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Qiu Z, Kang Y, Xu C, Ma W, Li G, Jia W, Wang P. Epidemiology and molecular characterization of carbapenem-resistant Klebsiella pneumoniae isolated from neonatal intensive care units in General Hospital of Ningxia Medical University, China, 2017-2021. Int Microbiol 2024:10.1007/s10123-024-00510-0. [PMID: 38512525 DOI: 10.1007/s10123-024-00510-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 02/23/2024] [Accepted: 03/10/2024] [Indexed: 03/23/2024]
Abstract
OBJECTIVES This study aimed to retrospectively investigate the epidemiology and molecular characteristics of carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates from neonatal intensive care units (NICU) between 2017 and 2021. METHODS The antibacterial susceptibility of all strains was assessed using the VITEK 2 compact system. The presence of antibiotic resistance, virulence genes, sequence types (STs), capsular (K) types, and the wzi genes was determined through polymerase chain reaction (PCR). Molecular typing was performed by pulsed-field gel electrophoresis (PFGE) using the restriction enzyme XbaI. Additionally, the virulence potential of peg344-positive strains was evaluated using the string test and mouse intraperitoneal infection models. Whole-genome sequencing was conducted on the DNB system and PacBio platforms. RESULTS A total of 46 CRKP isolates were collected during the study period. Out of these, 93.47% (43/46) were identified as CRKP strains belonging to the ST76-K10 type carrying blaNDM-5. It was observed that CRKP infection resulted in more severe clinical symptoms compared to CRKP colonization. Among the CRKP strains, a hypervirulent CRKP strain called KP-63, belonging to the ST23 type, was identified. This strain exhibited high mortality in the mouse infection model and was found to possess virulence genes. Genomic alignment analysis revealed a significant similarity between the virulence plasmid from KP-63 strain (pKP-63) and pK2044 from the hypervirulent K. pneumoniae strain NTUH-2044. CONCLUSIONS There has been a potential dissemination of ST76-K10 type CRKP carrying blaNDM-5 in the NICU at Ningxia Hospital. Neonatal CRKP infection has been found to cause more severe clinical symptoms than colonization. Furthermore, we have discovered a CR-hvKP strain of ST23 with serotype K1, which exhibits a significant resemblance in its virulent plasmid to pK2044. Therefore, it is crucial to enforce effective measures to restrict the spread and hinder the evolution of CRKP within the hospital.
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Affiliation(s)
- Zhuoran Qiu
- College of Clinical Medicine, Ningxia Medical University, Yinchuan, 750004, Ningxia, China
| | - Yuting Kang
- Ningxia Key Laboratory of Clinical and Pathogenic Microbiology, Institute of Medical Sciences, General Hospital of Ningxia Medical University, Technology Building 602, 804 Shengli Road, Yinchuan, 750004, Ningxia, China
| | - Chao Xu
- College of Clinical Medicine, Ningxia Medical University, Yinchuan, 750004, Ningxia, China
| | - Wanting Ma
- College of Clinical Medicine, Ningxia Medical University, Yinchuan, 750004, Ningxia, China
| | - Gang Li
- Center of Medical Laboratory, The General Hospital of Ningxia Medical University, Technology Building 601, 804 Shengli Road, Yinchuan, 750004, Ningxia, China
| | - Wei Jia
- Ningxia Key Laboratory of Clinical and Pathogenic Microbiology, Institute of Medical Sciences, General Hospital of Ningxia Medical University, Technology Building 602, 804 Shengli Road, Yinchuan, 750004, Ningxia, China.
- Center of Medical Laboratory, The General Hospital of Ningxia Medical University, Technology Building 601, 804 Shengli Road, Yinchuan, 750004, Ningxia, China.
| | - Pengtao Wang
- Ningxia Key Laboratory of Clinical and Pathogenic Microbiology, Institute of Medical Sciences, General Hospital of Ningxia Medical University, Technology Building 602, 804 Shengli Road, Yinchuan, 750004, Ningxia, China.
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Yang P, Liu C, Du P, Yi J, Wu Z, Zheng J, Shen N, Cui L, Lu M. ST218 Klebsiella pneumoniae became a high-risk clone for multidrug resistance and hypervirulence. BMC Microbiol 2024; 24:56. [PMID: 38347440 PMCID: PMC10860259 DOI: 10.1186/s12866-024-03205-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2023] [Accepted: 01/28/2024] [Indexed: 02/15/2024] Open
Abstract
BACKGROUND The occurrence of multidrug-resistant and hypervirulent Klebsiella pneumoniae (MDR-hvKp) worldwide poses a great challenge for public health. Few studies have focused on ST218 MDR-hvKp. METHODS Retrospective genomic surveillance was conducted at the Peking University Third Hospital from 2017 and clinical information was obtained. To understand genomic and microbiological characteristics, antimicrobial susceptibility testing, plasmid conjugation and stability, biofilm formation, serum killing, growth curves and whole-genome sequencing were performed. We also assessed the clinical and microbiological characteristics of ST218 compared with ST23. RESULTS A total of eleven ST218 Kp isolates were included. The most common infection type was lower respiratory tract infection (72.7%, 8/11) in our hospital, whereas ST23 hvKp (72.7%, 8/11) was closely associated with bloodstream infection. Notably, nosocomial infections caused by ST218 (54.5%, 6/11) was slightly higher than ST23 (36.4%, 4/11). All of the ST218 and ST23 strains presented with the virulence genes combination of iucA + iroB + peg344 + rmpA + rmpA2. Interestingly, the virulence score of ST218 was lower than ST23, whereas one ST218 strain (pPEKP3107) exhibited resistance to carbapenems, cephalosporins, β-lactamase/inhibitors and quinolones and harbored an ~ 59-kb IncN type MDR plasmid carrying resistance genes including blaNDM-1, dfrA14 and qnrS1. Importantly, blaNDM-1 and qnrS1 were flanked with IS26 located within the plasmid that could successfully transfer into E. coli J53. Additionally, PEKP2044 harbored an ~ 41-kb resistance plasmid located within tetA indicating resistance to doxycycline. CONCLUSION The emergence of blaNDM-1 revealed that there is great potential for ST218 Kp to become a high-risk clone for MDR-hvKp, indicating the urgent need for enhanced genomic surveillance.
