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Guitor AK, Yousuf EI, Raphenya AR, Hutton EK, Morrison KM, McArthur AG, Wright GD, Stearns JC. Capturing the antibiotic resistome of preterm infants reveals new benefits of probiotic supplementation. MICROBIOME 2022; 10:136. [PMID: 36008821 PMCID: PMC9414150 DOI: 10.1186/s40168-022-01327-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 07/14/2022] [Indexed: 05/28/2023]
Abstract
BACKGROUND Probiotic use in preterm infants can mitigate the impact of antibiotic exposure and reduce rates of certain illnesses; however, the benefit on the gut resistome, the collection of antibiotic resistance genes, requires further investigation. We hypothesized that probiotic supplementation of early preterm infants (born < 32-week gestation) while in hospital reduces the prevalence of antibiotic resistance genes associated with pathogenic bacteria in the gut. We used a targeted capture approach to compare the resistome from stool samples collected at the term corrected age of 40 weeks for two groups of preterm infants (those that routinely received a multi-strain probiotic during hospitalization and those that did not) with samples from full-term infants at 10 days of age to identify if preterm birth or probiotic supplementation impacted the resistome. We also compared the two groups of preterm infants up to 5 months of age to identify persistent antibiotic resistance genes. RESULTS At the term corrected age, or 10 days of age for the full-term infants, we found over 80 antibiotic resistance genes in the preterm infants that did not receive probiotics that were not identified in either the full-term or probiotic-supplemented preterm infants. More genes associated with antibiotic inactivation mechanisms were identified in preterm infants unexposed to probiotics at this collection time-point compared to the other infants. We further linked these genes to mobile genetic elements and Enterobacteriaceae, which were also abundant in their gut microbiomes. Various genes associated with aminoglycoside and beta-lactam resistance, commonly found in pathogenic bacteria, were retained for up to 5 months in the preterm infants that did not receive probiotics. CONCLUSIONS This pilot survey of preterm infants shows that probiotics administered after preterm birth during hospitalization reduced the diversity and prevented persistence of antibiotic resistance genes in the gut microbiome. The benefits of probiotic use on the microbiome and the resistome should be further explored in larger groups of infants. Due to its high sensitivity and lower sequencing cost, our targeted capture approach can facilitate these surveys to further address the implications of resistance genes persisting into infancy without the need for large-scale metagenomic sequencing. Video Abstract.
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Affiliation(s)
- Allison K Guitor
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Canada
| | - Efrah I Yousuf
- Department of Pediatrics, McMaster University, Hamilton, Canada
| | - Amogelang R Raphenya
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Canada
| | - Eileen K Hutton
- Department of Obstetrics & Gynecology, McMaster University, Hamilton, Canada
- The Baby & Mi and the Baby & Pre-Mi Cohort Studies, Hamilton, Canada
| | - Katherine M Morrison
- Department of Pediatrics, McMaster University, Hamilton, Canada
- The Baby & Mi and the Baby & Pre-Mi Cohort Studies, Hamilton, Canada
| | - Andrew G McArthur
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Canada
| | - Gerard D Wright
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada
- Michael G. DeGroote Institute for Infectious Disease Research, McMaster University, Hamilton, Canada
- David Braley Centre for Antibiotic Discovery, McMaster University, Hamilton, Canada
| | - Jennifer C Stearns
- Department of Biochemistry and Biomedical Sciences, McMaster University, Hamilton, Canada.
- The Baby & Mi and the Baby & Pre-Mi Cohort Studies, Hamilton, Canada.
- Department of Medicine, McMaster University, Hamilton, Canada.
- Farncombe Family Digestive Health Research Institute, McMaster University, Hamilton, Canada.
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202
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Conserved FimK Truncation Coincides with Increased Expression of Type 3 Fimbriae and Cultured Bladder Epithelial Cell Association in Klebsiella quasipneumoniae. J Bacteriol 2022; 204:e0017222. [PMID: 36005809 PMCID: PMC9487511 DOI: 10.1128/jb.00172-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Klebsiella spp. commonly cause both uncomplicated urinary tract infection (UTI) and recurrent UTI (rUTI). Klebsiella quasipneumoniae, a relatively newly defined species of Klebsiella, has been shown to be metabolically distinct from Klebsiella pneumoniae, but its type 1 and type 3 fimbriae have not been studied. K. pneumoniae uses both type 1 and type 3 fimbriae to attach to host epithelial cells. The type 1 fimbrial operon is well conserved between Escherichia coli and K. pneumoniae apart from fimK, which is unique to Klebsiella spp. FimK contains an N-terminal DNA binding domain and a C-terminal phosphodiesterase (PDE) domain that has been hypothesized to cross-regulate type 3 fimbriae expression via modulation of cellular levels of cyclic di-GMP. Here, we find that a conserved premature stop codon in K. quasipneumoniae fimK results in truncation of the C-terminal PDE domain and that K quasipneumoniae strain KqPF9 cultured bladder epithelial cell association and invasion are dependent on type 3 but not type 1 fimbriae. Further, we show that basal expression of both type 1 and type 3 fimbrial operons as well as cultured bladder epithelial cell association is elevated in KqPF9 relative to uropathogenic K. pneumoniae TOP52. Finally, we show that complementation of KqPF9ΔfimK with the TOP52 fimK allele reduced type 3 fimbrial expression and cultured bladder epithelial cell attachment. Taken together these data suggest that the C-terminal PDE of FimK can modulate type 3 fimbrial expression in K. pneumoniae and its absence in K. quasipneumoniae may lead to a loss of type 3 fimbrial cross-regulation. IMPORTANCE K. quasipneumoniae is often indicated as the cause of opportunistic infections, including urinary tract infection, which affects >50% of women worldwide. However, the virulence factors of K. quasipneumoniae remain uninvestigated. Prior to this work, K. quasipneumoniae and K. pneumoniae had only been distinguished phenotypically by metabolic differences. This work contributes to the understanding of K. quasipneumoniae by evaluating the contribution of type 1 and type 3 fimbriae, which are critical colonization factors encoded by all Klebsiella spp., to K. quasipneumoniae bladder epithelial cell attachment in vitro. We observe clear differences in bladder epithelial cell attachment and regulation of type 3 fimbriae between uropathogenic K. pneumoniae and K. quasipneumoniae that coincide with a structural difference in the fimbrial regulatory gene fimK.
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203
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Yan K, Yang T, Xu J, Dong L, Wang J, Cai Y. Synergistic effect of low-frequency ultrasound and antibiotics on the treatment of Klebsiella pneumoniae pneumonia in mice. Microb Biotechnol 2022; 15:2819-2830. [PMID: 36001465 PMCID: PMC9618311 DOI: 10.1111/1751-7915.14134] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2022] [Accepted: 08/10/2022] [Indexed: 12/03/2022] Open
Abstract
The antibiotic‐resistant Klebsiella pneumoniae (Kp) has become a significant crisis in treating pneumonia. Low‐frequency ultrasound (LFU) is promising to overcome the obstacles. Mice were infected with bioluminescent Kp Xen39 by intratracheal injection to study the therapeutic effect of LFU in combination with antibiotics. The counts per second (CPS) were assessed with an animal biophoton imaging system. Bacterial clearance, histopathology, and the concentrations of cytokines were determined to evaluate the therapeutic effect. LC–MS/MS was used to detect the distribution of antibiotics in the lung and plasma. LFU in combination with meropenem (MEM) or amikacin (AMK) significantly improved the behavioural state of mice. The CPS of the LFU combination group were more significantly decreased compared with those of the antibiotic alone groups. The average colony‐forming units of lung tissue in the LFU combination groups were also lower than those of the antibiotic groups. Although no significant changes of cytokines (IL‐6 and TNF‐α) in plasma and bronchoalveolar lavage fluid were observed, LFU in combination with antibiotics showed less inflammatory damage from histopathological results compared with the antibiotic‐alone groups. Moreover, 10 min of LFU treatment promoted the distribution of MEM and AMK in mouse lung tissue at 60 and 30 min, respectively, after dosage. LFU could enhance the effectiveness of MEM and AMK in the treatment of Kp‐induced pneumonia, which might be attributed to the fact that LFU could promote the distribution of antibiotics in lung tissue and reduce inflammatory injury.
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Affiliation(s)
- Kaicheng Yan
- Medical School of Chinese PLA, Beijing, China.,Department of Pharmacy, Center of Medicine Clinical Research, Medical Supplies Center, Chinese PLA General Hospital, Beijing, China
| | - Tianli Yang
- Medical School of Chinese PLA, Beijing, China.,Department of Pharmacy, Center of Medicine Clinical Research, Medical Supplies Center, Chinese PLA General Hospital, Beijing, China
| | - Juan Xu
- Department of Pharmacy, Center of Medicine Clinical Research, Medical Supplies Center, Chinese PLA General Hospital, Beijing, China
| | - Liuhan Dong
- Medical School of Chinese PLA, Beijing, China.,Department of Pharmacy, Center of Medicine Clinical Research, Medical Supplies Center, Chinese PLA General Hospital, Beijing, China
| | - Jin Wang
- Department of Pharmacy, Center of Medicine Clinical Research, Medical Supplies Center, Chinese PLA General Hospital, Beijing, China
| | - Yun Cai
- Department of Pharmacy, Center of Medicine Clinical Research, Medical Supplies Center, Chinese PLA General Hospital, Beijing, China
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204
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Hawkey J, Wyres KL, Judd LM, Harshegyi T, Blakeway L, Wick RR, Jenney AWJ, Holt KE. ESBL plasmids in Klebsiella pneumoniae: diversity, transmission and contribution to infection burden in the hospital setting. Genome Med 2022; 14:97. [PMID: 35999578 PMCID: PMC9396894 DOI: 10.1186/s13073-022-01103-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 08/05/2022] [Indexed: 12/24/2022] Open
Abstract
Background Resistance to third-generation cephalosporins, often mediated by extended-spectrum beta-lactamases (ESBLs), is a considerable issue in hospital-associated infections as few drugs remain for treatment. ESBL genes are often located on large plasmids that transfer horizontally between strains and species of Enterobacteriaceae and frequently confer resistance to additional drug classes. Whilst plasmid transmission is recognised to occur in the hospital setting, the frequency and impact of plasmid transmission on infection burden, compared to ESBL + strain transmission, is not well understood. Methods We sequenced the genomes of clinical and carriage isolates of Klebsiella pneumoniae species complex from a year-long hospital surveillance study to investigate ESBL burden and plasmid transmission in an Australian hospital. Long-term persistence of a key transmitted ESBL + plasmid was investigated via sequencing of ceftriaxone-resistant isolates during 4 years of follow-up, beginning 3 years after the initial study. Results We found 25 distinct ESBL plasmids. We identified one plasmid, which we called Plasmid A, that carried blaCTX-M-15 in an IncF backbone similar to pKPN-307. Plasmid A was transmitted at least four times into different Klebsiella species/lineages and was responsible for half of all ESBL episodes during the initial 1-year study period. Three of the Plasmid A-positive strains persisted locally 3–6 years later, and Plasmid A was detected in two additional strain backgrounds. Overall Plasmid A accounted for 21% of ESBL + infections in the follow-up period. Conclusions Here, we systematically surveyed ESBL strain and plasmid transmission over 1 year in a single hospital network. Whilst ESBL plasmid transmission events were rare in this setting, they had a significant and sustained impact on the burden of ceftriaxone-resistant and multidrug-resistant infections. If onward transmission of Plasmid A-carrying strains could have been prevented, this may have reduced the number of opportunities for Plasmid A to transmit and create novel ESBL + strains, as well as reducing overall ESBL infection burden.
Supplementary Information The online version contains supplementary material available at 10.1186/s13073-022-01103-0.
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Affiliation(s)
- Jane Hawkey
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia.
| | - Kelly L Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Louise M Judd
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Taylor Harshegyi
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Luke Blakeway
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Ryan R Wick
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia
| | - Adam W J Jenney
- Microbiology Unit & Department of Infectious Diseases, The Alfred Hospital, Melbourne, VIC, Australia
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, Australia. .,Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK.
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205
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Liu Y, Zhu S, Wei L, Feng Y, Cai L, Dunn S, McNally A, Zong Z. Arm race among closely-related carbapenem-resistant Klebsiella pneumoniae clones. ISME COMMUNICATIONS 2022; 2:76. [PMID: 37938732 PMCID: PMC9723571 DOI: 10.1038/s43705-022-00163-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 08/03/2022] [Accepted: 08/10/2022] [Indexed: 11/09/2023]
Abstract
Multiple carbapenem-resistant Klebsiella pneumoniae (CRKP) clones typically co-exist in hospital wards, but often certain clones will dominate. The factors driving this dominance are largely unclear. This study began from a genomic epidemiology analysis and followed by multiple approaches to identify the potential mechanisms driving the successful spread of a dominant clone. 638 patients in a 50-bed ICU were screened. 171 (26.8%) and 21 had CRKP from swabs and clinical specimens, respectively. Many (39.8% of those with ≥7-day ICU stay) acquired CRKP. After removing 18 unable to recover, 174 CRKP isolates were genome sequenced and belonged to six sequence types, with ST11 being the most prevalent (n = 154, 88.5%) and most (n = 169, 97.1%) carrying blaKPC-2. The 154 ST11 isolates belonged to 7 clones, with one (clone 1, KL64 capsular type) being dominant (n = 130, 84.4%). Clone 1 and the second-most common clone (clone 2, KL64, n = 15, 9.7%) emerged simultaneously, which was also detected by genome-based dating. Clone 1 exhibited decreased biofilm formation, shorter environment survival, and attenuated virulence. In murine gut, clone 1 outcompeted clone 2. Transcriptomic analysis showed significant upregulation of the ethanolamine operon in clone 1 when competing with clone 2. Clone 1 exhibited increased utilization of ethanolamine as a nitrogen source. This highlights that reduced virulence and enhanced ability to utilize ethanolamine may promote the success of nosocomial multidrug-resistant clones.
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Affiliation(s)
- Ying Liu
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China
| | - Shichao Zhu
- Department of Infection Control, West China Hospital, Sichuan University, Chengdu, China
| | - Li Wei
- Department of Infection Control, West China Hospital, Sichuan University, Chengdu, China
| | - Yu Feng
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China
- Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China
| | - Lin Cai
- Intensive Care Unit, West China Hospital, Sichuan University, Chengdu, China
| | - Steven Dunn
- Institute of Microbiology and Infection, College of Medical and Dental Science, University of Birmingham, Birmingham, UK
| | - Alan McNally
- Institute of Microbiology and Infection, College of Medical and Dental Science, University of Birmingham, Birmingham, UK
| | - Zhiyong Zong
- Center of Infectious Diseases, West China Hospital, Sichuan University, Chengdu, China.
- Center for Pathogen Research, West China Hospital, Sichuan University, Chengdu, China.
- Department of Infection Control, West China Hospital, Sichuan University, Chengdu, China.
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206
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Genetic Diversity of Virulent Polymyxin-Resistant Klebsiella aerogenes Isolated from Intensive Care Units. Antibiotics (Basel) 2022; 11:antibiotics11081127. [PMID: 36009996 PMCID: PMC9405322 DOI: 10.3390/antibiotics11081127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/15/2022] [Accepted: 08/17/2022] [Indexed: 11/18/2022] Open
Abstract
This study evaluated the scope and genetic basis of polymyxin-resistant Klebsiella aerogenes in Brazil. Eight polymyxin-resistant and carbapenemase-producing K. aerogenes strains were isolated from patients admitted to the ICU of a tertiary hospital. Bacterial species were identified by automated systems and antimicrobial susceptibility profile was confirmed using broth microdilution. The strains displayed a multidrug resistant profile and were subjected to whole-genome sequencing. Bioinformatic analysis revealed a variety of antimicrobial resistance genes, including the blaKPC-2. No plasmid-mediated colistin resistance gene was identified. Nonetheless, nonsynonymous mutations in mgrB, pmrA, pmrB, and eptA were detected, justifying the colistin resistance phenotype. Virulence genes encoding yersiniabactin, colibactin, and aerobactin were also found, associated with ICEKp4 and ICEKp10, and might be related to the high mortality observed among the patients. In fact, this is the first time ICEKp is identified in K. aerogenes in Brazil. Phylogenetic analysis grouped the strains into two clonal groups, belonging to ST93 and ST16. In summary, the co-existence of antimicrobial resistance and virulence factors is deeply worrying, as it could lead to the emergence of untreatable invasive infections. All these factors reinforce the need for surveillance programs to monitor the evolution and dissemination of multidrug resistant and virulent strains among critically ill patients.
