1
|
Silva JTP, Santos FF, Valiatti TB, Valêncio A, Ribeiro ÁCDS, Oliveira LFV, Cay R, Pignatari ACC, Gales AC. Unraveling the genomic characteristics of a Klebsiella quasipneumoniae clinical isolate carrying bla NDM-1. J Glob Antimicrob Resist 2024:S2213-7165(24)00110-3. [PMID: 38852850 DOI: 10.1016/j.jgar.2024.05.022] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2023] [Revised: 05/23/2024] [Accepted: 05/29/2024] [Indexed: 06/11/2024] Open
Abstract
OBJECTIVE Despite the increasing reports of blaNDM in Enterobacterales in Brazil, comprehensive whole genome sequencing (WGS) data remains scarce. To address this knowledge gap, our study focuses on the characterization of the genome of an NDM-1-producing Klebsiella quasipneumoniae subsp. quasipneumoniae (KQPN) clinical strain isolated in Brazil. METHODS The antimicrobial susceptibility profile of the A-73.113 strain was performed by agar dilution or broth microdilution following the BrCAST/EUCAST recommendations. WGS was performed using the Illumina® NextSeq platform and the generated reads were assembled using the SPAdes software. The sequences obtained were submitted to the bioinformatics pipelines to determine the sequence type, resistome, plasmidome, and virulome. RESULTS The A-73.113 strain was identified as KQPN and was susceptible to polymyxins (MICs, ≤0.25 µg/mL), tigecycline (MIC, 0.5 µg/mL), ciprofloxacin (MIC, 0.5 µg/mL), and levofloxacin (MIC, 1 µg/mL). WGS analysis revealed the presence of genes conferring resistance to β-lactams (blaNDM-1, blaCTX-M-15, blaOXA-9, blaOKP-A-5, blaTEM-1), aminoglycosides [aph(3')-VI, aadA1, aac(6')-Ib], and fluoroquinolones (oqxAB, qnrS1, aac(6')-Ib-cr]. Additionally, it was verified the presence of the plasmid replicons Col(pHAD28), IncFIA(HI1), IncFIB(K) (pCAV1099-114), IncFIB(pQil), and IncFII(K), as well as virulence-encoding genes: fimABCDEFGHIK (type 1 fimbria), pilW (type IV pili), iutA (aerobactin), entABCDEFS/fepABCDG/fes (Ent siderophores), iroE (salmochelin), and allABCDRS (allantoin utilization). Furthermore, we found that A-73.113 strain belongs to ST1040. CONCLUSION Here we report the genomic characteristics of an NDM-1-producing KQPN ST1040 strain isolated from blood culture in Brazil. These data will enhance our comprehension of how this species contributes to the acquisition and dissemination of blaNDM-1 in Brazilian nosocomial settings.
Collapse
Affiliation(s)
- Juliana Thalita P Silva
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil
| | - Fernanda F Santos
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil.
| | - Tiago B Valiatti
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil
| | - André Valêncio
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil
| | - Ághata Cardoso da Silva Ribeiro
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil
| | | | - Rodrigo Cay
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil; Universidade Federal de São Paulo (UNIFESP), Laboratório de Bacteriologia e Imunologia (LIB), Setor de Biologia Molecular, Microbiologia e Imunologia, Departamento de Ciências Biológicas (DCB), Instituto de Ciências Ambientais, Químicas e Farmacêuticas (ICAQF), Diadema SP, Brazil
| | - Antônio Carlos C Pignatari
- Universidade Federal de São Paulo (UNIFESP), Laboratório Especial de Microbiologia Clínica (LEMC), Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil
| | - Ana Cristina Gales
- Universidade Federal de São Paulo (UNIFESP), Laboratório Alerta, Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil; Universidade Federal de São Paulo (UNIFESP), Laboratório Especial de Microbiologia Clínica (LEMC), Division of Infectious Diseases, Department of Internal Medicine, Escola Paulista de Medicina (EPM), São Paulo SP, Brazil.
| |
Collapse
|
2
|
Miller WR, Arias CA. ESKAPE pathogens: antimicrobial resistance, epidemiology, clinical impact and therapeutics. Nat Rev Microbiol 2024:10.1038/s41579-024-01054-w. [PMID: 38831030 DOI: 10.1038/s41579-024-01054-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2024] [Indexed: 06/05/2024]
Abstract
The rise of antibiotic resistance and a dwindling antimicrobial pipeline have been recognized as emerging threats to public health. The ESKAPE pathogens - Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa and Enterobacter spp. - were initially identified as critical multidrug-resistant bacteria for which effective therapies were rapidly needed. Now, entering the third decade of the twenty-first century, and despite the introduction of several new antibiotics and antibiotic adjuvants, such as novel β-lactamase inhibitors, these organisms continue to represent major therapeutic challenges. These bacteria share several key biological features, including adaptations for survival in the modern health-care setting, diverse methods for acquiring resistance determinants and the dissemination of successful high-risk clones around the world. With the advent of next-generation sequencing, novel tools to track and combat the spread of these organisms have rapidly evolved, as well as renewed interest in non-traditional antibiotic approaches. In this Review, we explore the current epidemiology and clinical impact of this important group of bacterial pathogens and discuss relevant mechanisms of resistance to recently introduced antibiotics that affect their use in clinical settings. Furthermore, we discuss emerging therapeutic strategies needed for effective patient care in the era of widespread antimicrobial resistance.
Collapse
Affiliation(s)
- William R Miller
- Department of Internal Medicine, Division of Infectious Diseases, Houston Methodist Hospital, Houston, TX, USA
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX, USA
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA
| | - Cesar A Arias
- Department of Internal Medicine, Division of Infectious Diseases, Houston Methodist Hospital, Houston, TX, USA.
- Center for Infectious Diseases, Houston Methodist Research Institute, Houston, TX, USA.
- Department of Medicine, Weill Cornell Medical College, New York, NY, USA.
| |
Collapse
|
3
|
Bray AS, Zafar MA. Deciphering the gastrointestinal carriage of Klebsiella pneumoniae. Infect Immun 2024:e0048223. [PMID: 38597634 DOI: 10.1128/iai.00482-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024] Open
Abstract
Bacterial infections pose a significant global health threat, accounting for an estimated 7.7 million deaths. Hospital outbreaks driven by multi-drug-resistant pathogens, notably Klebsiella pneumoniae (K. pneumoniae), are of grave concern. This opportunistic pathogen causes pneumonia, urinary tract infections, and bacteremia, particularly in immunocompromised individuals. The rise of hypervirulent K. pneumoniae adds complexity, as it increasingly infects healthy individuals. Recent epidemiological data suggest that asymptomatic gastrointestinal carriage serves as a reservoir for infections in the same individual and allows for host-to-host transmission via the fecal-oral route. This review focuses on K. pneumoniae's gastrointestinal colonization, delving into epidemiological evidence, current animal models, molecular colonization mechanisms, and the protective role of the resident gut microbiota. Moreover, the review sheds light on in vivo high-throughput approaches that have been crucial for identifying K. pneumoniae factors in gut colonization. This comprehensive exploration aims to enhance our understanding of K. pneumoniae gut pathogenesis, guiding future intervention and prevention strategies.