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Affiliation(s)
- Ping Yang
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, China
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Chao Liu
- Department of Infectious Diseases, Peking University Third Hospital, Beijing, China
- Center of Infectious Disease, Peking University Third Hospital, Beijing, China
| | | | - Juan Yi
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
| | - Zhenchao Wu
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, China
| | - Jiajia Zheng
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China
| | - Ning Shen
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, China
- Institute of Medical Technology, Peking University Health Science Center, Beijing, China
- Department of Infectious Diseases, Peking University Third Hospital, Beijing, China
- Center of Infectious Disease, Peking University Third Hospital, Beijing, China
| | - Liyan Cui
- Department of Laboratory Medicine, Peking University Third Hospital, Beijing, China.
| | - Ming Lu
- Department of Pulmonary and Critical Care Medicine, Peking University Third Hospital, Beijing, China.
- Department of Infectious Diseases, Peking University Third Hospital, Beijing, China.
- Center of Infectious Disease, Peking University Third Hospital, Beijing, China.
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Yang Z, Zhou R, Chen Y, Zhang X, Liu L, Luo M, Chen J, Chen K, Zeng T, Liu B, Wu Y, Huang J, Liu Z, Ouyang J. Clinical and Molecular Characteristics and Antibacterial Strategies of Klebsiella pneumoniae in Pyogenic Infection. Microbiol Spectr 2023; 11:e0064023. [PMID: 37341605 PMCID: PMC10434161 DOI: 10.1128/spectrum.00640-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2023] [Accepted: 05/24/2023] [Indexed: 06/22/2023] Open
Abstract
Treatment of Klebsiella pneumoniae causing pyogenic infections is challenging. The clinical and molecular characteristics of Klebsiella pneumoniae causing pyogenic infections are poorly understood, and antibacterial treatment strategies are limited. We analyzed the clinical and molecular characteristics of K. pneumoniae from patients with pyogenic infections and used time-kill assays to reveal the bactericidal kinetics of antimicrobial agents against hypervirulent K. pneumoniae (hvKp). A total of 54 K. pneumoniae isolates were included, comprising 33 hvKp and 21 classic K. pneumoniae (cKp) isolates, and the hvKp and cKp isolates were identified using five genes (iroB, iucA, rmpA, rmpA2, and peg-344) that have been applied as hvKp strain markers. The median age of all cases was 54 years (25th and 75th percentiles, 50.5 to 70), 62.96% of individuals had diabetes, and 22.22% of isolates were sourced from individuals without underlying disease. The ratios of white blood cells/procalcitonin and C-reactive protein/procalcitonin were potential clinical markers for the identification of suppurative infection caused by hvKp and cKp. The 54 K. pneumoniae isolates were classified into 8 sequence type 11 (ST11) and 46 non-ST11 strains. ST11 strains carrying multiple drug resistance genes have a multidrug resistance phenotype, while non-ST11 strains carrying only intrinsic resistance genes are generally susceptible to antibiotics. Bactericidal kinetics revealed that hvKp isolates were not easily killed by antimicrobials at susceptible breakpoint concentrations compared with cKp. Given the varied clinical and molecular features and the catastrophic pathogenicity of K. pneumoniae, it is critical to determine the characteristics of such isolates for optimal management and effective treatment of K. pneumoniae causing pyogenic infections. IMPORTANCE Klebsiella pneumoniae may cause pyogenic infections, which are potentially life-threatening and bring great challenges for clinical management. However, the clinical and molecular characteristics of K. pneumoniae are poorly understood, and effective antibacterial treatment strategies are limited. We analyzed the clinical and molecular features of 54 isolates from patients with various pyogenic infections. We found that most patients with pyogenic infections had underlying diseases, such as diabetes. The ratio of white blood cells to procalcitonin and the ratio of C-reactive protein to procalcitonin were potential clinical markers for differentiating hypervirulent K. pneumoniae strains from classical K. pneumoniae strains that cause pyogenic infections. K. pneumoniae isolates of ST11 were generally more resistant to antibiotics than non-ST11 isolates. Most importantly, hypervirulent K. pneumoniae strains were more tolerant to antibiotics than classic K. pneumoniae isolates.
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Affiliation(s)
- Zhiyu Yang
- Department of Clinical Laboratory, Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Runmei Zhou
- Department of Pharmacy, Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Yusheng Chen
- Department of Pharmacy, Ningyuan County Hospital of Traditional Chinese Medicine, Ningyuan, Hunan, China
| | - Xiaotuan Zhang
- Department of Clinical Laboratory, Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Luogen Liu
- Clinical Research Center, Second Affiliated Hospital, University of South China, Hengyang, China
| | - Min Luo
- Department of Clinical Laboratory, Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Jinlin Chen
- Department of Clinical Laboratory, Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Kuilin Chen
- Department of Clinical Laboratory, Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Tong Zeng
- Key Laboratory of Medical Imaging and Artificial Intelligence of Hunan Province, Xiangnan University, Chenzhou, China
| | - Bin Liu
- Department of Clinical Laboratory, Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Yuan Wu
- Department of Clinical Laboratory, Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Jielite Huang
- Clinical Laboratory, Affiliated Nanhua Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Zhuoran Liu
- Department of Clinical Laboratory, Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
| | - Jinglin Ouyang
- Clinical Research Center, Second Affiliated Hospital, University of South China, Hengyang, China
- Department of Ultrasound Medicine, Second Affiliated Hospital, Hengyang Medical School, University of South China, Hengyang, China
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Alkompoz AK, Hamed SM, Zaid ASA, Almangour TA, Al-Agamy MH, Aboshanab KM. Correlation of CRISPR/Cas and Antimicrobial Resistance in Klebsiella pneumoniae Clinical Isolates Recovered from Patients in Egypt Compared to Global Strains. Microorganisms 2023; 11:1948. [PMID: 37630508 PMCID: PMC10459600 DOI: 10.3390/microorganisms11081948] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2023] [Revised: 07/27/2023] [Accepted: 07/28/2023] [Indexed: 08/27/2023] Open
Abstract
The CRISPR/Cas system has been long known to interfere with the acquisition of foreign genetic elements and was recommended as a tool for fighting antimicrobial resistance. The current study aimed to explore the prevalence of the CRISPR/Cas system in Klebsiella pneumoniae isolates recovered from patients in Egypt in comparison to global strains and correlate the CRISPR/Cas to susceptibility to antimicrobial agents. A total of 181 clinical isolates were PCR-screened for cas and selected antimicrobial resistance genes (ARGs). In parallel, 888 complete genome sequences were retrieved from the NCBI database for in silico analysis. CRISPR/Cas was found in 46 (25.4%) isolates, comprising 18.8% type I-E and 6.6% type I-E*. Multidrug resistance (MDR) and extensive drug resistance (XDR) were found in 73.5% and 25.4% of the isolates, respectively. More than 95% of the CRISPR/Cas-bearing isolates were MDR (65.2%) or XDR (32.6%). No significant difference was found in the susceptibility to the tested antimicrobial agents among the CRISPR/Cas-positive and -negative isolates. The same finding was obtained for the majority of the screened ARGs. Among the published genomes, 23.2% carried CRISPR/Cas, with a higher share of I-E* (12.8%). They were confined to specific sequence types (STs), most commonly ST147, ST23, ST15, and ST14. More plasmids and ARGs were carried by the CRISPR/Cas-negative group than others, but their distribution in the two groups was not significantly different. The prevalence of some ARGs, such as blaKPC, blaTEM, and rmtB, was significantly higher among the genomes of the CRISPR/Cas-negative strains. A weak, nonsignificant positive correlation was found between the number of spacers and the number of resistance plasmids and ARGs. In conclusion, the correlation between CRISPR/Cas and susceptibility to antimicrobial agents or bearing resistance plasmids and ARGs was found to be nonsignificant. Plasmid-targeting spacers might not be naturally captured by CRISPR/Cas. Spacer match analysis is recommended to provide a clearer image of the exact behavior of CRISPR/Cas towards resistance plasmids.
