, Keimyung University School of Medicine and Institute for Medical Science, Keimyung University, Daegu 42601, Republic of Korea; (M.H.); (J.Y.L.)
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Blaikie JM, Sapula SA, Siderius NL, Hart BJ, Amsalu A, Leong LE, Warner MS, Venter H. Resistome Analysis of Klebsiella pneumoniae Complex from Residential Aged Care Facilities Demonstrates Intra-facility Clonal Spread of Multidrug-Resistant Isolates. Microorganisms 2024; 12:751. [PMID: 38674695 PMCID: PMC11051875 DOI: 10.3390/microorganisms12040751] [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: 12/22/2023] [Revised: 03/14/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Antimicrobial-resistant Klebsiella pneumoniae is one of the predominant pathogens in healthcare settings. However, the prevalence and resistome of this organism within residential aged care facilities (RACFs), which are potential hotspots for antimicrobial resistance, remain unexplored. Here, we provide a phenotypic and molecular characterization of antimicrobial-resistant K. pneumoniae isolated from RACFs. K. pneumoniae was isolated from urine, faecal and wastewater samples and facility swabs. The antimicrobial susceptibility profiles of all the isolates were determined and the genomic basis for resistance was explored with whole-genome sequencing on a subset of isolates. A total of 147 K. pneumoniae were isolated, displaying resistance against multiple antimicrobials. Genotypic analysis revealed the presence of beta-lactamases and the ciprofloxacin-resistance determinant QnrB4 but failed to confirm the basis for the observed cephalosporin resistance. Clonal spread of the multidrug-resistant, widely disseminated sequence types 323 and 661 was observed. This study was the first to examine the resistome of K. pneumoniae isolates from RACFs and demonstrated a complexity between genotypic and phenotypic antimicrobial resistance. The intra-facility dissemination and persistence of multidrug-resistant clones is concerning, given that residents are particularly vulnerable to antimicrobial resistant infections, and it highlights the need for continued surveillance and interventions to reduce the risk of outbreaks.
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Affiliation(s)
- Jack M. Blaikie
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
| | - Sylvia A. Sapula
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
| | - Naomi L. Siderius
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
| | - Bradley J. Hart
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
| | - Anteneh Amsalu
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
- Department of Medical Microbiology, University of Gondar, Gondar 196, Ethiopia
| | - Lex E.X. Leong
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
- Microbiology and Infectious Diseases, SA Pathology, Adelaide, SA 5000, Australia;
| | - Morgyn S. Warner
- Microbiology and Infectious Diseases, SA Pathology, Adelaide, SA 5000, Australia;
- School of Medicine, University of Adelaide, Adelaide, SA 5000, Australia
- Infectious Diseases Unit, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
| | - Henrietta Venter
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
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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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Turton JF, Perry C, McGowan K, Turton JA, Hope R. Klebsiella pneumoniae sequence type 147: a high-risk clone increasingly associated with plasmids carrying both resistance and virulence elements. J Med Microbiol 2024; 73:001823. [PMID: 38629482 PMCID: PMC11084618 DOI: 10.1099/jmm.0.001823] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Accepted: 03/18/2024] [Indexed: 04/19/2024] Open
Abstract
