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Lam M, Leung KM, Lai GKK, Leung FCC, Griffin SDJ. Complete genome sequence of Klebsiella variicola subsp. variicola ML.9ba2, an endophytic strain isolated from aerial roots of Philodendron erubescens. Microbiol Resour Announc 2024; 13:e0116323. [PMID: 38509053 PMCID: PMC11008176 DOI: 10.1128/mra.01163-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Accepted: 03/02/2024] [Indexed: 03/22/2024] Open
Abstract
The endophytic strain Klebsiella variicola subsp. variicola ML.9ba2 was isolated from aerial roots of Philodendron erubescens in Hong Kong. Its complete genome of 5,682,083 bp (57.29% G+C), comprising a single chromosome and an IncF plasmid, was established through hybrid assembly.
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Affiliation(s)
- M. Lam
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong, China
| | - K. M. Leung
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong, China
| | - G. K. K. Lai
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong, China
| | - F. C. C. Leung
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong, China
| | - S. D. J. Griffin
- Shuyuan Molecular Biology Laboratory, The Independent Schools Foundation Academy, Hong Kong, China
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Blaikie JM, Sapula SA, Siderius NL, Hart BJ, Amsalu A, Leong LE, Warner MS, Venter H. Resistome Analysis of Klebsiella pneumoniae Complex from Residential Aged Care Facilities Demonstrates Intra-facility Clonal Spread of Multidrug-Resistant Isolates. Microorganisms 2024; 12:751. [PMID: 38674695 PMCID: PMC11051875 DOI: 10.3390/microorganisms12040751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2023] [Revised: 03/14/2024] [Accepted: 03/22/2024] [Indexed: 04/28/2024] Open
Abstract
Antimicrobial-resistant Klebsiella pneumoniae is one of the predominant pathogens in healthcare settings. However, the prevalence and resistome of this organism within residential aged care facilities (RACFs), which are potential hotspots for antimicrobial resistance, remain unexplored. Here, we provide a phenotypic and molecular characterization of antimicrobial-resistant K. pneumoniae isolated from RACFs. K. pneumoniae was isolated from urine, faecal and wastewater samples and facility swabs. The antimicrobial susceptibility profiles of all the isolates were determined and the genomic basis for resistance was explored with whole-genome sequencing on a subset of isolates. A total of 147 K. pneumoniae were isolated, displaying resistance against multiple antimicrobials. Genotypic analysis revealed the presence of beta-lactamases and the ciprofloxacin-resistance determinant QnrB4 but failed to confirm the basis for the observed cephalosporin resistance. Clonal spread of the multidrug-resistant, widely disseminated sequence types 323 and 661 was observed. This study was the first to examine the resistome of K. pneumoniae isolates from RACFs and demonstrated a complexity between genotypic and phenotypic antimicrobial resistance. The intra-facility dissemination and persistence of multidrug-resistant clones is concerning, given that residents are particularly vulnerable to antimicrobial resistant infections, and it highlights the need for continued surveillance and interventions to reduce the risk of outbreaks.
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Affiliation(s)
- Jack M. Blaikie
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
| | - Sylvia A. Sapula
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
| | - Naomi L. Siderius
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
| | - Bradley J. Hart
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
| | - Anteneh Amsalu
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
- Department of Medical Microbiology, University of Gondar, Gondar 196, Ethiopia
| | - Lex E.X. Leong
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
- Microbiology and Infectious Diseases, SA Pathology, Adelaide, SA 5000, Australia;
| | - Morgyn S. Warner
- Microbiology and Infectious Diseases, SA Pathology, Adelaide, SA 5000, Australia;
- School of Medicine, University of Adelaide, Adelaide, SA 5000, Australia
- Infectious Diseases Unit, Royal Adelaide Hospital, Adelaide, SA 5000, Australia
| | - Henrietta Venter
- UniSA Clinical and Health Sciences, Health and Biomedical Innovation, University of South Australia, Adelaide, SA 5000, Australia; (J.M.B.); (S.A.S.); (N.L.S.); (B.J.H.); (A.A.); (L.E.X.L.)
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Zhou C, Zhang H, Xu M, Liu Y, Yuan B, Lin Y, Shen F. Within-Host Resistance and Virulence Evolution of a Hypervirulent Carbapenem-Resistant Klebsiella pneumoniae ST11 Under Antibiotic Pressure. Infect Drug Resist 2023; 16:7255-7270. [PMID: 38023413 PMCID: PMC10658960 DOI: 10.2147/idr.s436128] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2023] [Accepted: 11/07/2023] [Indexed: 12/01/2023] Open
Abstract
Background Hypervirulent carbapenem-resistant Klebsiella pneumoniae (hv-CRKP) has recently aroused an extremely severe health challenge and public concern. However, the underlying mechanisms of fitness costs that accompany antibiotic resistance acquisition remain largely unexplored. Here, we report a hv-CRKP-associated fatal infection and reveal a reduction in virulence due to the acquisition of aminoglycoside resistance. Methods The bacterial identification, antimicrobial susceptibility, hypermucoviscosity, virulence factors, MLST and serotypes were profiled.The clonal homology and plasmid acquisition among hv-CRKP strains were detected by XbaI and S1-PFGE. The virulence potential of the strains was evaluated using Galleria mellonella larvae infection model, serum resistance assay, capsular polysaccharide quantification, and biofilm formation assay. Genomic variations were identified using whole-genome sequencing (WGS). Results Four K. pneumoniae carbapenemase (KPC)-producing CRKP strains were consecutively isolated from an 86-year-old patient with severe pneumonia. Whole-genome sequencing (WGS) showed that all four hv-CRKP strains belonged to the ST11-KL64 clone. PFGE analysis revealed that the four ST11-KL64 hv-CRKP strains could be grouped into the same PFGE type. Under the pressure of antibiotics, the antimicrobial resistance of the strains increased and the virulence potential decreased. Further sequencing, using the Nanopore platform, was performed on three representative isolates (WYKP586, WYKP589, and WYKP594). Genomic analysis showed that the plasmids of these three strains underwent a large number of breaks and recombination events under antibiotic pressure. We found that as aminoglycoside resistance emerged via acquisition of the rmtB gene, the hypermucoviscosity and virulence of the strains decreased because of internal mutations in the rmpA and rmpA2 genes. Conclusion This study shows that ST11-KL64 hv-CRKP can further evolve to acquire aminoglycoside resistance accompanied by decreased virulence to adapt to antibiotic pressure in the host.
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Affiliation(s)
- Cong Zhou
- Department of Clinical Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, People’s Republic of China
| | - Hui Zhang
- Department of Clinical Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, People’s Republic of China
| | - Maosuo Xu
- Department of Clinical Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, People’s Republic of China
| | - Yajuan Liu
- Department of Clinical Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, People’s Republic of China
| | - Baoyu Yuan
- Department of Clinical Laboratory, Shanghai Children’s Hospital, Shanghai Jiao Tong University, Shanghai, People’s Republic of China
| | - Yong Lin
- Department of Clinical Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, People’s Republic of China
| | - Fang Shen
- Department of Clinical Laboratory, Shanghai Fifth People’s Hospital, Fudan University, Shanghai, People’s Republic of China
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Haddadi MH, Khoshnood S, Koupaei M, Heidary M, Moradi M, Jamshidi A, Behrouj H, Movahedpour A, Maleki MH, Ghanavati R. Evaluating the incidence of ampC-β-lactamase genes, biofilm formation, and antibiotic resistance among hypervirulent and classical Klebsiella pneumoniae strains. J Appl Microbiol 2023; 134:lxad241. [PMID: 37881066 DOI: 10.1093/jambio/lxad241] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 09/18/2023] [Accepted: 10/21/2023] [Indexed: 10/27/2023]
Abstract
AIM Both immunocompetent and healthy individuals can become life-threateningly ill when exposed to the hypervirulent (hvKp) strains of Klebsiella pneumoniae (Kp). The main objectives of this study were to evaluate the presence of ampC-lactamase genes, biofilm formation, and antibiotic resistance in clinical strains of hvKp and cKp (classical K. pneumoniae). MATERIALS AND METHODS Kp strains were collected from patients referred to Shahidzadeh Hospital in Behbahan City, Khuzestan Province, Iran. Several techniques were used to identify hvKp. The hypermucoviscosity phenotype was determined using the string test. Isolates that developed dark colonies on tellurite agar were assumed to be hvKp strains. If any of the iucA, iutA, or peg-344 genes were detected, the isolates were classified as hvKp. Phenotypic and genotypic detection of AmpC β-lactamases of hvKp strains was performed by the combined disk method and polymerase chain reaction, respectively. In addition, crystal violet staining was used to determine the biofilm formation of these isolates. RESULTS For this study, 76 non-duplicative isolates of Kp were collected. Overall, 22 (28.94%) strains had positive string test results, and 31 (40.78%) isolates were grown in tellurite-containing medium. The genes iucA and iutA or peg-344 were found in 23.68% of all Kp strains and in 50% of tellurite-resistant isolates, respectively. The most effective antibiotics against hvKp isolates were tetracycline (85.52%) and chloramphenicol (63.15%). Using the cefoxitin disc diffusion method, we observed that 56.57% (43/76) of the strains were AmpC producer. A total of 30.26% (n = 23/76) of the isolates tested positive for at least one ampC gene, including blaDHA (52.63%, n = 40), blaCIT (40.78%, n = 31), blaACC (19.76%, n = 15), blaMOX (25%, n = 19), and blaFOX (43.42%, n = 33). Biofilm formation analysis revealed that most hvKp isolates were weak (n = 6, 40%) and moderate (n = 5, 33.33%) biofilm producers. CONCLUSION Healthcare practitioners should consider the possibility of the existence and acquisition of hvKp everywhere. The exact mechanisms of bacterial acquisition are also unknown, and it is unclear whether the occurrence of infections is related to healthcare or not. Thus, there are still many questions about hvKp that need to be investigated.