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207
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Altayb HN, Elbadawi HS, Alzahrani FA, Baothman O, Kazmi I, Nadeem MS, Hosawi S, Chaieb K. Co-Occurrence of β-Lactam and Aminoglycoside Resistance Determinants among Clinical and Environmental Isolates of Klebsiella pneumoniae and Escherichia coli: A Genomic Approach. Pharmaceuticals (Basel) 2022; 15:1011. [PMID: 36015159 PMCID: PMC9416466 DOI: 10.3390/ph15081011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2022] [Revised: 08/11/2022] [Accepted: 08/15/2022] [Indexed: 12/04/2022] Open
Abstract
The presence of antimicrobial-resistance genes (ARGs) in mobile genetic elements (MGEs) facilitates the rapid development and dissemination of multidrug-resistant bacteria, which represents a serious problem for human health. This is a One Health study which aims to investigate the co-occurrence of antimicrobial resistance determinants among clinical and environmental isolates of K. pneumoniae and E. coli. Various bioinformatics tools were used to elucidate the bacterial strains' ID, resistome, virulome, MGEs, and phylogeny for 42 isolates obtained from hospitalized patients (n = 20) and environmental sites (including fresh vegetables, fruits, and drinking water) (n = 22). The multilocus sequence typing (MLST) showed that K. pneumoniae belonged to ten sequence types (STs) while the E. coli belonged to seventeen STs. Multidrug-resistant isolates harbored β-lactam, aminoglycoside resistance determinants, and MGE were detected circulating in the environment (drinking water, fresh vegetables, and fruits) and in patients hospitalized with postoperative infections, neonatal sepsis, and urinary tract infection. Four K. pneumoniae environmental isolates (7E, 16EE, 1KE, and 19KE) were multidrug-resistant and were positive for different beta-lactam and aminoglycoside resistance determinants. blaCTX-M-15 in brackets of ISEc 9 and Tn 3 transposases was detected in isolates circulating in the pediatrics unit of Soba hospital and the environment. This study documented the presence of bacterial isolates harboring a similar pattern of antimicrobial resistance determinants circulating in hospitals and environments. A rapid response is needed from stakeholders to initiate a program for infection prevention and control measures to detect such clones disseminated in the communities and hospitals.
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Affiliation(s)
- Hisham N. Altayb
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Centre for Artificial Intelligence in Precision Medicine, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Hana S. Elbadawi
- Microbiology and Parasitology Department, Soba University Hospital, University of Khartoum, Khartoum 11115, Sudan
| | - Faisal A. Alzahrani
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Embryonic Stem Cells Unit, King Fahd Medical Research Center, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Othman Baothman
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Muhammad Shahid Nadeem
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Salman Hosawi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
| | - Kamel Chaieb
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Laboratory of Analysis, Treatment and Valorization of Pollutants of the Environmental and Products, Faculty of Pharmacy, University of Monastir, Monastir 5000, Tunisia
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208
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Spadar A, Phelan J, Elias R, Modesto A, Caneiras C, Marques C, Lito L, Pinto M, Cavaco-Silva P, Ferreira H, Pomba C, Da Silva GJ, Saavedra MJ, Melo-Cristino J, Duarte A, Campino S, Perdigão J, Clark TG. Genomic epidemiological analysis of Klebsiella pneumoniae from Portuguese hospitals reveals insights into circulating antimicrobial resistance. Sci Rep 2022; 12:13791. [PMID: 35963896 PMCID: PMC9375070 DOI: 10.1038/s41598-022-17996-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 08/03/2022] [Indexed: 11/30/2022] Open
Abstract
Klebsiella pneumoniae (Kp) bacteria are an increasing threat to public health and represent one of the most concerning pathogens involved in life-threatening infections and antimicrobial resistance (AMR). To understand the epidemiology of AMR of Kp in Portugal, we analysed whole genome sequencing, susceptibility testing and other meta data on 509 isolates collected nationwide from 16 hospitals and environmental settings between years 1980 and 2019. Predominant sequence types (STs) included ST15 (n = 161, 32%), ST147 (n = 36, 7%), ST14 (n = 26, 5%) or ST13 (n = 26, 5%), while 31% of isolates belonged to STs with fewer than 10 isolates. AMR testing revealed widespread resistance to aminoglycosides, fluoroquinolones, cephalosporins and carbapenems. The most common carbapenemase gene was blaKPC-3. Whilst the distribution of AMR linked plasmids appears uncorrelated with ST, their frequency has changed over time. Before year 2010, the dominant plasmid group was associated with the extended spectrum beta-lactamase gene blaCTX-M-15, but this group appears to have been displaced by another carrying the blaKPC-3 gene. Co-carriage of blaCTX-M and blaKPC-3 was uncommon. Our results from the largest genomics study of Kp in Portugal highlight the active transmission of strains with AMR genes and provide a baseline set of variants for future resistance monitoring and epidemiological studies.
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Affiliation(s)
- Anton Spadar
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Jody Phelan
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - Rita Elias
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Ana Modesto
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Cátia Caneiras
- Microbiology Research Laboratory of Environmental Health (EnviHealthMicro Lab), Institute of Environmental Health (ISAMB) and Institute of Preventive Medicine and Public Health (IMP&SP), Faculty of Medicine, Universidade de Lisboa, Lisbon, Portugal
| | - Cátia Marques
- Faculdade de Medicina Veterinária, Universidade Lusófona de Humanidades E Tecnologias, Lisbon, Portugal
| | - Luís Lito
- Laboratório de Microbiologia, Serviço de Patologia Clínica, Centro Hospitalar Universitário Lisboa Norte, Lisbon, Portugal
| | - Margarida Pinto
- Laboratório de Microbiologia, Serviço de Patologia Clínica, Centro Hospitalar Universitário Lisboa Central, Lisbon, Portugal
| | - Patrícia Cavaco-Silva
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Universitário Egas Moniz, Caparica, Portugal
- Technophage, Lisboa, Portugal
| | - Helena Ferreira
- UCIBIO, Microbiology Service, Biological Sciences Department, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Constança Pomba
- Centre of Interdisciplinary Research in Animal Health (CIISA), Faculty of Veterinary Medicine, University of Lisbon, Avenida da Universidade Técnica, 1300-477, Lisboa, Portugal
| | - Gabriela J Da Silva
- Faculty of Pharmacy and Center for Neurosciences and Cell Biology, University of Coimbra, Coimbra, Portugal
| | - Maria José Saavedra
- Laboratory Medical Microbiology, Department of Veterinary Sciences, CITAB-Centre for the Research and Technology Agro-Environmental and Biological Sciences, University of Trás-Os-Montes and Alto Douro, Vila Real, Portugal
| | - José Melo-Cristino
- Laboratório de Microbiologia, Serviço de Patologia Clínica, Centro Hospitalar Universitário Lisboa Norte, Lisbon, Portugal
- Instituto de Microbiologia, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Aida Duarte
- Centro de Investigação Interdisciplinar Egas Moniz, Instituto Universitário Egas Moniz, Caparica, Portugal
- Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Susana Campino
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK
| | - João Perdigão
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisbon, Portugal
| | - Taane G Clark
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
- Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, London, UK.
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209
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Zhao L, Xia X, Yuan T, Zhu J, Shen Z, Li M. Molecular Epidemiology of Antimicrobial Resistance, Virulence and Capsular Serotypes of Carbapenemase-Carrying Klebsiella pneumoniae in China. Antibiotics (Basel) 2022; 11:antibiotics11081100. [PMID: 36009969 PMCID: PMC9405458 DOI: 10.3390/antibiotics11081100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2022] [Revised: 08/10/2022] [Accepted: 08/11/2022] [Indexed: 11/16/2022] Open
Abstract
This study analyzed genomic data of 4643 strains of carbapenemase-carrying Klebsiella pneumoniae (KPN) in China by using the Kleborate software package. The data showed rich diversity in carbapenemase-carrying KPN genomes, which contain not only 152 sequence types but also 90 capsular serotypes. In 2013, the transfer of carbapenemase to hypervirulent Klebsiella pneumoniae (HvKP) of KL1 and KL2 occurred, and since 2014, the propagation of carbapenemase into mammals, poultry, and insects has been detected. The ST11 capsular serotype had a reversal of the prevalence of KL47 and KL64 in 2016, with KL64 replacing KL47 as the dominant serotype. Colibactin is a very suitable indicator to differentiate KL1-type HvKP and classic Klebsiella pneumoniae. The most prevalent yersiniabactin of KL1 is ybt1 ICEKp10, and that of ST11 carbapenem-resistant KPN(ST11-CRKP) is ybt9 ICEKp3. The virulence genes of KL1 carbapenem-resistant hypervirulent KPN (KL1-CRHvKP), as well as ST65- and ST86-type KL2-CRHvKP, were not lost after carbapenemase was obtained.
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Affiliation(s)
- Lina Zhao
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Xinxin Xia
- Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong SAR 999077, China
| | - Ting Yuan
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Junying Zhu
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Zhen Shen
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
| | - Min Li
- Department of Laboratory Medicine, Ren Ji Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200127, China
- Faculty of Medical Laboratory Science, College of Health Science and Technology, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
- Correspondence:
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210
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Komiya K, Yoshikawa H, Goto A, Yamamoto T, Yamasue M, Johkoh T, Hiramatsu K, Kadota JI. Radiological patterns and prognosis in elderly patients with acute Klebsiella pneumoniae pneumonia: A retrospective study. Medicine (Baltimore) 2022; 101:e29734. [PMID: 35960104 PMCID: PMC9371486 DOI: 10.1097/md.0000000000029734] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Although Klebsiella pneumoniae pneumonia is an insidious threat among the elderly, the role of radiological features has not been elucidated. We aimed to evaluate thin-section chest computed tomography (CT) features and assess its associations with disease prognosis in elderly patients with acute K. pneumoniae pneumonia. We retrospectively included elderly patients, admitted for acute K. pneumoniae pneumonia, and investigated thin-section CT findings to determine whether bronchopneumonia or lobar pneumonia was present. The association between the radiological pattern of pneumonia and in-hospital mortality was analyzed. Eighty-six patients with acute K. pneumoniae pneumonia were included, and among them, the bronchopneumonia pattern was observed in 70 (81%) patients. Twenty-five (29%) patients died in hospital, and they had a greater incidence of lobar pneumonia pattern (40% in nonsurvivors vs 10% in survivors; P = .008), low albumin level (2.7 g/dL, range, 1.6-3.8 in nonsurvivors vs 3.0 g/dL, range, 1.7-4.2 in survivors; P = .026) and higher levels of aspartate aminotransferase (30 U/L, range, 11-186 in nonsurvivors vs 23 U/L, range, 11-102 in survivors, P = .017) and C-reactive protein (8.0 mg/dL, range, 0.9-26.5 in nonsurvivors vs 4.7 mg/dL, range, 0.0-24.0 in survivors; P = .047) on admission. Multivariate analysis showed that lobar pneumonia pattern was independently associated with increased in-hospital mortality (adjusted hazard ratio, 3.906; 95% CI, 1.513-10.079; P = .005). In elderly patients with acute K. pneumoniae pneumonia, the lobar pneumonia pattern may be less commonly observed, and this pattern could relate to poor prognosis.
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Affiliation(s)
- Kosaku Komiya
- Department of Respiratory Medicine and Infectious Diseases, Oita University Faculty of Medicine, Oita, Japan
- Department of Internal Medicine, Tenshindo Hetsugi Hospital, Oita, Japan
- *Correspondence: Kosaku Komiya, Department of Respiratory Medicine and Infectious Diseases, 1-1 Idaigaoka, Hasama-machi, Yufu, Oita 879-5593, Japan (e-mail: )
| | - Hiroki Yoshikawa
- Department of Respiratory Medicine and Infectious Diseases, Oita University Faculty of Medicine, Oita, Japan
- Department of Internal Medicine, Tenshindo Hetsugi Hospital, Oita, Japan
| | - Akihiko Goto
- Department of Internal Medicine, Tenshindo Hetsugi Hospital, Oita, Japan
| | - Takashi Yamamoto
- Department of Internal Medicine, Tenshindo Hetsugi Hospital, Oita, Japan
| | - Mari Yamasue
- Department of Respiratory Medicine and Infectious Diseases, Oita University Faculty of Medicine, Oita, Japan
| | - Takeshi Johkoh
- Radiology, Kinki Central Hospital of Mutual Aid Association of Public School Teachers, Hyogo, Japan
| | - Kazufumi Hiramatsu
- Department of Medical Safety Management, Oita University Faculty of Medicine, Oita, Japan
| | - Jun-ichi Kadota
- Department of Respiratory Medicine and Infectious Diseases, Oita University Faculty of Medicine, Oita, Japan
- Director, Nagasaki Harbor Medical Center, Nagasaki, Japan
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211
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Spadar A, Perdigão J, Campino S, Clark TG. Genomic analysis of hypervirulent Klebsiella pneumoniae reveals potential genetic markers for differentiation from classical strains. Sci Rep 2022; 12:13671. [PMID: 35953553 PMCID: PMC9372168 DOI: 10.1038/s41598-022-17995-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Accepted: 08/03/2022] [Indexed: 11/23/2022] Open
Abstract
The majority of Klebsiella pneumoniae (Kp) infections are nosocomial, but a growing number of community-acquired infections are caused by hypervirulent strains (hvKp) characterised by liver invasion and rapid metastasis. Unlike nosocomial Kp infections, hvKp are generally susceptible to antibiotics. Due to the rapid progression of hvKp infections, timely and accurate diagnosis is required for effective treatment. To identify potential drivers of the hypervirulent phenotype, we performed a genome-wide association study (GWAS) analysis on single nucleotide variants and accessory genome loci across 79 publicly available Kp isolates collected from patients’ liver and a diverse global Kp dataset (n = 646). The GWAS analysis revealed 29 putative genes (P < 10–10) associated with higher risk of liver phenotype, including hypervirulence linked salmochelin iro (odds ratio (OR): 29.8) and aerobactin iuc (OR: 14.1) loci. A minority of liver isolates (n = 15, 19%) had neither of these siderophores nor any other shared biomarker, suggesting possible unknown drivers of hypervirulence and an intrinsic ability of Kp to invade the liver. Despite identifying potential novel loci linked to a liver invasive Kp phenotype, our work highlights the need for large-scale studies involving more sequence types to identify further hypervirulence biomarkers to assist clinical decision making.
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Affiliation(s)
- Anton Spadar
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - João Perdigão
- Research Institute for Medicines (iMed.ULisboa), Faculdade de Farmácia, Universidade de Lisboa, Lisboa, Portugal
| | - Susana Campino
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK
| | - Taane G Clark
- Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London, UK. .,Faculty of Epidemiology and Population Health, London School of Hygiene and Tropical Medicine, Keppel Street, London, WC1E 7HT, UK.