Collapse
Affiliation(s)
- Andrew S Bray
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| | - M Ammar Zafar
- Department of Microbiology and Immunology, Wake Forest School of Medicine, Winston-Salem, North Carolina, USA
| |
Collapse
|
4
|
Chen H, Xu H, Liu R, Shen J, Zheng B, Li L. Coexistence of bla IMP-4 and bla SFO-1 in an IncHI5B plasmid harbored by tigecycline-non-susceptible Klebsiella variicola strain. Ann Clin Microbiol Antimicrob 2024; 23:24. [PMID: 38448920 PMCID: PMC10918965 DOI: 10.1186/s12941-024-00680-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Accepted: 02/19/2024] [Indexed: 03/08/2024] Open
Abstract
BACKGROUND Klebsiella variicola is considered a newly emerging human pathogen. Clinical isolates of carbapenemase and broad-spectrum β-lactamase-producing K. variicola remain relatively uncommon. A strain of K. variicola 4253 was isolated from a clinical sample, and was identified to carry the blaIMP-4 and blaSFO-1 genes. This study aims to discern its antibiotic resistance phenotype and genomic characteristics. METHODS Species identification was conducted using MALDI-TOF/MS. PCR identification confirmed the presence of the blaIMP-4 and blaSFO-1 genes. Antibiotic resistance phenotype and genomic characteristics were detected by antimicrobial susceptibility testing and whole-genome sequencing. Plasmid characterization was carried out through S1-PFGE, conjugation experiments, Southern blot, and comparative genomic analysis. RESULTS K. variicola 4253 belonged to ST347, and demonstrated resistance to broad-spectrum β-lactamase drugs and tigecycline while being insensitive to imipenem and meropenem. The blaIMP-4 and blaSFO-1 genes harbored on the plasmid p4253-imp. The replicon type of p4253-imp was identified as IncHI5B, representing a multidrug-resistant plasmid capable of horizontal transfer and mediating the dissemination of drug resistance. The blaIMP-4 gene was located on the In809-like integrative element (Intl1-blaIMP-4-aacA4-catB3), which circulates in Acinetobacter and Enterobacteriaceae. CONCLUSIONS This study reports the presence of a strain of K. variicola, which is insensitive to tigecycline, carrying a plasmid harboring blaIMP-4 and blaSFO-1. It is highly likely that the strain acquired this plasmid through horizontal transfer. The blaIMP-4 array (Intl1-blaIMP-4-aacA4-catB3) is also mobile in Acinetobacter and Enterobacteriaceae. So it is essential to enhance clinical awareness and conduct epidemiological surveillance on multidrug-resistant K. variicola, conjugative plasmids carrying blaIMP-4, and the In809 integrative element.
Collapse
Affiliation(s)
- Hui Chen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd, Hangzhou City, 310003, China
| | - Hao Xu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd, Hangzhou City, 310003, China
| | - Ruishan Liu
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd, Hangzhou City, 310003, China
| | - Jian Shen
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd, Hangzhou City, 310003, China
| | - Beiwen Zheng
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd, Hangzhou City, 310003, China.
| | - Lanjuan Li
- State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, National Clinical Research Center for Infectious Diseases, National Medical Center for Infectious Diseases, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, The First Affiliated Hospital, Zhejiang University School of Medicine, 79 Qingchun Rd, Hangzhou City, 310003, China.
| |
Collapse
|
5
|
Li YT, Xiao YH, Liu Y, Hu N, Wu C, Huang X, Zeng L. Characterisation of highly virulent and colistin-resistant ST367-KL1 Klebsiella quasipneumoniae subsp. similipneumoniae Strain. J Glob Antimicrob Resist 2024; 36:267-275. [PMID: 38272213 DOI: 10.1016/j.jgar.2024.01.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Revised: 12/27/2023] [Accepted: 01/12/2024] [Indexed: 01/27/2024] Open
Abstract
OBJECTIVES To elucidate the characteristics of a colistin-resistant and hypervirulent Klebsiella quasipneumoniae subsp. similipneumoniae strain (KP8) using whole genome sequencing and various phenotypic assays. METHODS Antimicrobial susceptibility testing was performed using broth microdilution. Whole genome sequencing and comparative genomics were utilised to elucidate genomic characteristics. Phenotypic assays to evaluate virulence factors included measurements of mucosal viscosity, biofilm production, siderophore production, infection of A549 cells, serum-killing assays, and Galleria mellonella infection models. RESULTS Whole-genome sequencing revealed that the strain (KP8) belongs to sequence type 367 (ST367) and capsular type 1 (KL1), and it harbours several virulence genes, including regulator of mucoid phenotype (rmpA/A2), salmochelin (iroBCDN) and aerobactin (iucABCDiutA). Antibiotic susceptibility tests showed that KP8 was resistant to colistin. Genome analysis showed that the colistin resistance of KP8 might be related to amino acid insertions in pmrB (L215_D217, insL) and pagP (M1_S3, insV). Importantly, KP8 demonstrated comparable mucosal viscosity, biofilm production capacity, siderophore production levels to hvKP. Serum-killing experiments, A549 cell infection models, and G. mellonella infection models further indicated that KP8 displayed high virulence, akin to the hypervirulent strain NUTH-K2044. Notably, global genome analysis of the K. quasipneumoniae subsp. similipneumoniae strains highlighted that the ST367 lineage has a higher tendency to carry virulence-associated genes compared to other sequence types. The prevalence of virulence-associated factors concentrated within Chinese ST367 isolates reinforces this observation. CONCLUSION These findings further enhance our understanding of the resistance and pathogenicity of ST367 K. quasipneumoniae subsp. similipneumoniae strain and also providing a broader perspective on the global epidemiological landscape.
Collapse
Affiliation(s)
- Yu-Ting Li
- Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China; School of Public Health, Nanchang University, Nanchang, China
| | - Yang-Hua Xiao
- Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China; School of Public Health, Nanchang University, Nanchang, China
| | - Yanling Liu
- Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Niya Hu
- Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China
| | - Chengwei Wu
- School of Public Health, Nanchang University, Nanchang, China
| | - Xiaotian Huang
- Department of Medical Microbiology, School of Medicine, Nanchang University, Nanchang, China
| | - Lingbing Zeng
- Department of Clinical Laboratory, The First Affiliated Hospital, Jiangxi Medical College, Nanchang University, Nanchang, China.
| |
Collapse
|
6
|
Chen C, Wang W, Zhang J, Zhang L, Zhao J, Deng J, Li W, Li X, Zhuo W, Huang L, Chen J. Genomic characteristics of two strains of ESBL-producing Klebsiella pneumoniae ST268 isolated from different samples of one patient. J Glob Antimicrob Resist 2024; 36:319-325. [PMID: 38266958 DOI: 10.1016/j.jgar.2024.01.007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 11/20/2023] [Accepted: 01/13/2024] [Indexed: 01/26/2024] Open
Abstract
OBJECTIVES This study reports the whole-genome sequences of two strains of extended-spectrum beta-lactamase (ESBL)-producing and multidrug-resistant (MDR) K. pneumoniae ST268 and explores their acquired antibiotic resistance genes (ARGs) and the mobile genetic elements (MGEs). METHODS Two strains of K. pneumoniae ST268 were isolated from different samples of one patient. Assessment of antimicrobial susceptibility was performed, and then whole-genome sequencing was conducted. Acquired ARGs, insertion sequences, and transposons harboured by the two strains of K. pneumoniae ST268 were identified, and then the genetic contexts associated with the ARGs were analysed systematically. RESULTS Two strains of K. pneumoniae ST268 were found to carry the 118.6-kb hybrid IncFIIK:IncQ1:repBR1701 plasmid. All the acquired ARGs carried by the IncF plasmid were found to be situated on the 25.3-kb MDR region bracketed by ISKpn19 and IS26, which was widely present in the plasmids in 14 STs of strains in K. pneumoniae but also in IncF plasmids from Shigella flexneri and Klebsiella quasipneumoniae. Notably, the IncF plasmids harbouring the 25.3-kb MDR region were geographically distributed mainly in China, and the pKP161637-1/pKP160802-1 in our study was the first report on the IncF plasmid carrying the 25.3-kb MDR region bracketed in K. pneumoniae ST268. CONCLUSIONS Two strains of ESBL-producing K. pneumoniae ST268 with a MDR IncF plasmid were identified in a hospital in China. The ARGs were identified on the 25.3-kb MDR region, bracketed by ISKpn19 and IS26, of the IncF plasmids, which were present not only in the K. pneumoniae but also in the S. flexneri and K. quasipneumoniae.