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Affiliation(s)
| | - Saeed Khoshnood
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam 69316, Iran
| | - Maryam Koupaei
- Department of Microbiology and Immunology, School of Medicine, Kashan University of Medical Sciences, Kashan 8759187131, Iran
| | - Mohsen Heidary
- Department of Laboratory Sciences, School of Paramedical Sciences, Sabzevar University of Medical Sciences, Sabzevar 6971938668 , Iran
| | - Melika Moradi
- Department of Microbiology, School of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz 6136763316, Iran
| | - Ali Jamshidi
- Behbahan Faculty of Medical Sciences, Behbahan 6361796819, Iran
| | - Hamid Behrouj
- Behbahan Faculty of Medical Sciences, Behbahan 6361796819, Iran
| | | | - Mohammad Hassan Maleki
- Clinical Microbiology Research Center, Ilam University of Medical Sciences, Ilam 69316, Iran
| | - Roya Ghanavati
- School of Paramedical Sciences, Behbahan Faculty of Medical Sciences, Behbahan 63617, Iran
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Arcari G, Carattoli A. Global spread and evolutionary convergence of multidrug-resistant and hypervirulent Klebsiella pneumoniae high-risk clones. Pathog Glob Health 2023; 117:328-341. [PMID: 36089853 PMCID: PMC10177687 DOI: 10.1080/20477724.2022.2121362] [Citation(s) in RCA: 19] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Abstract
For people living in developed countries life span is growing at a faster pace than ever. One of the main reasons for such success is attributable to the introduction and extensive use in the clinical practice of antibiotics over the course of the last seven decades. In hospital settings, Klebsiella pneumoniae represents a well-known and commonly described opportunistic pathogen, typically characterized by resistance to several antibiotic classes. On the other hand, the broad wedge of population living in Low and/or Middle Income Countries is increasing rapidly, allowing the spread of several commensal bacteria which are transmitted via human contact. Community transmission has been the original milieu of K. pneumoniae isolates characterized by an outstanding virulence (hypervirulent). These two characteristics, also defined as "pathotypes", originally emerged as different pathways in the evolutionary history of K. pneumoniae. For a long time, the Sequence Type (ST), which is defined by the combination of alleles of the 7 housekeeping genes of the Multi-Locus Sequence Typing, has been a reliable marker of the pathotype: multidrug-resistant clones (e.g. ST258, ST147, ST101) in the Western world and hypervirulent clones (e.g. ST23, ST65, ST86) in the Eastern. Currently, the boundaries separating the two pathotypes are fading away due to several factors, and we are witnessing a worrisome convergence in certain high-risk clones. Here we review the evidence available on confluence of multidrug-resistance and hypervirulence in specific K. pneumoniae clones.
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Affiliation(s)
- Gabriele Arcari
- Department of Molecular Medicine, Sapienza University of Rome, Rome, Italy
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Saki M, Amin M, Savari M, Hashemzadeh M, Seyedian SS. Beta-lactamase determinants and molecular typing of carbapenem-resistant classic and hypervirulent Klebsiella pneumoniae clinical isolates from southwest of Iran. Front Microbiol 2022; 13:1029686. [PMID: 36406386 PMCID: PMC9669656 DOI: 10.3389/fmicb.2022.1029686] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2022] [Accepted: 09/26/2022] [Indexed: 08/27/2023] Open
Abstract
This study investigated the molecular epidemiology of carbapenem-resistant classic Klebsiella pneumoniae (CR-cKp) and carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp) isolates in southwestern Iran. From 2019 to 2021, 136 (88.9%) cKp and 17 (11.1%) hvKp isolates were identified using biochemical tests and polymerase chain reaction (PCR). Antibiotic resistance, beta-lactamases, and clonal relatedness of carbapenem-resistant isolates were investigated using disk diffusion, PCR, and enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR), respectively. The different markers of hvKp isolates were as follows: string test (35.3%, n = 6/17), magA (11.8%, n = 2/17), rmpA (11.8%, n = 2/17), rmpA2 (52.9%, n = 9/17), iucA (52.9%, n = 9/17), and peg344 (35.3%, n = 6/17). Also, 55.1% (n = 75/136) of cKp and 47.1% (n = 8/17) of hvKp isolates were CR-cKp and CR-hvKp, respectively. All CR-hvKp (100.0%, n = 8) isolates were MDR. Colistin, tetracycline, and tigecycline were the most effective antibiotics. The occurrence of beta-lactamase genes in 75 CR-cKp and 8 CR-hvKp isolates was as follows: bla NDM (41.3, 25.0%), bla IMP (4.0, 0.0%), bla VIM (8.0, 0.0%), bla GES (14.7, 25.0%), bla OXA-48-like (20.0, 0.0%), bla CTX-M (26.7, 12.5%), bla SHV (24.0, 12.5%), bla TEM (10.7, 0.0%), bla FOX (6.7, 0.0%), bla DHA (6.7, 0.0%), bla CMY (5.3, 0.0%), bla LAT (12.0, 0.0%), and bla ACT (8.0, 0.0%). ERIC-PCR showed a high diversity among isolates. In this study, the occurrence of MDR CR-hvKp isolates harboring bla NDM and bla GES was detected for the first time in southwestern Iran. To prevent the spread of CR-hvKp and reduce selection pressure, long-term surveillance and more effective treatment strategies should be implemented.
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Affiliation(s)
- Morteza Saki
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mansour Amin
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Savari
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Mohammad Hashemzadeh
- Infectious and Tropical Diseases Research Center, Health Research Institute, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
- Department of Microbiology, Faculty of Medicine, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
| | - Seyed Saeid Seyedian
- Alimentary Tract Research Center, Ahvaz Jundishapur University of Medical Sciences, Ahvaz, Iran
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Molecular mechanisms and genomic basis of tigecycline-resistant Enterobacterales from swine slaughterhouses. Microbiol Res 2022; 264:127151. [DOI: 10.1016/j.micres.2022.127151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 07/27/2022] [Accepted: 07/28/2022] [Indexed: 11/15/2022]
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Wang Y, Xu E, Li M, Chen W, Liu Z, Huo W, Chen G. Genomic characterization of hypervirulent carbapenem-resistant clinical Klebsiella pneumoniae ST11 isolate from China. J Glob Antimicrob Resist 2022; 30:276-278. [PMID: 35781063 DOI: 10.1016/j.jgar.2022.06.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 06/07/2022] [Accepted: 06/18/2022] [Indexed: 11/30/2022] Open
Affiliation(s)
- Yuanyuan Wang
- College of Medical Technology, Shaanxi University of Chinese Medicine, Xi Xian New Area, People's Republic of China
| | - E'e Xu
- College of Medical Technology, Shaanxi University of Chinese Medicine, Xi Xian New Area, People's Republic of China
| | - Meng Li
- School of Medicine, Northwest University, Xi'an, People's Republic of China
| | - Wei Chen
- School of Medicine, Northwest University, Xi'an, People's Republic of China
| | - Zhimeng Liu
- School of Medicine, Northwest University, Xi'an, People's Republic of China
| | - Weiping Huo
- School of Medicine, Northwest University, Xi'an, People's Republic of China
| | - Gukui Chen
- School of Medicine, Northwest University, Xi'an, People's Republic of China.
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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: 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: 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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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: 79] [Impact Index Per Article: 39.5] [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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11
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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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12
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Extensively Drug-Resistant Klebsiella pneumoniae Counteracts Fitness and Virulence Costs That Accompanied Ceftazidime-Avibactam Resistance Acquisition. Microbiol Spectr 2022; 10:e0014822. [PMID: 35435751 PMCID: PMC9241641 DOI: 10.1128/spectrum.00148-22] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
The ability of extensively drug-resistant (XDR) Klebsiella pneumoniae to rapidly acquire resistance to novel antibiotics is a global concern. Moreover, Klebsiella clonal lineages that successfully combine resistance and hypervirulence have increasingly occurred during the last years. However, the underlying mechanisms of counteracting fitness costs that accompany antibiotic resistance acquisition remain largely unexplored. Here, we investigated whether and how an XDR sequence type (ST)307 K. pneumoniae strain developed resistance against the novel drug combination ceftazidime-avibactam (CAZ-AVI) using experimental evolution. In addition, we performed in vitro and in vivo assays, molecular modeling, and bioinformatics to identify resistance-conferring processes and explore the resulting decrease in fitness and virulence. The subsequent amelioration of the initial costs was also addressed. We demonstrate that distinct mutations of the major nonselective porin OmpK36 caused CAZ-AVI resistance that persists even upon following a second experimental evolution without antibiotic selection pressure and that the Klebsiella strain compensates the resulting fitness and virulence costs. Furthermore, the genomic and transcriptomic analyses suggest the envelope stress response regulator rpoE and associated RpoE-regulated genes as drivers of this compensation. This study verifies the crucial role of OmpK36 in CAZ-AVI resistance and shows the rapid adaptation of a bacterial pathogen to compensate fitness- and virulence-associated resistance costs, which possibly contributes to the emergence of successful clonal lineages. IMPORTANCE Extensively drug-resistant Klebsiella pneumoniae causing major outbreaks and severe infections has become a significant challenge for health care systems worldwide. Rapid resistance development against last-resort therapeutics like ceftazidime-avibactam is a significant driver for the accelerated emergence of such pathogens. Therefore, it is crucial to understand what exactly mediates rapid resistance acquisition and how bacterial pathogens counteract accompanying fitness and virulence costs. By combining bioinformatics with in vitro and in vivo phenotypic approaches, this study revealed the critical role of mutations in a particular porin channel in ceftazidime-avibactam resistance development and a major metabolic regulator for ameliorating fitness and virulence costs. These results highlight underlying mechanisms and contribute to the understanding of factors important for the emergence of successful bacterial pathogens.
