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Beig M, Majidzadeh N, Asforooshani MK, Rezaie N, Abed S, Khiavi EHG, Sholeh M, Aghamohammad S. Antibiotic resistance rates in hypervirulent Klebsiella pneumoniae strains: a systematic review and meta-analysis. J Glob Antimicrob Resist 2024:S2213-7165(24)00127-9. [PMID: 39069234 DOI: 10.1016/j.jgar.2024.06.018] [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: 11/19/2023] [Revised: 05/26/2024] [Accepted: 06/16/2024] [Indexed: 07/30/2024] Open
Abstract
OBJECTIVES In response to the growing global concerns regarding antibiotic resistance, we conducted a meta-analysis to assess the prevalence of antibiotic resistance in hypervirulent Klebsiella pneumoniae (hvKp) strains. METHODS We conducted a meta-analysis of antibiotic resistance in the hvKp strains. Eligible studies published in English until April 10, 2023, were identified through a systematic search of various databases. After removing duplicates, two authors independently assessed and analyzed the relevant publications, and a third author resolved any discrepancies. Data extraction included publication details and key information on antibiotic resistance. Data synthesis employed a random-effects model to account for heterogeneity, and various statistical analyses were conducted using R and the metafor package. RESULTS This meta-analysis of 77 studies from 17 countries revealed the prevalence of antibiotic resistance in hvKp strains. A high resistance rates have been observed against various classes of antibiotics. Ampicillin-sulbactam faced 45.3% resistance, respectively, rendering them largely ineffective. The first-generation cephalosporin cefazolin exhibited a resistance rate of 38.1%, whereas second-generation cefuroxime displayed 26.7% resistance. Third-generation cephalosporins, cefotaxime (65.8%) and ceftazidime (57.1%), and fourth-generation cephalosporins, cefepime (51.3%), showed substantial resistance. The last-resort carbapenems, imipenem (45.7%), meropenem (51.0%), and ertapenem (40.6%), were not spared. Conclusion CONCLUSION: This study emphasizes the growing issue of antibiotic resistance in hvKp strains, with notable resistance to both older and newer antibiotics, increasing resistance over time, regional disparities, and methodological variations. Effective responses should involve international cooperation, standardized testing, and tailored regional interventions.
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Affiliation(s)
- Masoumeh Beig
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | | | - Mahshid Khazani Asforooshani
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran; Department of Microbiology, Faculty of Biological Sciences, Alzahra University, Tehran, Iran
| | - Niloofar Rezaie
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Sahar Abed
- Department of Microbial Biotechnology, Faculty of Basic Sciences and Advanced Technologies in Biology, University of Science and Culture, Tehran, Iran
| | | | - Mohammad Sholeh
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran.
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Sohrabi M, Pirbonyeh N, Alizade Naini M, Rasekhi A, Ayoub A, Hashemizadeh Z, Shahcheraghi F. A challenging case of carbapenem resistant Klebsiella pneumoniae-related pyogenic liver abscess with capsular polysaccharide hyperproduction: a case report. BMC Infect Dis 2024; 24:433. [PMID: 38654215 PMCID: PMC11040961 DOI: 10.1186/s12879-024-09314-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2023] [Accepted: 04/11/2024] [Indexed: 04/25/2024] Open
Abstract
BACKGROUND Carbapenem-resistant Klebsiella pneumoniae (CRKP) infections are a major public health problem, necessitating the administration of polymyxin E (colistin) as a last-line antibiotic. Meanwhile, the mortality rate associated with colistin-resistant K. pneumoniae infections is seriously increasing. On the other hand, importance of administration of carbapenems in promoting colistin resistance in K. pneumoniae is unknown. CASE PRESENTATION We report a case of K. pneumoniae-related pyogenic liver abscess in which susceptible K. pneumoniae transformed into carbapenem- and colistin-resistant K. pneumoniae during treatment with imipenem. The case of pyogenic liver abscess was a 50-year-old man with diabetes and liver transplant who was admitted to Abu Ali Sina Hospital in Shiraz. The K. pneumoniae isolate responsible for community-acquired pyogenic liver abscess was isolated and identified. The K. pneumoniae isolate was sensitive to all tested antibiotics except ampicillin in the antimicrobial susceptibility test and was identified as a non-K1/K2 classical K. pneumoniae (cKp) strain. Multilocus sequence typing (MLST) identified the isolate as sequence type 54 (ST54). Based on the patient's request, he was discharged to continue treatment at another center. After two months, he was readmitted due to fever and progressive constitutional symptoms. During treatment with imipenem, the strain acquired blaOXA-48 and showed resistance to carbapenems and was identified as a multidrug resistant (MDR) strain. The minimum inhibitory concentration (MIC) test for colistin was performed by broth microdilution method and the strain was sensitive to colistin (MIC < 2 µg/mL). Meanwhile, on blood agar, the colonies had a sticky consistency and adhered to the culture medium (sticky mucoviscous colonies). Quantitative real-time PCR and biofilm formation assay revealed that the CRKP strain increased capsule wzi gene expression and produced slime in response to imipenem. Finally, K. pneumoniae-related pyogenic liver abscess with resistance to a wide range of antibiotics, including the last-line antibiotics colistin and tigecycline, led to sepsis and death. CONCLUSIONS Based on this information, can we have a theoretical hypothesis that imipenem is a promoter of resistance to carbapenems and colistin in K. pneumoniae? This needs more attention.