Collapse
Affiliation(s)
- Chao Chen
- Department of Neurology, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Wei Wang
- Department of Pulmonary and Critical Care Medicine, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Jiechang Zhang
- Department of Cardiology, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Limei Zhang
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Jianhua Zhao
- Department of Neurosurgery, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Jinming Deng
- Department of Neurology, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Wang Li
- Shandong Provincial Engineering and Technology Research Center for Wild Plant Resources Development and Application of Yellow River Delta, College of Biological and Environmental Engineering, Binzhou University, Binzhou, China
| | - Xiaobin Li
- Guangdong Provincial Key Laboratory of Tumor Interventional Diagnosis and Treatment, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China
| | - Wenyan Zhuo
- Department of Neurology, Zhuhai People's Hospital (Zhuhai Hospital affiliated with Jinan University), Zhuhai, China.
| | - Lian Huang
- Department of Neurology, The First Affiliated Hospital of Jinan University, Guangzhou, China.
| | - Jing Chen
- Laboratory Medicine Center, Nanfang Hospital, Southern Medical University, Guangzhou, China.
| |
Collapse
|
7
|
Luna-Pineda VM, Rodríguez-Martínez G, Salazar-García M, Romo-Castillo M. Plant-Origin Components: New Players to Combat Antibiotic Resistance in Klebsiella pneumoniae. Int J Mol Sci 2024; 25:2134. [PMID: 38396811 PMCID: PMC10888558 DOI: 10.3390/ijms25042134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 01/09/2024] [Accepted: 01/13/2024] [Indexed: 02/25/2024] Open
Abstract
Klebsiella pneumoniae (Kpn) is an opportunistic pathogen that causes intrahospital complications such as pneumonia, liver abscesses, soft tissue infections, urinary infections, bacteraemia, and, in some cases, death. Since this bacterium has a higher frequency than other Gram-negative pathogens, it has become an important pathogen to the health sector. The adaptative genome of Kpn likely facilitates increased survival of the pathogen in diverse situations. Therefore, several studies have been focused on developing new molecules, synergistic formulations, and biomaterials that make it possible to combat and control infections with and dispersion of this pathogen. Note that the uncontrolled antibiotic administration that occurred during the pandemic led to the emergence of new multidrug-resistant strains, and scientists were challenged to overcome them. This review aims to compile the latest information on Kpn that generates intrahospital infections, specifically their pathogenicity-associated factors. Furthermore, it explains the natural-product-based treatments (extracts and essential oils) developed for Kpn infection and dispersion control.
Collapse
Affiliation(s)
- Victor M. Luna-Pineda
- Laboratorio de Investigación en COVID-19, Hospital Infantil de México Federico Gómez, Ciudad de México 06720, Mexico; (V.M.L.-P.); (G.R.-M.)
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Ciudad de México 06720, Mexico
| | - Griselda Rodríguez-Martínez
- Laboratorio de Investigación en COVID-19, Hospital Infantil de México Federico Gómez, Ciudad de México 06720, Mexico; (V.M.L.-P.); (G.R.-M.)
- Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Ciudad de México 06720, Mexico
| | - Marcela Salazar-García
- Departamento de Investigación Biomédica, Hospital Infantil de México Federico Gómez, Ciudad de México 06720, Mexico;
| | - Mariana Romo-Castillo
- IxM/CONAHCYT-HIMFG, Laboratorio de Investigación en Inmunología y Proteómica, Hospital Infantil de México Federico Gómez, Ciudad de México 06720, Mexico
| |
Collapse
|
8
|
Metcalf R, Messer LF, White HL, Ormsby MJ, Matallana-Surget S, Quilliam RS. Evidence of interspecific plasmid uptake by pathogenic strains of Klebsiella isolated from microplastic pollution on public beaches. JOURNAL OF HAZARDOUS MATERIALS 2024; 461:132567. [PMID: 37741206 DOI: 10.1016/j.jhazmat.2023.132567] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Revised: 08/22/2023] [Accepted: 09/14/2023] [Indexed: 09/25/2023]
Abstract
Microplastic beads are becoming a common feature on beaches, and there is increasing evidence that such microplastics can become colonised by potential human pathogens. However, whether the concentrations and pathogenicity of these pathogens pose a public health risk are still unclear. Therefore, the aim of this study was to determine realistic environmental concentrations of potential pathogens colonising microplastic beads, and quantify the expression of virulence and antimicrobial resistance genes (ARGs). Microplastic beads were collected from beaches and a culture-dependent approach was used to determine the concentrations of seven target bacteria (Campylobacter spp.; E. coli; intestinal enterococci; Klebsiella spp.; Pseudomonas aeruginosa; Salmonella spp.; Vibrio spp.). All seven target bacteria were detected without the need for a pre-enrichment step; urban sites had higher bacterial concentrations, whilst polymer type had no influence on bacterial concentrations. Klebsiella was the most abundant target bacteria and possessed virulence and ARGs, some of which were present on plasmids from other species, and showed pathogenicity in a Galleria melonella infection model. Our findings demonstrate how pathogen colonised microplastic beads can pose a heightened public health risk at the beach, and highlights the urgency for improved monitoring and enforcement of regulations on the release of microplastics into the environment.
Collapse
Affiliation(s)
- Rebecca Metcalf
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK.
| | - Lauren F Messer
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - Hannah L White
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - Michael J Ormsby
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - Sabine Matallana-Surget
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| | - Richard S Quilliam
- Biological and Environmental Sciences, Faculty of Natural Sciences, University of Stirling, Stirling FK9 4LA, UK
| |
Collapse
|
9
|
Zhang PJ, Lu ZH, Cao LJ, Chen H, Sun Y. Successful treatment of invasive liver abscess syndrome caused by Klebsiella variicola with intracranial infection and septic shock: A case report. World J Gastrointest Surg 2023; 15:2938-2944. [PMID: 38222021 PMCID: PMC10784832 DOI: 10.4240/wjgs.v15.i12.2938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Revised: 10/11/2023] [Accepted: 11/10/2023] [Indexed: 12/27/2023] Open
Abstract
BACKGROUND Klebsiella variicola (K. variicola) is a member of the Klebsiella genus and is often misidentified as Klebsiella pneumoniae. In this report, we present a rare case of invasive liver abscess caused by K. variicola. CASE SUMMARY We report a rare case of liver abscess due to K. variicola. A 57-year-old female patient presented with back pain for a month. She developed a high-grade fever associated with chills, and went into a coma and developed shock. The clinical examinations and tests after admission confirmed a diagnosis of primary liver abscess caused by K. variicola complicated by intracranial infection and septic shock. The patient successfully recovered following early percutaneous drainage of the abscess, prompt appropriate antibiotic administration, and timely open surgical drainage. CONCLUSION This is a case of successful treatment of invasive liver abscess syndrome caused by K. variicola, which has rarely been reported. The findings of this report point to the need for further study of this disease.