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Molecular Characteristics of Antimicrobial Resistance and Virulence in Klebsiella pneumoniae Strains Isolated from Goose Farms in Hainan, China. Appl Environ Microbiol 2022; 88:e0245721. [PMID: 35389252 DOI: 10.1128/aem.02457-21] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023] Open
Abstract
We retrospectively investigated 326 samples that were collected from goose farms in Hainan Province, China, in 2017. A total of 33 carbapenem-resistant Klebsiella pneumoniae (CRKP) isolates were identified from 326 samples, and the 33 CRKP isolates were characterized based on whole-genome sequencing (WGS) data from the Illumina and Oxford Nanopore Technologies (ONT) platforms. All of these 33 CRKP isolates possessed blaNDM-5, and a single isolate coharbored mcr-1 and blaNDM-5, while 4 isolates carried multiple virulence and metal tolerance gene clusters. One CRKP strain (CMG-35-2) was selected for long sequence reading. A hybrid plasmid carrying the virulence, resistance, and metal resistance gene in the strain was found. It possessed 2 backbones [IncFIB(K)-IncFII(K)] within a single plasmid that were closely related to K. pneumoniae plasmids from a human-associated habitat in the United States and from a human isolate in Hong Kong. A mouse abdominal infection model indicated that that strain was of the moderate virulence phenotype. This study revealed that K. pneumoniae on goose farms is an important reservoir for blaNDM-5 and these bacteria are represented by a diversity of sequence types. The heterozygous multiple drug resistance genes carried on plasmids highlighted the genetic complexity of CRKP and the urgent need for continued active surveillance. IMPORTANCE CRKP is one of the most important pathogens, which can cause infection not only in humans but also in waterfowl. The discovery of blaNDM-5-producing K. pneumoniae in waterfowl farms in recent years suggests that waterfowl are an important reservoir for blaNDM-5-producing Enterobacteriaceae. However, there are few studies on the spread of blaNDM-5-producing bacteria in waterfowl farms. Our study showed that the IncX3 plasmid carrying blaNDM-5 in goose farms is widely present in K. pneumoniae isolates and a large number of resistance genes are accumulated in it. We found a transferable IncFIB-FII hybrid plasmid that combines virulence, resistance, and metal resistance genes, which allow transfer of these traits between bacteria in different regions. The results of this study contribute to a better understanding of the prevalence and transmission of carbapenem-resistant K. pneumoniae in goose farms.
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The Role of Plasmid and Resistance Gene Acquisition in the Emergence of ST23 Multi-Drug Resistant, Hypervirulent Klebsiella pneumoniae. Microbiol Spectr 2022; 10:e0192921. [PMID: 35297657 PMCID: PMC9045268 DOI: 10.1128/spectrum.01929-21] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Multidrug-resistant (MDR) hypervirulent Klebsiella pneumoniae (hvKp) sequence type (ST) 23 (MDR-ST23-hvKp) is emerging in China. Despite its increasing importance, this pathogen has not yet been subject to detailed genomic interrogation. We identified 28 ST23 Kp isolated from three hospitals in China. The organisms were subjected to antimicrobial susceptibility testing and whole-genome sequencing (WGS). These novel genomic sequences were analyzed in combination with 218 publicly available genome sequences. We performed molecular serotyping and subtyping, assessed the composition of virulence-associated and antimicrobial resistance (AMR) genes, and determined mobile elements associated with horizontal gene transfer. Two MDR-ST23-hvKp were sequenced by long-read sequencing. The genetic characteristics of MDR and non-MDR isolates were compared. Among the 28 novel ST23 isolates, all were hvKp and 2/28 (7.1%) were MDR-hvKp. From the collection of 246 genomes, KL1 was the predominant serotype (224/246; 91.1%) and the siderophore combination of YbST46-CbST29-AbST1-SmST2 was dominant (101/246; 41.1%); 34/246 (13.8%) organisms belonged to MDR-ST23-hvKp. IncF and IncR plasmid replicons were significantly more prevalent in the MDR group (P < 0.05) than in the non-MDR group. IS26 was commonly involved in AMR acquisition. We observed that the acquisition of AMR genes within the ST23-hvKp was not associated with a loss of virulence genes. A 28-bp fusion site was highly conserved with two copies of the virulence-associated plasmid in ST23-hvKp, and we harbored by some of the IncFII plasmids of MDR-ST23-hvKp. Our data suggest that MDR-ST23-hvKp has undergone multiple independent genetic acquisition and recombination events within different sublineages. Notably, the acquisition of IncFII plasmids and/or IS26 contributed to the horizontal transfer of AMR genes within ST23-hvKp. Genomic surveillance is essential for further tracking of kMDR-ST23-hvKp. IMPORTANCE Hypervirulent Klebsiella pneumoniae (hvKp) has become the dominant pathotype in hospitals recently. The sequence type (ST) 23 hvKp, which are more commonly associated with the community-acquired infections previously, may have the capacity to acquire multidrug-resistant (MDR) phenotypes creating a new "superbug" (MDR-hvKp) in hospital. In the present study, we studied the associations of MDR and hypervirulence among ST23 K. pneumoniae from our strain collection and publicly accessible genome data. By comparative analysis of the carriage of resistance genes, virulence genes plasmid replicon types, and plasmid sequences, we found that IncFII plasmids were significantly more prevalent in MDR isolates and IS26 were commonly involved in resistance gene acquisition. We also discovered new MDR plasmids. These results provided an overview landscape of the genetic elements associated with MDR-ST23-hvKp based on currently accessible genome data and calling for further genomic surveillance and well-designed control studies of MDR-ST23-hvKp.
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Li L, Olsen RH, Wang C, Song A, Xiao J, Meng H, Ronco T, Shi L. First report of two foodborne Salmonella enterica subsp. enterica serovar Bovismorbificans isolates carrying a novel mega-plasmid harboring bla DHA-1 and qnrB4 genes. Int J Food Microbiol 2021; 360:109439. [PMID: 34688125 DOI: 10.1016/j.ijfoodmicro.2021.109439] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 08/30/2021] [Accepted: 10/12/2021] [Indexed: 11/18/2022]
Abstract
Salmonella enterica displaying resistance to extended-spectrum cephalosporins and fluoroquinolone (FQs) has been deemed a high-priority pathogen by the World Health Organization (WHO). While CTX-M type acquired β-lactamases have been detected in S. enterica serovar Bovismorbificans, DHA enzymes have been rarely reported in S. Bovismorbificans. In this study, we here report for the first time the isolation of two multi-drug resistant (MDR) S. Bovismorbificans strains co-harboring plasmid-encoded AmpC (pAmpC) β-lactamase gene (blaDHA-1) and qnrB gene, 16Sal017 isolated from a chicken meat sample and 16Sal018 from a grass carp fish sample, collected from retail markets in Guangzhou, China. The blaDHA-1 and qnrB genes in these two strains were both located on the same novel 217,773 bp IncHI2 plasmid belonged to ST2. The plasmid contained 16 additional acquired antimicrobial resistance genes encoding resistance to eight antibiotic classes and quaternary ammonium compound. Besides, 16Sal017 contained an additional 10,124 bp Col (pHAD28)-like plasmid harboring qnrS1. The blaDHA-1 and qnrB4 genes were located in an 18,198 bp region, sul1-qacEΔ1-ampR-blaDHA-1-pspABCDF-qnrB4-sapABC-IS91-sul1-qacEΔ1, which has been identified in various bacteria species, indicating the high transfer ability of blaDHA-1 and qnrB4 genes within this gene cluster. The IncHI2 plasmid was found to be transferable to Escherichia coli J53 by conjugation and resulted in the acquiring of multiple resistance in the transconjugants. Genome sequence comparisons by cgMLST and MAUVE alignment indicated 16Sal017 and 16Sal018 are highly similar and are not epidemiologically linked with strains from other sources and countries. Our findings suggest S. Bovismorbificans as a new host for conjugative mega-plasmid harboring blaDHA-1 and qnrB4 genes, and highlight the potential transmission opportunity of these S. Bovismorbificans clones through the food chain, which need continuous investigation.
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Affiliation(s)
- Lili Li
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou, Guangdong, China; School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, China
| | - Rikke Heidemann Olsen
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Chong Wang
- Shandong New Hope Liuhe Group Ltd., Qingdao, China
| | - Anhua Song
- Guangzhou Food Inspection Institute, Guangdong, China
| | - Jian Xiao
- Guangzhou Food Inspection Institute, Guangdong, China
| | - Hecheng Meng
- School of Food Science and Engineering, South China University of Technology, Guangzhou, Guangdong, China.
| | - Troels Ronco
- Department of Veterinary and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Frederiksberg C, Denmark
| | - Lei Shi
- Institute of Food Safety and Nutrition, Jinan University, Guangzhou, Guangdong, China; State Key Laboratory of Food Safety Technology for Meat Products, Xiamen 361100, China
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Chen R, Liu Z, Xu P, Qi X, Qin S, Wang Z, Li R. Deciphering the Epidemiological Characteristics and Molecular Features of bla KPC-2- or bla NDM-1-Positive Klebsiella pneumoniae Isolates in a Newly Established Hospital. Front Microbiol 2021; 12:741093. [PMID: 34858362 PMCID: PMC8631570 DOI: 10.3389/fmicb.2021.741093] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2021] [Accepted: 09/27/2021] [Indexed: 01/01/2023] Open
Abstract
The emergence of hypervirulent carbapenem-resistant Klebsiella pneumoniae (hv-CRKP) was regarded as an emerging threat in clinical settings. Here, we investigated the prevalence of CRKP strains among inpatients in a new hospital over 1 year since its inception with various techniques, and carried out a WGS-based phylogenetic study to dissect the genomic background of these isolates. The genomes of three representative blaNDM–1-positive strains and the plasmids of four blaKPC–2-positive strains were selected for Nanopore long-read sequencing to resolve the complicated MDR structures. Thirty-five CRKP strains were identified from 193 K. pneumoniae isolates, among which 30 strains (85.7%) harbored blaKPC–2, whereas the remaining five strains (14.3%) were positive for blaNDM–1. The antimicrobial resistance profiles of blaNDM–1-positive isolates were narrower than that of blaKPC–2-positive isolates. Five isolates including two blaNDM–1-positive isolates and three blaKPC–2-positive strains could successfully transfer the carbapenem resistance phenotype by conjugation. All CRKP strains were categorized into six known multilocus sequence types, with ST11 being the most prevalent type. Phylogenetic analysis demonstrated that the clonal spread of ST11 blaKPC–2-positive isolates and local polyclonal spread of blaNDM–1-positive isolates have existed in the hospital. The blaNDM–1 gene was located on IncX3, IncFIB/IncHI1B, and IncHI5-like plasmids, of which IncFIB/IncHI1B plasmid has a novel structure. By contrast, all ST11 isolates shared the similar blaKPC–2-bearing plasmid backbone, and 11 of them possessed pLVPK-like plasmids. In addition, in silico virulome analysis, Galleria mellonella larvae infection assay, and siderophore secretion revealed the hypervirulence potential of most blaKPC–2-positive strains. Given that these isolates also had remarkable environmental adaptability, targeted measures should be implemented to prevent the grave consequences caused by hv-CRKP strains in nosocomial settings.