Introduction. The first hybrid resistance/virulence plasmid, combining elements from virulence plasmids described in hypervirulent types of Klebsiella pneumoniae with those from conjugative resistance plasmids, was described in an isolate of sequence type (ST) 147 from 2016. Subsequently, this type has been increasingly associated with these plasmids.Hypothesis or gap statement. The extent of carriage of hybrid virulence/resistance plasmids in nosocomial isolates of K. pneumoniae requires further investigation.Aim. To describe the occurrence of virulence/resistance plasmids among isolates of K. pneumoniae received by the UK reference laboratory, particularly among representatives of ST147, and to compare their sequences.Methodology. Isolates received by the laboratory during 2022 and the first half of 2023 (n=1278) were screened for virulence plasmids by PCR detection of rmpA/rmpA2 and typed by variable-number tandem repeat analysis. Twenty-nine representatives of ST147 (including a single-locus variant) from seven hospital laboratories were subjected to long-read nanopore sequencing using high-accuracy q20 chemistry to provide complete assemblies.Results. rmpA/rmpA2 were detected in 110 isolates, of which 59 belonged to hypervirulent K1-ST23, K2-ST86 and K2-ST65/375. Of the remainder, representatives of ST147 formed the largest group, with 22 rmpA/rmpA2-positive representatives (out of 47 isolates). Representatives were from 19 hospital laboratories, with rmpA/rmpA2-positive isolates from 10. Nanopore sequencing of 29 representatives of ST147 divided them into those with no virulence plasmid (n=12), those with non-New Delhi metallo-β-lactamase (NDM) virulence plasmids (n=6) and those carrying bla NDM-5 (n=9) or bla NDM-1 (n=2) virulence plasmids. These plasmids were of IncFIB(pNDM-Mar)/IncHI1B(pNDM-MAR) replicon types. Most of the non-NDM virulence plasmids were highly similar to the originally described KpvST147L_NDM plasmid. Those carrying bla NDM-5 were highly similar to one another and to previously described plasmids in ST383 and carried an extensive array of resistance genes. Comparison of the fully assembled chromosomes indicated multiple introductions of ST147 in UK hospitals.Conclusion. This study highlights the high proportion of representatives of ST147 that carry IncFIB(pNDM-Mar)/IncHI1B(pNDM-MAR) hybrid resistance virulence plasmids. It is important to be aware of the high probability that representatives of this type carry these plasmids combining resistance and virulence determinants and of the consequent increased risk to patients.
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Affiliation(s)
- Jane F. Turton
- HealthCare Associated Infections, Fungal, Antimicrobial Resistance, Antimicrobial Use and Sepsis Division, UK Health Security Agency, 61, Colindale Avenue, London NW9 5HT, UK
| | - Claire Perry
- Public Health Microbiology, UK Health Security Agency, 61, Colindale Avenue, London NW9 5HT, UK
| | - Kim McGowan
- Public Health Microbiology, UK Health Security Agency, 61, Colindale Avenue, London NW9 5HT, UK
| | - Jack A. Turton
- HealthCare Associated Infections, Fungal, Antimicrobial Resistance, Antimicrobial Use and Sepsis Division, UK Health Security Agency, 61, Colindale Avenue, London NW9 5HT, UK
| | - Russell Hope
- HealthCare Associated Infections, Fungal, Antimicrobial Resistance, Antimicrobial Use and Sepsis Division, UK Health Security Agency, 61, Colindale Avenue, London NW9 5HT, UK
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Greičius P, Linkevicius M, Razmuk J, Sinotova J, Alm E, Svartström O, Bortolaia V, Kudirkienė E, Roer L, Hendriksen RS, Tamoliūnaitė G, Palm D, Monnet DL, Kohlenberg A, Griškevičius A. Emergence of OXA-48-producing Klebsiella pneumoniae in Lithuania, 2023: a multi-cluster, multi-hospital outbreak. Euro Surveill 2024; 29:2400188. [PMID: 38639094 PMCID: PMC11027475 DOI: 10.2807/1560-7917.es.2024.29.16.2400188] [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: 03/28/2024] [Accepted: 04/17/2024] [Indexed: 04/20/2024] Open
Abstract
In 2023, an increase of OXA-48-producing Klebsiella pneumoniae was noticed by the Lithuanian National Public Health Surveillance Laboratory. Whole genome sequencing (WGS) of 106 OXA-48-producing K. pneumoniae isolates revealed three distinct clusters of carbapenemase-producing K. pneumoniae high-risk clones, including sequence type (ST) 45 (n = 35 isolates), ST392 (n = 32) and ST395 (n = 28), involving six, six and nine hospitals in different regions, respectively. These results enabled targeted investigation and control, and underscore the value of national WGS-based surveillance for antimicrobial resistance.