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212
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Feriotti C, Sá-Pessoa J, Calderón-González R, Gu L, Morris B, Sugisawa R, Insua JL, Carty M, Dumigan A, Ingram RJ, Kissenpfening A, Bowie AG, Bengoechea JA. Klebsiella pneumoniae hijacks the Toll-IL-1R protein SARM1 in a type I IFN-dependent manner to antagonize host immunity. Cell Rep 2022; 40:111167. [PMID: 35947948 PMCID: PMC9638020 DOI: 10.1016/j.celrep.2022.111167] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Revised: 05/18/2022] [Accepted: 07/14/2022] [Indexed: 02/06/2023] Open
Abstract
Many bacterial pathogens antagonize host defense responses by translocating effector proteins into cells. It remains an open question how those pathogens not encoding effectors counteract anti-bacterial immunity. Here, we show that Klebsiella pneumoniae exploits the evolutionary conserved innate protein SARM1 to regulate negatively MyD88- and TRIF-governed inflammation, and the activation of the MAP kinases ERK and JNK. SARM1 is required for Klebsiella induction of interleukin-10 (IL-10) by fine-tuning the p38-type I interferon (IFN) axis. SARM1 inhibits the activation of Klebsiella-induced absent in melanoma 2 inflammasome to limit IL-1β production, suppressing further inflammation. Klebsiella exploits type I IFNs to induce SARM1 in a capsule and lipopolysaccharide O-polysaccharide-dependent manner via the TLR4-TRAM-TRIF-IRF3-IFNAR1 pathway. Absence of SARM1 reduces the intracellular survival of K. pneumoniae in macrophages, whereas sarm1-deficient mice control the infection. Altogether, our results illustrate an anti-immunology strategy deployed by a human pathogen. SARM1 inhibition will show a beneficial effect to treat Klebsiella infections.
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Affiliation(s)
- Claudia Feriotti
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, UK
| | - Joana Sá-Pessoa
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, UK
| | - Ricardo Calderón-González
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, UK
| | - Lili Gu
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Brenda Morris
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, UK
| | - Ryoichi Sugisawa
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Jose L Insua
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, UK
| | - Michael Carty
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - Amy Dumigan
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, UK
| | - Rebecca J Ingram
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, UK
| | - Adrien Kissenpfening
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, UK
| | - Andrew G Bowie
- School of Biochemistry and Immunology, Trinity Biomedical Sciences Institute, Trinity College Dublin, Dublin 2, Ireland
| | - José A Bengoechea
- Wellcome-Wolfson Institute for Experimental Medicine, School of Medicine, Dentistry and Biomedical Sciences, Queen's University Belfast, 97 Lisburn Road, Belfast, UK.
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213
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Pinpimai K, Banlunara W, Roe WD, Dittmer K, Biggs PJ, Tantilertcharoen R, Chankow K, Bunpapong N, Boonkam P, Pirarat N. Genetic characterization of hypervirulent Klebsiella pneumoniae responsible for acute death in captive marmosets. Front Vet Sci 2022; 9:940912. [PMID: 36016808 PMCID: PMC9397405 DOI: 10.3389/fvets.2022.940912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/08/2022] [Indexed: 11/18/2022] Open
Abstract
Klebsiella pneumoniae is a Gram-negative bacterium implicated as the causative pathogen in several medical health issues with different strains causing different pathologies including pneumonia, bloodstream infections, meningitis and infections from wounds or surgery. In this study, four captive African marmosets housed in Thailand were found dead. Necropsy and histology revealed congestion of hearts, kidneys and adrenal glands. Twenty-four bacterial isolates were obtained from these four animals with all isolates yielding identical phenotypes indicative of K. pneumoniae based on classical identification schema. All the isolates show the susceptibility to amikacin, cephalexin, doxycycline, gentamicin, and enrofloxacin with intermediate susceptibility to amoxycillin/clavulanic acid. One isolate (20P167W) was chosen for genome analysis and determined to belong to sequence type 65 (ST65). The genome of 20P167W possessed multiple virulence genes including mrk gene cluster and iro and iuc gene cluster (salmochelin and aerobactin, respectively) as well as multiple antibiotic resistance genes including bla SHV-67, bla SHV-11, oqxA, oqxB, and fosA genes resembling those found in human isolates; this isolate has a close genetic relationship with isolates from humans in Ireland, but not from Thailand and California sea lions. Phylogenetic studies using SNP show that there was no relation between genetic and geographic distributions of all known strains typing ST65, suggesting that ST65 strains may spread worldwide through multiple international transmission events rather than by local expansions in humans and/or animals. We also predict that K. pneumoniae ST65 has an ability to acquire genetic mobile element from other bacteria, which would allow Klebsiella to become an even greater public health concern.
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Affiliation(s)
- Komkiew Pinpimai
- Aquatic Resources Research Institute, Chulalongkorn University, Bangkok, Thailand
| | - Wijit Banlunara
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Wendi D. Roe
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Keren Dittmer
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Patrick J. Biggs
- School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Rachod Tantilertcharoen
- Veterinary Diagnostic Laboratory, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Katriya Chankow
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Napawan Bunpapong
- Veterinary Diagnostic Laboratory, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Center of Excellence for Emerging and Re-Emerging Diseases in Animals, Chulalongkorn University, Bangkok, Thailand
| | - Pongthai Boonkam
- Veterinary Diagnostic Laboratory, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
| | - Nopadon Pirarat
- Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
- Wildlife Exotic and Aquatic Pathology Research Unit (WEAP RU), Department of Pathology, Faculty of Veterinary Science, Chulalongkorn University, Bangkok, Thailand
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214
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Shoja S, Ansari M, Bengar S, Rafiei A, Shamseddin J, Alizade H. Bacteriological characteristics of hypervirulent Klebsiella pneumoniae rmpA gene (hvKp- rmpA)-harboring strains in the south of Iran. IRANIAN JOURNAL OF MICROBIOLOGY 2022; 14:475-483. [PMID: 36721517 PMCID: PMC9867641 DOI: 10.18502/ijm.v14i4.10233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Background and Objectives To provide data on the occurrence of classical K. pneumoniae (cKp) and hypervirulent Klebsiella pneumoniae (hvKp) strains harboring the gene encoding regulator of mucoid phenotype A (rmpA) and evaluated characteristics of virulence biomarkers, carbapenemase, extended-spectrum-β-lactamase (ESBL)-producing, and capsule serotypes among K. pneumoniae clinical isolates collected in the south of Iran. Materials and Methods A total of 400 K. pneumoniae isolates were collected. First, the K. pneumoniae isolates were screened for rmpA gene by PCR, and then they were characterized for the presence of the virulence genes (pagO, iucA, iroB, luxR), capsular serotype genes (K1, K2, K5, K20, K54, and K57), carbapenemase (bla NDM, bla IMP, bla VIM, bla KPC, bla SPM, bla OXA-48, and bla OXA-181) and ESBL (bla CTX-M, bla SHV and bla TEM) genes. For all K. pneumoniae isolates phenotypic tests include of string test and disk diffusion test were performed. Results In total, 16 (4%) hvKp-rmpA+ and 384 (96%) cKp were observed. Of hvKp-rmpA+ strains, 16 (100%) were carried pagO, iroB, and luxR genes, and 13 (81.3%) strains harbored iucA gene. The most prevalent capsular type genes were K1 (62%) and K2 (19%) in hvKp-rmpA+ strains. The incidence of bla SHV gene in hvKp and cKp was 94% (15/16) and 87.5% (336/384), respectively. The cKp isolates carried bla NDM (30/384; 7.8%) gene. Conclusion Our data suggest that the incidence of hvKp was low. Also, hvKp-rmpA+ strains have less antibiotic resistance than cKp isolates. Serotypes K1 and K2, and bla SHV gene were strongly associated with hvKp-rmpA+.
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Affiliation(s)
- Saeed Shoja
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Maryam Ansari
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Saman Bengar
- Student Research Committee, Faculty of Medicine, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Azam Rafiei
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Jebreil Shamseddin
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran
| | - Hesam Alizade
- Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran,Corresponding author: Hesam Alizade, Ph.D, Infectious and Tropical Diseases Research Center, Hormozgan Health Institute, Hormozgan University of Medical Sciences, Bandar Abbas, Iran. Tel: +98-7633710393 Fax: +98-7633710393
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215
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Van Hooste W, Vanrentergem M, Nulens E, Snauwaert C, De Geyter D, Mertens R, Van Praet JT. Infections caused by hypervirulent Klebsiella pneumoniae in non-endemic countries: three case reports and review of the literature. Acta Clin Belg 2022; 78:229-233. [PMID: 35904343 DOI: 10.1080/17843286.2022.2106705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
OBJECTIVES Spontaneous liver abscess caused by a hypervirulent Klebsiella pneumoniae strain was first described several decades ago in Taiwan and has been an emerging clinical entity worldwide ever since. We aimed to describe the clinical and microbiological characteristics of this infection in a non-endemic setting. METHODS A narrative literature review was conducted in PubMed for European case reports of hypervirulent Klebsiella pneumoniae from 2016 to 2021. RESULTS Forty case reports were retrieved. Mean age of the patients was 59 years and 72% were male. Diabetes mellitus was present in 33%. Twenty percent of the patients originated from an endemic region. A liver abscess and bacteremia were observed in, respectively, 83% and 80% of the cases. The most frequent metastatic infections were found in the eye (28%) and the lungs (28%). The sensitivity of molecular capsular antigen detection and the string test was 87% and 92%, respectively. Sixty-three percent of the strains had a wildtype resistance. CONCLUSION Hypervirulent Klebsiella pneumoniae infections in non-endemic countries are most frequently observed in middle-aged males. Clinicians should be vigilant for metastatic infections.
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Affiliation(s)
- Wannes Van Hooste
- Department of Nephrology and Infectious Diseases, AZ Sint-Jan Brugge-Oostende AVBrugge, Belgium
| | - Marthe Vanrentergem
- Department of Medical Microbiology, AZ Sint-Jan Brugge-Oostende AVBrugge, Belgium
| | - Eric Nulens
- Department of Medical Microbiology, AZ Sint-Jan Brugge-Oostende AVBrugge, Belgium
| | - Christophe Snauwaert
- Department of Hepatology and Gastroenterology, AZ Sint-Jan Brugge-Oostende AVBrugge, Belgium
| | - Deborah De Geyter
- Department of Microbiology and Infection Control, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - Rembert Mertens
- Department of Internal Medicine and Infectious Diseases, Universitair Ziekenhuis Brussel, Vrije Universiteit Brussel, Brussels, Belgium
| | - Jens T Van Praet
- Department of Nephrology and Infectious Diseases, AZ Sint-Jan Brugge-Oostende AVBrugge, Belgium.,Faculty of Medicine and Health sciences, Ghent University, Ghent, Belgium
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216
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Yang X, Liu X, Xu Y, Yang C, Chan EWC, Shum HP, Chen S. Genetic and Functional Characterization of a Conjugative KpVP-2-Type Virulence Plasmid From a Clinical Klebsiella pneumoniae Strain. Front Microbiol 2022; 13:914884. [PMID: 35935210 PMCID: PMC9354667 DOI: 10.3389/fmicb.2022.914884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/23/2022] [Indexed: 11/23/2022] Open
Abstract
The main mechanism of virulence in Klebsiella pneumoniae is the acquisition of K. pneumoniae virulence plasmids (KpVPs), which include two dominant types, namely, KpVP-1 (carrying iuc1, iro1, rmpA, and rmpA2) and KpVP-2 (carrying iuc2, iro2, and rmpA). Both are non-conjugative and associated with different hypervirulent clones. In contrast to KpVP-1 reported in K1, K2, and other serotypes of K. pneumoniae, KpVP-2 was only reported in K2 strains and rarely characterized. In this study, we identified a conjugative KpVP-2-type virulence plasmid from a clinical hypervirulent K. pneumoniae strain. This plasmid was generated by the integration of conjugative transfer genes into the KpVP-2-type plasmid Kp52.145 II and could be readily conjugated to Escherichia coli strain EC600 and K. pneumoniae strains of various types which are clinically existing, mediating hypervirulence. Furthermore, this kind of conjugative KpVP-2-type virulence plasmid has been disseminated in clinical settings in Hong Kong and other regions of the world. The generation of conjugative virulence plasmid may promote its transmission and explain the evolution of this type of virulence plasmid.
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Affiliation(s)
- Xuemei Yang
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Xiaoxuan Liu
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Yating Xu
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Chen Yang
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
| | - Edward Wai-Chi Chan
- State Key Lab of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Hong Kong SAR, China
| | - Hoi-ping Shum
- Department of Intensive Care, Pamela Youde Nethersole Eastern Hospital, Chai Wan, Hong Kong SAR, China
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong SAR, China
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217
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de Sousa ATHI, Costa MTDS, Cândido SL, Makino H, Morgado TO, Pavelegini LAD, Colodel EM, Nakazato L, Dutra V. Determination of multidrug-resistant populations and molecular characterization of complex Klebsiella spp. in wild animals by multilocus sequence typing. Vet World 2022; 15:1691-1698. [PMID: 36185529 PMCID: PMC9394135 DOI: 10.14202/vetworld.2022.1691-1698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 05/26/2022] [Indexed: 11/23/2022] Open
Abstract
Background and Aim: One of the most significant public health concerns is multidrug-resistant (MDR) microorganisms. Klebsiella spp. have been at the forefront of causing different types of infections such as bacteremia, urinary tract infections, pneumonia, enteritis, and sepsis in humans as well as animals. This study aimed to determine the genomic similarity between Klebsiella spp. isolated from wild animal samples and those described in the Institut Pasteur genomic database to verify the spread of resistant clones regionally in the state of Mato Grosso, and to compare the epidemiological data in different regions of Brazil and the world. Materials and Methods: Isolates from various sites of injury in wild animals were identified by sequencing the 16S rRNA gene. Antimicrobial susceptibility testing was performed using the disk diffusion method to verify the resistance profile, and then, multilocus sequence typing was performed to verify the population structure and compare the isolates from other regions of Brazil and the world. Results: Twenty-three sequence types (STs) were observed; of these, 11 were new STs, as new alleles were detected. There was no predominant ST among the isolates. All isolates were MDR, with high rates of resistance to sulfonamides, ampicillin, amoxicillin, and nitrofurantoin and low resistance to meropenem, imipenem, and amikacin. Conclusion: Improving our understanding of the population structure of Klebsiella spp. in wild animals may help determine the source of infection during outbreaks in humans or animals, as the One Health concept emphasizes the interlinks between humans, animals, and environmental health.
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Affiliation(s)
| | - Marco Túlio dos Santos Costa
- Microbiology Laboratory of the Veterinary Hospital, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Stefhano Luis Cândido
- Microbiology Laboratory of the Veterinary Hospital, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Herica Makino
- Microbiology Laboratory of the Veterinary Hospital, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Thais Oliveira Morgado
- Center for Medicine and Research of Wild Animals, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | | | - Edson Moleta Colodel
- Pathology Laboratory of the Veterinary Hospital, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Luciano Nakazato
- Microbiology Laboratory of the Veterinary Hospital, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
| | - Valéria Dutra
- Microbiology Laboratory of the Veterinary Hospital, Universidade Federal de Mato Grosso, Cuiabá, Mato Grosso, Brazil
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218
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Migliaccio A, Stabile M, Bagattini M, Triassi M, Berisio R, De Gregorio E, Zarrilli R. Resveratrol Reverts Tolerance and Restores Susceptibility to Chlorhexidine and Benzalkonium in Gram-Negative Bacteria, Gram-Positive Bacteria and Yeasts. Antibiotics (Basel) 2022; 11:antibiotics11070961. [PMID: 35884215 PMCID: PMC9311544 DOI: 10.3390/antibiotics11070961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/13/2022] [Accepted: 07/15/2022] [Indexed: 11/16/2022] Open
Abstract
The spread of microorganisms causing health-care associated infection (HAI) is contributed to by their intrinsic tolerance to a variety of biocides, used as antiseptics or disinfectants. The natural monomeric stilbenoid resveratrol (RV) is able to modulate the susceptibility to the chlorhexidine digluconate (CHX) biocide in Acinetobacter baumannii. In this study, a panel of reference strains and clinical isolates of Gram-negative bacteria, Gram-positive bacteria and yeasts were analyzed for susceptibility to CHX and benzalkonium chloride (BZK) and found to be tolerant to one or both biocides. The carbonyl cyanide m-chlorophenylhydrazine protonophore (CCCP) efflux pump inhibitor reduced the minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) of CHX and BZK in the majority of strains. RV reduced dose-dependently MIC and MBC of CHX and BZK biocides when used as single agents or in combination in all analyzed strains, but not CHX MIC and MBC in Pseudomonas aeruginosa, Candida albicans, Klebsiella pneumoniae, Stenotrophomonas maltophilia and Burkholderia spp. strains. In conclusion, RV reverts tolerance and restores susceptibility to CHX and BZK in the majority of microorganisms responsible for HAI. These results indicates that the combination of RV, CHX and BZK may represent a useful strategy to maintain susceptibility to biocides in several nosocomial pathogens.