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Affiliation(s)
- Ruifei Chen
- Department of Clinical Laboratory, Henan Provincial People's Hospital, Department of Clinical Laboratory of Central China Fuwai Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, China
| | - Ziyi Liu
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, China.,Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
| | - Poshi Xu
- Department of Clinical Laboratory, Henan Provincial People's Hospital, Department of Clinical Laboratory of Central China Fuwai Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, China
| | - Xinkun Qi
- Department of Clinical Laboratory, Henan Provincial People's Hospital, Department of Clinical Laboratory of Central China Fuwai Hospital, Central China Fuwai Hospital of Zhengzhou University, Zhengzhou, China
| | - Shangshang Qin
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, China
| | - Zhiqiang Wang
- Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, College of Veterinary Medicine, Yangzhou University, Yangzhou, 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, China.,Institute of Comparative Medicine, Yangzhou University, Yangzhou, China
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Plasmids Shape the Current Prevalence of tmexCD1-toprJ1 among Klebsiella pneumoniae in Food Production Chains. mSystems 2021; 6:e0070221. [PMID: 34609171 PMCID: PMC8547460 DOI: 10.1128/msystems.00702-21] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
The emergence of novel antimicrobial resistance genes conferring resistance to last-resort antimicrobials poses a serious challenge to global public health security. Recently, one plasmid-mediated RND family multidrug resistance efflux pump gene cluster named tmexCD1-toprJ1, which confers resistance to tigecycline, was identified in bacteria of animal and human origins. However, the comprehensive landscape of the genomic epidemiology of this novel resistance determinant remained unclear. To fill this knowledge gap, we isolated 25 tmexCD1-toprJ1-positive bacteria from 682 samples collected along the pork production chain, including swine farms, slaughterhouses, and retail pork, and characterized the positive strains systematically using antimicrobial susceptibility testing, conjugation assays, single-molecule sequencing, and genomic analyses. We found that tmexCD1-toprJ1-positive bacteria were most prevalent in slaughterhouses (7.32%), followed by retail pork (0.72%). Most of the positive strains were Klebsiella pneumoniae (23/25), followed by Proteus mirabilis (2/25). IncFIB(Mar)/IncHI1B hybrid plasmids were mainly vectors for tmexCD1-toprJ1 and dominated the horizontal dissemination of tmexCD1-toprJ1 among K. pneumoniae isolates. However, in this study, we identified the IncR plasmid as a tmexCD1-toprJ1-positive plasmid with a broad host range, which evidenced that the widespread prevalence of tmexCD1-toprJ1 is possible due to such kinds of plasmids in the future. In addition, we found diversity and heterogeneity of translocatable units containing tmexCD1-toprJ1 in the plasmids. We also investigated the genetic features of tmexCD1-toprJ1 in online databases, which led to the proposal of the umuC gene as the potential insertion site of tmexCD1-toprJ1. Collectively, this study enriches the epidemiological and genomic characterization of tmexCD1-toprJ1 and provides a theoretical basis for preventing an increase in tmexCD1-toprJ1 prevalence. IMPORTANCE Tigecycline, the first member of the glycylcycline class of antibacterial agents, is frequently used to treat complicated infections caused by multidrug-resistant Gram-positive and Gram-negative bacteria. The emergence of a novel plasmid-mediated efflux pump, TmexCD1-ToprJ1, conferring resistance to multiple antimicrobials, including tigecycline, poses a huge risk to human health. In this study, we investigated the prevalence of tmexCD1-toprJ1-positive strains along the food production chain and found that tmexCD1-toprJ1 was mainly distributed in IncFIB(Mar)/HI1B hybrid plasmids of K. pneumoniae. We also observed a potential risk of transmission of such plasmids along the pork processing chain, which finally may incur a threat to humans. Furthermore, the IncFIB(Mar)/HI1B tmexCD1-toprJ1-positive plasmids with a limited host range and specific insertion sites of tmexCD1-toprJ1 are strong evidence to prevent a fulminant epidemic of tmexCD1-toprJ1 among diverse pathogens. The mobilization and dissemination of tmexCD1-toprJ1, especially when driven by plasmids, deserve sustained attention and investigations.
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Wijesinghe HGS, Hare DJ, Mohamed A, Shah AK, Harris PNA, Hill MM. Detecting antimicrobial resistance in Escherichia coli using benchtop attenuated total reflectance-Fourier transform infrared spectroscopy and machine learning. Analyst 2021; 146:6211-6219. [PMID: 34522918 DOI: 10.1039/d1an00546d] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The widespread dissemination of resistance to third-generation cephalosporins in the Enterobacterales through the production of extended-spectrum β-lactamase (ESBL) is considered a critical global crisis requiring urgent attention of clinicians and scientists alike. Rapid diagnostic methods that can identify microbial resistance profiles closer to the point of care are crucial to minimize the overuse of antimicrobial agents and improve patient outcomes. Although Fourier transform infrared (FTIR) microscopy has shown promise in distinguishing between bacterial species, the high cost and technical requirements of the IR microscope may limit broad clinical use. To address the practical needs of a clinical microbiology laboratory, here, we examine the ability of a lower cost portable benchtop attenuated total reflectance (ATR)-FTIR spectrometer to achieve antimicrobial resistance detection, using a simple, clinically aligned sampling protocol. The technical reproducibility was confirmed through multi-day analysis of an Escherichia coli type strain, which serves as quality control. We generated a dataset of 100 E. coli clinical bloodstream isolates with 63 ceftriaxone resistant blaCTX-M ESBL gene variant strains and developed a classifier for blaCTX-M genotype detection. After assessing 35 machine learning methods using the training set (n = 71), four methods were further optimised, and the best performing method was evaluated using the held-out testing set (n = 29). A tuned support vector machine model with a polynomial kernel, using the 700-1500 cm-1 range achieved a sensitivity of 89.2%, and specificity of 66.7% for detecting blaCTX-M in independent testing, approaching the reported performance of FTIR microscopy. With further algorithm improvement, these data suggest the potential deployment of a portable FTIR spectrometer as a rapid antimicrobial susceptibility prediction platform to enable the efficient use of antimicrobials.
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Affiliation(s)
- Hewa G S Wijesinghe
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, QLD, 4006, Australia.,School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, 4067, Australia
| | - Dominic J Hare
- Atomic Medicine Initiative, University of Technology Sydney, Broadway, NSW, 2007, Australia
| | - Ahmed Mohamed
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD, 4006, Australia.
| | - Alok K Shah
- QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD, 4006, Australia.
| | - Patrick N A Harris
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, QLD, 4006, Australia.,Herston Infectious Disease Institute, Royal Brisbane & Women's Hospital, Herston, QLD, 4029, Australia.,Central Microbiology, Pathology Queensland, Royal Brisbane & Women's Hospital, Herston, QLD, 4029, Australia
| | - Michelle M Hill
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, Herston, QLD, 4006, Australia.,QIMR Berghofer Medical Research Institute, Herston, Brisbane, QLD, 4006, Australia.
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19
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Xu Y, Zhang J, Wang M, Liu M, Liu G, Qu H, Liu J, Deng Z, Sun J, Ou HY, Qu J. Mobilization of the nonconjugative virulence plasmid from hypervirulent Klebsiella pneumoniae. Genome Med 2021; 13:119. [PMID: 34294113 PMCID: PMC8299605 DOI: 10.1186/s13073-021-00936-5] [Citation(s) in RCA: 64] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2021] [Accepted: 07/09/2021] [Indexed: 11/28/2022] Open
Abstract
Background Klebsiella pneumoniae, as a global priority pathogen, is well known for its capability of acquiring mobile genetic elements that carry resistance and/or virulence genes. Its virulence plasmid, previously deemed nonconjugative and restricted within hypervirulent K. pneumoniae (hvKP), has disseminated into classic K. pneumoniae (cKP), particularly carbapenem-resistant K. pneumoniae (CRKP), which poses alarming challenges to public health. However, the mechanism underlying its transfer from hvKP to CRKP is unclear. Methods A total of 28 sequence type (ST) 11 bloodstream infection-causing CRKP strains were collected from Ruijin Hospital in Shanghai, China, and used as recipients in conjugation assays. Transconjugants obtained from conjugation assays were confirmed by XbaI and S1 nuclease pulsed-field gel electrophoresis, PCR detection and/or whole-genome sequencing. The plasmid stability of the transconjugants was evaluated by serial culture. Genetically modified strains and constructed mimic virulence plasmids were employed to investigate the mechanisms underlying mobilization. The level of extracellular polysaccharides was measured by mucoviscosity assays and uronic acid quantification. An in silico analysis of 2608 plasmids derived from 814 completely sequenced K. pneumoniae strains available in GenBank was performed to investigate the distribution of putative helper plasmids and mobilizable virulence plasmids. Results A nonconjugative virulence plasmid was mobilized by the conjugative plasmid belonging to incompatibility group F (IncF) from the hvKP strain into ST11 CRKP strains under low extracellular polysaccharide-producing conditions or by employing intermediate E. coli strains. The virulence plasmid was mobilized via four modes: transfer alone, cotransfer with the conjugative IncF plasmid, hybrid plasmid formation due to two rounds of single-strand exchanges at specific 28-bp fusion sites or homologous recombination. According to the in silico analysis, 31.8% (242) of the putative helper plasmids and 98.8% (84/85) of the virulence plasmids carry the 28-bp fusion site. All virulence plasmids carry the origin of the transfer site. Conclusions The nonconjugative virulence plasmid in ST11 CRKP strains is putatively mobilized from hvKP or E. coli intermediates with the help of conjugative IncF plasmids. Our findings emphasize the importance of raising public awareness of the rapid dissemination of virulence plasmids and the consistent emergence of hypervirulent carbapenem-resistant K. pneumoniae (hv-CRKP) strains. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00936-5.