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Affiliation(s)
| | - Samira M. Hamed
- Department of Microbiology and Immunology, Faculty of Pharmacy, October University for Modern Sciences and Arts (MSA), 6th of October, Giza 12451, Egypt;
| | - Ahmed S. Abu Zaid
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt;
| | - Thamer A. Almangour
- Department of Clinical Pharmacy, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
| | - Mohamed H. Al-Agamy
- Department of Pharmaceutics, College of Pharmacy, King Saud University, Riyadh 11451, Saudi Arabia;
- Department of Microbiology and Immunology, Faculty of Pharmacy, Al-Azhar University, Cairo 11651, Egypt
| | - Khaled M. Aboshanab
- Department of Microbiology and Immunology, Faculty of Pharmacy, Ain Shams University, Cairo 11566, Egypt;
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Yang M, Zhou X, Bao Y, Zhang Y, Liu B, Gan L, Tao W, Tuo J, Gong H. Comprehensive Genomic Analysis Reveals Extensive Diversity of Type I and Type IV Secretion Systems in Klebsiella pneumoniae. Curr Microbiol 2023; 80:270. [PMID: 37402963 DOI: 10.1007/s00284-023-03362-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2023] [Accepted: 06/02/2023] [Indexed: 07/06/2023]
Abstract
The diversity and distribution of secretion systems in Klebsiella pneumoniae are unclear. In this study, the six common secretion systems (T1SS-T6SS) were comprehensively investigated in the genomes of 952 K. pneumoniae strains. T1SS, T2SS, type T subtype of T4SS, T5SS, and subtype T6SSi of T6SS were found. The findings indicated fewer types of secretion systems in K. pneumoniae than reported in Enterobacteriaceae, such as Escherichia coli. One conserved T2SS, one conserved T5SS, and two conserved T6SS were detected in more than 90% of the strains. In contrast, the strains displayed extensive diversity of T1SS and T4SS. Notably, T1SS and T4SS were enriched in the hypervirulent and classical multidrug resistance pathotypes of K. pneumoniae, respectively. The results expand the epidemiological knowledge of the virulence and transmissibility of pathogenic K. pneumoniae and contribute to identify the potential strains for safe applications.
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Affiliation(s)
- Menglei Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Xiaoqin Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Yangyang Bao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Yang Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Boya Liu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Luxi Gan
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Weihua Tao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Jinyou Tuo
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China
| | - Heng Gong
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai, 200237, People's Republic of China.
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Yuan Y, Liu X, Zhou L, Ding W, Zhang L, Zheng J. Case report: A case of acute postoperative endophthalmitis following penetrating keratoplasty due to carbapenem-resistant Klebsiella Pneumoniae and literature review. Front Med (Lausanne) 2023; 10:1110411. [PMID: 37265480 PMCID: PMC10229784 DOI: 10.3389/fmed.2023.1110411] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2022] [Accepted: 05/04/2023] [Indexed: 06/03/2023] Open
Abstract
A 22-year-old lady underwent penetrating keratoplasty for serious keratoconus. The following day, it was complicated by the development of infectious endophthalmitis. The source of infection was identified as carbapenem-resistant Klebsiella pneumoniae. The donor corneal button might be playing a role in infection transmission due to carbapenem-resistant Klebsiella pneumoniae in a sputum culture when the donor was still alive. Nosocomial infections were typically severe, rapidly progressive, and difficult to treat. Finally, the patient underwent therapeutic penetrating keratoplasty again with complete resolution of the infection.
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Affiliation(s)
- Ying Yuan
- Department of Ophthalmology, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou Province, China
- School of Clinical Medical, Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Xiaoyuan Liu
- Department of Ophthalmology, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou Province, China
- School of Clinical Medical, Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Li Zhou
- Department of Ophthalmology, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou Province, China
- School of Clinical Medical, Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Wuchun Ding
- Department of Ophthalmology, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou Province, China
- School of Clinical Medical, Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Liying Zhang
- Department of Ophthalmology, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou Province, China
- School of Clinical Medical, Guizhou Medical University, Guiyang, Guizhou Province, China
| | - Jinhua Zheng
- Department of Ophthalmology, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou Province, China
- School of Clinical Medical, Guizhou Medical University, Guiyang, Guizhou Province, China
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Rodrigues IC, Ribeiro-Almeida M, Ribeiro J, Silveira L, Prata JC, Pista A, Martins da Costa P. Occurrence of Multidrug-Resistant Bacteria Resulting from the Selective Pressure of Antibiotics: A Comprehensive Analysis of ESBL K. pneumoniae and MRSP Isolated in a Dog with Rhinorrhea. Vet Sci 2023; 10:vetsci10050326. [PMID: 37235409 DOI: 10.3390/vetsci10050326] [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: 03/31/2023] [Revised: 04/28/2023] [Accepted: 04/29/2023] [Indexed: 05/28/2023] Open
Abstract
Because of public health concerns, much greater scrutiny is now placed on antibiotic use in pets, especially for antimicrobial agents that have human analogs. Therefore, this study aimed to characterize the phenotypic and genotypic profiles of multidrug-resistant bacteria isolated from nasal swabs samples taken from a one-year-old male Serra da Estrela dog with rhinorrhea that was treated with amikacin. An extended-spectrum β-lactamases (ESBL) Klebsiella pneumoniae was isolated in the first sample taken from the left nasal cavity of the dog. Seven days later, methicillin-resistant (MRSP) Staphylococcus pseudintermedius was also isolated. Nevertheless, no alterations to the therapeutic protocol were performed. Once the inhibitory action of the antibiotic disappeared, the competitive advantage of the amikacin-resistant MRSP was lost, and only commensal flora was observed on both nasal cavities. The genotypic profile of extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae revealed the same characteristics and close relation to other strains, mainly from Estonia, Slovakia and Romania. Regarding MRSP isolates, although resistance to aminoglycosides was present in the first MRSP, the second isolate carried aac(6')-aph(2″), which enhanced its resistance to amikacin. However, the veterinary action was focused on the treatment of the primary agent (ESBL K. pneumoniae), and the antibiotic applied was according to its phenotypic profile, which may have led to the resolution of the infectious process. Therefore, this study highlights the importance of targeted therapy, proper clinical practice and laboratory-hospital communication to safeguard animal, human and environmental health.