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Affiliation(s)
- Paulius Greičius
- National Public Health Surveillance Laboratory (NVSPL), Vilnius, Lithuania
| | - Marius Linkevicius
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Jelena Razmuk
- National Public Health Surveillance Laboratory (NVSPL), Vilnius, Lithuania
| | | | - Erik Alm
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Olov Svartström
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | | | | | - Louise Roer
- Statens Serum Institut (SSI), Copenhagen, Denmark
| | - Rene S Hendriksen
- Technical University of Denmark, National Food Institute (DTU Food), Kongens Lyngby, Denmark
| | | | - Daniel Palm
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Dominique L Monnet
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Anke Kohlenberg
- European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
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48
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Chen H, Xu H, Liu R, Shen J, Zheng B, Li L. Coexistence of bla IMP-4 and bla SFO-1 in an IncHI5B plasmid harbored by tigecycline-non-susceptible Klebsiella variicola strain. Ann Clin Microbiol Antimicrob 2024; 23:24. [PMID: 38448920 PMCID: PMC10918965 DOI: 10.1186/s12941-024-00680-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/19/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND Klebsiella variicola is considered a newly emerging human pathogen. Clinical isolates of carbapenemase and broad-spectrum β-lactamase-producing K. variicola remain relatively uncommon. A strain of K. variicola 4253 was isolated from a clinical sample, and was identified to carry the blaIMP-4 and blaSFO-1 genes. This study aims to discern its antibiotic resistance phenotype and genomic characteristics. METHODS Species identification was conducted using MALDI-TOF/MS. PCR identification confirmed the presence of the blaIMP-4 and blaSFO-1 genes. Antibiotic resistance phenotype and genomic characteristics were detected by antimicrobial susceptibility testing and whole-genome sequencing. Plasmid characterization was carried out through S1-PFGE, conjugation experiments, Southern blot, and comparative genomic analysis. RESULTS K. variicola 4253 belonged to ST347, and demonstrated resistance to broad-spectrum β-lactamase drugs and tigecycline while being insensitive to imipenem and meropenem. The blaIMP-4 and blaSFO-1 genes harbored on the plasmid p4253-imp. The replicon type of p4253-imp was identified as IncHI5B, representing a multidrug-resistant plasmid capable of horizontal transfer and mediating the dissemination of drug resistance. The blaIMP-4 gene was located on the In809-like integrative element (Intl1-blaIMP-4-aacA4-catB3), which circulates in Acinetobacter and Enterobacteriaceae. CONCLUSIONS This study reports the presence of a strain of K. variicola, which is insensitive to tigecycline, carrying a plasmid harboring blaIMP-4 and blaSFO-1. It is highly likely that the strain acquired this plasmid through horizontal transfer. The blaIMP-4 array (Intl1-blaIMP-4-aacA4-catB3) is also mobile in Acinetobacter and Enterobacteriaceae. So it is essential to enhance clinical awareness and conduct epidemiological surveillance on multidrug-resistant K. variicola, conjugative plasmids carrying blaIMP-4, and the In809 integrative element.
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Affiliation(s)
- Hui 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, 79 Qingchun Rd, Hangzhou City, 310003, China
| | - Hao Xu
- 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, 79 Qingchun Rd, Hangzhou City, 310003, China
| | - Ruishan Liu
- 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, 79 Qingchun Rd, Hangzhou City, 310003, China
| | - Jian 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, 79 Qingchun Rd, Hangzhou City, 310003, China
| | - Beiwen Zheng
- 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, 79 Qingchun Rd, Hangzhou City, 310003, China.
| | - Lanjuan Li
- 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, 79 Qingchun Rd, Hangzhou City, 310003, China.
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Liu Y, Wang J, Zhao R, Liu X, Dong Y, Shi W, Jiang H, Guan X. Bacterial isolation and genome analysis of a novel Klebsiella quasipneumoniae phage in southwest China's karst area. Virol J 2024; 21:56. [PMID: 38448926 PMCID: PMC10916049 DOI: 10.1186/s12985-024-02321-1] [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: 12/08/2023] [Accepted: 02/19/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND Southwest China is one of the largest karst regions in the world. Karst environment is relatively fragile and vulnerable to human activities. Due to the discharge of sewage and domestic garbage, the karst system may be polluted by pathogenic bacteria. The detection of bacterial distribution and identification of phage capable of infecting them is an important approach for environmental assessment and resource acquisition. METHODS Bacteria and phages were isolated from karst water in southwest China using the plate scribing and double plate method, respectively. Isolated phage was defined by transmission electron microscopy, one-step growth curve and optimal multiplicity of infection (MOI). Genomic sequencing, phylogenetic analysis, comparative genomic and proteomic analysis were performed. RESULTS A Klebsiella quasipneumoniae phage was isolated from 32 isolates and named KL01. KL01 is morphologically identified as Caudoviricetes with an optimal MOI of 0.1, an incubation period of 10 min, and a lysis period of 60 min. The genome length of KL01 is about 45 kb, the GC content is 42.5%, and it contains 59 open reading frames. The highest average nucleotide similarity between KL01 and a known Klebsiella phage 6939 was 83.04%. CONCLUSIONS KL01 is a novel phage, belonging to the Autophagoviridae, which has strong lytic ability. This study indicates that there were not only some potential potentially pathogenic bacteria in the karst environment, but also phage resources for exploration and application.