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Affiliation(s)
- Antonella Migliaccio
- Department of Public Health, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy; (A.M.); (M.S.); (M.B.); (M.T.)
| | - Maria Stabile
- Department of Public Health, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy; (A.M.); (M.S.); (M.B.); (M.T.)
| | - Maria Bagattini
- Department of Public Health, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy; (A.M.); (M.S.); (M.B.); (M.T.)
| | - Maria Triassi
- Department of Public Health, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy; (A.M.); (M.S.); (M.B.); (M.T.)
| | - Rita Berisio
- Institute of Biostructures and Bioimaging, National Research Council, 80131 Naples, Italy;
| | - Eliana De Gregorio
- Department of Molecular Medicine and Medical Biotechnology, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy
- Correspondence: (E.D.G.); (R.Z.)
| | - Raffaele Zarrilli
- Department of Public Health, University of Naples Federico II, Via S. Pansini 5, 80131 Naples, Italy; (A.M.); (M.S.); (M.B.); (M.T.)
- Correspondence: (E.D.G.); (R.Z.)
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Zhang Z, Wang H, Guo Y, Liu Z, Chang Z. Metagenome Analysis of the Bacterial Characteristics in Invasive Klebsiella Pneumoniae Liver Abscesses. Front Cell Infect Microbiol 2022; 12:812542. [PMID: 35909970 PMCID: PMC9334793 DOI: 10.3389/fcimb.2022.812542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 06/01/2022] [Indexed: 11/17/2022] Open
Abstract
Background Klebsiella pneumoniae liver abscess (KPLA) combined with extrahepatic migratory infection (EMI) is defined as invasive KPLA (IKPLA) and is associated with a poor prognosis. The mechanism of IKPLA formation is yet to be elucidated. In this study, metagenomic sequencing was used to compare the bacterial characteristics between IKPLA and KPLA to explore the underlying mechanism of invasiveness. Methods Clinical details, imaging, and microbial features were retrospectively evaluated by medical record review. Metagenomic sequencing was performed on the pus samples of liver abscesses whose culture results were indicative of monomicrobial Klebsiella pneumoniae (K. pneumoniae). Bacterial diversity and composition in IKPLA and KPLA were comparatively analyzed, and the key pathways and genes that may affect invasiveness were further explored. Results Sixteen patients were included in this study. Five patients with EMI were included in the IKPLA group, and the other eleven patients without EMI were assigned to the KPLA group. There was no statistical difference in the hypermucoviscous phenotype and serotype of K. pneumoniae between the two groups. The bacterial diversity of IKPLA was lower than that of KPLA. The abundant taxa in the IKPLA group were primarily species of unclassified Enterobacteriaceae and K. pneumoniae. The KPLA group had a high abundance of the genera Tetrasphaera and Leuconostoc. Metabolic pathway genes represented most of the enriched genes in IKPLA. Fourteen pathogenic genes with significant differences in abundance were identified between the two groups, including ybtS, fepC, phoQ, acrB, fimK, magA, entC, arnT, iucA, fepG, oqxB, entA, tonB, and entF (p < 0.001). Conclusion The diversity and bacterial composition of IKPLA were significantly different from those of KPLA. Microbiological changes in the abscess, activation of the related metabolic pathways, and the pathogenic gene expression may constitute a novel mechanism that regulates the invasiveness of KPLA.
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Affiliation(s)
- Zhijie Zhang
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Hairui Wang
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yawen Guo
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhaoyu Liu
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhihui Chang
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, China
- *Correspondence: Zhihui Chang,
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Denissen J, Reyneke B, Waso-Reyneke M, Havenga B, Barnard T, Khan S, Khan W. Prevalence of ESKAPE pathogens in the environment: Antibiotic resistance status, community-acquired infection and risk to human health. Int J Hyg Environ Health 2022; 244:114006. [PMID: 35841823 DOI: 10.1016/j.ijheh.2022.114006] [Citation(s) in RCA: 80] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2022] [Revised: 06/30/2022] [Accepted: 06/30/2022] [Indexed: 01/10/2023]
Abstract
The ESKAPE (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter spp.) pathogens are characterised by increased levels of resistance towards multiple classes of first line and last-resort antibiotics. Although these pathogens are frequently isolated from clinical environments and are implicated in a variety of life-threatening, hospital-associated infections; antibiotic resistant ESKAPE strains have been isolated from environmental reservoirs such as surface water, wastewater, food, and soil. Literature on the persistence and subsequent health risks posed by the ESKAPE isolates in extra-hospital settings is however, limited and the current review aims to elucidate the primary reservoirs of these pathogens in the environment, their antibiotic resistance profiles, and the link to community-acquired infections. Additionally, information on the current state of research regarding health-risk assessments linked to exposure of the ESKAPE pathogens in the natural environment, is outlined.
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Affiliation(s)
- Julia Denissen
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Brandon Reyneke
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Monique Waso-Reyneke
- Faculty of Health Sciences, University of Johannesburg, PO Box 17011, Doornfontein, 2028, South Africa
| | - Benjamin Havenga
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa
| | - Tobias Barnard
- Water and Health Research Centre, University of Johannesburg, PO Box 17011, Doornfontein, 7305, South Africa
| | - Sehaam Khan
- Faculty of Health Sciences, University of Johannesburg, PO Box 17011, Doornfontein, 2028, South Africa
| | - Wesaal Khan
- Department of Microbiology, Faculty of Science, Stellenbosch University, Private Bag X1, Stellenbosch, 7602, South Africa.
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Pandemic Clones of CTX-M-15 Producing Klebsiella pneumoniae ST15, ST147, and ST307 in Companion Parrots. Microorganisms 2022; 10:microorganisms10071412. [PMID: 35889131 PMCID: PMC9320316 DOI: 10.3390/microorganisms10071412] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 12/22/2022] Open
Abstract
Psittacine birds are commonly kept as companion birds and the maintenance of these birds in captivity may represent a zoonotic risk and contribute to the propagation of multidrug-resistant and β-lactamase extended-spectrum (ESBLs)-producing pathogens. This study aimed to identify and characterize strains of the Klebsiella pneumoniae complex isolated from diseased psittacine birds, determining virulence and resistance profiles. K. pneumoniae strains were isolated from 16 birds (16/46). All strains carried more than three virulence genes, with a high frequency of fimH and kpn (93.75%), uge (87.52%), and irp-2 (81.25%) genes. The antimicrobial susceptibility revealed that 3/16 strains were ESBL producers. Genomic analysis revealed that CTX-M-15-positive strains belonged to sequence types (STs) ST15, ST147, and ST307, characterized as international clones associated with outbreaks of healthcare-associated infections (HAIs) worldwide.
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Nonogaki R, Iijima A, Kawamura K, Kayama S, Sugai M, Yagi T, Arakawa Y, Doi Y, Suzuki M. PCR-based ORF typing of Klebsiella pneumoniae for rapid identification of global clones and transmission events. J Appl Microbiol 2022; 133:2050-2062. [PMID: 35797348 DOI: 10.1111/jam.15701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 06/30/2022] [Accepted: 07/04/2022] [Indexed: 11/28/2022]
Abstract
AIMS Klebsiella pneumoniae is a major cause of healthcare-associated infections. In this study, we aimed to develop a rapid and simple genotyping method that can characterize strains causing nosocomial infections. METHODS AND RESULTS The PCR-based open reading frame (ORF) typing (POT) method consists of two multiplex PCR reactions which were designed to detect 25 ORFs specific to bacterial genetic lineages, species, antimicrobial resistant genes (blaCTX-M group-1 , blaCTX-M group-9 , blaIMP and blaKPC ), a capsular K1-specific gene, and a virulence factor gene (rmpA/A2). The electrophoresis results are then digitized. A total of 192 strains (136 clinical and 8 reference strains of K. pneumoniae, 33 clinical and 1 reference strains of K. variicola, and 14 clinical strains of K. quasipneumoniae) were classified into 95, 26, and 11 POT values, respectively. The distribution patterns of ORFs among K. pneumoniae correlated well with multilocus sequence typing (MLST). Furthermore, closely related species could be distinguished and key antimicrobial resistance and hypervirulence genes were identified as part of POT. CONCLUSIONS The POT method was developed and validated for K. pneumoniae. In comparison to MLST, the POT method is a rapid and easy genotyping method for monitoring transmission events by K. pneumoniae in clinical microbiology laboratories. SIGNIFICANCE AND IMPACT OF THE STUDY The POT method supplies clear and informative molecular typing results for K. pneumoniae. The method would facilitate molecular epidemiological analysis in infection control and hospital epidemiology investigations.
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Affiliation(s)
- Rina Nonogaki
- Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Anna Iijima
- Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Kumiko Kawamura
- Department of Integrated Health Sciences, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Shizuo Kayama
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan.,Department of Antimicrobial Resistance, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Motoyuki Sugai
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan.,Department of Antimicrobial Resistance, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Tetsuya Yagi
- Department of Infectious Diseases, Nagoya University Graduate School of Medicine, Japan
| | - Yoshichika Arakawa
- Department of Bacteriology, Nagoya University Graduate School of Medicine, Aichi, Japan
| | - Yohei Doi
- Department of Microbiology, Fujita Health University School of Medicine, Aichi, Japan.,Department of Infectious Diseases, Fujita Health University School of Medicine, Aichi, Japan.,Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Masahiro Suzuki
- Department of Microbiology, Fujita Health University School of Medicine, Aichi, Japan
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Kochan TJ, Nozick SH, Medernach RL, Cheung BH, Gatesy SWM, Lebrun-Corbin M, Mitra SD, Khalatyan N, Krapp F, Qi C, Ozer EA, Hauser AR. Genomic surveillance for multidrug-resistant or hypervirulent Klebsiella pneumoniae among United States bloodstream isolates. BMC Infect Dis 2022; 22:603. [PMID: 35799130 PMCID: PMC9263067 DOI: 10.1186/s12879-022-07558-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Accepted: 06/21/2022] [Indexed: 02/07/2023] Open
Abstract
BACKGROUND Klebsiella pneumoniae strains have been divided into two major categories: classical K. pneumoniae, which are frequently multidrug-resistant and cause hospital-acquired infections in patients with impaired defenses, and hypervirulent K. pneumoniae, which cause severe community-acquired and disseminated infections in normal hosts. Both types of infections may lead to bacteremia and are associated with significant morbidity and mortality. The relative burden of these two types of K. pneumoniae among bloodstream isolates within the United States is not well understood. METHODS We evaluated consecutive K. pneumoniae isolates cultured from the blood of hospitalized patients at Northwestern Memorial Hospital (NMH) in Chicago, Illinois between April 2015 and April 2017. Bloodstream isolates underwent whole genome sequencing, and sequence types (STs), capsule loci (KLs), virulence genes, and antimicrobial resistance genes were identified in the genomes using the bioinformatic tools Kleborate and Kaptive. Patient demographic, comorbidity, and infection information, as well as the phenotypic antimicrobial resistance of the isolates were extracted from the electronic health record. Candidate hypervirulent isolates were tested in a murine model of pneumonia, and their plasmids were characterized using long-read sequencing. We also extracted STs, KLs, and virulence and antimicrobial resistance genes from the genomes of bloodstream isolates submitted from 33 United States institutions between 2007 and 2021 to the National Center for Biotechnology Information (NCBI) database. RESULTS Consecutive K. pneumoniae bloodstream isolates (n = 104, one per patient) from NMH consisted of 75 distinct STs and 51 unique capsule loci. The majority of these isolates (n = 58, 55.8%) were susceptible to all tested antibiotics except ampicillin, but 17 (16.3%) were multidrug-resistant. A total of 32 (30.8%) of these isolates were STs of known high-risk clones, including ST258 and ST45. In particular, 18 (17.3%) were resistant to ceftriaxone (of which 17 harbored extended-spectrum beta-lactamase genes) and 9 (8.7%) were resistant to meropenem (all of which harbored a carbapenemase genes). Four (3.8%) of the 104 isolates were hypervirulent K. pneumoniae, as evidenced by hypermucoviscous phenotypes, high levels of virulence in a murine model of pneumonia, and the presence of large plasmids similar to characterized hypervirulence plasmids. These isolates were cultured from patients who had not recently traveled to Asia. Two of these hypervirulent isolates belonged to the well characterized ST23 lineage and one to the re-emerging ST66 lineage. Of particular concern, two of these isolates contained plasmids with tra conjugation loci suggesting the potential for transmission. We also analyzed 963 publicly available genomes of K. pneumoniae bloodstream isolates from locations within the United States. Of these, 465 (48.3%) and 760 (78.9%) contained extended-spectrum beta-lactamase genes or carbapenemase genes, respectively, suggesting a bias towards submission of antibiotic-resistant isolates. The known multidrug-resistant high-risk clones ST258 and ST307 were the predominant sequence types. A total of 32 (3.3%) of these isolates contained aerobactin biosynthesis genes and 26 (2.7%) contained at least two genetic features of hvKP strains, suggesting elevated levels of virulence. We identified 6 (0.6%) isolates that were STs associated with hvKP: ST23 (n = 4), ST380 (n = 1), and ST65 (n = 1). CONCLUSIONS Examination of consecutive isolates from a single center demonstrated that multidrug-resistant high-risk clones are indeed common, but a small number of hypervirulent K. pneumoniae isolates were also observed in patients with no recent travel history to Asia, suggesting that these isolates are undergoing community spread in the United States. A larger collection of publicly available bloodstream isolate genomes also suggested that hypervirulent K. pneumoniae strains are present but rare in the USA; however, this collection appears to be heavily biased towards highly antibiotic-resistant isolates (and correspondingly away from hypervirulent isolates).
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Affiliation(s)
- Travis J Kochan
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA.
| | - Sophia H Nozick
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Rachel L Medernach
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Bettina H Cheung
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Samuel W M Gatesy
- Division of Infectious Diseases, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Marine Lebrun-Corbin
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Sumitra D Mitra
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Natalia Khalatyan
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Fiorella Krapp
- Division of Infectious Diseases, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Chao Qi
- Department of Pathology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
| | - Egon A Ozer
- Division of Infectious Diseases, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Center for Pathogen Genomics and Microbial Evolution, Havey Institute for Global Health, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Alan R Hauser
- Department of Microbiology-Immunology, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
- Division of Infectious Diseases, Department of Medicine, Northwestern University, Feinberg School of Medicine, Chicago, IL, USA
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Hunt M, Letcher B, Malone KM, Nguyen G, Hall MB, Colquhoun RM, Lima L, Schatz MC, Ramakrishnan S, Iqbal Z. Minos: variant adjudication and joint genotyping of cohorts of bacterial genomes. Genome Biol 2022; 23:147. [PMID: 35791022 PMCID: PMC9254434 DOI: 10.1186/s13059-022-02714-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Accepted: 06/20/2022] [Indexed: 12/30/2022] Open
Abstract
There are many short-read variant-calling tools, with different strengths and weaknesses. We present a tool, Minos, which combines outputs from arbitrary variant callers, increasing recall without loss of precision. We benchmark on 62 samples from three bacterial species and an outbreak of 385 Mycobacterium tuberculosis samples. Minos also enables joint genotyping; we demonstrate on a large (N=13k) M. tuberculosis cohort, building a map of non-synonymous SNPs and indels in a region where all such variants are assumed to cause rifampicin resistance. We quantify the correlation with phenotypic resistance and then replicate in a second cohort (N=10k).