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Affiliation(s)
- Inês C Rodrigues
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Terminal de Cruzeiros do Porto, de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
| | - Marisa Ribeiro-Almeida
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
- UCIBIO-Applied Molecular Biosciences Unit, Rede de Química e Tecnologia (REQUIMTE), Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, 4050-313 Porto, Portugal
| | - Jorge Ribeiro
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
| | - Leonor Silveira
- Department of Infectious Diseases, National Institute of Health, Av. Padre Cruz, 1600-609 Lisbon, Portugal
| | - Joana C Prata
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
- TOXRUN-Toxicology Research Unit, University Institute of Health Sciences, Cooperativa de Ensino Superior Politécnico e Universitário (CESPU), 4585-116 Gandra, Portugal
| | - Angela Pista
- Department of Infectious Diseases, National Institute of Health, Av. Padre Cruz, 1600-609 Lisbon, Portugal
| | - Paulo Martins da Costa
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Rua de Jorge Viterbo Ferreira, 228, 4050-313 Porto, Portugal
- Interdisciplinary Centre of Marine and Environmental Research (CIIMAR), Terminal de Cruzeiros do Porto, de Leixões, Av. General Norton de Matos s/n, 4450-208 Matosinhos, Portugal
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Hallal Ferreira Raro O, Nordmann P, Dominguez Pino M, Findlay J, Poirel L. Emergence of Carbapenemase-Producing Hypervirulent Klebsiella pneumoniae in Switzerland. Antimicrob Agents Chemother 2023; 67:e0142422. [PMID: 36853006 PMCID: PMC10019205 DOI: 10.1128/aac.01424-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Accepted: 01/19/2023] [Indexed: 03/01/2023] Open
Abstract
Increasing occurrence of multidrug-resistant (MDR) and hypervirulent (hv) Klebsiella pneumoniae (MDR-hvKp) convergent clones is being observed. Those strains have the potential of causing difficult-to-treat infections in healthy adults with an increased capacity for mortality. It is therefore crucial to track their dissemination to prevent their further spread. The aim of our study was to investigate the occurrence of carbapenemase-producing hvKp isolates in Switzerland and to determine their genetic profile. A total of 279 MDR carbapenemase-producing K. pneumoniae from patients hospitalized all over Switzerland was investigated, and a rate of 9.0% K. pneumoniae presenting a virulence genotype was identified. Those isolates produced either KPC, NDM, or OXA-48 and had been either recovered from rectal swabs, urine, and blood. A series of previously reported K. pneumoniae clones such as ST23-K1, ST395-K2, and ST147-K20 or ST147-K64 were identified. All the isolates defined as MDR-hvKp (4.7%) possessed the aerobactin and the yersiniabactin clusters. The ST23-K1s were the only isolates presenting the colibactin cluster and achieved higher virulence scores. This study highlights the occurrence and circulation of worrisome MDR-hvKp and MDR nonhypervirulent K. pneumoniae (MDR-nhv-Kp) isolates in Switzerland. Our findings raise an alert regarding the need for active surveillance networks to track and monitor the spread of such successful hybrid clones representing a public health threat worldwide.
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Affiliation(s)
- Otávio Hallal Ferreira Raro
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Patrice Nordmann
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland
- Institute for Microbiology, University Hospital, Lausanne, Switzerland
| | - Manuel Dominguez Pino
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Jacqueline Findlay
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
| | - Laurent Poirel
- Medical and Molecular Microbiology, Faculty of Science and Medicine, University of Fribourg, Fribourg, Switzerland
- Swiss National Reference Center for Emerging Antibiotic Resistance (NARA), University of Fribourg, Fribourg, Switzerland
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9
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Narendrakumar L, Chakraborty M, Kumari S, Paul D, Das B. β-Lactam potentiators to re-sensitize resistant pathogens: Discovery, development, clinical use and the way forward. Front Microbiol 2023; 13:1092556. [PMID: 36970185 PMCID: PMC10036598 DOI: 10.3389/fmicb.2022.1092556] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/29/2022] [Indexed: 03/12/2023] Open
Abstract
β-lactam antibiotics are one of the most widely used and diverse classes of antimicrobial agents for treating both Gram-negative and Gram-positive bacterial infections. The β-lactam antibiotics, which include penicillins, cephalosporins, monobactams and carbapenems, exert their antibacterial activity by inhibiting the bacterial cell wall synthesis and have a global positive impact in treating serious bacterial infections. Today, β-lactam antibiotics are the most frequently prescribed antimicrobial across the globe. However, due to the widespread use and misapplication of β-lactam antibiotics in fields such as human medicine and animal agriculture, resistance to this superlative drug class has emerged in the majority of clinically important bacterial pathogens. This heightened antibiotic resistance prompted researchers to explore novel strategies to restore the activity of β-lactam antibiotics, which led to the discovery of β-lactamase inhibitors (BLIs) and other β-lactam potentiators. Although there are several successful β-lactam-β-lactamase inhibitor combinations in use, the emergence of novel resistance mechanisms and variants of β-lactamases have put the quest of new β-lactam potentiators beyond precedence. This review summarizes the success stories of β-lactamase inhibitors in use, prospective β-lactam potentiators in various phases of clinical trials and the different strategies used to identify novel β-lactam potentiators. Furthermore, this review discusses the various challenges in taking these β-lactam potentiators from bench to bedside and expounds other mechanisms that could be investigated to reduce the global antimicrobial resistance (AMR) burden.