Collapse
Affiliation(s)
- Pin-Jie Zhang
- The First Department of Critical Care Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, Anhui Province, China
| | - Zhong-Hua Lu
- The First Department of Critical Care Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, Anhui Province, China
| | - Li-Jun Cao
- The First Department of Critical Care Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, Anhui Province, China
| | - Hu Chen
- The First Department of Critical Care Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, Anhui Province, China
| | - Yun Sun
- The First Department of Critical Care Medicine, The Second Affiliated Hospital of Anhui Medical University, Hefei 230601, Anhui Province, China
| |
Collapse
|
10
|
Seethalakshmi PS, RU VPN, Prabhakaran A, Prathiviraj R, Pamanji R, Kiran GS, Selvin J. Genomic investigation unveils high-risk ESBL producing Enterobacteriaceae within a rural environmental water body. CURRENT RESEARCH IN MICROBIAL SCIENCES 2023; 6:100216. [PMID: 38274946 PMCID: PMC10809108 DOI: 10.1016/j.crmicr.2023.100216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024] Open
Abstract
Antimicrobial resistance is regarded as a global threat to public health, animals, and the environment, emerging in response to extensive utilization of antimicrobials. The determinants of antimicrobial resistance are transported to susceptible bacterial populations through genetic recombination or through gene transfer, mediated by bacteriophages, plasmids, transposons, and insertion sequences. To determine the penetration of antimicrobial resistance into the bacterial population of the Thiruvandarkoil Lake, a water body located in the rural settings of Puducherry, India, culture-based microbiological and genomic approaches were used. Resistant bacterial isolates obtained from microbiological screening were subjected to whole genome sequencing and the genetic determinants of antimicrobial resistance were identified using in silico genomic tools. Cephalosporin-resistant isolates were found to produce extended spectrum beta lactamases, encoded by blaVEB-6 (in Proteus mirabilis PS01), blaSHV-12 and ompK36 mutation (in Klebsiella quasipneumoniae PS02) and blaSHV-12, blaACT-16, blaCTX-M and blaNDM-1 in (Enterobacter hormaechei PS03). Genes encoding heavy metal resistance, virulence and resistance to detergents were also detected in these resistant isolates. Among ESBL-producing organisms, one mcr-9-positive Enterobacter hormaechei was also identified in this study. To our knowledge, this is the first report of mcr-9 carrying bacterium in the environment in India. This study seeks the immediate attention of policy makers, researchers, government officials and environmental activists in India, to develop surveillance programs to monitor the dissemination of antimicrobial resistance in the environment.
Collapse
Affiliation(s)
- P S Seethalakshmi
- Department of Microbiology, Pondicherry University, Puducherry 605014, India
| | | | | | | | - Rajesh Pamanji
- Department of Microbiology, Pondicherry University, Puducherry 605014, India
| | - George Seghal Kiran
- Department of Food Science and Technology, Pondicherry University, Puducherry 605014, India
| | - Joseph Selvin
- Department of Microbiology, Pondicherry University, Puducherry 605014, India
| |
Collapse
|
11
|
Nikapitiya C, Chandrarathna HPSU, Dias MKHM, Lee J, De Zoysa M. Characterization and biocontrol efficacy of lytic phage (KPP-1) that infects multidrug resistant Klebsiella variicola. Braz J Microbiol 2023; 54:2509-2520. [PMID: 37368195 PMCID: PMC10484831 DOI: 10.1007/s42770-023-01037-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2022] [Accepted: 05/30/2023] [Indexed: 06/28/2023] Open
Abstract
Klebsiella variicola strain was identified from a natural water stream. Novel phage (KPP-1) infecting K. variicola was isolated and characterized. The biocontrol efficacy of KPP-1 against K. variicola-infected adult zebrafish was also investigated. The host K. variicola strain was resistant to six of the antibiotics tested and comprised the virulence genes kfuBC, fim, ureA, and Wza-Wzb-Wzccps. Morphological analysis by transmission electron microscopy revealed that KPP-1 has icosahedron head and tail structures. The latent period and burst size of KPP-1 were 20 min and 88 PFU per infected cell, respectively, at a multiplicity of infection of 0.1. KPP-1 was stable over a broad pH range (3-11), temperature (4-50 °C), and salinity (0.1-3%). KPP-1 inhibits the growth of K. variicola in vitro and in vivo. In the zebrafish infection model, treatment with KPP-1-infected K. variicola demonstrated 56% of cumulative survival. This suggests the possibility of developing KPP-1 as a potential biocontrol agent against multidrug-resistant K. variicola that belongs to the K. pneumoniae complex.
Collapse
Affiliation(s)
- Chamilani Nikapitiya
- College of Veterinary Medicine and Research Institute of Veterinary Medicine, Chungnam National University, Daejeon, 34134, Republic of Korea
| | - H P S U Chandrarathna
- College of Veterinary Medicine and Research Institute of Veterinary Medicine, Chungnam National University, Daejeon, 34134, Republic of Korea
| | | | - Jehee Lee
- Department of Marine Life Sciences & Fish Vaccine Research Center, Jeju National University, Jeju, 63243, Republic of Korea.
- Marine Science Institute, Jeju National University, Jeju, 63333, Republic of Korea.
| | - Mahanama De Zoysa
- College of Veterinary Medicine and Research Institute of Veterinary Medicine, Chungnam National University, Daejeon, 34134, Republic of Korea.
| |
Collapse
|
12
|
Wu Y, Zhao J, Li Z, Liu X, Hu Y, Zhang F, Zhang Y, Pu D, Li C, Zhuo X, Shi H, Lu B. Within-host acquisition of colistin-resistance of an NDM-producing Klebsiella quasipneumoniae subsp. similipneumoniae strain through the insertion sequence- 903B-mediated inactivation of mgrB gene in a lung transplant child in China. Front Cell Infect Microbiol 2023; 13:1153387. [PMID: 37743865 PMCID: PMC10513040 DOI: 10.3389/fcimb.2023.1153387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2023] [Accepted: 08/10/2023] [Indexed: 09/26/2023] Open
Abstract
Background Colistin, as the antibiotic of "last resort" for carbapenem-resistant Klebsiella, develop resistance during administration of this antimicrobial agent. We identified an NDM-1-producing Klebsiella quasipneumonuae subsp. similipneumoniae (KQSS) strain KQ20605 recovered from a child, which developed resistance to colistin (KQ20786) through acquiring an IS903B element between the -27th and -26th bp of mgrB promoter region after 6-day colistin usage. Objectives The aim of this study is to explore the source of IS903B in the disruptive mgrB gene and its underlying mechanisms. Materials and methods Antibiotics susceptibility testing was conducted via microbroth dilution method. The in vitro colistin-induced experiment of KQ20605 was performed to mimic the in vivo transition from colistin-sensitive to resistant. Whole-genome sequencing was used to molecular identification of colistin resistance mechanism. Results The IS903B element integrated into mgrB gene of KQ20786 had a 100% nucleotide identity and coverage match with one IS903B on plasmid IncR, and only 95.1% (1005/1057) identity to those on chromosome. In vitro, upon the pressure of colistin, KQ20605 could also switch its phenotype from colistin-sensitive to resistant with IS elements (e.g., IS903B and IS26) frequently inserted into mgrB gene at "hotspots", with the insertion site of IS903B nearly identical to that of KQ20786. Furthermore, IS26 elements in this isolate were only encoded by plasmids, including IncR and conjugative plasmid IncN harboring bla NDM. Conclusion Mobilizable IS elements on plasmids tend to be activated and integrated into mgrB gene at "hotspots" in this KQSS, thereby causing the colistin resistance emergence and further dissemination.