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Affiliation(s)
- Martin Hunt
- EMBL-EBI, Cambridge, UK
- Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | | | | | | | | | - Rachel M Colquhoun
- Institute of Evolutionary Biology, Ashworth Laboratories, University of Edinburgh, Edinburgh, UK
| | | | - Michael C Schatz
- Department of Computer Science, Johns Hopkins University, Baltimore, MD, USA
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Genomic and Immunological Characterization of Hypermucoviscous Carbapenem-Resistant Klebsiella pneumoniae ST25 Isolates from Northwest Argentina. Int J Mol Sci 2022; 23:ijms23137361. [PMID: 35806365 PMCID: PMC9266295 DOI: 10.3390/ijms23137361] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Revised: 06/14/2022] [Accepted: 06/27/2022] [Indexed: 02/05/2023] Open
Abstract
In recent years, an increase in the prevalence hypermucoviscous carbapenem-resistant Klebsiella pneumoniae with sequence type 25 (ST25) was detected in hospitals of Tucuman (Northwest Argentina). In this work, the virulence and the innate immune response to two K. pneumoniae ST25 strains (LABACER 01 and LABACER 27) were evaluated in a murine model after a respiratory challenge. In addition, comparative genomics was performed with K. pneumoniae LABACER01 and LABACER27 to analyze genes associated with virulence. Both LABACER01 and LABACER27 were detected in the lungs of infected mice two days after the nasal challenge, with LABACER01 counts significantly higher than those of LABACER27. Only LABACER01 was detected in hemocultures. Lactate dehydrogenase (LDH) and albumin levels in bronchoalveolar lavage (BAL) samples were significantly higher in mice challenged with LABACER01 than in LABACER27-infected animals, indicating greater lung tissue damage. Both strains increased the levels of neutrophils, macrophages, TNF-α, IL-1β, IL-6, KC, MCP-1, IFN-γ, and IL-17 in the respiratory tract and blood, with the effect of LABACER01 more marked than that of LABACER27. In contrast, LABACER27 induced higher levels of IL-10 in the respiratory tract than LABACER01. Genomic analysis revealed that K. pneumoniae LABACER01 and LABACER27 possess virulence factors found in other strains that have been shown to be hypervirulent, including genes required for enterobactin (entABCDEF) and salmochelin (iroDE) biosynthesis. In both strains, the genes of toxin–antitoxin systems, as well as regulators of the expression of virulence factors and adhesion genes were also detected. Studies on the genetic potential of multiresistant K. pneumoniae strains as well as their cellular and molecular interactions with the host are of fundamental importance to assess the association of certain virulence factors with the intensity of the inflammatory response. In this sense, this work explored the virulence profile based on genomic and in vivo studies of hypermucoviscous carbapenem-resistant K. pneumoniae ST25 strains, expanding the knowledge of the biology of the emerging ST25 clone in Argentina.
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Burbick CR, Alexander TL, Wolking R, Gull T, Ceric O, Reimschuessel R. Non-carbapenemase producing carbapenem-resistant Klebsiella pneumoniae isolated from the urinary tract of a dog. THE CANADIAN VETERINARY JOURNAL = LA REVUE VETERINAIRE CANADIENNE 2022; 63:740-744. [PMID: 35784769 PMCID: PMC9207975] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Subscribe] [Scholar Register] [Indexed: 04/01/2023]
Abstract
Objective Carbapenems are broad-spectrum β-lactams with excellent activity against multidrug-resistant (MDR) Enterobacterales. Unfortunately, resistance to carbapenems within this bacterial family, known as carbapenem-resistant Enterobacterales (CRE), occurs and challenges the ability to treat difficult MDR infections. Although the impact of carbapenem-resistance has been greatest in human medicine, reports in the veterinary literature are increasing especially as national veterinary antimicrobial resistance surveillance programs are now in place. In this brief communication, we report the isolation of a non-carbapenemase-producing, carbapenem-resistant Klebsiella pneumoniae from the urine of a dog, discuss the likely mechanism of resistance, and wider implications. Animal Canine. Procedure Whole genome sequencing and phenotypic antimicrobial susceptibility testing was performed on a K. pneumoniae isolated from the urine of a dog. Results Antimicrobial susceptibility testing identified phenotypic resistance to imipenem and meropenem. Phenotypic detection of carbapenemase production was negative. Whole genome sequencing identified efflux pump genes associated with carbapenem resistance and point mutations in membrane porin genes. No carbapenemase gene was identified. Conclusion Phenotypic antimicrobial susceptibility testing identified the K. pneumoniae as a non-carbapenemase producing carbapenem-resistant organism with the proposed genotypic mechanism including alteration of efflux pumps and membrane porin activity and/or expression. Clinical significance Currently, there is limited use of carbapenem antimicrobial drugs in veterinary medicine, and practitioners may be unfamiliar or unaware of this type of resistance, its significance on routine antimicrobial susceptibility test reports, and implications for antimicrobial therapy and public health. Carbapenem-resistant Enterobacterales are infrequently isolated from companion animals; however, due to increasing adoption of advanced medical and surgical interventions, they may become more prevalent.
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Affiliation(s)
- Claire R Burbick
- Washington Animal Disease Diagnostic Laboratory, Washington State University, 1940 SE Olympia Ave, Pullman, Washington 99164, USA (Burbick, Alexander, Wolking); Department of Veterinary Microbiology and Pathology, Washington State University, PO Box 647040, Pullman, Washington 99164, USA (Burbick); Veterinary Medical Diagnostic Laboratory, University of Missouri, PO Box 6023, Columbia, Missouri 65205, USA (Gull); Veterinary Laboratory Investigation and Response Network, Center for Veterinary Medicine, United States Food and Drug Administration, 8491 Muirkirk Road, Laurel, Maryland 20708, USA (Ceric, Reimschuessel)
| | - Trevor L Alexander
- Washington Animal Disease Diagnostic Laboratory, Washington State University, 1940 SE Olympia Ave, Pullman, Washington 99164, USA (Burbick, Alexander, Wolking); Department of Veterinary Microbiology and Pathology, Washington State University, PO Box 647040, Pullman, Washington 99164, USA (Burbick); Veterinary Medical Diagnostic Laboratory, University of Missouri, PO Box 6023, Columbia, Missouri 65205, USA (Gull); Veterinary Laboratory Investigation and Response Network, Center for Veterinary Medicine, United States Food and Drug Administration, 8491 Muirkirk Road, Laurel, Maryland 20708, USA (Ceric, Reimschuessel)
| | - Rebecca Wolking
- Washington Animal Disease Diagnostic Laboratory, Washington State University, 1940 SE Olympia Ave, Pullman, Washington 99164, USA (Burbick, Alexander, Wolking); Department of Veterinary Microbiology and Pathology, Washington State University, PO Box 647040, Pullman, Washington 99164, USA (Burbick); Veterinary Medical Diagnostic Laboratory, University of Missouri, PO Box 6023, Columbia, Missouri 65205, USA (Gull); Veterinary Laboratory Investigation and Response Network, Center for Veterinary Medicine, United States Food and Drug Administration, 8491 Muirkirk Road, Laurel, Maryland 20708, USA (Ceric, Reimschuessel)
| | - Tamara Gull
- Washington Animal Disease Diagnostic Laboratory, Washington State University, 1940 SE Olympia Ave, Pullman, Washington 99164, USA (Burbick, Alexander, Wolking); Department of Veterinary Microbiology and Pathology, Washington State University, PO Box 647040, Pullman, Washington 99164, USA (Burbick); Veterinary Medical Diagnostic Laboratory, University of Missouri, PO Box 6023, Columbia, Missouri 65205, USA (Gull); Veterinary Laboratory Investigation and Response Network, Center for Veterinary Medicine, United States Food and Drug Administration, 8491 Muirkirk Road, Laurel, Maryland 20708, USA (Ceric, Reimschuessel)
| | - Olgica Ceric
- Washington Animal Disease Diagnostic Laboratory, Washington State University, 1940 SE Olympia Ave, Pullman, Washington 99164, USA (Burbick, Alexander, Wolking); Department of Veterinary Microbiology and Pathology, Washington State University, PO Box 647040, Pullman, Washington 99164, USA (Burbick); Veterinary Medical Diagnostic Laboratory, University of Missouri, PO Box 6023, Columbia, Missouri 65205, USA (Gull); Veterinary Laboratory Investigation and Response Network, Center for Veterinary Medicine, United States Food and Drug Administration, 8491 Muirkirk Road, Laurel, Maryland 20708, USA (Ceric, Reimschuessel)
| | - Renate Reimschuessel
- Washington Animal Disease Diagnostic Laboratory, Washington State University, 1940 SE Olympia Ave, Pullman, Washington 99164, USA (Burbick, Alexander, Wolking); Department of Veterinary Microbiology and Pathology, Washington State University, PO Box 647040, Pullman, Washington 99164, USA (Burbick); Veterinary Medical Diagnostic Laboratory, University of Missouri, PO Box 6023, Columbia, Missouri 65205, USA (Gull); Veterinary Laboratory Investigation and Response Network, Center for Veterinary Medicine, United States Food and Drug Administration, 8491 Muirkirk Road, Laurel, Maryland 20708, USA (Ceric, Reimschuessel)
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Baier-Grabner S, Equiluz-Bruck S, Endress D, Blaschitz M, Schubert S, Indra A, Fudel M, Frischer T, Götzinger F. A Yersiniabactin-producing Klebsiella aerogenes Strain Causing an Outbreak in an Austrian Neonatal Intensive Care Unit. Pediatr Infect Dis J 2022; 41:593-599. [PMID: 35421055 DOI: 10.1097/inf.0000000000003553] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
BACKGROUND Yersiniabactin, a siderophore with a high affinity to iron, has been described as a potential virulence factor in Enterobacteriaceae. Klebsiella aerogenes is a Gram-negative rod known to cause invasive infection in very low birth weight infants but is an unusual pathogen to cause outbreaks in neonatal intensive care units (NICU). METHODS We performed a retrospective analysis of all patients colonized with K. aerogenes in our NICU from September to December 2018. Each infant with an occurrence of K. aerogenes in any microbiological culture was defined as a case. Clinical data were taken from medical charts. K. aerogenes isolates were genotyped using whole-genome sequencing combined with core genome multilocus sequencing type analysis. Yersiniabactin production was evaluated by luciferase assay. RESULTS In total 16 patients were colonized with K. aerogenes over the 3-month period and 13 patients remained asymptomatic or developed late-onset neonatal sepsis from another pathogen. Three patients developed necrotizing enterocolitis, 2 complicated by sepsis and 1 of them died. All symptomatic patients were premature infants with low birth weight. Genetic sequencing confirmed an outbreak with the same strain, all samples expressed the high-pathogenicity island, necessary for the production of yersiniabactin. Six exemplary cases were proven to produce yersiniabactin in vitro. CONCLUSION This is the first report of an outbreak of a yersiniabactin-producing K. aerogenes strain causing invasive infection in preterm infants. We hypothesize that, due to improved iron uptake, this strain was associated with higher virulence than non-yersiniabactin-producing strains. Extended search for virulence factors and genetic sequencing could be pivotal in the management of NICU outbreaks in the future.
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Affiliation(s)
| | | | - David Endress
- From the Department of Pediatrics and Adolescent Medicine
| | | | - Sören Schubert
- Max von Pettenkofer-Institute, Faculty of Medicine, LMU Munich, Germany
| | - Alexander Indra
- Paracelsus Medical University of Salzburg, Salzburg, Austria
| | - Marta Fudel
- Department of Hospital Hygiene, Klinik Ottakring, Vienna, Austria
| | - Thomas Frischer
- Sigmund Freud Private University, Sigmund Freud Platz 3, Vienna, Austria
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Ballaben AS, Galetti R, Ferreira JC, Paziani MH, Kress MRVZ, Garcia DDO, Silva PD, Doi Y, Darini ALC, Andrade LN. Different virulence genetic context of multidrug-resistant CTX-M- and KPC-producing Klebsiella pneumoniae isolated from cerebrospinal fluid. Diagn Microbiol Infect Dis 2022; 104:115784. [DOI: 10.1016/j.diagmicrobio.2022.115784] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2022] [Revised: 06/30/2022] [Accepted: 07/22/2022] [Indexed: 11/03/2022]
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Al Fadhli AH, Jamal WY, Rotimi VO. Elucidating the virulence genes harboured by carbapenemase- and non-carbapenemase-producing carbapenem-resistant Klebsiella pneumoniae rectal isolates from patients admitted to intensive care units using whole-genome sequencing in Kuwait. J Med Microbiol 2022; 71. [PMID: 35819900 DOI: 10.1099/jmm.0.001554] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. Klebsiella pneumoniae is a Gram-negative pathogen responsible for community- and nosocomial-acquired infections. The presence of an accessory genome determines the bacterial pathogenicity and the host immune response, and thus indicates multidrug-resistant strains or more virulent groups. Little is known about the virulence genes in K. pneumoniae in Kuwait.Hypothesis/Gap Statement. The diversity of virulence genes and capsule loci in K. pneumoniae isolates warrants further genomic studies to better understand their transmission within the hospitals in Kuwait.Aim. We aimed to investigate the virulence genes harboured by K. pneumoniae isolated from rectal swabs of intensive care unit (ICU) patients in two Kuwaiti teaching hospitals.Methodology. Six isolates from patients in the ICUs of Al Razi and Mubarak hospitals, designated RZH144, RZH132 RZH108 and RZH173, and MKH381 and MKH347, respectively, were subjected to whole-genome sequencing (WGS) assays. RZH144 and RZH132 were non-carbapenemase-producing K. pneumoniae (NCKP) isolates negative for genes encoding carbapenemase production by PCR assays, and the remaining four were carbapenemase-producing K. pneumoniae (CPKP) isolates. Isolates were characterized by phenotypic, PCR and WGS methods. Susceptibility testing was performed by E test and clonality by multilocus sequence typing. Analysis of the isolates' assembled contigs was carried out using Kleborate (https://pathogen.watch).Results. An NCPE RZH132 K. pneumoniae isolate belonged to ST231-wzi104 and harboured gene clusters encoding the biosynthesis of the siderophore aerobactin (iuc5) on 62-3LV. The capsular locus variants were KL51 and O locus O1v2. Another NCPKP RZH144 isolate was confirmed as ST43-wzi412 and harboured KL61 and O1v1. The four CPKP isolates harboured two virulence loci - ybt14 and iuc5 - encoding the siderophores yersiniabactin and aerobactin, respectively. They belonged to ST231-wzi104 and harboured yersiniabactin on ICEKp5. The sequence type of ybt was YbST145-1LV. Strain RZ108 was devoid of virulence loci. Its sequence type was ST15-wzi151 and harboured KL48 and O1V1. ST231 clonal lineage isolates shared common virulence plasmid variants.Conclusion. The CPKP ST231 had the highest virulence score and contained iuc5, which was found for the first time in ST231-CPKP isolates in Kuwait.