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Affiliation(s)
- Lekshmi Narendrakumar
- Functional Genomics Laboratory, Infection and Immunology Division, Translational Health Science and Technology Institute, Faridabad, India
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10
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Shaidullina ER, Schwabe M, Rohde T, Shapovalova VV, Dyachkova MS, Matsvay AD, Savochkina YA, Shelenkov AA, Mikhaylova YV, Sydow K, Lebreton F, Idelevich EA, Heiden SE, Becker K, Kozlov RS, Shipulin GA, Akimkin VG, Lalk M, Guenther S, Zautner AE, Bohnert JA, Mardanova AM, Bouganim R, Marchaim D, Hoff KJ, Schaufler K, Edelstein MV. Genomic analysis of the international high-risk clonal lineage Klebsiella pneumoniae sequence type 395. Genome Med 2023; 15:9. [PMID: 36782220 PMCID: PMC9926764 DOI: 10.1186/s13073-023-01159-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 01/20/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND Klebsiella pneumoniae, which is frequently associated with hospital- and community-acquired infections, contains multidrug-resistant (MDR), hypervirulent (hv), non-MDR/non-hv as well as convergent representatives. It is known that mostly international high-risk clonal lineages including sequence types (ST) 11, 147, 258, and 307 drive their global spread. ST395, which was first reported in the context of a carbapenemase-associated outbreak in France in 2010, is a less well-characterized, yet emerging clonal lineage. METHODS We computationally analyzed a large collection of K. pneumoniae ST395 genomes (n = 297) both sequenced in this study and reported previously. By applying multiple bioinformatics tools, we investigated the core-genome phylogeny and evolution of ST395 as well as distribution of accessory genome elements associated with antibiotic resistance and virulence features. RESULTS Clustering of the core-SNP alignment revealed four major clades with eight smaller subclades. The subclades likely evolved through large chromosomal recombination, which involved different K. pneumoniae donors and affected, inter alia, capsule and lipopolysaccharide antigen biosynthesis regions. Most genomes contained acquired resistance genes to extended-spectrum cephalosporins, carbapenems, and other antibiotic classes carried by multiple plasmid types, and many were positive for hypervirulence markers, including the siderophore aerobactin. The detection of "hybrid" resistance and virulence plasmids suggests the occurrence of the convergent ST395 pathotype. CONCLUSIONS To the best of our knowledge, this is the first study that investigated a large international collection of K. pneumoniae ST395 genomes and elucidated phylogenetics and detailed genomic characteristics of this emerging high-risk clonal lineage.
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Affiliation(s)
- Elvira R. Shaidullina
- grid.446122.70000 0004 0620 2113Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia
| | - Michael Schwabe
- grid.5603.0Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Thomas Rohde
- grid.5603.0Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Valeria V. Shapovalova
- grid.513078.8Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, Russia
| | - Marina S. Dyachkova
- grid.513078.8Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, Russia
| | - Alina D. Matsvay
- grid.513078.8Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, Russia
| | - Yuliya A. Savochkina
- grid.513078.8Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, Russia
| | | | | | - Katharina Sydow
- grid.5603.0Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - François Lebreton
- grid.507680.c0000 0001 2230 3166Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, USA
| | - Evgeny A. Idelevich
- grid.5603.0Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany ,grid.16149.3b0000 0004 0551 4246Institute of Medical Microbiology, University Hospital Münster, Münster, Germany
| | - Stefan E. Heiden
- grid.5603.0Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Karsten Becker
- grid.5603.0Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Roman S. Kozlov
- grid.446122.70000 0004 0620 2113Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia
| | - German A. Shipulin
- grid.513078.8Federal State Budgetary Institution “Centre for Strategic Planning and Management of Biomedical Health Risks” of the Federal Medical Biological Agency, Moscow, Russia
| | | | - Michael Lalk
- grid.5603.0Institute of Biochemistry, University of Greifswald, Greifswald, Germany
| | - Sebastian Guenther
- grid.5603.0Pharmaceutical Biology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany
| | - Andreas E. Zautner
- grid.5807.a0000 0001 1018 4307Institute of Medical Microbiology and Hospital Hygiene, Medical Faculty, Otto-Von-Guericke University Magdeburg, Magdeburg, Germany
| | - Jürgen A. Bohnert
- grid.5603.0Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, Greifswald, Germany
| | - Ayslu M. Mardanova
- grid.77268.3c0000 0004 0543 9688Institute of Fundamental Medicine and Biology, Kazan Federal University, Kazan, Russia
| | - Ruth Bouganim
- grid.413990.60000 0004 1772 817XDepartment of Internal Medicine A, Shamir (Assaf Harofeh) Medical Center, Zerifin, Israel
| | - Dror Marchaim
- grid.12136.370000 0004 1937 0546Infection Control Unit, Shamir (Assaf Harofeh) Medical Center and Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Katharina J. Hoff
- grid.5603.0Institute of Mathematics and Computer Science, University of Greifswald, Greifswald, Germany
| | - Katharina Schaufler
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, Greifswald, Germany. .,Institute of Infection Medicine, Christian-Albrecht University Kiel and University Medical Center Schleswig-Holstein, Kiel, Germany.
| | - Mikhail V. Edelstein
- grid.446122.70000 0004 0620 2113Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, Smolensk, Russia
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11
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Kuzina ES, Kislichkina AA, Sizova AA, Skryabin YP, Novikova TS, Ershova ON, Savin IA, Khokhlova OE, Bogun AG, Fursova NK. High-Molecular-Weight Plasmids Carrying Carbapenemase Genes blaNDM-1, blaKPC-2, and blaOXA-48 Coexisting in Clinical Klebsiella pneumoniae Strains of ST39. Microorganisms 2023; 11:microorganisms11020459. [PMID: 36838424 PMCID: PMC9961262 DOI: 10.3390/microorganisms11020459] [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: 01/25/2023] [Revised: 02/07/2023] [Accepted: 02/09/2023] [Indexed: 02/15/2023] Open
Abstract
BACKGROUND Klebsiella pneumoniae, a member of the ESKAPE group of bacterial pathogens, has developed multi-antimicrobial resistance (AMR), including resistance to carbapenems, which has increased alarmingly due to the acquisition of carbapenemase genes located on specific plasmids. METHODS Four clinical K. pneumoniae isolates were collected from four patients of a neuro-intensive care unit in Moscow, Russia, during the point prevalence survey. The AMR phenotype was estimated using the Vitec-2 instrument, and whole genome sequencing (WGS) was done using Illumina and Nanopore technologies. RESULTS All strains were resistant to beta-lactams, nitrofurans, fluoroquinolones, sulfonamides, aminoglycosides, and tetracyclines. WGS analysis revealed that all strains were closely related to K. pneumoniae ST39, capsular type K-23, with 99.99% chromosome identity. The novelty of the study is the description of the strains carrying simultaneously three large plasmids of the IncHI1B, IncC, and IncFIB groups carrying the carbapenemase genes of three types, blaOXA-48, blaNDM-1, and blaKPC-2, respectively. The first of them, highly identical in all strains, was a hybrid plasmid that combined two regions of the resistance genes (blaOXA-48 and blaTEM-1 + blaCTX-M-15 + blaOXA-1 + catB + qnrS1 + int1) and a region of the virulence genes (iucABCD, iutA, terC, and rmpA2::IS110). CONCLUSION The spread of K. pneumoniae strains carrying multiple plasmids conferring resistance even to last-resort antibiotics is of great clinical concern.