Collapse
Affiliation(s)
- Yongli Wu
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Jiankang Zhao
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Ziyao Li
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Institute of Clinical Medical Sciences, China-Japan Friendship Hospital, Beijing, China
| | - Xinmeng Liu
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
| | - Yanning Hu
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
| | - Feilong Zhang
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
| | - Yulin Zhang
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Danni Pu
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Chen Li
- Department of Pulmonary and Critical Care Medicine, Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
| | - Xianxia Zhuo
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Capital Medical University China-Japan Friendship School of Clinical Medicine, Beijing, China
| | - Huihui Shi
- Department of Clinical Laboratory, Affiliated Nantong Hospital of Shanghai University, Nantong, China
| | - Binghuai Lu
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Institute of Clinical Medical Sciences, China-Japan Friendship Hospital, Beijing, China
- Department of Pulmonary and Critical Care Medicine, Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
| |
Collapse
|
13
|
Wang S, Wang L, Jin J, Li G, Shao H, Song Y, Sun Y, Zhang Y, Cheng J, Li L. Genomic Epidemiology and Characterization of Carbapenem-Resistant Klebsiella pneumoniae in ICU Inpatients in Henan Province, China: a Multicenter Cross-Sectional Study. Microbiol Spectr 2023; 11:e0419722. [PMID: 37212684 PMCID: PMC10269698 DOI: 10.1128/spectrum.04197-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2022] [Accepted: 04/19/2023] [Indexed: 05/23/2023] Open
Abstract
Carbapenem-resistant Klebsiella pneumoniae (CRKP) has disseminated globally and is difficult to treat, causing increased morbidity and mortality rates in critically ill patients. We conducted a multicenter cross-sectional study of intensive care unit (ICU) inpatients in 78 hospitals to investigate the prevalence and molecular characteristics of CRKP in Henan Province, China, a hyperepidemic region. A total of 327 isolates were collected and downsampled to 189 for whole-genome sequencing. Molecular typing revealed that sequence type 11 (ST11) of clonal group 258 (CG258) was predominant (88.9%, n = 168), followed by ST2237 (5.8%, n = 11) and ST15 (2.6%, n = 5). We used core genome multilocus sequence typing (cgMLST) to further classified the population into 13 subtypes. Capsule polysaccharide (K-antigen) and lipopolysaccharide (LPS; O-antigen) typing revealed that K64 (48.1%, n = 91) and O2a (49.2%, n = 93) were the most common. We studied isolates collected from both the airway and the gut of the same patients and showed that intestinal carriage was associated with respiratory colonization (odds ratio = 10.80, P < 0.0001). Most isolates (95.2%, n = 180) showed multiple drug resistance (MDR), while 59.8% (n = 113) exhibited extensive drug resistance (XDR), and all isolates harbored either blaKPC-2 (98.9%, n = 187) or blaCTX-M and blaSHV extended-spectrum beta-lactamases (ESBLs) (75.7%, n = 143). However, most were susceptible to ceftazidime-avibactam (CZA) (94.7%, n = 179) and colistin (97.9%, n = 185). We found mgrB truncations in isolates conferring resistance to colistin and mutations in blaSHV and OmpK35 and OmpK36 osmoporins in CZA-resistant isolates. Using a regularized regression model, we found that the aerobactin sequence type and the salmochelin sequence type, among others, were predictors of the hypermucoviscosity phenotype. IMPORTANCE In this study, we address the ongoing epidemic of carbapenem-resistant Klebsiella pneumoniae, a critical threat to public health. The alarming genotypic and phenotypic convergence of multidrug resistance and virulence highlights the increasingly aggravated threat posed by K. pneumoniae. This calls for a combined effort of physicians and scientists to study the potential mechanisms and establish guidelines for antimicrobial therapies and interventions. To this end, we have conducted a genomic epidemiology and characterization study using isolates collected in a coordinated effort of multiple hospitals. Innovative biological discoveries of clinical importance are made and brought to the attention of clinical researchers and practitioners. This study presents an important advance in the application of genomics and statistics to recognize, understand, and control an infectious disease of concern.
Collapse
Affiliation(s)
- Shanmei Wang
- Department of Clinical Microbiology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, Henan, China
| | - Lei Wang
- Department of Bioinformatics Research, Genskey Co., Ltd., Beijing, China
| | - Jing Jin
- Department of Pathogen Biology and Immunology, Henan Medical College, Zhengzhou, Henan, China
| | - Gang Li
- Department of Clinical Microbiology, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, Henan, China
| | - Huanzhang Shao
- Department of Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, Henan, China
| | - Yang Song
- Department of Bioinformatics Research, Genskey Co., Ltd., Beijing, China
| | - Yuanzheng Sun
- Clinical Laboratory, Yuzhou Jundu Hospital, Xuchang, Henan, China
| | - Yan Zhang
- Clinical Laboratory, Yima People’s Hospital, Sanmenxia, Henan, China
| | - Jianjian Cheng
- Department of Respiratory and Critical Care Medicine, Henan Provincial People's Hospital, Zhengzhou University People's Hospital, Henan University People's Hospital, Zhengzhou, Henan, China
| | - Lifeng Li
- Department of Bioinformatics Research, Genskey Co., Ltd., Beijing, China
| |
Collapse
|
14
|
Hussain A, Mazumder R, Ahmed A, Saima U, Phelan JE, Campino S, Ahmed D, Asadulghani M, Clark TG, Mondal D. Genome dynamics of high-risk resistant and hypervirulent Klebsiella pneumoniae clones in Dhaka, Bangladesh. Front Microbiol 2023; 14:1184196. [PMID: 37303793 PMCID: PMC10248448 DOI: 10.3389/fmicb.2023.1184196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 05/05/2023] [Indexed: 06/13/2023] Open
Abstract
Klebsiella pneumoniae is recognized as an urgent public health threat because of the emergence of difficult-to-treat (DTR) strains and hypervirulent clones, resulting in infections with high morbidity and mortality rates. Despite its prominence, little is known about the genomic epidemiology of K. pneumoniae in resource-limited settings like Bangladesh. We sequenced genomes of 32 K. pneumoniae strains isolated from patient samples at the International Center for Diarrhoeal Disease Research, Bangladesh (icddr,b). Genome sequences were examined for their diversity, population structure, resistome, virulome, MLST, O and K antigens and plasmids. Our results revealed the presence of two K. pneumoniae phylogroups, namely KpI (K. pneumoniae) (97%) and KpII (K. quasipneumoniae) (3%). The genomic characterization revealed that 25% (8/32) of isolates were associated with high-risk multidrug-resistant clones, including ST11, ST14, ST15, ST307, ST231 and ST147. The virulome analysis confirmed the presence of six (19%) hypervirulent K. pneumoniae (hvKp) and 26 (81%) classical K. pneumoniae (cKp) strains. The most common ESBL gene identified was blaCTX-M-15 (50%). Around 9% (3/32) isolates exhibited a difficult-to-treat phenotype, harboring carbapenem resistance genes (2 strains harbored blaNDM-5 plus blaOXA-232, one isolate blaOXA-181). The most prevalent O antigen was O1 (56%). The capsular polysaccharides K2, K20, K16 and K62 were enriched in the K. pneumoniae population. This study suggests the circulation of the major international high-risk multidrug-resistant and hypervirulent (hvKp) K. pneumoniae clones in Dhaka, Bangladesh. These findings warrant immediate appropriate interventions, which would otherwise lead to a high burden of untreatable life-threatening infections locally.