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Affiliation(s)
- Yanping Xu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, China
| | - Jianfeng Zhang
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Meng Wang
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Meng Liu
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Guitian Liu
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Hongping Qu
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Jialin Liu
- Department of Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China
| | - Zixin Deng
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China
| | - Jingyong Sun
- Department of Laboratory Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China. .,Department of Clinical Microbiology, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai, 200025, China.
| | - Hong-Yu Ou
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, 200030, China.
| | - Jieming Qu
- Department of Pulmonary and Critical Care Medicine, Ruijin Hospital, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Institute of Respiratory Diseases, Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China; Shanghai Key Laboratory of Emergency Prevention, Diagnosis and Treatment of Respiratory Infectious Diseases, Shanghai, 200025, China.
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20
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Mahfouz N, Ferreira I, Beisken S, von Haeseler A, Posch AE. Large-scale assessment of antimicrobial resistance marker databases for genetic phenotype prediction: a systematic review. J Antimicrob Chemother 2021; 75:3099-3108. [PMID: 32658975 PMCID: PMC7566382 DOI: 10.1093/jac/dkaa257] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Revised: 05/04/2020] [Accepted: 05/11/2020] [Indexed: 02/07/2023] Open
Abstract
Background Antimicrobial resistance (AMR) is a rising health threat with 10 million annual casualties estimated by 2050. Appropriate treatment of infectious diseases with the right antibiotics reduces the spread of antibiotic resistance. Today, clinical practice relies on molecular and PCR techniques for pathogen identification and culture-based antibiotic susceptibility testing (AST). Recently, WGS has started to transform clinical microbiology, enabling prediction of resistance phenotypes from genotypes and allowing for more informed treatment decisions. WGS-based AST (WGS-AST) depends on the detection of AMR markers in sequenced isolates and therefore requires AMR reference databases. The completeness and quality of these databases are material to increase WGS-AST performance. Methods We present a systematic evaluation of the performance of publicly available AMR marker databases for resistance prediction on clinical isolates. We used the public databases CARD and ResFinder with a final dataset of 2587 isolates across five clinically relevant pathogens from PATRIC and NDARO, public repositories of antibiotic-resistant bacterial isolates. Results CARD and ResFinder WGS-AST performance had an overall balanced accuracy of 0.52 (±0.12) and 0.66 (±0.18), respectively. Major error rates were higher in CARD (42.68%) than ResFinder (25.06%). However, CARD showed almost no very major errors (1.17%) compared with ResFinder (4.42%). Conclusions We show that AMR databases need further expansion, improved marker annotations per antibiotic rather than per antibiotic class and validated multivariate marker panels to achieve clinical utility, e.g. in order to meet performance requirements such as provided by the FDA for clinical microbiology diagnostic testing.
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Affiliation(s)
- Norhan Mahfouz
- Ares Genetics GmbH, Karl-Farkas-Gasse 18, Vienna 1030, Austria
| | - Inês Ferreira
- Ares Genetics GmbH, Karl-Farkas-Gasse 18, Vienna 1030, Austria.,Center for Integrative Bioinformatics Vienna, Max Perutz Laboratories, University of Vienna and Medical University of Vienna, Vienna 1030, Austria
| | - Stephan Beisken
- Ares Genetics GmbH, Karl-Farkas-Gasse 18, Vienna 1030, Austria
| | - Arndt von Haeseler
- Center for Integrative Bioinformatics Vienna, Max Perutz Laboratories, University of Vienna and Medical University of Vienna, Vienna 1030, Austria.,Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Andreas E Posch
- Ares Genetics GmbH, Karl-Farkas-Gasse 18, Vienna 1030, Austria
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Li Y, Li Z, Qian S, Dong F, Wang Q, Zhang P, Yao K. A fatal case of liver abscess caused by hypervirulent Klebsiella pneumoniae in a diabetic adolescent: A clinical and laboratory study. Pediatr Investig 2021; 5:118-124. [PMID: 34179708 PMCID: PMC8212719 DOI: 10.1002/ped4.12238] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 08/20/2020] [Indexed: 01/17/2023] Open
Abstract
IMPORTANCE Hypervirulent variants of Klebsiella pneumoniae (hvKp) are capable of causing life-threatening pyogenic liver abscesses (PLAs), but hvKp caused PLAs was seldom reported in pediatric populations. Hence, there is an urgent need to raise our awareness of this phenomenon in pediatric populations. OBJECTIVE This study aimed to report the clinical characteristics of hvKp that caused fatal PLA complicated by bacteremia in an adolescent and further identify the microbiological and genomic features of the causative strain. METHODS A 14-year-old boy with diabetes mellitus was admitted to our hospital with a diagnosis of PLA complicated by bacteremia. A hypermucoviscous hvKp strain, KPN_19-106, was isolated from the drainage fluid present within the liver abscess cavity and blood. The hypermucoviscosity phenotype of the causative strain was determined by string test. Its virulence was measured using serum resistance assay and Galleria mellonella larvae-killing assay. Antimicrobial susceptibility was determined by broth microdilution method. Genetic information was obtained by whole-genome sequencing and bioinformatics analysis. RESULTS KPN_19-106 belonged to sequence type 380 and serotype K2 and exhibited stronger serum resistance and higher in vivo lethality than the well-characterized hvKp NTUH-K2044 strain. Although KPN_19-106 is susceptible to most antibiotics, no sign of improvement was observed during treatment with such drugs. Whole-genome sequencing revealed that the isolate had integrated multiple mobile genetic elements related to virulence. INTERPRETATION Antibiotic-susceptible hvKp can cause fatal PLA complicated by bacteremia in adolescents, with no improvement during antimicrobial therapy. The causative strain in this case had integrated multiple virulence genes and thus exhibited higher virulence both in vitro and in vivo when compared with NTUH-K2044.
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Affiliation(s)
- Yue Li
- MOE Key Laboratory of Major Diseases in ChildrenNational Key Discipline of Pediatrics (Capital Medical University)National Clinical Research Center for Respiratory DiseasesBeijing Key Laboratory of Pediatric Respiratory Infection DiseasesBeijing Pediatric Research InstituteBeijing Children’s HospitalCapital Medical UniversityNational Center for Children’s HealthChina
| | - Zheng Li
- Department of Pediatric Intensive Care UnitBeijing Children’s HospitalCapital Medical UniversityNational Center for Children’s HealthChina
| | - Suyun Qian
- Department of Pediatric Intensive Care UnitBeijing Children’s HospitalCapital Medical UniversityNational Center for Children’s HealthChina
| | - Fang Dong
- Department of Clinical Microbiology LaboratoryBeijing Children’s HospitalCapital Medical UniversityNational Center for Children’s HealthChina
| | - Qing Wang
- MOE Key Laboratory of Major Diseases in ChildrenNational Key Discipline of Pediatrics (Capital Medical University)National Clinical Research Center for Respiratory DiseasesBeijing Key Laboratory of Pediatric Respiratory Infection DiseasesBeijing Pediatric Research InstituteBeijing Children’s HospitalCapital Medical UniversityNational Center for Children’s HealthChina
| | - Pengfei Zhang
- Department of Pediatric Intensive Care UnitBeijing Children’s HospitalCapital Medical UniversityNational Center for Children’s HealthChina
| | - Kaihu Yao
- MOE Key Laboratory of Major Diseases in ChildrenNational Key Discipline of Pediatrics (Capital Medical University)National Clinical Research Center for Respiratory DiseasesBeijing Key Laboratory of Pediatric Respiratory Infection DiseasesBeijing Pediatric Research InstituteBeijing Children’s HospitalCapital Medical UniversityNational Center for Children’s HealthChina
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Identification of Two Plasmids Coharboring Carbapenemase Genes and tmexCD1-toprJ1 in Clinical Klebsiella pneumoniae ST2667. Antimicrob Agents Chemother 2021; 65:AAC.00625-21. [PMID: 33846130 DOI: 10.1128/aac.00625-21] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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Tian D, Wang M, Zhou Y, Hu D, Ou HY, Jiang X. Genetic diversity and evolution of the virulence plasmids encoding aerobactin and salmochelin in Klebsiella pneumoniae. Virulence 2021; 12:1323-1333. [PMID: 33970792 PMCID: PMC8115583 DOI: 10.1080/21505594.2021.1924019] [Citation(s) in RCA: 36] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Virulence plasmids of hypervirulent Klebsiella pneumoniae (hvKp) have the potential to transfer to drug-resistant strains or integrate with other plasmids, facilitating the genome evolution of threatening pathogens. We conducted an in-depth analysis of the publicly available 156 complete genome sequences of hvKp together with a multi-region clinical cohort of 171 hvKp strains from China to provide evidence for the virulence plasmid evolution. Virulence plasmids were frequently detected in the ST23 and ST11 K. pneumoniae strains. Multidrug-resistant hvKp (MDR-hvKp) occupied a large proportion of hvKp, and the coexistence of virulence and resistance plasmids may be the major cause. Virulence plasmids commonly possessed multiple replicons, of which IncFIBK was the most prevalent (84.6%). We identified 49 IncFIBK alleles among 583 IncFIBK plasmids, and they could be divided into Clades I, II, and III. We further observed that conjugative and non-conjugative virulence plasmids could be distinguished by IncFIBK genetic diversity, and IncFIBK subtyping could also indirectly indicate a chimeric preference of conjugative virulence plasmids. On this basis, we developed an open-access web tool called KpVR for IncFIBK subtyping. In conclusion, the genetic diversity of IncFIBK virulence plasmids could be used for tracking the evolution of virulence plasmids, and further preventing the emergence of MDR-hvKp strains.