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Affiliation(s)
- Amani H Al Fadhli
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait
| | - Wafaa Y Jamal
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait
| | - Vincent O Rotimi
- Department of Microbiology, Faculty of Medicine, Kuwait University, Kuwait
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Xiao T, Peng K, Chen Q, Hou X, Huang W, Lv H, Yang X, Lei G, Li R. Coexistence of tmexCD-toprJ, blaNDM-1, and blaIMP-4 in One Plasmid Carried by Clinical Klebsiella spp. Microbiol Spectr 2022; 10:e0054922. [PMID: 35647621 PMCID: PMC9241619 DOI: 10.1128/spectrum.00549-22] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 04/21/2022] [Indexed: 12/31/2022] Open
Abstract
In clinical practice, carbapenems and tigecycline are considered significant options for treating infections caused by multidrug-resistant Klebsiella spp. The continual evolution of resistance mechanisms to carbapenems and tigecycline is shattering the present condition. Meanwhile, convergence of the two resistance mechanisms in a single strain has been reported repeatedly, posing a significant threat to public health and safety. In this study, two carbapenem- and tigecycline-resistant Klebsiella species were obtained from patients and investigated using antimicrobial susceptibility testing, conjugation assay, whole-genome sequencing, and bioinformatics analysis. In Klebsiella variicola FK2020ZBJ35, an untransferable multidrug IncFIB(Mar)/IncHI1B-like plasmid carrying tmexCD2-toprJ2, blaIMP-4, and blaNDM-1 was discovered, as was a similar plasmid carrying tmexCD1-toprJ1 and blaIMP-4 in Klebsiella quasipneumoniae 2019SCSN059. Genetic context analysis found that two distinct tmexCD-toprJ variants were detected in comparable mobile units with genetic array int-int-hp-hp-tnfxB-tmexCD-toprJ and integrated into separate genetic locations. blaIMP-4 and blaNDM-1 were carried by an integron In1377 and a truncated Tn3000, respectively. These findings revealed that the carbapenem and tigecycline resistance genes carried by the two strains were located on mobile elements and might potentially transmit horizontally to additional strains. Furthermore, our findings showed that IncFIB(Mar)/IncHI1B-like plasmids represent a significant reservoir of essential resistance genes that warrants continued monitoring. IMPORTANCE Tigecycline is an essential antibiotic that is used to treat infections caused by carbapenem-resistant Klebsiella pneumoniae (CRKP). The emergence of high-level tigecycline-resistant CRKP poses a serious hazard to human health. This work screened two tigecycline-resistant CRKP strains from clinical patients and found a type of plasmid that encoded carbapenemase and TmexCD-ToprJ in Klebsiella. Importantly, one plasmid cocarried tmexCD-toprJ, blaNDM-1, and blaIMP-4, hinting that this plasmid could be a critical vector for superbug development. Furthermore, we discovered that the carbapenem and tigecycline resistance genes are located in mobile units by genetic structure analysis. Our research tracks the formation of clinically super-resistant Gram-negative bacteria.
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Affiliation(s)
- Tao Xiao
- Center for Disease Control and Prevention of Sichuan Province, Chengdu, Sichuan Province, People’s Republic of China
| | - Kai Peng
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, People’s Republic of China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu Province, People’s Republic of China
| | - Qi Chen
- Suining Center for Disease Control and Prevention, Suining, Sichuan Province, People’s Republic of China
| | - Xueqin Hou
- Guangyuan Center for Disease Control and Prevention, Guangyuan, Sichuan Province, People’s Republic of China
| | - Weifeng Huang
- Center for Disease Control and Prevention of Sichuan Province, Chengdu, Sichuan Province, People’s Republic of China
| | - Hong Lv
- Center for Disease Control and Prevention of Sichuan Province, Chengdu, Sichuan Province, People’s Republic of China
| | - Xiaorong Yang
- Center for Disease Control and Prevention of Sichuan Province, Chengdu, Sichuan Province, People’s Republic of China
| | - Gaopeng Lei
- Center for Disease Control and Prevention of Sichuan Province, Chengdu, Sichuan Province, People’s Republic of China
| | - Ruichao Li
- Jiangsu Co-Innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, Jiangsu Province, People’s Republic of China
- Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu Province, People’s Republic of China
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Venturini C, Bowring B, Partridge SR, Ben Zakour NL, Fajardo-Lubian A, Lopez Ayala A, Qin J, Totsika M, van Galen G, Norris J, Iredell J. Co-Occurrence of Multidrug Resistant Klebsiella pneumoniae Pathogenic Clones of Human Relevance in an Equine Pneumonia Case. Microbiol Spectr 2022; 10:e0215821. [PMID: 35579468 PMCID: PMC9241755 DOI: 10.1128/spectrum.02158-21] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 04/13/2022] [Indexed: 11/20/2022] Open
Abstract
The global epidemiology of multidrug resistant Klebsiella pneumoniae, a serious threat to both animal and human health, is dominated by the spread of pathogenic clones, each separately evolving via acquisition of transferable antibiotic resistance or niche-specific virulence determinants. In horses, K. pneumoniae infection can lead to severe respiratory illness. Here, we characterized multiple isolates recovered from bronchial aspirates of a mare with pneumonia refractory to antibiotics. First, we used a combination of standard microbiology, bacteriophage cross-susceptibility and antibiotic resistance testing to profile the infecting K. pneumoniae population. The genomes of isolates with distinct fingerprints (pulsed-field gel electrophoresis) and unique combined bacteriophage/antibiotic profiles were then further analyzed using whole-genome sequencing. Adhesion to human epithelial cells and biofilm production were also measured as virulence indicators. Although it is commonly expected for one clone to dominate an infection episode, we identified five coexisting multidrug resistant K. pneumoniae sharing the same niche. One was a novel sequence type (ST4656), while the other four were all members of emerging human pathogenic clonal groups (ST307, ST628, ST893 and ST392). These isolates did not display significant differences from one another in terms of virulence or resistance and differed only in plasmid content from isolates implicated in severe human infections, with equal potential to prolong duration and severity of infection when sharing the same niche. This study highlights the importance of more precise surveillance and detection measures to uncover bacterial heterogeneity, reminding us that the "single clone" concept is not an absolute in invasive bacterial infections. IMPORTANCE Multidrug resistant Klebsiella pneumoniae are agents of life-threatening infections in animals and humans, with several multidrug resistant clones causing outbreaks of disease worldwide. It is generally accepted that only one clone will be dominant in an infection episode. In this study, we investigated K. pneumoniae isolates from a horse with severe pneumonia and demonstrated co-occurrence of multiple sequence types previously identified as emerging human pathogens. The equine isolates are not significantly different from one another in terms of virulence or resistance, with equal potential to prolong duration and severity of infection, and are indistinguishable from isolates recovered from humans, except for plasmid content. Our study highlights how the "one dominant clone" concept is not an absolute in severe infection, illustrating the need for improved diagnostics to track heterogeneity of infection, and reinforces the importance of cross-monitoring of environmental and human reservoirs of multidrug resistant pathogens.
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Affiliation(s)
- Carola Venturini
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Sydney School of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - Bethany Bowring
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
| | - Sally R. Partridge
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Sydney School of Medicine, University of Sydney, Sydney, New South Wales, Australia
- Westmead Hospital, Western Sydney Local Health District (WSLHD), Westmead, New South Wales, Australia
| | - Nouri L. Ben Zakour
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Sydney School of Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Alicia Fajardo-Lubian
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Sydney School of Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Ariana Lopez Ayala
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Sydney School of Medicine, University of Sydney, Sydney, New South Wales, Australia
| | - Jilong Qin
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Makrina Totsika
- Centre for Immunology and Infection Control, School of Biomedical Sciences, Queensland University of Technology, Brisbane, Queensland, Australia
| | - Gaby van Galen
- Sydney School of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - Jacqueline Norris
- Sydney School of Veterinary Science, University of Sydney, Sydney, New South Wales, Australia
| | - Jonathan Iredell
- Centre for Infectious Diseases and Microbiology, Westmead Institute for Medical Research, Westmead, New South Wales, Australia
- Sydney School of Medicine, University of Sydney, Sydney, New South Wales, Australia
- Westmead Hospital, Western Sydney Local Health District (WSLHD), Westmead, New South Wales, Australia
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232
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Hisyam Bin Ismail CMK, Raihan Mohammad Shabani N, Chuah C, Hassan Z, Bakar Abdul Majeed A, Herng Leow C, Kaur Banga Singh K, Yee Leow C. Shigella iron-binding proteins: An insight into molecular physiology, pathogenesis, and potential target vaccine development. Vaccine 2022; 40:3991-3998. [PMID: 35660036 DOI: 10.1016/j.vaccine.2022.05.061] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 11/21/2021] [Accepted: 05/19/2022] [Indexed: 12/01/2022]
Abstract
Shigella is a well-known etiological agent responsible for intestinal infection among children, the elderly, and immunocompromised people ranging from mild to severe cases. Shigellosis remains endemic in Malaysia and yet there is no commercial vaccine available to eradicate the disease. Iron is an essential element for the survival of Shigella within the host. Hence, it is required for regulating metabolic mechanisms and virulence determinants. Alteration of iron status in the extracellular environment directly triggers the signal in enteropathogenic bacterial, providing information that they are in a hostile environment. To survive in an iron-limited environment, molecular regulation of iron-binding proteins plays a vital role in facilitating the transportation and utilization of sufficient iron sources. Given the importance of iron molecules for bacterial survival and pathogenicity, this review summarizes the physiological role of iron-binding proteins in bacterial survival and their potential use in vaccine and therapeutic developments.
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Affiliation(s)
| | - Nor Raihan Mohammad Shabani
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia; Faculty of Health Sciences, Universiti Teknologi MARA, Kampus Bertam, 13200 Kepala Batas, Penang, Malaysia
| | - Candy Chuah
- Department of Medical and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia; Faculty of Health Sciences, Universiti Teknologi MARA, Kampus Bertam, 13200 Kepala Batas, Penang, Malaysia
| | - Zurina Hassan
- Centre for Drug Research, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Abu Bakar Abdul Majeed
- Faculty of Pharmacy, Universiti Teknologi MARA, Kampus Puncak Alam, 42300 Kuala Selangor, Selangor, Malaysia
| | - Chiuan Herng Leow
- Institute for Research in Molecular Medicine (INFORMM), Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia
| | - Kirnpal Kaur Banga Singh
- Department of Medical and Parasitology, School of Medical Sciences, Universiti Sains Malaysia, 16150 Kubang Kerian, Kelantan, Malaysia
| | - Chiuan Yee Leow
- School of Pharmaceutical Sciences, Universiti Sains Malaysia, 11800 Minden, Penang, Malaysia.
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233
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Xie M, Chen K, Chan EWC, Zhang R, Chen S. Characterization of clinical carbapenem-resistant K1 Klebsiella quasipneumoniae subsp. similipneumoniae strains harboring virulence plasmid. Int J Antimicrob Agents 2022; 60:106628. [PMID: 35760224 DOI: 10.1016/j.ijantimicag.2022.106628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 06/16/2022] [Accepted: 06/19/2022] [Indexed: 11/05/2022]
Abstract
The continuous emergence of carbapenem-resistant and hypervirulent Klebsiella pneumoniae (CR-HvKP) poses great challenges to human health due to the extremely high morbidity and mortality. Klebsiella quasipneumoniae is a newly described bacterial species and often mis-identified as Klebsiella pneumoniae. Clinical K. quasipneumoniae strains have been reported worldwide, in which multidrug-resistant lineages have become a severe health problem, while less has been understood on this important pathogen. In this study, we characterized three clinical carbapenem-resistant K. quasipneumoniae subsp. similipneumoniae isolates, which belonged to sequence type (ST) ST367 and capsular type K1 and contained several virulence genes, including salmochelin (iroBCDN), aerobactin (iucABCDiutA), regulator of mucoid phenotype (rmpA/A2), as well as some resistance genes, including blaKPC-2, blaOKP-B-9, and oqxAB. These carbapenem-resistant K. quasipneumoniae subsp. similipneumoniae strains that containing virulence genes exhibited higher level of virulence and serum resistance than classical K. pneumoniae strain, while their virulence levels were slightly lower when compared with typical ST11 CR-HvKP and ST23 K1 HvKP strains. This study reported for the first time the genetic and virulence characterization of clinical K. quasipneumoniae subsp. similipneumoniae strains that simultaneously contained blaKPC-2 gene and virulence genes, which contributed to a better understanding of their resistance and pathogenicity as well as for epidemic surveillance worldwide.
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Affiliation(s)
- Miaomiao Xie
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Kaichao Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Edward Wai-Chi Chan
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Rong Zhang
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China.
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong.
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234
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Rocha J, Henriques I, Gomila M, Manaia CM. Common and distinctive genomic features of Klebsiella pneumoniae thriving in the natural environment or in clinical settings. Sci Rep 2022; 12:10441. [PMID: 35729190 PMCID: PMC9213442 DOI: 10.1038/s41598-022-14547-6] [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: 11/05/2021] [Accepted: 06/08/2022] [Indexed: 01/17/2023] Open
Abstract
The Klebsiella pneumoniae complex is comprised of ubiquitous bacteria that can be found in soils, plants or water, and as humans' opportunistic pathogens. This study aimed at inferring common and distinctive features in clinical and environmental K. pneumoniae. Whole genome sequences of members of the K. pneumoniae complex (including K. variicola, n = 6; and K. quasipneumoniae, n = 7), of clinical (n = 78) and environmental (n = 61) origin from 21 countries were accessed from the GenBank. These genomes were compared based on phylogeny, pangenome and selected clinically relevant traits. Phylogenetic analysis based on 2704 genes of the core genome showed close relatedness between clinical and environmental strains, in agreement with the multi-locus sequence typing. Eight out of the 62 sequence types (STs) identified, included both clinical and environmental genomes (ST11, ST14, ST15, ST37, ST45, ST147, ST348, ST437). Pangenome-wide association studies did not evidence significant differences between clinical and environmental genomes. However, the genomes of clinical isolates presented significantly more exclusive genes related to antibiotic resistance/plasmids, while the environmental isolates yielded significantly higher allelic diversity of genes related with functions such as efflux or oxidative stress. The study suggests that K. pneumoniae can circulate among the natural environment and clinical settings, probably under distinct adaptation pressures.
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Affiliation(s)
- Jaqueline Rocha
- Universidade Católica Portuguesa, CBQF-Centro de Biotecnologia e Química Fina-Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Isabel Henriques
- Department of Life Sciences, Faculty of Science and Technology, University of Coimbra, Coimbra, Portugal.,CESAM, University of Aveiro, Aveiro, Portugal
| | - Margarita Gomila
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | - Célia M Manaia
- Universidade Católica Portuguesa, CBQF-Centro de Biotecnologia e Química Fina-Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal.
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235
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Klebsiella pneumonia and Its Antibiotic Resistance: A Bibliometric Analysis. BIOMED RESEARCH INTERNATIONAL 2022; 2022:1668789. [PMID: 35707374 PMCID: PMC9192197 DOI: 10.1155/2022/1668789] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 05/03/2022] [Accepted: 05/18/2022] [Indexed: 11/18/2022]
Abstract
The rapid development of antibiotic resistance in K. pneumonia has led to a major concern. In order to analyze the hotspots and develop trends in this field through visual the analysis, this study used CiteSpace software to summarize the available data in the literature to provide insights. A total of 9366 research articles were retrieved from the Web of Science Core Collection, and the number of published papers is increasing year by year. The country with the most articles was the USA, followed by China and India. The institution with the highest number of publications was LERU. The author with the highest number of articles was Li. The journal with the highest citation rate was Antimicrobial Agents and Chemotherapy. In addition, based on keyword coword analysis and cited literature prominence analysis by CiteSpace, the current research focus in the field was therapy, CRKP, and resistance genes. This paper provides a new quantitative visualization way for the development of the field in the recent ten years. The results show global trends that researchers can use to determine future directions.
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236
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Hennart M, Guglielmini J, Bridel S, Maiden MCJ, Jolley KA, Criscuolo A, Brisse S. A dual barcoding approach to bacterial strain nomenclature: Genomic taxonomy of Klebsiella pneumoniae strains. Mol Biol Evol 2022; 39:6608353. [PMID: 35700230 PMCID: PMC9254007 DOI: 10.1093/molbev/msac135] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Sublineages (SLs) within microbial species can differ widely in their ecology and pathogenicity, and their precise definition is important in basic research and for industrial or public health applications. Widely accepted strategies to define SLs are currently missing, which confuses communication in population biology and epidemiological surveillance. Here, we propose a broadly applicable genomic classification and nomenclature approach for bacterial strains, using the prominent public health threat Klebsiella pneumoniae as a model. Based on a 629-gene core genome multilocus sequence typing (cgMLST) scheme, we devised a dual barcoding system that combines multilevel single linkage (MLSL) clustering and life identification numbers (LINs). Phylogenetic and clustering analyses of >7,000 genome sequences captured population structure discontinuities, which were used to guide the definition of 10 infraspecific genetic dissimilarity thresholds. The widely used 7-gene multilocus sequence typing (MLST) nomenclature was mapped onto MLSL SLs (threshold: 190 allelic mismatches) and clonal group (threshold: 43) identifiers for backwards nomenclature compatibility. The taxonomy is publicly accessible through a community-curated platform (https://bigsdb.pasteur.fr/klebsiella), which also enables external users’ genomic sequences identification. The proposed strain taxonomy combines two phylogenetically informative barcode systems that provide full stability (LIN codes) and nomenclatural continuity with previous nomenclature (MLSL). This species-specific dual barcoding strategy for the genomic taxonomy of microbial strains is broadly applicable and should contribute to unify global and cross-sector collaborative knowledge on the emergence and microevolution of bacterial pathogens.