Collapse
Affiliation(s)
- Arif Hussain
- Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Razib Mazumder
- Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Abdullah Ahmed
- Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Umme Saima
- Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| | - Jody E. Phelan
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Susana Campino
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Dilruba Ahmed
- Clinical Microbiology and Immunology Laboratory, Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Md Asadulghani
- Biosafety and BSL3 Laboratory, Biosafety Office, International Centre for Diarrhoeal Disease Research, Bangladesh, Dhaka, Bangladesh
| | - Taane G. Clark
- Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Dinesh Mondal
- Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka, Bangladesh
| |
Collapse
|
15
|
Tanii R, Harada S, Saito H, Okamoto K, Doi Y, Suzuki M. A case report of fatal COVID-19 complicated by rapidly progressive sepsis caused by Klebsiella variicola. BMC Infect Dis 2023; 23:184. [PMID: 36991335 DOI: 10.1186/s12879-023-08128-9] [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: 07/24/2022] [Accepted: 02/27/2023] [Indexed: 03/31/2023] Open
Abstract
BACKGROUND There is a growing interest in Klebsiella variicola as a causative pathogen in humans, though its clinical features and the impact of co-infection or secondary infection with COVID-19 remain unknown. CASE PRESENTATION A 71-year-old man presented with fever, altered mental status and generalized weakness and was admitted to ICU due to severe COVID-19 pneumonia. He was newly diagnosed with type II diabetes mellitus upon admission. On hospital day 3, his respiratory status deteriorated, requiring invasive mechanical ventilation. On hospital day 10, superimposed bacterial pneumonia was suspected and subsequently, broad-spectrum antibiotics were administered for the associated bloodstream infection. On hospital day 13, despite administration of active antibiotics and appropriate source control, he decompensated and died. The causative organism isolated from blood cultures was initially reported as K. pneumoniae, but it was identified as K. variicola by a genetic analysis. A representative isolate (FUJ01370) had a novel multilocus sequence typing allelic profile (gapA-infB-mdh-pgi-phoE-rpoB-tonB: 16-24-21-27-52-17-152), to which sequence type 5794 was assigned (GenBank assembly accession: GCA_019042755.1). CONCLUSIONS We report a fatal case of respiratory and bloodstream infection due to K. variicola complicating severe COVID-19. Co-infection or secondary infection of K. variicola in COVID-19 is likely under-recognized and can be fulminant as in this case.
Collapse
Affiliation(s)
- Rimi Tanii
- Department of Emergency and Critical Care Medicine, St. Marianna University Yokohama Seibu Hospital, 1197-1, Yasashi-cho, Asahi-ku, Yokohama, Kanagawa, Japan.
| | - Sohei Harada
- Department of Infection Control and Prevention, The University of Tokyo Hospital, Tokyo, Japan
| | - Hiroki Saito
- Department of Emergency and Critical Care Medicine, St. Marianna University Yokohama Seibu Hospital, 1197-1, Yasashi-cho, Asahi-ku, Yokohama, Kanagawa, Japan
| | - Koh Okamoto
- Department of Infectious Diseases, The University of Tokyo Hospital, Tokyo, Japan
| | - Yohei Doi
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- Department of Infectious Diseases, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
- Division of Infectious Diseases, University of Pittsburgh School of Medicine, Pittsburgh, PA, USA
| | - Masahiro Suzuki
- Department of Microbiology, Fujita Health University School of Medicine, Toyoake, Aichi, Japan
| |
Collapse
|
16
|
Ge H, Qiao J, Xu H, Liu R, Zhao J, Chen R, Li C, Chen M, Guo X. Emergence of OXA-484-Producing Klebsiella variicola in China. Infect Drug Resist 2023; 16:1767-1775. [PMID: 37008750 PMCID: PMC10065429 DOI: 10.2147/idr.s404551] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 03/23/2023] [Indexed: 03/29/2023] Open
Abstract
Purpose The frequent and inappropriate use of antibiotics has caused a dramatic rise in the number, species, and degree of multi-drug resistant bacteria, making them more prevalent and difficult to treat. In this context, the aim of the present study was to characterize the OXA-484-producing strains isolated from a perianal swab of a patient by using whole-genome analysis. Patients and Methods In this study, carbapenemase-producing Klebsiella variicola was identified by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS), average nucleotide identity (ANI) and PCR. S1 nuclease pulsed-field gel electrophoresis (S1-PFGE) and Southern blotting were utilized to characterize the plasmid profiles of K. variicola 4717. In particular, WGS was performed to obtain genomic information on this clinical isolate, and assemble all the plasmids of the bla OXA-484-harboring strain. Results The antimicrobial susceptibility pattern of K. variicola 4717 revealed that it was resistant to a range of antibiotics, including aztreonam, imipenem, meropenem, ceftriaxone, cefotaxime, ceftazidime, levofloxacin, ciprofloxacin, piperacillin-tazobactam, methylene-sulfamer oxazole, amoxicillin-clavulanic acid, cefepime, and tigecycline. Its susceptibility to chloromycin was intermediate, while it was still susceptible to amikacin, gentamicin, fosfomycin, and polymyxin B. The presence of two companion plasmids, p4717_1 and p4717_2, together with a plasmid carrying the bla OXA-484 gene was observed. An in-depth investigation of p4717-OXA-484 uncovered that it is an IncX3-type plasmid and shares a similar segment encoded by IS26. Given the similar genetic background, it was conceivable that bla OXA-484 could have developed from bla OXA-181 through a series of mutations. Conclusion Herein, we described the first genome sequence of K. variicola strain harbouring the class D β-actamase bla OXA-484 in an Inc-X3-type plasmid. Our work also uncovered the genetic characterization of K. variicola 4717 and the importance of initiating antimicrobial detection promptly.