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Affiliation(s)
- Dongxing Tian
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Meng Wang
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Ying Zhou
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Dakang Hu
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
| | - Hong-Yu Ou
- State Key Laboratory of Microbial Metabolism, Joint International Laboratory on Metabolic & Developmental Sciences, School of Life Sciences & Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Xiaofei Jiang
- Department of Laboratory Medicine, Huashan Hospital, Shanghai Medical College, Fudan University, Shanghai, China
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Shankar C, Jacob JJ, Vasudevan K, Biswas R, Manesh A, Sethuvel DPM, Varughese S, Biswas I, Veeraraghavan B. Emergence of Multidrug Resistant Hypervirulent ST23 Klebsiella pneumoniae: Multidrug Resistant Plasmid Acquisition Drives Evolution. Front Cell Infect Microbiol 2020; 10:575289. [PMID: 33330125 PMCID: PMC7718023 DOI: 10.3389/fcimb.2020.575289] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Accepted: 10/23/2020] [Indexed: 12/15/2022] Open
Abstract
Background In recent years, the emergence of multidrug resistant hypervirulent K. pneumoniae (MDR hvKp) isolates poses severe therapeutic challenge to global public health. The present study used the complete genome sequence of two MDR hvKp isolates belonging to ST23 to characterize the phylogenetic background and plasmid diversity. Methods Two hvKp isolates from patients with bacteremia were sequenced using Ion Torrent PGM and Oxford Nanopore MinION platforms and assembled by hybrid genome assembly approach. Comparative genomics approaches were used to investigate the population structure, evolution, virulence, and antimicrobial resistance of MDR hvKp strains. Results The study isolates exhibited typical features of hvKp phenotypes associated with ST23. The convergence of multidrug resistance and hypervirulence were attributed by the presence of multiple plasmids including a 216 kb virulence plasmid and MDR plasmids belonging to IncA/C2, IncFIB, IncX3, and ColKP3 groups. The insertion of catA1 gene into virulence plasmid was observed along with genetic factors such as aerobactin, salmochelin, and rmpA2 that confer hvKp’s hypervirulent phenotype. The core genome single nucleotide polymorphism (SNP) phylogenetic analyses of the isolates showed the evolution of ST23 hvKp was predominantly driven by ICEKp acquisitions. Conclusion To the best of our knowledge, this is the first report of MDR hvKp isolates of ST23 with insertion of catA1 gene into the virulence plasmid which presents the possibility of hotspot integration sites on the plasmids to aid acquisition of AMR genes. ST23 is no longer confined to susceptible strains of hvKp. Our findings emphasize the need for more studies on recombinant events, plasmid transmission dynamics and evolutionary process involving hvKp.
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Affiliation(s)
- Chaitra Shankar
- Department of Clinical Microbiology, Christian Medical College and Hospital, Vellore, India
| | - Jobin John Jacob
- Department of Clinical Microbiology, Christian Medical College and Hospital, Vellore, India
| | - Karthick Vasudevan
- Department of Clinical Microbiology, Christian Medical College and Hospital, Vellore, India
| | - Rohit Biswas
- College of Biological Sciences, University of Minnesota, Saint Paul, MN, United States
| | - Abi Manesh
- Department of Infectious Diseases, Christian Medical College and Hospital, Vellore, India
| | | | - Santosh Varughese
- Department of Nephrology, Christian Medical College and Hospital, Vellore, India
| | - Indranil Biswas
- Department of Microbiology, Molecular Genetics and Immunology, University of Kansas Medical Centre, Kansas City, KS, United States
| | - Balaji Veeraraghavan
- Department of Clinical Microbiology, Christian Medical College and Hospital, Vellore, India
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Tang M, Kong X, Hao J, Liu J. Epidemiological Characteristics and Formation Mechanisms of Multidrug-Resistant Hypervirulent Klebsiella pneumoniae. Front Microbiol 2020; 11:581543. [PMID: 33329444 PMCID: PMC7714786 DOI: 10.3389/fmicb.2020.581543] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/14/2020] [Indexed: 12/18/2022] Open
Abstract
Multi-drug resistance (MDR) and hypervirulence (hv) were exhibited by different well-separated Klebsiella pneumoniae lineages in the past, but their convergence clones—MDR-hypervirulent K. pneumoniae (HvKPs)—both highly pathogenic and resistant to most available antibiotics, have increasingly been reported. In light of the clonal lineages and molecular characteristics of the studied MDR-HvKP strains found in the literature since 2014, this review discusses the epidemiology of MDR-HvKPs, in particular summarizing the three general aspects of plasmids-associated mechanisms underlying the formation of MDR-HvKPs clones: MDR-classic K. pneumoniae (cKPs) acquiring hv plasmids, hvKPs obtaining MDR plasmids, and the acquisition of hybrid plasmids harboring virulence and resistance determinants. A deeper understanding of epidemiological characteristics and possible formation mechanisms of MDR-HvKPs is greatly needed for the proper surveillance and management of this potential threat.
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Affiliation(s)
- Miran Tang
- Clinical Laboratory Department, Santai People's Hospital, Mianyang, China
| | - Xin Kong
- Department of Laboratory Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jingchen Hao
- Department of Laboratory Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jinbo Liu
- Department of Laboratory Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
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Sen S, Sarkar K. Effective Biocidal and Wound Healing Cogency of Biocompatible Glutathione: Citrate-Capped Copper Oxide Nanoparticles Against Multidrug-Resistant Pathogenic Enterobacteria. Microb Drug Resist 2020; 27:616-627. [PMID: 33048008 DOI: 10.1089/mdr.2020.0131] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Multidrug-resistant (MDR) superficial bacterial infections caused by carbapenem-resistant Enterobacter sp. and Klebsiella sp. have emerged as major threats toward global health care management. In search of a novel antimicrobial, our main objectives were to explore the antimicrobial, antibiofilm, and wound healing potential of glutathione and citrate-capped copper oxide nanoparticles (CuNPs) against gram-negative MDR pathogens Klebsiella quasipneumoniae and Enterobacter sp., ensuring the lowest possible host cell nano-cytotoxicity and minimum susceptibility of the CuNPs toward oxidation. The CuNPs were found to elicit reactive oxygen species (ROS) generation within bacterial cells, inhibiting the bacterial growth and division. They contributed to the remodeling of the bacterial lipopolysaccharide, induced membrane lysis, and promoted antibiofilm activities by reduced cell-cell aggregation and matrix destabilization while displaying excellent biocompatibility against HEK-293 and HeLa cell lines. The CuNPs were also instrumental in preventing postsurgical wound infections and aiding in wound closure in the murine excisional wound model, as observed in albino Wistar rats, forcing us to believe that the CuNPs are bioactive in wound therapy. The results are encouraging and demands further experimental exploitation of the particles in treating other MDR gram-negative infections, irrespective of their resistance status.
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Affiliation(s)
- Samya Sen
- Department of Microbiology, University of Kalyani, Kalyani, India
| | - Keka Sarkar
- Department of Microbiology, University of Kalyani, Kalyani, India
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Li R, Cheng J, Dong H, Li L, Liu W, Zhang C, Feng X, Qin S. Emergence of a novel conjugative hybrid virulence multidrug-resistant plasmid in extensively drug-resistant Klebsiella pneumoniae ST15. Int J Antimicrob Agents 2020; 55:105952. [PMID: 32335274 DOI: 10.1016/j.ijantimicag.2020.105952] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2019] [Revised: 03/10/2020] [Accepted: 03/19/2020] [Indexed: 11/28/2022]
Abstract
INTRODUCTION Co-existence of both virulence and multidrug-resistant (MDR) determinants on a self-transmissible plasmid facilitates simultaneous transfer of virulence and resistance in a single event and rapid emergence of virulent and MDR Klebsiella pneumoniae clones. METHOD This study identified extensively drug-resistant ST15 strains, KP17-15 and KP17-16, from clinical cases with microbiological and genomical approaches. RESULTS The chromosomes of KP17-15 and KP17-16 were highly homologous with 12 SNP differences, indicating that the two strains were derived from the same clone. Multiple plasmids existed in the isolates, including novel virulence plasmids p17-15-vir (479 kb) and p17-16-vir (290 kb) for KP17-15 and KP17-16, respectively. Notably, the plasmid p17-15-vir (479 kb) was a hybrid plasmid that might be formed by recombination of two homologous regions encoding group II intron reverse transcriptase and mobile element ISShes11 shared by p17-16-vir (290 kb) and a conjugative MDR plasmid p17-16-CTX (188 kb). p17-15-vir was readily transferable to ST11 Klebsiella pneumoniae by conjugation. Moreover, p17-16-vir, a non-conjugative virulence plasmid lacking the transfer (tra) operon, was also transferable by conjugation under the help of p17-16-CTX or p17-16-KPC. Fusion of p17-16-vir with p17-16-CTX into a p17-15-vir-like plasmid was also observed in the transconjugant. CONCLUSION The findings uncover the evolutionary pathway of a novel hybrid virulence MDR plasmid and transfer mechanism of a non-conjugative virulence plasmid. Systematic surveillance of such hybrid virulence MDR plasmids in clinical Klebsiella pneumoniae should be performed.
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Affiliation(s)
- 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, China; Institute of Comparative Medicine, Yangzhou University, Yangzhou, Jiangsu, China
| | - Jing Cheng
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Huiyue Dong
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Leyuan Li
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Wentian Liu
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Chunli Zhang
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China
| | - Xianju Feng
- The First Affiliated Hospital of Zhengzhou University, Zhengzhou, Henan, China
| | - Shangshang Qin
- School of Pharmaceutical Sciences, Zhengzhou University, Zhengzhou, Henan, China; Key Laboratory of Advanced Drug Preparation Technologies, Ministry of Education, Zhengzhou University, Zhengzhou, Henan, China.