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Affiliation(s)
- Melanie Hennart
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
- Sorbonne Université, Collège Doctoral, Paris, France
| | - Julien Guglielmini
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
| | - Sébastien Bridel
- Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | | | - Keith A. Jolley
- Department of Zoology, University of Oxford, Oxford, United Kingdom
| | - Alexis Criscuolo
- Institut Pasteur, Université Paris Cité, Bioinformatics and Biostatistics Hub, Paris, France
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237
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Zhou X, Chu Q, Li S, Yang M, Bao Y, Zhang Y, Fu S, Gong H. A new and effective genes-based method for phylogenetic analysis of Klebsiella pneumoniae. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2022; 100:105275. [PMID: 35339697 DOI: 10.1016/j.meegid.2022.105275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/02/2021] [Revised: 03/16/2022] [Accepted: 03/21/2022] [Indexed: 06/14/2023]
Abstract
The exponential increase in the number of genomes deposited in public databases can help us gain a more holistic understanding of the phylogeny and epidemiology of Klebsiella pneumoniae. However, inferring the evolutionary relationships of K. pneumoniae based on big genomic data is challenging for existing methods. In this study, core genes of K. pneumoniae were determined and analysed in terms of differences in GC content, mutation rate, size, and potential functions. We then developed a stable genes-based method for big data analysis and compared it with existing methods. Our new method achieved a higher resolution phylogenetic analysis of K. pneumoniae. Using this genes-based method, we explored global phylogenetic relationships based on a public database of nearly 953 genomes. The results provide useful information to facilitate the phylogenetic and epidemiological analysis of K. pneumoniae, and the findings are relevant for security applications.
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Affiliation(s)
- Xiaoqin Zhou
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Qiyu Chu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China; College of Life and Environment Sciences, Shanghai Normal University, 100 Guilin Road, Shanghai 200234, PR China
| | - Shengming Li
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Menglei Yang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Yangyang Bao
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Yang Zhang
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Shuilin Fu
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China
| | - Heng Gong
- State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, 130 Meilong Road, Shanghai 200237, PR China.
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238
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Gorrie CL, Mirčeta M, Wick RR, Judd LM, Lam MMC, Gomi R, Abbott IJ, Thomson NR, Strugnell RA, Pratt NF, Garlick JS, Watson KM, Hunter PC, Pilcher DV, McGloughlin SA, Spelman DW, Wyres KL, Jenney AWJ, Holt KE. Genomic dissection of Klebsiella pneumoniae infections in hospital patients reveals insights into an opportunistic pathogen. Nat Commun 2022; 13:3017. [PMID: 35641522 PMCID: PMC9156735 DOI: 10.1038/s41467-022-30717-6] [Citation(s) in RCA: 49] [Impact Index Per Article: 24.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/04/2022] [Indexed: 12/11/2022] Open
Abstract
Klebsiella pneumoniae is a major cause of opportunistic healthcare-associated infections, which are increasingly complicated by the presence of extended-spectrum beta-lactamases (ESBLs) and carbapenem resistance. We conducted a year-long prospective surveillance study of K. pneumoniae clinical isolates in hospital patients. Whole-genome sequence (WGS) data reveals a diverse pathogen population, including other species within the K. pneumoniae species complex (18%). Several infections were caused by K. variicola/K. pneumoniae hybrids, one of which shows evidence of nosocomial transmission. A wide range of antimicrobial resistance (AMR) phenotypes are observed, and diverse genetic mechanisms identified (mainly plasmid-borne genes). ESBLs are correlated with presence of other acquired AMR genes (median n = 10). Bacterial genomic features associated with nosocomial onset are ESBLs (OR 2.34, p = 0.015) and rhamnose-positive capsules (OR 3.12, p < 0.001). Virulence plasmid-encoded features (aerobactin, hypermucoidy) are observed at low-prevalence (<3%), mostly in community-onset cases. WGS-confirmed nosocomial transmission is implicated in just 10% of cases, but strongly associated with ESBLs (OR 21, p < 1 × 10-11). We estimate 28% risk of onward nosocomial transmission for ESBL-positive strains vs 1.7% for ESBL-negative strains. These data indicate that K. pneumoniae infections in hospitalised patients are due largely to opportunistic infections with diverse strains, with an additional burden from nosocomially-transmitted AMR strains and community-acquired hypervirulent strains.
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Affiliation(s)
- Claire L Gorrie
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Vic, Australia.
| | - Mirjana Mirčeta
- Microbiology Unit, Alfred Pathology Service, The Alfred Hospital, Melbourne, Vic, Australia
| | - Ryan R Wick
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia
| | - Louise M Judd
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia
- Doherty Applied Microbial Genomics (DAMG), Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Vic, Australia
| | - Margaret M C Lam
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia
| | - Ryota Gomi
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia
- Department of Environmental Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Iain J Abbott
- Microbiology Unit, Alfred Pathology Service, The Alfred Hospital, Melbourne, Vic, Australia
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia
| | - Nicholas R Thomson
- Wellcome Sanger Institute, Hinxton, Cambs, UK
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Richard A Strugnell
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Vic, Australia
| | - Nigel F Pratt
- Infectious Diseases Clinical Research Unit, The Alfred Hospital, Melbourne, Vic, Australia
| | - Jill S Garlick
- Infectious Diseases Clinical Research Unit, The Alfred Hospital, Melbourne, Vic, Australia
| | - Kerrie M Watson
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia
| | - Peter C Hunter
- Aged Care, Caulfield Hospital, Alfred Health, Melbourne, Vic, Australia
| | - David V Pilcher
- Intensive Care Unit, The Alfred Hospital, Melbourne, Vic, Australia
- Australian and New Zealand Intensive Care Research Centre, School of Public Health and Preventative Medicine, Monash University, Melbourne, Vic, Australia
| | - Steve A McGloughlin
- Intensive Care Unit, The Alfred Hospital, Melbourne, Vic, Australia
- Australian and New Zealand Intensive Care Research Centre, School of Public Health and Preventative Medicine, Monash University, Melbourne, Vic, Australia
| | - Denis W Spelman
- Microbiology Unit, Alfred Pathology Service, The Alfred Hospital, Melbourne, Vic, Australia
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia
| | - Kelly L Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia
| | - Adam W J Jenney
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Vic, Australia
- Microbiology Unit, Alfred Pathology Service, The Alfred Hospital, Melbourne, Vic, Australia
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia.
- Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK.
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239
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Le MNT, Kayama S, Wyres KL, Yu L, Hisatsune J, Suzuki M, Yahara K, Terachi T, Sawa K, Takahashi S, Okuhara T, Kohama K, Holt KE, Mizutani T, Ohge H, Sugai M. Genomic epidemiology and temperature dependency of hypermucoviscous Klebsiella pneumoniae in Japan. Microb Genom 2022; 8. [PMID: 35622495 PMCID: PMC9465067 DOI: 10.1099/mgen.0.000827] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Klebsiella pneumoniae (Kp) has emerged as a global life-threatening pathogen owing to its multidrug resistance and hypervirulence phenotype. Several fatal outbreaks of carbapenem-resistant hypervirulent Kp have been reported recently. Hypermucoviscosity (HMV) is a phenotype commonly associated with hypervirulence of Kp, which is usually regulated by rmpA or rmpA2 (regulators of the mucoid phenotype). Here, we found that temperature was important in the HMV phenotype of Kp, and the impact of temperature on HMV was not uniform among strains. We investigated the HMV phenotype at 37 °C and room temperature (20–25 °C) in 170 clinically isolated hypermucoviscous Kp strains in Japan and analysed the association between the HMV phenotype, virulence genes and antimicrobial resistance (AMR) genes. String length distribution at different temperatures was correlated with the genomic population of Kp. The strains carrying rmpA/rmpA2 frequently showed the HMV phenotype at 37 °C, while the strains negative for these genes tended to show the HMV phenotype at room temperature. Hypervirulent Kp clusters carrying rmpA/rmpA2 without extended-spectrum beta-lactamases (ESBL)/carbapenemases produced higher string lengths at 37 °C than at room temperature, and were mostly isolated from the respiratory tract. Other HMV strains showed distinct characteristics of not carrying rmpA/rmpA2 but were positive for ESBL/carbapenemases, with a higher string length at room temperature than at 37 °C, and were frequently isolated from bloodstream infections. In total, 21 (13.5 %) HMV isolates carried ESBL and carbapenemases, among which five isolates were carbapenem-resistant hypervirulent Kp with a pLVPK-like plasmid (an epidemic virulence plasmid) and a pKPI-6-like plasmid (an epidemic blaIMP-6-bearing plasmid in Japan), suggesting the convergence of worldwide hypervirulence and epidemic AMR in Japan.
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Affiliation(s)
- Mi Nguyen-Tra Le
- Department of Antimicrobial Resistance, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan.,Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan.,Department of Bacteriology, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan
| | - Shizuo Kayama
- Department of Antimicrobial Resistance, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan.,Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan.,Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Japan
| | - Kelly L Wyres
- Department of Infectious Diseases, Monash University, Melboune, Victoria, Australia
| | - Liansheng Yu
- Department of Antimicrobial Resistance, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan.,Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan.,Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Japan
| | - Junzo Hisatsune
- Department of Antimicrobial Resistance, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan.,Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan.,Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Japan
| | - Masato Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Japan
| | - Koji Yahara
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Japan
| | - Tsuneko Terachi
- Department of Clinical Laboratory, Osaka Police Hospital, Osaka, Japan
| | - Kana Sawa
- Department of Clinical Laboratory, Osaka Police Hospital, Osaka, Japan
| | | | | | - Kunihiko Kohama
- Department of Clinical Laboratory, Chugoku Rosai Hospital, Hiroshima, Japan
| | - Kathryn E Holt
- Department of Infectious Diseases, Monash University, Melboune, Victoria, Australia.,London School of Hygiene and Tropical Medicine, London, UK
| | - Tetsu Mizutani
- Department of Clinical Laboratory, Osaka Police Hospital, Osaka, Japan
| | - Hiroki Ohge
- Department of Infectious Diseases, Hiroshima University Hospital, Hiroshima, Japan.,Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan
| | - Motoyuki Sugai
- Department of Antimicrobial Resistance, Hiroshima University Graduate School of Biomedical and Health Sciences, Hiroshima, Japan.,Project Research Center for Nosocomial Infectious Diseases, Hiroshima University, Hiroshima, Japan.,Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Japan
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240
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Study of Plasmid-Mediated Quinolone Resistance in Klebsiella pneumoniae: Relation to Extended-Spectrum Beta-Lactamases. JOURNAL OF PURE AND APPLIED MICROBIOLOGY 2022. [DOI: 10.22207/jpam.16.2.36] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Klebsiella pneumoniae (K. pneumoniae) is an important pathogen associated with various infections. The emergence of antibiotic resistances, such as quinolone resistance and those due to extended-spectrum beta-lactamases (ESBL), reduces the available choices for treatment. The objectives of the current study include the evaluation of the prevalence of the plasmid-mediated quinolone resistance genes qepA, acrA, acrB, and aac(6’)-Ib-cr by polymerase chain reaction (PCR) in K. pneumoniae and the determination of the mechanism relating these genes to the ESBL phenotype and resistance to other groups of antibiotics. In total, 300 clinical isolates of K. pneumoniae were included in the study. Isolates were subjected to antibiotic sensitivity tests using the disc diffusion method. Quinolone resistance by the minimum inhibitory concentration method and detection of ESBL resistance by the double disc diffusion method were also determined. PCR analyses revealed the prevalence of acrA, aac(6’)-Ib-cr, acrB, and qepA in 74.3%, 73.7%, 71%, and 6.7% of the isolates, respectively. Quinolone-resistant isolates positive for plasmid-encoded genes represented 82.7% of K. pneumoniae isolates positive for ESBL activity. The results also showed that the isolates of K. pneumoniae carrying plasmid-encoded quinolone resistance genes had significantly increased resistance to amikacin, amoxicillin/clavulanate, gentamicin, and cefoxitin than those isolates without quinolone resistance genes. Therefore, there was a high prevalence of acrA, acrB, and aac(6’)-Ib-cr among K. pneumoniae and the prevalence of quinolone resistance was significantly associated with the ESBL resistance phenotype. Moreover, the presence of quinolone resistance genes was associated with resistance to aminoglycosides, namely amikacin and gentamicin.
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241
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A Small KPC-2-Producing Plasmid in Klebsiella pneumoniae: Implications for Diversified Vehicles of Carbapenem Resistance. Microbiol Spectr 2022; 10:e0268821. [PMID: 35579474 PMCID: PMC9241637 DOI: 10.1128/spectrum.02688-21] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
The convergence of hypervirulence to carbapenem-resistant K. pneumoniae (CRKP) in a highly transmissible ST11 clone poses a great challenge to public health and anti-infection therapy. Recently, we revealed that an expanding repertoire of diversified KPC-2-producing plasmids occurs in these high-risk clones. Here, we report a clinical case infected with a rare isolate of ST437 CRKP, K186, which exhibited KPC-2 production. Apart from its 5,322,657-bp long chromosome, whole-genome sequencing of strain K186 elucidated three distinct resistance plasmids (designated pK186_1, pK186_2, and pK186_KPC, respectively). Unlike the prevalently larger form of KPC-2-producing plasmids (~120 to ~170 kb) earlier we observed, pK186_KPC is an IncN-type, small plasmid of 26,012bp in length. Combined with the colinear alignment of plasmid genome, the analyses of insertion sequences further suggested that this carbapenem-resistant pK186_KPC might arise from the cointegration of its ancestral IncN and IncFII plasmids, exclusively relying on IS26-based transposition events. Taken together, the result represents an unusual example of blaKPC-2-bearing small plasmids, and highlights an ongoing arsenal of diversified carriers benefiting the transferability of KPC-2 carbapenem resistance. IMPORTANCE A rare ST437 isolate termed K186 was clinically determined which was unlike ST11, the dominant sequence type of CRKP. Whole-genome sequencing enabled us to discover three distinct resistance plasmids, namely, pK186_1, pK186_2, and pK186_KPC. Among them, pK186_KPC appears as a unique plasmid ~26 kb in size, much smaller than the prevalent forms (~120 to ~170 kb). Intriguingly, genetic analysis suggests that it might originate from Proteus mirabilis. This result constitutes an additional example of differentiated plasmid vehicles dedicated to the emergence and dissemination of KPC-2 carbapenem resistance.
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242
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Giannattasio-Ferraz S, Ene A, Johnson G, Maskeri L, Oliveira AP, Banerjee S, Barbosa-Stancioli EF, Putonti C. Multidrug-Resistant Klebsiella variicola Isolated in the Urine of Healthy Bovine Heifers, a Potential Risk as an Emerging Human Pathogen. Appl Environ Microbiol 2022; 88:e0004422. [PMID: 35416681 PMCID: PMC9088279 DOI: 10.1128/aem.00044-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2022] [Accepted: 03/06/2022] [Indexed: 11/20/2022] Open
Abstract
Klebsiella variicola, a member of Klebsiella pneumoniae complex, is found to infect plants, insects, and animals and is considered an emerging pathogen in humans. While antibiotic resistance is often prevalent among K. variicola isolates from humans, this has not been thoroughly investigated in isolates from nonhuman sources. Prior evidence suggests that K. variicola can be transmitted between agricultural products as well as between animals, and the use of antibiotics in agriculture has increased antibiotic resistance in other emerging pathogens. Furthermore, in animals that contain K. variicola as a normal member of the rumen microbiota, the same bacteria can also cause infections, such as clinical mastitis in dairy cows. Here, we describe K. variicola UFMG-H9 and UFMG-H10, both isolated from the urine of healthy Gyr heifers. These two genomes represent the first isolates from the urine of cattle and exhibit greater similarity with strains from the human urinary tract than isolates from bovine fecal or milk samples. Unique to the UFMG-H9 genome is the presence of flagellar genes, the first such observation for K. variicola. Neither of the sampled animals had symptoms associated with K. variicola infection, even though genes associated with virulence and antibiotic resistance were identified in both strains. Both strains were resistant to amoxicillin, erythromycin, and vancomycin, and UFMG-H10 is resistant to fosfomycin. The observed resistances emphasize the concern regarding the emergence of this species as a human pathogen given its circulation in healthy livestock animals. IMPORTANCE Klebsiella variicola is an opportunistic pathogen in humans. It also has been associated with bovine mastitis, which can have significant economic effects. While numerous isolates have been sequenced from human infections, only 12 have been sequenced from cattle (fecal and milk samples) to date. Recently, we discovered the presence of K. variicola in the urine of two healthy heifers, the first identification of K. variicola in the bovine urinary tract and the first confirmed K. variicola isolate encoding for flagella-mediated motility. Here, we present the genome sequences and analysis of these isolates. The bovine urinary genomes are more similar to isolates from the human urinary tract than they are to other isolates from cattle, suggesting niche specialization. The presence of antibiotic resistance genes is concerning, as prior studies have found transmission between animals. These findings are important to understand the circulation of K. variicola in healthy livestock animals.