Collapse
Affiliation(s)
- Haoyu Ge
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Jie Qiao
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Hao Xu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Ruishan Liu
- Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, State Key Laboratory for Diagnosis and Treatment of Infectious Diseases, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Junhui Zhao
- School of Basic Medical Sciences, Zhejiang Chinese Medical University, Hangzhou, People’s Republic of China
| | - Ruyan Chen
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Chenyu Li
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
| | - Mantao Chen
- Department of Neurosurgery, the First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, People’s Republic of China
| | - Xiaobing Guo
- Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, People’s Republic of China
- Correspondence: Xiaobing Guo, Department of Laboratory Medicine, The First Affiliated Hospital of Zhengzhou University, Jianshe East Road, Zhengzhou, Henan Province, 450000, People’s Republic of China, Tel +86 371 6627 8237, Fax +86 371 6691 3569, Email
| |
Collapse
|
17
|
Li Z, Liu X, Lei Z, Li C, Zhang F, Wu Y, Yang X, Zhao J, Zhang Y, Hu Y, Shen F, Wang P, Yang J, Liu Y, Lu B. Genetic Diversity of Polymyxin-Resistance Mechanisms in Clinical Isolates of Carbapenem-Resistant Klebsiella pneumoniae: a Multicenter Study in China. Microbiol Spectr 2023; 11:e0523122. [PMID: 36847569 PMCID: PMC10100843 DOI: 10.1128/spectrum.05231-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/06/2023] [Indexed: 03/01/2023] Open
Abstract
Polymyxin has been the last resort to treat multidrug-resistant Klebsiella pneumonia. However, recent studies have revealed that polymyxin-resistant carbapenem-resistant Klebsiella pneumonia (PR-CRKP) emerged due to the mutations in chromosomal genes or the plasmid-harboring mcr gene, leading to lipopolysaccharide modification or efflux of polymyxin through pumps. Further surveillance was required. In the present study we collected PR-CRKP strains from 8 hospitals in 6 provinces/cities across China to identify the carbapenemase and polymyxin resistance genes and epidemiological features by whole-genome sequencing (WGS). The broth microdilution method (BMD) was performed to determine the MIC of polymyxin. Of 662 nonduplicate CRKP strains, 15.26% (101/662) were defined as PR-CRKP; 10 (9.90%) were confirmed as Klebsiella quasipneumoniae by WGS. The strains were further classified into 21 individual sequence types (STs) by using multilocus sequence typing (MLST), with ST11 being prevalent (68/101, 67.33%). Five carbapenemase types were identified among 92 CR-PRKP, blaKPC-2 (66.67%), blaNDM-1 (16.83%), blaNDM-5 (0.99%), blaIMP-4 (4.95%), and blaIMP-38 (0.99%). Notably, 2 PR-CRKP strains harbored both blaKPC-2 and blaNDM-1. The inactivation of mgrB, associated significantly with high-level polymyxin resistance, was mainly caused by the insertion sequence (IS) insertion (62.96%, 17/27). Furthermore, acrR was inserted coincidently by ISkpn26 (67/101, 66.33%). The deletion or splicing mutations of crrCAB were significantly associated with ST11 and KL47 (capsule locus types), and diverse mutations of the ramR gene were identified. Only one strain carried the mcr gene. In summary, the high IS-inserted mgrB inactivation, the close relationship between ST11 and the deletion or splicing mutations of the crrCAB, and the specific features of PR-K. quasipneumoniae constituted notable features of our PR-CRKP strains in China. IMPORTANCE Polymyxin-resistant CRKP is a serious public health threat whose resistance mechanisms should be under continuous surveillance. Here, we collected 662 nonduplicate CRKP strains across China to identify the carbapenemase and polymyxin resistance genes and epidemiological features. Polymyxin resistance mechanism in 101 PR-CRKP strains in China were also investigated, 9.8% of which (10/101) were K. quasipneumoniae, as determined via WGS, and inactivation of mgrB remained the most crucial polymyxin resistance mechanism, significantly related to high-level resistance. Deletion or splicing mutations of crrCAB were significantly associated with ST11 and KL47. Diverse mutations of the ramR gene were identified. The plasmid complementation experiment and mRNA expression analysis further confirmed that the mgrB promoter and ramR played a critical role in polymyxin resistance. This multicenter study contributed to the understanding of antibiotic resistance forms in China.
Collapse
Affiliation(s)
- Ziyao Li
- China-Japan Friendship Institute of Clinical Medical Sciences, Beijing, China
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xinmeng Liu
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
| | - Zichen Lei
- China-Japan Friendship Institute of Clinical Medical Sciences, Beijing, China
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Chen Li
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
- Liuyang Traditional Chinese Medicine Hospital, Changsha, Hunan, China
| | - Feilong Zhang
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
| | - Yongli Wu
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Xinrui Yang
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
| | - Jiankang Zhao
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Yulin Zhang
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
| | - Yanning Hu
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
| | - Fangfang Shen
- Heping Hospital affiliated with Changzhi Medical College, Changzhi, Shanxi, China
| | - Pingbang Wang
- The People’s Hospital of Liuyang, Changsha, Hunan, China
| | - Junwen Yang
- Department of Laboratory Medicine, Zhengzhou Key Laboratory of Children’s Infection and Immunity, Children’s Hospital Affiliated with Zhengzhou University, Zhengzhou, Henan, China
| | - Yulei Liu
- Department of Laboratory Medicine, Beijing Anzhen Hospital, Beijing, China
| | - Binghuai Lu
- China-Japan Friendship Institute of Clinical Medical Sciences, Beijing, China
- Laboratory of Clinical Microbiology and Infectious Diseases, Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, National Center for Respiratory Medicine, China-Japan Friendship Hospital, Beijing, China
- Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Beijing, China
- Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, China
- Peking University China-Japan Friendship School of Clinical Medicine, Beijing, China
| |
Collapse
|
18
|
Donchev D, Ivanov IN, Stoikov I, Sabtcheva S, Kalchev Y, Murdjeva M, Dobreva E, Hristova R. Improvement and Validation of a Multi-Locus Variable Number of Tandem Repeats Analysis (MLVA8+) for Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae. Microorganisms 2023; 11:microorganisms11020444. [PMID: 36838409 PMCID: PMC9965953 DOI: 10.3390/microorganisms11020444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 02/02/2023] [Accepted: 02/08/2023] [Indexed: 02/12/2023] Open
Abstract
The genotyping of the multidrug-resistant Klebsiella pneumoniae species complex is essential to identify outbreaks and to track their source and spread. The aim of this study was to improve and extend the typeability, availability, cost and time efficiency of an existing multi-locus VNTR analysis (MLVA). A modified scheme (MLVA8+) was adopted and validated for strain-level differentiation of the three Klebsiella species involved in human pathology. A diverse set of 465 K. pneumoniae clinical isolates from 22 hospitals and 3 outpatient laboratories in Bulgaria were studied, where 315 were carbapenem-resistant. The MLVA8+ typeability was significantly improved and the typing data were validated against 158 isolates which were previously typed by WGS. The MLVA8+ results were highly concordant with the classic 7-locus MLST and the novel K. variicola MLST, but had greater congruency coefficients (adjusted Wallace). A major advantage was the differentiation of the hybrid cluster ST258 into its corresponding clades. Furthermore, the applicability of MLVA8+ was demonstrated by conducting a retrospective investigation of the intra-hospital spread of blaKPC-, blaNDM- and blaOXA-48-like producers. The MLVA8+ has improved utility and extended typing scope to K. variicola and K. quasipneumoniae, while its cost and time-to-result were reduced.