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Affiliation(s)
- Maryam Sohrabi
- Department of Bacteriology, Pasteur Institute of Iran, Tehran, Iran
| | - Neda Pirbonyeh
- Department of Microbiology, Burn and Wound Healing Research Center, Shiraz University of Medical Sciences, Shiraz, Iran
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Mahvash Alizade Naini
- Department of Internal Medicine, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Alireza Rasekhi
- Department of Radiology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Abbas Ayoub
- Department of Radiology, Shiraz University of Medical Sciences, Shiraz, Iran
| | - Zahra Hashemizadeh
- Department of Bacteriology and Virology, School of Medicine, Shiraz University of Medical Sciences, Shiraz, Iran
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Li L, Li S, Wei X, Lu Z, Qin X, Li M. Infection with Carbapenem-resistant Hypervirulent Klebsiella Pneumoniae: clinical, virulence and molecular epidemiological characteristics. Antimicrob Resist Infect Control 2023; 12:124. [PMID: 37953357 PMCID: PMC10642049 DOI: 10.1186/s13756-023-01331-y] [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: 03/24/2023] [Accepted: 11/05/2023] [Indexed: 11/14/2023] Open
Abstract
BACKGROUND Carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) is gradually becoming the dominant nosocomial pathogens in the healthcare setting. METHODS A retrospective study was conducted on patients with CR-KP from July 2021 to May 2022 in a teaching hospital. We identified bacterial isolates, collected the clinical data, and performed antimicrobial susceptibility testing, hypermucoviscosity string test, antimicrobial and virulence-associated genotype, as well as multi-locus sequence typing. CR-hvKP was defined as the presence of some combination of rmpA and/or rmpA2 with iucA, iroB, or peg-344. SPSS was used for data analysis. Univariate logistic regression analyses were used for risk factor and all statistically significant variables were included in the multivariate model. Statistical significance was taken to be P < 0.05. RESULTS A total of 69 non-duplicated CR-KP isolates were collected, 27 of which were CR-hvKP. Out of the 69 CR-KP strains under investigation, they were distributed across 14 distinct sequence types (STs), wherein ST11 exhibited the highest prevalence, constituting 65.2% (45/69) of the overall isolates. The principal carbapenemase genes identified encompassed blakpc-2, blaNDM-1, and blaOXA-48, with blakpc-2 prevailing as the predominant type, accounting for 73.9% (51/69). A total of 69 CR-KP strains showed high resistance to common clinical antibiotics, with the exception of ceftazidime/avibactam. The ST11 (P = 0.040), ST65 (P = 0.030) and blakpc-2 ST11 clones (P = 0.010) were found to be highly related to hvKp. Regarding the host, tracheal intubation (P = 0.008), intracranial infection (P = 0.020) and neutrophil count (P = 0.049) were significantly higher in the patients with CR-hvKP. Multivariate analysis showed tracheal intubation to be an independent risk factor for CR-hvKP infection (P = 0.030, OR = 4.131). According to the clinical data we collected, tracheal intubation was performed mainly in the elderly with severe underlying diseases, which implied that CR-hvKP has become prevalent among elderly patients with comorbidities. CONCLUSIONS The prevalence of CR-hvKP may be higher than expected in the healthcare setting. CR-hvKP is gradually becoming the dominant nosocomial pathogen, and its prevalence and treatment will be a major challenge. It is essential to enhance clinical awareness and management of CR-hvKP infection.