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Affiliation(s)
- Ekaterina S. Kuzina
- Department of Training and Improvement of Specialists, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
| | - Angelina A. Kislichkina
- Department of Culture Collection, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
| | - Angelika A. Sizova
- Department of Culture Collection, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
| | - Yury P. Skryabin
- Department of Molecular Microbiology, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
| | - Tatiana S. Novikova
- Department of Molecular Microbiology, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
| | - Olga N. Ershova
- Department of Clinical Epidemiology, National Medical Research Center of Neurosurgery Named after Academician N.N. Burdenko, 125047 Moscow, Russia
| | - Ivan A. Savin
- Department of Clinical Epidemiology, National Medical Research Center of Neurosurgery Named after Academician N.N. Burdenko, 125047 Moscow, Russia
| | - Olga E. Khokhlova
- Department of Molecular Microbiology, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
| | - Alexander G. Bogun
- Department of Culture Collection, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
| | - Nadezhda K. Fursova
- Department of Molecular Microbiology, State Research Center for Applied Microbiology and Biotechnology, Territory “Kvartal A”, 142279 Obolensk, Russia
- Correspondence:
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12
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Biedrzycka M, Izdebski R, Urbanowicz P, Polańska M, Hryniewicz W, Gniadkowski M, Literacka E. MDR carbapenemase-producing Klebsiella pneumoniae of the hypervirulence-associated ST23 clone in Poland, 2009-19. J Antimicrob Chemother 2022; 77:3367-3375. [PMID: 36177793 DOI: 10.1093/jac/dkac326] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/05/2022] [Indexed: 12/13/2022] Open
Abstract
OBJECTIVES To characterize carbapenemase-producing isolates of the Klebsiella pneumoniae hypervirulent (hvKp) clone ST23 in Poland. METHODS Fifteen K. pneumoniae ST23 isolates were identified by the Polish surveillance of carbapenemase-producing Enterobacterales. These comprised a cluster with KPC-2 + NDM-1 (n = 7), KPC-2 (n = 1) or NDM-1 (n = 1) enzymes from one hospital from 2018, and sporadic isolates with KPC-2 (n = 1), NDM-1 (n = 1), VIM-1 (n = 1) or OXA-48 (n = 3), recovered from 2009 to 2019 in different towns. The isolates were sequenced by Illumina MiSeq, followed by MinION for six representatives. Clonality, phylogeny, serotypes, virulomes, resistomes and plasmids of the isolates were analysed and compared with international ST23 strains, using various bioinformatic tools. RESULTS Only two diverse isolates with KPC-2 or VIM-1 were of typical hvKp ST23 serotypes K1 and O1v.2, and its predominant phylogenetic clade. These contained multiple chromosomal (ybt, clb) and pK2044/KpVP-1 plasmid (iuc, iro, rmpADC, rmpA2) virulence loci, whereas carbapenemase and other antimicrobial resistance (AMR) genes were on single additional plasmids. All remaining isolates were of K57 and O2v.2 serotypes, and a minor, distant clade of unclear phylogeny, including also ∼10 isolates from other European countries. These had fewer virulence loci (ybt, iuc, rmpADC, rmpA2) but abounded in plasmids, which with several chromosomal AMR mutations conferred more extensive MDR phenotypes than in K1 O1v.2. Lower clonal diversity than in K1, and numerous common characteristics of the isolates supported the hypothesis of the emerging character of the ST23 K57 clade. CONCLUSIONS A new MDR ST23 lineage has emerged in Europe, causing a potential threat to public health.
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Affiliation(s)
| | - R Izdebski
- National Medicines Institute, Warsaw, Poland
| | | | - M Polańska
- Faculty of Biology, Warsaw University, Warsaw, Poland
| | | | | | - E Literacka
- National Medicines Institute, Warsaw, Poland
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13
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Shapovalova V, Shaidullina E, Azizov I, Sheck E, Martinovich A, Dyachkova M, Matsvay A, Savochkina Y, Khafizov K, Kozlov R, Shipulin G, Edelstein M. Molecular Epidemiology of mcr-1-Positive Escherichia coli and Klebsiella pneumoniae Isolates: Results from Russian Sentinel Surveillance (2013-2018). Microorganisms 2022; 10:microorganisms10102034. [PMID: 36296310 PMCID: PMC9607333 DOI: 10.3390/microorganisms10102034] [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: 09/27/2022] [Revised: 10/11/2022] [Accepted: 10/12/2022] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND The dissemination of mobile colistin resistance (mcr) genes is a serious healthcare threat because polymyxins represent "last-line" therapeutics for multi-drug-resistant Gram-negative pathogens. This study aimed to assess the prevalence of colistin resistance and mcr genes and characteristics of clinical Escherichia coli (Eco) and Klebsiella pneumoniae (Kpn) isolates and plasmids carrying these genes in Russia. METHODS A total of 4324 Eco and 4530 Kpn collected in the frame of sentinel surveillance in 2013-2018 were tested for susceptibility to colistin and other antibiotics using the broth microdilution method. mcr genes were screened by real-time PCR. Phylogeny, genomic features and plasmids of mcr-positive isolates were assessed using whole-genome sequencing and subsequent bioinformatic analysis. RESULTS Colistin resistance was detected in 2.24% Eco and 9.3% Kpn. Twenty-two (0.51%) Eco and two (0.04%) Kpn from distant sites carried mcr-1.1. Most mcr-positive isolates co-harbored ESBLs and other resistance determinants to various antibiotic classes. The mcr-positive Eco belonged to 16 MLST types, with ST359 being most common; Kpn belonged to ST307 and ST23. mcr-1.1 was carried mainly in IncI2 (n = 18) and IncX4 (n = 5) plasmids highly similar to those identified previously in human, animal and environmental isolates. CONCLUSION This study demonstrated a dissemination of "typical" mcr-bearing plasmids among diverse Eco and Kpn genotypes and across a wide geographic area in Russia. Given the frequent association of mcr with other resistance determinants and potential clinical impact, the continual surveillance of this threat is warranted.