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Abstract
Klebsiella pneumoniae is a common cause of antimicrobial-resistant opportunistic infections in hospitalized patients. The species is naturally resistant to penicillins, and members of the population often carry acquired resistance to multiple antimicrobials. However, knowledge of K. pneumoniae ecology, population structure or pathogenicity is relatively limited. Over the past decade, K. pneumoniae has emerged as a major clinical and public health threat owing to increasing prevalence of healthcare-associated infections caused by multidrug-resistant strains producing extended-spectrum β-lactamases and/or carbapenemases. A parallel phenomenon of severe community-acquired infections caused by 'hypervirulent' K. pneumoniae has also emerged, associated with strains expressing acquired virulence factors. These distinct clinical concerns have stimulated renewed interest in K. pneumoniae research and particularly the application of genomics. In this Review, we discuss how genomics approaches have advanced our understanding of K. pneumoniae taxonomy, ecology and evolution as well as the diversity and distribution of clinically relevant determinants of pathogenicity and antimicrobial resistance. A deeper understanding of K. pneumoniae population structure and diversity will be important for the proper design and interpretation of experimental studies, for interpreting clinical and public health surveillance data and for the design and implementation of novel control strategies against this important pathogen.
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Yu X, Zhang W, Zhao Z, Ye C, Zhou S, Wu S, Han L, Han Z, Ye H. Molecular characterization of carbapenem-resistant Klebsiella pneumoniae isolates with focus on antimicrobial resistance. BMC Genomics 2019; 20:822. [PMID: 31699025 PMCID: PMC6839148 DOI: 10.1186/s12864-019-6225-9] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2019] [Accepted: 10/25/2019] [Indexed: 01/02/2023] Open
Abstract
Background The enhancing incidence of carbapenem-resistant Klebsiella pneumoniae (CRKP)-mediated infections in Mengchao Hepatobiliary Hospital of Fujian Medical University in 2017 is the motivation behind this investigation to study gene phenotypes and resistance-associated genes of emergence regarding the CRKP strains. In current study, seven inpatients are enrolled in the hospital with complete treatments. The carbapenem-resistant K. pneumoniae whole genome is sequenced using MiSeq short-read and Oxford Nanopore long-read sequencing technology. Prophages are identified to assess genetic diversity within CRKP genomes. Results The investigation encompassed eight CRKP strains that collected from the patients enrolled as well as the environment, which illustrate that blaKPC-2 is responsible for phenotypic resistance in six CRKP strains that K. pneumoniae sequence type (ST11) is informed. The plasmid with IncR, ColRNAI and pMLST type with IncF[F33:A-:B-] co-exist in all ST11 with KPC-2-producing CRKP strains. Along with carbapenemases, all K. pneumoniae strains harbor two or three extended spectrum β-lactamase (ESBL)-producing genes. fosA gene is detected amongst all the CRKP strains. The single nucleotide polymorphisms (SNP) markers are indicated and validated among all CRKP strains, providing valuable clues for distinguishing carbapenem-resistant strains from conventional K. pneumoniae. Conclusions ST11 is the main CRKP type, and blaKPC-2 is the dominant carbapenemase gene harbored by clinical CRKP isolates from current investigations. The SNP markers detected would be helpful for characterizing CRKP strain from general K. pneumoniae. The data provides insights into effective strategy developments for controlling CRKP and nosocomial infection reductions.
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Affiliation(s)
- Xiaoling Yu
- Department of Infectious Diseases, Mengchao Hepatobiliary Hospital of Fujian Medical University, Xihong Road 312, Fuzhou, 350025, Fujian, People's Republic of China
| | - Wen Zhang
- Friedman Brain Institute, Icahn School of Medicine at Mount Sinai, New York, NY, 10029, USA
| | - Zhiping Zhao
- Department of Infectious Diseases, Mengchao Hepatobiliary Hospital of Fujian Medical University, Xihong Road 312, Fuzhou, 350025, Fujian, People's Republic of China
| | - Chengsong Ye
- Key Lab of Urban Environment and Health, Institute of Urban Environment, Chinese Academy of Sciences, Xiamen, 361021, Fujian, People's Republic of China
| | - Shuyan Zhou
- Department of Microbiology, Mengchao Hepatobiliary Hospital of Fujian Medical University, Xihong Road 312, Fuzhou, 350025, Fujian, People's Republic of China
| | - Shaogui Wu
- Department of Microbiology, Mengchao Hepatobiliary Hospital of Fujian Medical University, Xihong Road 312, Fuzhou, 350025, Fujian, People's Republic of China
| | - Lifen Han
- Department of Infectious Diseases, Mengchao Hepatobiliary Hospital of Fujian Medical University, Xihong Road 312, Fuzhou, 350025, Fujian, People's Republic of China
| | - Zhaofang Han
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, Fujian, People's Republic of China. .,Xiamen Cingene Science and Technology co., LTD, Xiamen, 361021, Fujian, People's Republic of China.
| | - Hanhui Ye
- Department of Infectious Diseases, Mengchao Hepatobiliary Hospital of Fujian Medical University, Xihong Road 312, Fuzhou, 350025, Fujian, People's Republic of China.
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Li J, Huang ZY, Yu T, Tao XY, Hu YM, Wang HC, Zou MX. Isolation and characterization of a sequence type 25 carbapenem-resistant hypervirulent Klebsiella pneumoniae from the mid-south region of China. BMC Microbiol 2019; 19:219. [PMID: 31533609 PMCID: PMC6749629 DOI: 10.1186/s12866-019-1593-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2019] [Accepted: 09/09/2019] [Indexed: 12/29/2022] Open
Abstract
Background The molecular characterization of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) isolates is not well studied. Our goal was to investigate the molecular epidemiology of CR-hvKP strains that were isolated from a Chinese hospital. Results All clinical carbapenem-resistant K. pneumoniae (CR-KP) isolates were collected and identified from patient samples between 2014 and 2017 from a Chinese hospital. The samples were subjected to screening for CR-hvKP by string test and the detection of the aerobactin gene. CR-hvKP isolates were further confirmed through neutrophil phagocytosis and a mice lethality assay. The CR-hvKP isolates were investigated for their capsular genotyping, virulence gene profiles, and the expression of carbapenemase genes by PCR and DNA sequencing. Multilocus sequence type (MLST) and pulsed-field gel electrophoresis (PFGE) were performed to exclude the homology of these isolates. Twenty strains were identified as CR-hvKP. These strains were resistant to imipenem and several other antibiotics, however, most were susceptible to amikacin. Notably, two isolates were not susceptible to tigecycline. Capsular polysaccharide synthesis genotyping revealed that 17 of the 20 CR-hvKP strains belonged to the K2 serotype, while the others belonged to serotypes other than K1, K2, K5, K20, and K57. The strains were found to be positive for 10 types of virulence genes and a variety of these genes coexisted in the same strain. Two carbapenemase genes were identified: blaKPC-2 (13/20) and blaNDM-1 (1/20). PFGE typing revealed eight clusters comprising isolates that belonged to MLST types ST25, ST11 and ST375, respectively. PFGE cluster A was identified as the main cluster, which included 11 isolates that belong to ST25 and mainly from ICU department. Conclusions Our findings suggest that hospital-acquired infections may contribute in part to the CR-hvKP strains identified in this study. It also suggests that ST25 CR-hvKP strain has a clonal distribution in our hospital. Therefore, effective surveillance and strict infection control strategies should be implemented to prevent outbreak by CR-hvKP strains in hospitals setting.
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Affiliation(s)
- Jun Li
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Zi-Yan Huang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Ting Yu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Xiao-Yan Tao
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Yong-Mei Hu
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Hai-Chen Wang
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Ming-Xiang Zou
- Department of Clinical Laboratory, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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Lü Y, Zhao S, Liang H, Zhang W, Liu J, Hu H. The first report of a novel IncHI1B bla SIM-1-carrying megaplasmid pSIM-1-BJ01 from a clinical Klebsiella pneumoniae isolate. Infect Drug Resist 2019; 12:2103-2112. [PMID: 31413597 PMCID: PMC6657655 DOI: 10.2147/idr.s212333] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Accepted: 07/03/2019] [Indexed: 12/03/2022] Open
Abstract
Background: A rare member of metallo-β-lactamases genes, blaSIM-1, carried by a 316-kb plasmid designated pSIM-1-BJ01 was isolated from a clinical cephalosporins- and carbapenem-resistant Klebsiellapneumoniae 13624. This is the first sequence report of a transferable blaSIM-1-carrying conjugative plasmid isolated from K. pneumoniae. Purpose: The sequence analysis of pSIM-1-BJ01 will help us to identify genes responsible for conjugation, plasmid maintenance and drug resistance, to understand the evolution and control the dissemination of resistance plasmids. Patients and methods:K. pneumoniae 13624 was isolated from the urine specimen of a patient. Bacterial genomic DNA was sequenced with PacBio RSII platform. Results: Most of the pSIM-1-BJ01 backbone matches that of pRJA166a, which was isolated from a clinical hypervirulent K. pneumoniae ST23 strain at Shanghai, China, recently. The highly homologous backbones between the two plasmids imply the close relationship of evolution. Two different multidrug-resistant regions both carrying the class 1 integrons with different resistance genes have been assembled into the pSIM-1-BJ01. Besides, the other two resistance plasmids, pKP13624-1 carrying blaTEM-1 and blaCTX-M-15 and pKP13624-2 carrying blaCTX-M-14 and blaLAP-2 were also identified. Conclusion: The emergence of the blaSIM-1-carrying IncHI1B pSIM-1-BJ01 suggests the spread of blaSIM among Enterobacteriaceae is possible. We should pay more attention to supervise and control the dissemination of hypervirulent carbapenem-resistant K. pneumonia in public hospitals.