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Affiliation(s)
- Linlin Li
- Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Department of Clinical Laboratory, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Shan Li
- Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Department of Clinical Laboratory, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xianzhen Wei
- Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Department of Clinical Laboratory, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Zhaolu Lu
- Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Department of Clinical Laboratory, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Xue Qin
- Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Department of Clinical Laboratory, the First Affiliated Hospital of Guangxi Medical University, Nanning, China
| | - Meng Li
- Key Laboratory of Clinical Laboratory Medicine of Guangxi Department of Education, Department of Clinical Laboratory, the First Affiliated Hospital of Guangxi Medical University, Nanning, 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: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 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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Liu P, Yang A, Tang B, Wang Z, Jian Z, Liu Y, Wang J, Zhong B, Yan Q, Liu W. Molecular epidemiology and clinical characteristics of the type VI secretion system in Klebsiella pneumoniae causing abscesses. Front Microbiol 2023; 14:1181701. [PMID: 37266024 PMCID: PMC10230222 DOI: 10.3389/fmicb.2023.1181701] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 04/28/2023] [Indexed: 06/03/2023] Open
Abstract
Purpose The type VI system (T6SS) has the potential to be a new virulence factor for hypervirulent Klebsiella pneumoniae (hvKp) strains. This study aimed to characterize the molecular and clinical features of T6SS-positive and T6SS-negative K. pneumoniae isolates that cause abscesses. Patients and methods A total of 169 non-duplicate K. pneumoniae strains were isolated from patients with abscesses in a tertiary hospital in China from January 2018 to June 2022, and clinical data were collected. For all isolates, capsular serotypes, T6SS genes, virulence, and drug resistance genes, antimicrobial susceptibility testing, and biofilm formation assays were assessed. Multilocus sequence typing was used to analyze the genotypes of hvKp. T6SS-positive hvKp, T6SS-negative hvKp, T6SS-positive cKP, and T6SS-negative cKP (n = 4 strains for each group) were chosen for the in vivo Galleria mellonella infection model and in vitro competition experiments to further explore the microbiological characteristics of T6SS-positive K. pneumoniae isolates. Results The positive detection rate for T6SS was 36.1%. The rates of hvKp, seven virulence genes, K1 capsular serotype, and ST23 in T6SS-positive strains were all higher than those in T6SS-negative strains (p < 0.05). Multivariate logistic regression analysis indicated that the carriage of aerobactin (OR 0.01) and wcaG (OR 33.53) were independent risk factors for T6SS-positive strains (p < 0.05). The T6SS-positive strains had a stronger biofilm-forming ability than T6SS-negative strains (p < 0.05). The T6SS-positive and T6SS-negative strains showed no significant differences in competitive ability (p = 0.06). In the in vivo G. mellonella infection model, the T6SS(+)/hvKP group had the worst prognosis. Except for cefazolin and tegacyclin, T6SS-positive isolates displayed a lower rate of antimicrobial resistance to other drugs (p < 0.05). The T6SS-positive isolates were more likely to be acquired from community infections (p < 0.05). Conclusion Klebsiella pneumoniae isolates causing abscesses have a high prevalence of T6SS genes. T6SS-positive K. pneumoniae isolates are associated with virulence, and the T6SS genes may be involved in the hvKp virulence mechanism.
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Affiliation(s)
- Peilin Liu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Awen Yang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Bin Tang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zhiqian Wang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Zijuan Jian
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Yanjun Liu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Jiahui Wang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
| | - Baiyun Zhong
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Qun Yan
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, China
| | - Wenen Liu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, Hunan, China
- National Clinical Research Center for Geriatric Disorders, Xiangya Hospital, Changsha, Hunan, China
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Zhu Q, Xu J, Chen X, Ren Y, Zhao L. Risk factors and molecular epidemiology of bloodstream infections due to carbapenem-resistant Klebsiella pneumoniae. Diagn Microbiol Infect Dis 2023; 106:115955. [PMID: 37167651 DOI: 10.1016/j.diagmicrobio.2023.115955] [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: 09/29/2022] [Revised: 03/24/2023] [Accepted: 04/11/2023] [Indexed: 05/13/2023]
Abstract
PURPOSE Carbapenem-resistant Klebsiella pneumoniae (CRKP) is emerging as a worldwide public health concern; however, molecular epidemiological surveillance of clinical CRKP bloodstream infection (BSI) in China is limited. We conducted a retrospective observational study to assess risk factors and the molecular epidemiology of CRKP BSI. METHODS We reviewed the medical records of enrolled patients to assess risk factors of CRKP BSI. Characteristics of CRKP isolates were analyzed by whole genome sequencing and Kleborate. Evolutionary diversification in CRKP isolates was described through Single Nucleotide Polymorphisms analysis and phylogenetic tree construction. RESULTS We found that prior ICU hospitalization and use of carbapenems were independent risk factors for CRKP BSI. The main CRKP sequence type (ST) and capsular serotype were ST11 and KL64, and KPC-2 was the most prevalent enzyme type of carbapenemase-carrying Klebsiella pneumoniae. The most prevalent aerobactin and yersiniabactin of ST11-CRKP were iuc-1 and ybt9 ICEKp3, as for KL64-CRKP. Phylogenomic analysis showed that the antibacterial resistance genes on plasmids were highly consistent, but the genetic background of the chromosomes was still different. CONCLUSIONS Our findings are important for hospitals, allowing them to limit dissemination of CRKP and optimize antibiotic administration.