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Affiliation(s)
- Valeria Shapovalova
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks, Federal Medical Biological Agency, 119121 Moscow, Russia
- Correspondence:
| | - Elvira Shaidullina
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia
| | - Ilya Azizov
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia
| | - Eugene Sheck
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia
| | - Alexey Martinovich
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia
| | - Marina Dyachkova
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks, Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Alina Matsvay
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks, Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Yulia Savochkina
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks, Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Kamil Khafizov
- Central Research Institute of Epidemiology, 111123 Moscow, Russia
| | - Roman Kozlov
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia
| | - German Shipulin
- Federal State Budgetary Institution, Centre for Strategic Planning and Management of Biomedical Health Risks, Federal Medical Biological Agency, 119121 Moscow, Russia
| | - Mikhail Edelstein
- Institute of Antimicrobial Chemotherapy, Smolensk State Medical University, 214019 Smolensk, Russia
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Harbaoui S, Ferjani S, Abbassi M, Saidani M, Gargueh T, Ferjani M, Hammi Y, Boutiba‐Ben Boubaker I. Genetic heterogeneity and predominance of
bla
CTX‐M
‐15
in cefotaxime‐resistant
Enterobacteriaceae
isolates colonizing hospitalized children in Tunisia. Lett Appl Microbiol 2022; 75:1460-1474. [DOI: 10.1111/lam.13812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2022] [Revised: 07/25/2022] [Accepted: 08/08/2022] [Indexed: 11/28/2022]
Affiliation(s)
- S. Harbaoui
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche « Résistance aux antimicrobiens » 1006 Tunis Tunisie
| | - S. Ferjani
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche « Résistance aux antimicrobiens » 1006 Tunis Tunisie
| | - M.S. Abbassi
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche « Résistance aux antimicrobiens » 1006 Tunis Tunisie
- Université de Tunis El Manar, Institut de la recherche vétérinaire de Tunisie Tunis Tunisie
| | - M. Saidani
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche « Résistance aux antimicrobiens » 1006 Tunis Tunisie
- CHU Charles Nicolle Service de Microbiologie 1006 Tunis Tunisie
| | - T. Gargueh
- CHU Charles Nicolle Service de Pédiatrie 1006 Tunis Tunisie
| | - M. Ferjani
- CHU Charles Nicolle Service de Pédiatrie 1006 Tunis Tunisie
| | - Y. Hammi
- CHU Charles Nicolle Service de Pédiatrie 1006 Tunis Tunisie
| | - I. Boutiba‐Ben Boubaker
- Université de Tunis El Manar, Faculté de Médecine de Tunis, LR99ES09 Laboratoire de recherche « Résistance aux antimicrobiens » 1006 Tunis Tunisie
- CHU Charles Nicolle Service de Microbiologie 1006 Tunis Tunisie
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15
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Khrulnova S, Fedorova A, Frolova I, Tandilova K, Likold E, Klyasova PG. Distribution of virulence genes and capsule types in Klebsiella pneumoniae among bloodstream isolates from patients with hematological malignancies. Diagn Microbiol Infect Dis 2022; 104:115744. [DOI: 10.1016/j.diagmicrobio.2022.115744] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 05/13/2022] [Accepted: 06/10/2022] [Indexed: 11/03/2022]
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Simultaneous Hospital Outbreaks of New Delhi Metallo-β-Lactamase-Producing Enterobacterales Unraveled Using Whole-Genome Sequencing. Microbiol Spectr 2022; 10:e0228721. [PMID: 35311539 PMCID: PMC9045244 DOI: 10.1128/spectrum.02287-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Multidrug-resistant Enterobacterales, including carbapenemase producers, are currently spreading in health care facilities and the community. The Bichat Claude Bernard hospital in Paris faced a prolonged NDM-producing Enterobacterales (NDM-CPE) outbreak. Whole-genome sequencing (WGS) was performed on all isolated NDM-CPE to evaluate its benefits for outbreak surveillance and comprehension. All NDM-CPE isolates collected during the outbreak period (August 2016 to January 2018) were sequenced using the Illumina NextSeq platform. Gene content and core genomes were compared. Genomics results underwent epidemiological analysis which classified NDM-CPE cases as imported (positive sample during the 48 h after admission), hospital acquired, or uncertain. Over the epidemic period, 61 patients were colonized or infected with 81 distinct NDM-CPE isolates. Klebsiella pneumoniae was the most common species (n = 52, 64%), followed by Escherichia coli (13.5%) and other species (22.5%). In all, 43/52 (83%) K. pneumoniae isolates were clonal (≤18 single nucleotide polymorphisms [SNPs] except for three isolates) and belonged to ST307. The IncFIIK [K2:A-/B-] plasmid carrying blaNDM-1 present in all ST307 K. pneumoniae isolates was also detected in 18 other NDM-CPE isolates. Additionally, eight clonal ST144 Klebsiella oxytoca (≤18 SNPs) isolates lacking the epidemic plasmid were observed. The WGS analyses confirmed the acquired and imported cases except for two patients and resolved uncertain cases, which all turned out to be hospital acquisitions. WGS coupled with epidemiological analysis unraveled three epidemic phenomena: mainly the spread of a clonal ST307 K. pneumoniae strain and its conjugative plasmid carrying blaNDM-1 but also the unexpected clonal spread of an ST144 K. oxytoca strain. IMPORTANCE Carbapenemase-producing Enterobacterales (CPE) can spread and cause outbreaks in health care facilities, resulting in increased lengths of stay and morbidity. Control of outbreaks requires epidemiological surveillance, usually based on microbiological screening and patient follow-up. These data are sometimes insufficient to identify the routes of dissemination. There is therefore a need for more accurate tools such as whole-genome sequencing (WGS), which allows comparison of isolates but also plasmids carrying resistance with a high definition. In this work, we retrospectively sequenced the genomes of all NDM-producing Enterobacterales isolated during a prolonged NDM outbreak in our hospital. We demonstrated the value of combining WGS with epidemiological data that unveiled the multiple mechanisms of dissemination involved in the outbreak and confirmed transmission cases. This work reinforces the potential of WGS in outbreak surveillance and suggests that it could improve outbreak control if used in real time by confirming transmission cases more rapidly.