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Affiliation(s)
- Silvia Giannattasio-Ferraz
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Adriana Ene
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
| | - Genevieve Johnson
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
| | - Laura Maskeri
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
| | - André Penido Oliveira
- Empresa de Pesquisa Agropecuária de Minas Gerais – EPAMIG, Uberaba, Minas Gerais, Brazil
| | - Swarnali Banerjee
- Department of Mathematics and Statistics, Loyola University Chicago, Chicago, Illinois, USA
| | - Edel F. Barbosa-Stancioli
- Departamento de Microbiologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, Minas Gerais, Brazil
| | - Catherine Putonti
- Bioinformatics Program, Loyola University Chicago, Chicago, Illinois, USA
- Department of Biology, Loyola University Chicago, Chicago, Illinois, USA
- Department of Microbiology and Immunology, Stritch School of Medicine, Loyola University Chicago, Maywood, Illinois, USA
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243
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Inosine and D-Mannose Secreted by Drug-Resistant Klebsiella pneumoniae Affect Viability of Lung Epithelial Cells. Molecules 2022; 27:molecules27092994. [PMID: 35566345 PMCID: PMC9106066 DOI: 10.3390/molecules27092994] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2022] [Revised: 04/30/2022] [Accepted: 05/03/2022] [Indexed: 11/29/2022] Open
Abstract
The antibiotic resistance rates of Klebsiella pneumoniae have been steadily increasing in recent years. Nevertheless, the metabolic features of the drug-resistant Klebsiella pneumoniae and its associated benefits for bacterial pathogenicity are far from expounded. This study aims to unravel the unique physiological and metabolic properties specific to drug-resistant K. pneumoniae. Using scanning electron microscopy (SEM), we observed a thicker extracellular mucus layer around a drug-resistant K. pneumonia strain (Kp-R) than a drug-sensitive K. pneumonia strain (Kp-S). Kp-R also produced more capsular polysaccharide (CPS) and biofilm, and appeared to have a significant competitive advantage when co-cultured with Kp-S. Moreover, Kp-R was easier to adhere to and invade A549 epithelial cells than Kp-S but caused less cell-viability damage according to cell counting kit-8 (CCK-8) tests. Immunofluorescence revealed that both Kp-R and Kp-S infection destroyed the tight junctions and F-actin of epithelial cells, while the damage caused by Kp-S was more severe than Kp-R. We detected the extracellular metabolites secreted by the two strains with UHPLC-Q-TOF MS to explore the critical secretion products. We identified 16 predominant compounds that were differentially expressed. Among them, inosine increased the viability of epithelial cells in a dose-dependent manner, and an A2AR antagonist can abolish such enhancement. D-mannose, which was secreted less in Kp-R, inhibited the viability of A549 cells in the range of low doses. These findings provide potential targets and research strategies for preventing and treating drug-resistant K. pneumoniae infections.
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Chen C, Xu H, Liu R, Hu X, Han J, Wu L, Fu H, Zheng B, Xiao Y. Emergence of Neonatal Sepsis Caused by MCR-9- and NDM-1-Co-Producing Enterobacter hormaechei in China. Front Cell Infect Microbiol 2022; 12:879409. [PMID: 35601097 PMCID: PMC9120612 DOI: 10.3389/fcimb.2022.879409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2022] [Accepted: 04/05/2022] [Indexed: 01/01/2023] Open
Abstract
Mobile colistin resistance (mcr) genes represent an emerging threat to public health. Reports on the prevalence, antimicrobial profiles, and clonality of MCR-9-producing Enterobacter cloacae complex (ECC) isolates on a national scale in China are limited. We screened 3,373 samples from humans, animals, and the environment and identified eleven MCR-9-positive ECC isolates. We further investigated their susceptibility, epidemiology, plasmid profiles, genetic features, and virulence potential. Ten strains were isolated from severe bloodstream infection cases, especially three of them were recovered from neonatal sepsis. Enterobacter hormaechei was the most predominant species among the MCR-9-producing ECC population. Moreover, the co-existence of MCR-9, CTX-M, and SHV-12 encoding genes in MCR-9-positive isolates was globally observed. Notably, mcr-9 was mainly carried by IncHI2 plasmids, and we found a novel ~187 kb IncFII plasmid harboring mcr-9, with low similarity with known plasmids. In summary, our study presented genomic insights into genetic characteristics of MCR-9-producing ECC isolates retrieved from human, animal, and environment samples with one health perspective. This study is the first to reveal NDM-1- and MCR-9-co-producing ECC from neonatal sepsis in China. Our data highlights the risk for the hidden spread of the mcr-9 colistin resistance gene.
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Affiliation(s)
- Chunlei Chen
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Hao Xu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
| | - Ruishan Liu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Xinjun Hu
- Department of Infectious Diseases, The First Affiliated Hospital, College of Clinical Medicine, Henan University of Science and Technology, Luoyang, China
| | - Jianfeng Han
- Sansure Biotech Inc. Medical Affairs Department, National Joint Local Engineering Research Center for Genetic Diagnosis of Infection Diseases and Tumors, Beijing, China
| | - Lingjiao Wu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Hao Fu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Beiwen Zheng
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
- Research Units of Infectious Diseases and Microecology, Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Beiwen Zheng, ; Yonghong Xiao,
| | - Yonghong Xiao
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
- Jinan Microecological Biomedicine Shandong Laboratory, Jinan, China
- Research Units of Infectious Diseases and Microecology, Chinese Academy of Medical Sciences, Beijing, China
- *Correspondence: Beiwen Zheng, ; Yonghong Xiao,
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Muraya A, Kyany’a C, Kiyaga S, Smith HJ, Kibet C, Martin MJ, Kimani J, Musila L. Antimicrobial Resistance and Virulence Characteristics of Klebsiella pneumoniae Isolates in Kenya by Whole-Genome Sequencing. Pathogens 2022; 11:545. [PMID: 35631066 PMCID: PMC9144577 DOI: 10.3390/pathogens11050545] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2022] [Revised: 04/27/2022] [Accepted: 04/28/2022] [Indexed: 02/04/2023] Open
Abstract
Klebsiella pneumoniae is a globally significant opportunistic pathogen causing healthcare-associated and community-acquired infections. This study examined the epidemiology and the distribution of resistance and virulence genes in clinical K. pneumoniae strains in Kenya. A total of 89 K. pneumoniae isolates were collected over six years from five counties in Kenya and were analyzed using whole-genome sequencing and bioinformatics. These isolates were obtained from community-acquired (62/89) and healthcare-associated infections (21/89), and from the hospital environment (6/89). Genetic analysis revealed the presence of blaNDM-1 and blaOXA-181 carbapenemase genes and the armA and rmtF genes known to confer pan-aminoglycoside resistance. The most abundant extended-spectrum beta-lactamase genes identified were blaCTX-M-15 (36/89), blaTEM (35/89), and blaOXA (18/89). In addition, one isolate had a mobile colistin resistance gene (mcr-8). Fluoroquinolone resistance-conferring mutations in gyrA and parC genes were also observed. The most notable virulence factors were those associated with hyper-virulence (rmpA/A2 and magA), yersiniabactin (ybt), salmochelin (iro), and aerobactin (iuc and iutA). A total of 38 distinct sequence types were identified, including known global lineages ST14, ST15, ST147, and ST307, and a regional clone ST17 implicated in regional outbreaks. In addition, this study genetically characterized two potential hypervirulent isolates and two community-acquired ST147 high-risk clones that contained carbapenemase genes, yersiniabactin, and other multidrug resistance genes. These results demonstrate that the resistome and virulome of Kenyan clinical and hospital environmental K. pneumoniae isolates are diverse. The reservoir of high-risk clones capable of spreading resistance, and virulence factors have the potential to cause unmanageable infection outbreaks with high morbidity and mortality.
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Affiliation(s)
- Angela Muraya
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62000-00200, Kenya; (A.M.); (C.K.); (J.K.)
| | - Cecilia Kyany’a
- United States Army Medical Research Directorate-Africa, Village Market, Nairobi P.O. Box 606-00621, Kenya; (C.K.); (H.J.S.)
- Kenya Medical Research Institute, Nairobi P.O. Box 54840-00200, Kenya
| | - Shahiid Kiyaga
- Department of Immunology and Molecular Biology, School of Biomedical Sciences, College of Health Sciences, Makerere University, Kampala P.O. Box 7072, Uganda;
| | - Hunter J. Smith
- United States Army Medical Research Directorate-Africa, Village Market, Nairobi P.O. Box 606-00621, Kenya; (C.K.); (H.J.S.)
| | - Caleb Kibet
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62000-00200, Kenya; (A.M.); (C.K.); (J.K.)
- International Center for Insect Physiology and Ecology, Nairobi P.O. Box 30772-00100, Kenya
| | - Melissa J. Martin
- Multidrug-Resistant Organism Repository and Surveillance Network (MRSN), Walter Reed Army Institute of Research, Silver Spring, MD 20910, USA;
| | - Josephine Kimani
- Department of Biochemistry, Jomo Kenyatta University of Agriculture and Technology, Nairobi P.O. Box 62000-00200, Kenya; (A.M.); (C.K.); (J.K.)
| | - Lillian Musila
- United States Army Medical Research Directorate-Africa, Village Market, Nairobi P.O. Box 606-00621, Kenya; (C.K.); (H.J.S.)
- Kenya Medical Research Institute, Nairobi P.O. Box 54840-00200, Kenya
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Håkonsholm F, Hetland MA, Svanevik CS, Lunestad BT, Löhr IH, Marathe NP. Insights into the genetic diversity, antibiotic resistance and pathogenic potential of Klebsiella pneumoniae from the Norwegian marine environment using whole-genome analysis. Int J Hyg Environ Health 2022; 242:113967. [DOI: 10.1016/j.ijheh.2022.113967] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 02/25/2022] [Accepted: 03/25/2022] [Indexed: 01/08/2023]
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247
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Hawkey J, Vezina B, Monk JM, Judd LM, Harshegyi T, López-Fernández S, Rodrigues C, Brisse S, Holt KE, Wyres KL. A curated collection of Klebsiella metabolic models reveals variable substrate usage and gene essentiality. Genome Res 2022; 32:1004-1014. [PMID: 35277433 PMCID: PMC9104693 DOI: 10.1101/gr.276289.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 03/08/2022] [Indexed: 11/24/2022]
Abstract
The Klebsiella pneumoniae species complex (KpSC) is a set of seven Klebsiella taxa that are found in a variety of niches and are an important cause of opportunistic health care-associated infections in humans. Because of increasing rates of multi-drug resistance within the KpSC, there is a growing interest in better understanding the biology and metabolism of these organisms to inform novel control strategies. We collated 37 sequenced KpSC isolates isolated from a variety of niches, representing all seven taxa. We generated strain-specific genome-scale metabolic models (GEMs) for all 37 isolates and simulated growth phenotypes on 511 distinct carbon, nitrogen, sulfur, and phosphorus substrates. Models were curated and their accuracy was assessed using matched phenotypic growth data for 94 substrates (median accuracy of 96%). We explored species-specific growth capabilities and examined the impact of all possible single gene deletions using growth simulations in 145 core carbon substrates. These analyses revealed multiple strain-specific differences, within and between species, and highlight the importance of selecting a diverse range of strains when exploring KpSC metabolism. This diverse set of highly accurate GEMs could be used to inform novel drug design, enhance genomic analyses, and identify novel virulence and resistance determinants. We envisage that these 37 curated strain-specific GEMs, covering all seven taxa of the KpSC, provide a valuable resource to the Klebsiella research community.
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Affiliation(s)
- Jane Hawkey
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
| | - Ben Vezina
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
| | - Jonathan M Monk
- Department of Bioengineering, University of California, San Diego, San Diego, California 92093, USA
| | - Louise M Judd
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
| | - Taylor Harshegyi
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
| | - Sebastián López-Fernández
- Institut Pasteur, Université de Paris, Biodiversity and Epidemiology of Bacterial Pathogens, 75015 Paris, France
| | - Carla Rodrigues
- Institut Pasteur, Université de Paris, Biodiversity and Epidemiology of Bacterial Pathogens, 75015 Paris, France
| | - Sylvain Brisse
- Institut Pasteur, Université de Paris, Biodiversity and Epidemiology of Bacterial Pathogens, 75015 Paris, France
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London WC1E 7HT, United Kingdom
| | - Kelly L Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
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248
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Klebsiella pneumoniae hipervirulenta ST66 como causa de neumonía necrosante. Enferm Infecc Microbiol Clin 2022. [DOI: 10.1016/j.eimc.2022.03.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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249
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Dong N, Yang X, Chan EWC, Zhang R, Chen S. Klebsiella species: Taxonomy, hypervirulence and multidrug resistance. EBioMedicine 2022; 79:103998. [PMID: 35405387 PMCID: PMC9010751 DOI: 10.1016/j.ebiom.2022.103998] [Citation(s) in RCA: 82] [Impact Index Per Article: 41.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2021] [Revised: 03/25/2022] [Accepted: 03/28/2022] [Indexed: 11/24/2022] Open
Abstract
Members of the genus Klebsiella have rapidly evolved within the past decade, generating organisms that simultaneously exhibit both multidrug resistance and hypervirulence (MDR-hv) phenotypes; such organisms are associated with severe hospital- and community-acquired infections. Carbapenem-resistant infections with unknown optimal treatment regime were of particular concern among the MDR-hv Klebsiella strains. Recent studies have revealed the molecular features and the mobile resistance elements they harbour, allowing identification of genetic loci responsible for transmission, stable inheritance, and expression of mobile resistance or virulence-encoding elements that confer the new phenotypic characteristics of MDR-hv Klebsiella spp. Here, we provide a comprehensive review on the taxonomic position, species composition and different phylotypes of Klebsiella spp., describing the diversity and worldwide distribution of the MDR-hv clones, the genetic mutation and horizontal gene transfer events that drive the evolution of such clones, and the potential impact of MDR-hv infections on human health.
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Affiliation(s)
- Ning Dong
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Xuemei Yang
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, China
| | - Edward Wai-Chi Chan
- State Key Lab of Chemical Biology and Drug Discovery, Department of Applied Biology and Chemical Technology, The Hong Kong polytechnic University, Hung Hom, Hong Kong, China
| | - Rong Zhang
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong, China.
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250
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Sundaresan AK, Vincent K, Mohan GBM, Ramakrishnan J. Association of Sequence types, Antimicrobial Resistance and Virulence Genes in Indian isolates of Klebsiella pneumoniae: A Comparative Genomics Study. J Glob Antimicrob Resist 2022; 30:431-441. [DOI: 10.1016/j.jgar.2022.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2022] [Revised: 05/06/2022] [Accepted: 05/07/2022] [Indexed: 10/18/2022] Open
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