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Affiliation(s)
- Qiongfang Zhu
- Center of Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Jie Xu
- Center of Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Xu Chen
- Center of Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Yalu Ren
- Center of Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China
| | - Lina Zhao
- Center of Clinical Laboratory, The First Affiliated Hospital of Soochow University, Suzhou, Jiangsu, China; Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, China.
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Wang YC, Lu MC, Li YT, Tang HL, Hsiao PY, Chen BH, Teng RH, Chiou CS, Lai YC. Microevolution of CG23-I Hypervirulent Klebsiella pneumoniae during Recurrent Infections in a Single Patient. Microbiol Spectr 2022; 10:e0207722. [PMID: 36129301 PMCID: PMC9602619 DOI: 10.1128/spectrum.02077-22] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2022] [Accepted: 09/05/2022] [Indexed: 12/31/2022] Open
Abstract
CG23-I lineage constitutes the majority of hypervirulent Klebsiella pneumoniae. A diabetic patient suffered six episodes of infections caused by CG23-I K. pneumoniae. A total of nine isolates were collected in 2020. We performed whole-genome sequencing to elucidate the within-patient evolution of CG23-I K. pneumoniae. The maximum pairwise difference among the nine longitudinally collected isolates was five single nucleotide polymorphisms. One of the mutations was at the Asp87 position of GyrA. Four indels were identified, including an initiator tRNAfMet duplication, a tRNAArg deletion, a 7-bp insertion, and a 22-bp deletion. All 9 isolates had the genomic features of CG23-I K. pneumoniae, a chromosome-borne ICEKp10, and a large virulence plasmid. The carriage of a complete set of genes for the biosynthesis of colibactin by ICEKp10 gave the nine isolates an ability to cause DNA damage to RAW264.7 cells. Compared with the initial isolate, the last isolate with an additional copy of initiator tRNAfMet grew faster in a nutrient-limiting condition and exhibited enhanced virulence in BALB/c mice. Collectively, we characterized the within-patient microevolution of CG23-I K. pneumoniae through an in-depth comparison of genome sequences. Using the in vitro experiments and mouse models, we also demonstrated that these genomic alterations endowed the isolates with advantages to pass through in vivo selection. IMPORTANCE CG23-I is a significant lineage of hypervirulent Klebsiella pneumoniae. This study characterizes the within-patient microevolution of CG23-I K. pneumoniae. Selective pressures from continuous use of antibiotics favored point mutations contributing to bacterial resistance to antibiotics. The duplication of an initiator tRNAfMet gene helped CG23-I K. pneumoniae proliferate to reach a maximal population size during infections. For longer persistence inside a human host, the large virulence plasmid evolved with more flexible control of replication through duplication of the iteron-1 region. With the genomic alterations, the last isolate had a growth advantage over the initial isolate and exhibited enhanced virulence in BALB/c mice. This study gives us a deeper understanding of the genome evolution during the within-patient pathoadaptation of CG23-I K. pneumoniae.
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Affiliation(s)
- Yao-Chen Wang
- Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
- School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Min-Chi Lu
- Department of Microbiology and Immunology, School of Medicine, China Medical University, Taichung, Taiwan
- Division of Infectious Diseases, Department of Internal Medicine, China Medical University Hospital, Taichung, Taiwan
| | - Yia-Ting Li
- Division of Respiratory Therapy, Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
| | - Hui-Ling Tang
- Department of Microbiology and Immunology, School of Medicine, China Medical University, Taichung, Taiwan
| | - Pei-Yi Hsiao
- Department of Microbiology and Immunology, School of Medicine, Chung Shan Medical University, Taichung, Taiwan
| | - Bo-Han Chen
- Central Region Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Ru-Hsiou Teng
- Central Region Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Chien-Shun Chiou
- Central Region Laboratory, Center for Diagnostics and Vaccine Development, Centers for Disease Control, Ministry of Health and Welfare, Taipei, Taiwan
| | - Yi-Chyi Lai
- Department of Internal Medicine, Chung Shan Medical University Hospital, Taichung, Taiwan
- Department of Microbiology and Immunology, School of Medicine, Chung Shan Medical University, Taichung, Taiwan
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