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Manyahi J, Majigo M, Kibwana U, Kamori D, Lyamuya EF. Colonization of Extended-spectrum β-lactamase producing Enterobacterales and meticillin-resistant S. aureus in the intensive care unit at a tertiary hospital in Tanzania: Implications for Infection control and prevention. Infect Prev Pract 2022; 4:100212. [PMID: 35495173 PMCID: PMC9046873 DOI: 10.1016/j.infpip.2022.100212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Accepted: 03/24/2022] [Indexed: 11/24/2022] Open
Abstract
Background Multi-drug resistant (MDR) bacteria pose a major global threat to public-health and are of particular concern to hospitalized intensive care unit (ICU) patients. This study aimed at addressing the burden of MDR and the associated factors at admission to ICU. Methods This was a cross-sectional study conducted at the ICU of a tertiary hospital in Tanzania. Rectal and anterior nares swabs were collected within 48 hours of ICU admission to screen for extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-PE) and meticillin-resistant Staphylococcus aureus (MRSA), respectively. Results The proportion of fecal carriage for ESBL-PE at admission to ICU was 54.54% (95% CI, 47.52–61.39), and nasal carriage for MRSA was 9.32% (95%CI, 5.67–14.93). The nasal MRSA colonization (OR = 1.52) and fecal carriage for ESBL-PE (OR=1.38) were more likely in participants who had received antibiotics before ICU admission than not, but association was not statistically significant. Hospitalization for ≥2 days (OR=1.18) was associated with fecal carriage of ESBL-PE, though not statistically significant. Overall, 66% and 73.5% of patients received antibiotics before and upon admission to ICU, respectively. Ceftriaxone, metronidazole and meropenem were commonly prescribed antibiotics. More than 84% of Enterobacterales were resistant to ciprofloxacin and trimethoprim-sulfamethoxazole, and 2.90% were resistant to meropenem. MRSA isolates showed a high rate of resistance to gentamicin and erythromycin. Conclusion MDR bacteria are common in patients admitted to ICU. To reduce the risk associated with MDR, we recommend use of simple screening methods to screen for MDR at ICU admission as part of infection control and prevention.
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Affiliation(s)
- Joel Manyahi
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
- Corresponding author. Address: Muhimbili University of Health and Allied Sciences, P.O. Box 65001, Dar es Salaam, Tanzania. +255712251709.
| | - Mtebe Majigo
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Upendo Kibwana
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Doreen Kamori
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
| | - Eligius F. Lyamuya
- Department of Microbiology and Immunology, Muhimbili University of Health and Allied Sciences, Dar es Salaam, Tanzania
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18
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Early Response of Antimicrobial Resistance and Virulence Genes Expression in Classical, Hypervirulent, and Hybrid hvKp-MDR Klebsiella pneumoniae on Antimicrobial Stress. Antibiotics (Basel) 2021; 11:antibiotics11010007. [PMID: 35052884 PMCID: PMC8773033 DOI: 10.3390/antibiotics11010007] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Revised: 12/19/2021] [Accepted: 12/20/2021] [Indexed: 12/16/2022] Open
Abstract
Klebsiella pneumoniae is an increasingly important hospital pathogen. Classical K. pneumoniae (cKp) and hypervirulent K. pneumoniae (hvKp) are two distinct evolutionary genetic lines. The recently ongoing evolution of K. pneumoniae resulted in the generation of hybrid hvKP-MDR strains. K. pneumoniae distinct isolates (n = 70) belonged to 20 sequence types with the prevalence of ST395 (27.1%), ST23 (18.6%), ST147 (15.7%), and ST86 (7.1%), and 17 capsular types with the predominance of K2 (31.4%), K57 (18.6%), K64 (10.0%), K1 (5.7%) were isolated from patients of the Moscow neurosurgery ICU in 2014-2019. The rate of multi-drug resistant (MDR) and carbapenem-resistant phenotypes were 84.3% and 45.7%, respectively. Whole-genome sequencing of five selected strains belonging to cKp (ST395K47 and ST147K64), hvKp (ST86K2), and hvKp-MDR (ST23K1 and ST23K57) revealed blaSHV, blaTEM, blaCTX, blaOXA-48, and blaNDM beta-lactamase genes; acr, oqx, kpn, kde, and kex efflux genes; and K. pneumoniae virulence genes. Selective pressure of 100 mg/L ampicillin or 10 mg/L ceftriaxone induced changes of expression levels for named genes in the strains belonging to cKp, hvKp, and hybrid hvKp-MDR. Obtained results seem to be important for epidemiologists and clinicians for enhancing knowledge about hospital pathogens.
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Gómez M, Valverde A, del Campo R, Rodríguez JM, Maldonado-Barragán A. Phenotypic and Molecular Characterization of Commensal, Community-Acquired and Nosocomial Klebsiella spp. Microorganisms 2021; 9:2344. [PMID: 34835469 PMCID: PMC8625991 DOI: 10.3390/microorganisms9112344] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 11/17/2022] Open
Abstract
Klebsiella spp. is a relevant pathogen that can present acquired resistance to almost all available antibiotics, thus representing a serious threat for public health. While most studies have been focused on isolates causing community-acquired and nosocomial infections, little is known about the commensal isolates colonizing healthy subjects. We describe the molecular identification and the phenotypic characterization of commensal Klebsiella spp. from breast milk of healthy women and faeces from healthy breast-fed infants, which were compared with isolates from community-acquired infections and from a nosocomial NICU outbreak. The phylogenetic analysis of a 454-bp sequence of the rpoB gene was useful for species identification (K. pneumoniae, K. variicola, K. quasipneumoniae, K. oxytoca, K. grimontii, K. michiganensis, Raoultella planticola and R. ornithinolytica), previously misidentified as K. pneumoniae or K. oxytoca by biochemical methods. Globally, we report that commensal strains present virulence traits (virulence genes, siderophores and biofilms) comparable to community-acquired and NICU-infective isolates, thus suggesting that the human microbiota could constitute a reservoir for infection. Isolates causing NICU outbreak were multi-drug resistant (MDR) and ESBLs producers, although an imipenem-resistant commensal MDR K. quasipneumoniae isolate was also found. A commensal K. pneumoniae strain showed a potent bacteriocin-like inhibitory activity against MDR Klebsiella isolates, thus highlighting the potential role of commensal Klebsiella spp. in health and disease.
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Affiliation(s)
- Marta Gómez
- Department of Nutrition and Food Science, Complutense University of Madrid, 28040 Madrid, Spain; (M.G.); (J.M.R.)
| | - Arancha Valverde
- Department of Microbiology, Hospital Universitario Ramón y Cajal IRYCIS, 28034 Madrid, Spain; (A.V.); (R.d.C.)
| | - Rosa del Campo
- Department of Microbiology, Hospital Universitario Ramón y Cajal IRYCIS, 28034 Madrid, Spain; (A.V.); (R.d.C.)
| | - Juan Miguel Rodríguez
- Department of Nutrition and Food Science, Complutense University of Madrid, 28040 Madrid, Spain; (M.G.); (J.M.R.)
| | - Antonio Maldonado-Barragán
- Department of Nutrition and Food Science, Complutense University of Madrid, 28040 Madrid, Spain; (M.G.); (J.M.R.)
- Infection and Global Health Research Division, School of Medicine, University of St. Andrews, North Haugh, St Andrews KY16 9TF, UK
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