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Affiliation(s)
- Yanju Liu
- School of Ocean Sciences, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, 100083, Beijing, China
| | - Jinfeng Wang
- College of Food Science & Nutritional Engineering, China Agricultural University, 100083, Beijing, China
| | - Ruoyu Zhao
- School of Ocean Sciences, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, 100083, Beijing, China
| | - Xiaoping Liu
- School of Ocean Sciences, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, 100083, Beijing, China
| | - Yang Dong
- School of Ocean Sciences, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, 100083, Beijing, China
| | - Wenyu Shi
- College of Food Science & Nutritional Engineering, China Agricultural University, 100083, Beijing, China
| | - Hongchen Jiang
- School of Ocean Sciences, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, 100083, Beijing, China
| | - Xiangyu Guan
- School of Ocean Sciences, China University of Geosciences (Beijing), No. 29 Xueyuan Road, Haidian District, 100083, Beijing, China.
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50
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Kwon RS, Lee GY, Lee S, Song J. Antimicrobial properties of tomato juice and peptides against typhoidal Salmonella. Microbiol Spectr 2024; 12:e0310223. [PMID: 38289090 PMCID: PMC10913428 DOI: 10.1128/spectrum.03102-23] [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: 08/16/2023] [Accepted: 12/22/2023] [Indexed: 03/06/2024] Open
Abstract
Tomatoes are readily available and affordable vegetables that offer a range of health benefits due to their bioactive molecules, such as antioxidants and antimicrobials. In contrast to the widely recognized antioxidant properties of tomatoes, their antimicrobial properties remain largely unexplored. Here, we present our findings on the antimicrobial properties of tomato juice and peptides, namely, tomato-derived antimicrobial peptides (tdAMPs), in relation to their effectiveness against typhoidal Salmonella. Our research has revealed that tomato juice demonstrates significant antimicrobial properties against Salmonella Typhi, a pathogen that specifically affects humans and is responsible for causing typhoid fever. By employing computational analysis of the tomato genome sequence, conducting molecular dynamics simulation, and performing functional analyses, we have successfully identified two tdAMPs, namely, tdAMP-1 and tdAMP-2. These tdAMPs have demonstrated potent antimicrobial properties by effectively disrupting bacterial membranes. The efficacy of tdAMP-2 is shown to be more effective than tdAMP-1. The efficacy of tdAMP-1 and tdAMP-2 has been demonstrated against drug-resistant S. Typhi, as well as hyper-capsular S. Typhi variants that possess hypervirulent characteristics, which are presently circulating in countries with endemicity. Tomato juice, along with the two tdAMPs, has demonstrated effectiveness against uropathogenic Escherichia coli as well. This underscores their potential as viable agents in combating certain Gram-negative pathogens. This study provides valuable insights into the development of effective and sustainable public health strategies that utilize tomato and its derivatives as lifestyle interventions.IMPORTANCEIn this study, we investigate the antimicrobial properties of tomato juice, the most widely consumed affordable vegetables, as well as tomato-derived antimicrobial peptides, in relation to their effectiveness against foodborne pathogens with an emphasis on Salmonella Typhi, a deadly human-specific pathogen.
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Affiliation(s)
- Ryan S. Kwon
- Department of Microbiology and Immunology, Cornell University, Ithaca, New York, USA
| | - Gi Young Lee
- Department of Microbiology and Immunology, Cornell University, Ithaca, New York, USA
| | - Sohyoung Lee
- Department of Microbiology and Immunology, Cornell University, Ithaca, New York, USA
| | - Jeongmin Song
- Department of Microbiology and Immunology, Cornell University, Ithaca, New York, USA
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