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Affiliation(s)
- Yang Lü
- State Key Laboratory of Mycology, Institute of Microbiology, Chinese Academy of Sciences, Beijing, People's Republic of China
| | - Shulong Zhao
- Department of Laboratory Medicine, The Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, People's Republic of China
| | - Hui Liang
- Department of Laboratory Medicine, The Third Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Wei Zhang
- Department of Laboratory Medicine, The Third Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Jia Liu
- Department of Laboratory Medicine, The Third Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
| | - Hongyan Hu
- Department of Laboratory Medicine, The Third Medical Center, Chinese PLA General Hospital, Beijing, People's Republic of China
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32
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Abstract
Hypervirulent K. pneumoniae (hvKp) is an evolving pathotype that is more virulent than classical K. pneumoniae (cKp). hvKp usually infects individuals from the community, who are often healthy. Infections are more common in the Asian Pacific Rim but are occurring globally. hvKp infection frequently presents at multiple sites or subsequently metastatically spreads, often requiring source control. hvKp has an increased ability to cause central nervous system infection and endophthalmitis, which require rapid recognition and site-specific treatment. The genetic factors that confer hvKp's hypervirulent phenotype are present on a large virulence plasmid and perhaps integrative conjugal elements. Increased capsule production and aerobactin production are established hvKp-specific virulence factors. Similar to cKp, hvKp strains are becoming increasingly resistant to antimicrobials via acquisition of mobile elements carrying resistance determinants, and new hvKp strains emerge when extensively drug-resistant cKp strains acquire hvKp-specific virulence determinants, resulting in nosocomial infection. Presently, clinical laboratories are unable to differentiate cKp from hvKp, but recently, several biomarkers and quantitative siderophore production have been shown to accurately predict hvKp strains, which could lead to the development of a diagnostic test for use by clinical laboratories for optimal patient care and for use in epidemiologic surveillance and research studies.
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Affiliation(s)
- Thomas A Russo
- Department of Medicine, University at Buffalo-State University of New York, Buffalo, New York, USA
- Department of Microbiology and Immunology, University at Buffalo-State University of New York, Buffalo, New York, USA
- The Witebsky Center for Microbial Pathogenesis, University at Buffalo-State University of New York, Buffalo, New York, USA
- The Veterans Administration Western New York Healthcare System, Buffalo, New York, USA
| | - Candace M Marr
- Department of Medicine, University at Buffalo-State University of New York, Buffalo, New York, USA
- Erie County Medical Center, Buffalo, New York, USA
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Visual and Rapid Detection of Klebsiella pneumoniae by Magnetic Immunocapture-Loop-Mediated Isothermal Amplification Assay. Jundishapur J Microbiol 2019. [DOI: 10.5812/jjm.90016] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
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Wyres KL, Wick RR, Judd LM, Froumine R, Tokolyi A, Gorrie CL, Lam MMC, Duchêne S, Jenney A, Holt KE. Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae. PLoS Genet 2019; 15:e1008114. [PMID: 30986243 PMCID: PMC6483277 DOI: 10.1371/journal.pgen.1008114] [Citation(s) in RCA: 195] [Impact Index Per Article: 39.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 04/25/2019] [Accepted: 03/29/2019] [Indexed: 11/19/2022] Open
Abstract
Klebsiella pneumoniae has emerged as an important cause of two distinct public health threats: multi-drug resistant (MDR) healthcare-associated infections and drug susceptible community-acquired invasive infections. These pathotypes are generally associated with two distinct subsets of K. pneumoniae lineages or 'clones' that are distinguished by the presence of acquired resistance genes and several key virulence loci. Genomic evolutionary analyses of the most notorious MDR and invasive community-associated ('hypervirulent') clones indicate differences in terms of chromosomal recombination dynamics and capsule polysaccharide diversity, but it remains unclear if these differences represent generalised trends. Here we leverage a collection of >2200 K. pneumoniae genomes to identify 28 common clones (n ≥ 10 genomes each), and perform the first genomic evolutionary comparison. Eight MDR and 6 hypervirulent clones were identified on the basis of acquired resistance and virulence gene prevalence. Chromosomal recombination, surface polysaccharide locus diversity, pan-genome, plasmid and phage dynamics were characterised and compared. The data showed that MDR clones were highly diverse, with frequent chromosomal recombination generating extensive surface polysaccharide locus diversity. Additional pan-genome diversity was driven by frequent acquisition/loss of both plasmids and phage. In contrast, chromosomal recombination was rare in the hypervirulent clones, which also showed a significant reduction in pan-genome diversity, largely driven by a reduction in plasmid diversity. Hence the data indicate that hypervirulent clones may be subject to some sort of constraint for horizontal gene transfer that does not apply to the MDR clones. Our findings are relevant for understanding the risk of emergence of individual K. pneumoniae strains carrying both virulence and acquired resistance genes, which have been increasingly reported and cause highly virulent infections that are extremely difficult to treat. Specifically, our data indicate that MDR clones pose the greatest risk, because they are more likely to acquire virulence genes than hypervirulent clones are to acquire resistance genes.
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Affiliation(s)
- Kelly L. Wyres
- Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia
| | - Ryan R. Wick
- Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia
| | - Louise M. Judd
- Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia
| | - Roni Froumine
- Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia
| | - Alex Tokolyi
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Claire L. Gorrie
- Department of Infectious Diseases and Microbiology Unit, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Margaret M. C. Lam
- Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia
| | - Sebastián Duchêne
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Adam Jenney
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Kathryn E. Holt
- Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
- London School of Hygiene and Tropical Medicine, London, United Kingdom
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Fu Y, Xu M, Liu Y, Li A, Zhou J. Virulence and genomic features of a bla CTX-M-3 and bla CTX-M-14 coharboring hypermucoviscous Klebsiella pneumoniae of serotype K2 and ST65. Infect Drug Resist 2019; 12:145-159. [PMID: 30655681 PMCID: PMC6322562 DOI: 10.2147/idr.s187289] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Background Capsular serotype K2 Klebsiella pneumoniae of sequence type (ST) 65 has been recognized as a hypervirulent clone. Simultaneous presence of different blaCTX-M genes has never been reported in this clone. In the present study, the genetic characteristics and virulence phenotype of a CTX-M-3 and CTX-M-14 coproducing ST65 K. pneumoniae human isolate, KP_06, that caused an intracranial infection, are evaluated. Methods The potential virulence of KP_06 was assayed by in vitro and in vivo methods. The molecular biology and whole-genome sequencing technology were used to analyze the genomic features associated with the virulence of this strain. Results The KP_06 exhibited typical features of hypervirulent K. pneumoniae (hvKP), showing hypermucoviscosity phenotype and belonging to K2 and ST65. Apart from virulence genes linked to hvKP, including rmpA, rmpA2, and clb cluster and genes encoding siderophores, it was found to harbor a ~170 kb pLVPK-like virulence plasmid. In contrast to most hvKP, KP_06 was resistant to cephalosporins and the coexistence of blaCTX-M-3 and blaCTX-M-14 was detected. Further experiments demonstrated that this strain was classified as a nonbiofilm producer and serum sensitivity (grade 1) and killed only 30% of Galleria mellonella inoculated with 1×106 colony-forming unit of the specimen within 48 hours, suggesting relatively low virulence. Comparative genomic analysis of KP_06 with five K2 hypermucoviscous K. pneumoniae (HMKP) revealed seven unique orthologies with varied function in this strain. Intriguingly, the virulence genes identified in KP-06 were unexpectedly more diverse than those observed in five other K2 HMKP strains. Conclusion Our data support the notion that neither virulence-associated genes (clusters) nor the pLVPK-like virulence plasmid is sufficient for the hypervirulence of K. pneumoniae. Future studies aiming to explore the virulence of K. pneumoniae should take genome-based profile together with experimental work. The detailed mechanism involving in the impaired virulence of KP_06 remains to be further explored.
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Affiliation(s)
- Yiqi Fu
- Department of Respiratory Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China,
| | - Min Xu
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Center of Clinical Laboratory, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yanchao Liu
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Center of Clinical Laboratory, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ang Li
- Department of Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jianying Zhou
- Department of Respiratory Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China,
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The β-Lactamase Gene Profile and a Plasmid-Carrying Multiple Heavy Metal Resistance Genes of Enterobacter cloacae. Int J Genomics 2018; 2018:4989602. [PMID: 30671441 PMCID: PMC6317114 DOI: 10.1155/2018/4989602] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Accepted: 10/17/2018] [Indexed: 01/01/2023] Open
Abstract
In this work, by high-throughput sequencing, antibiotic resistance genes, including class A (blaCTX-M, blaZ, blaTEM, blaVEB, blaKLUC, and blaSFO), class C (blaSHV, blaDHA, blaMIR, blaAZECL-29, and blaACT), and class D (blaOXA) β-lactamase genes, were identified among the pooled genomic DNA from 212 clinical Enterobacter cloacae isolates. Six blaMIR-positive E. cloacae strains were identified, and pulsed-field gel electrophoresis (PFGE) showed that these strains were not clonally related. The complete genome of the blaMIR-positive strain (Y546) consisted of both a chromosome (4.78 Mb) and a large plasmid pY546 (208.74 kb). The extended-spectrum β-lactamases (ESBLs) (blaSHV-12 and blaCTX-M-9a) and AmpC (blaMIR) were encoded on the chromosome, and the pY546 plasmid contained several clusters of genes conferring resistance to metals, such as copper (pco), arsenic (ars), tellurite (ter), and tetrathionate (ttr), and genes encoding many divalent cation transporter proteins. The comparative genomic analyses of the whole plasmid sequence and of the heavy metal resistance gene-encoding regions revealed that the plasmid sequences of Klebsiella pneumoniae (such as pKPN-332, pKPN-3967, and pKPN-262) shared the highest similarity with those of pY546. It may be concluded that a variety of β-lactamase genes present in E. cloacae which confer resistance to β-lactam antibiotics and the emergence of plasmids carrying heavy metal resistance genes in clinical isolates are alarming and need further surveillance.
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