Collapse
Affiliation(s)
- Deyan Donchev
- National Reference Laboratory for Control and Monitoring of Antimicrobial Resistance, Department of Microbiology, National Center of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
- Correspondence:
| | - Ivan N. Ivanov
- National Reference Laboratory for Control and Monitoring of Antimicrobial Resistance, Department of Microbiology, National Center of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Ivan Stoikov
- National Reference Laboratory for Control and Monitoring of Antimicrobial Resistance, Department of Microbiology, National Center of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
- Laboratory for Clinical Microbiology, National Oncology Center, 6 Plovdivsko pole Str., 1797 Sofia, Bulgaria
| | - Stefana Sabtcheva
- Laboratory for Clinical Microbiology, National Oncology Center, 6 Plovdivsko pole Str., 1797 Sofia, Bulgaria
| | - Yordan Kalchev
- Department of Medical Microbiology and Immunology, “Prof. Dr. Elissay Yanev”, Medical University—Plovdiv, 15-A Vasil Aprilov Blvd., 4002 Plovdiv, Bulgaria
| | - Marianna Murdjeva
- Department of Medical Microbiology and Immunology, “Prof. Dr. Elissay Yanev”, Medical University—Plovdiv, 15-A Vasil Aprilov Blvd., 4002 Plovdiv, Bulgaria
| | - Elina Dobreva
- National Reference Laboratory for Control and Monitoring of Antimicrobial Resistance, Department of Microbiology, National Center of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| | - Rumyana Hristova
- National Reference Laboratory for Control and Monitoring of Antimicrobial Resistance, Department of Microbiology, National Center of Infectious and Parasitic Diseases, 26 Yanko Sakazov Blvd., 1504 Sofia, Bulgaria
| |
Collapse
|
19
|
Altayb HN, Hosawi S, Baothman O, Kazmi I, Chaieb K, Abu Zeid IM, Elbadawi HS, Lopes BS, Moglad E. Molecular insights into novel environmental strains of Klebsiella quasipneumoniae harboring different antimicrobial-resistance genes. Front Public Health 2023; 10:1068888. [PMID: 36711372 PMCID: PMC9878601 DOI: 10.3389/fpubh.2022.1068888] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2022] [Accepted: 12/21/2022] [Indexed: 01/14/2023] Open
Abstract
Introduction The emergence of bacterial pathogens in environmental hosts represents a major risk to public health. This study aimed at characterizing seven novel environmental strains of K. quasipneumoniae using a genomic approach which was misidentified by phenotypic methods in a previous batch of 27 species thought to be K. pneumoniae. Methods Whole-genome sequencing was performed using the Illumina platform, and the generated raw reads were de novo assembled. Comparative genomic, resistome, virulome, mobilome, and phylogeny were then investigated using dierent bioinformatics tools. Results Six strains were identified as K. quasipneumoniae subsp similipneumoniae and one as K. quasipneumoniae subsp. quasipneumoniae. All isolates were resistant to ampicillin, cephalexin, and amoxicillin-clavulanic acid and harbored the fosA, bla OKP types, oqxB, and oqxA genes. One isolate additionally harbored a gene cassettes consisting of bla SHV-1, bla OXA-1, aac(6')-Ib-cr, catB genes. The aminoglycoside-modifying enzyme gene aph(3")-Ia was bracketed by two insertion elements. Plasmid analyses showed that IncFIBK was the most prevalent plasmid, circulating in six isolates, while one isolate exhibited seven different plasmids. The isolates have virulence genes responsible for capsule formation, lipopolysaccharide, iron uptake aerobactin (iutA), salmochelins (iroE, iroN), enterobactin siderophore, adherence, and biofilm formation (mrkA, mrkB, mrkC, mrkD, mrkF, and mrkH). Conclusion Our study highlights the ecology and transmission of K. quasipneumoniae (which have the ability to disseminate to other environmental sources including animals) outside the clinical setting and the contribution of water, vegetables, and table surfaces as potential reservoirs of farm-to-fork transmission of disease via local markets in Khartoum, Sudan.
Collapse
Affiliation(s)
- Hisham N. Altayb
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia,Center of Artificial Intelligence in Precision Medicines, King Abdulaziz University, Jeddah, Saudi Arabia,*Correspondence: Hisham N. Altayb ✉
| | - Salman Hosawi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Othman Baothman
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Imran Kazmi
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Kamel Chaieb
- Department of Biochemistry, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Isam M. Abu Zeid
- Department of Biological Sciences, Faculty of Science, King Abdulaziz University, Jeddah, Saudi Arabia
| | - Hana S. Elbadawi
- Microbiology and Parasitology Department, Soba University Hospital, University of Khartoum, Khartoum, Sudan
| | - Bruno Silvester Lopes
- School of Health and Life Sciences, Teesside University, Middlesbrough, United Kingdom,National Horizons Centre, Teesside University, Darlington, United Kingdom,Bruno Silvester Lopes ✉
| | - Ehssan Moglad
- Department of Pharmaceutics, College of Pharmacy, Prince Sattam bin Abdulaziz University, Al-Kharj, Saudi Arabia
| |
Collapse
|
20
|
Chomkatekaew C, Thaipadungpanit J, Hearn P, Soeng S, Pol S, Neou L, Hopkins J, Turner P, Batty EM. Detection of maternal transmission of resistant Gram-negative bacteria in a Cambodian hospital setting. Front Microbiol 2023; 14:1158056. [PMID: 37125167 PMCID: PMC10140293 DOI: 10.3389/fmicb.2023.1158056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Accepted: 03/23/2023] [Indexed: 05/02/2023] Open
Abstract
Infection with Extended-spectrum beta-lactamase -producing Enterobacterales (ESBL-E) is common in infants and leads to increased intensive care unit admission and mortality, but the role of maternal transmission in colonization of infants is unclear. Using paired isolates from 50 pairs of mothers and neonates admitted to a Cambodian hospital, we investigated antimicrobial resistance in Escherichia coli and Klebsiella pneumoniae using whole genome sequencing. We detected a wide variety of ESBL-E genes present in this population along with high levels of multidrug resistance. From 21 pairs where the same organism was present in both mother and neonate, we identified eight pairs with identical or near-identical isolates from both individuals suggestive of transmission at or around birth, including a pair with transmission of multiple strains. We found no evidence for transmission of plasmids only from mother to infant. This suggests vertical transmission outside hospitals as a common cause of ESBL-E colonization in neonates.
Collapse
Affiliation(s)
- Chalita Chomkatekaew
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Janjira Thaipadungpanit
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Department of Clinical Tropical Medicine, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
| | - Pasco Hearn
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Sona Soeng
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Sreymom Pol
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Leakhena Neou
- Neonatal Unit, Angkor Hospital for Children, Siem Reap, Cambodia
| | - Jill Hopkins
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Center for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Paul Turner
- Cambodia-Oxford Medical Research Unit, Angkor Hospital for Children, Siem Reap, Cambodia
- Center for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
| | - Elizabeth M. Batty
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical Medicine, Mahidol University, Bangkok, Thailand
- Center for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, United Kingdom
- *Correspondence: Elizabeth M. Batty,
| |
Collapse
|
21
|
Wang L, Zhu M, Yan C, Zhang Y, He X, Wu L, Xu J, Lu J, Bao Q, Hu Y, Xu T, Liang J. Class 1 integrons and multiple mobile genetic elements in clinical isolates of the Klebsiella pneumoniae complex from a tertiary hospital in eastern China. Front Microbiol 2023; 14:985102. [PMID: 36950157 PMCID: PMC10026359 DOI: 10.3389/fmicb.2023.985102] [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: 07/03/2022] [Accepted: 02/07/2023] [Indexed: 03/08/2023] Open
Abstract
Background The emergence of highly drug-resistant K. pneumoniae, has become a major public health challenge. In this work, we aim to investigate the diversity of species and sequence types (STs) of clinical Klebsiella isolates and to characterize the prevalence and structure of class 1 integrons. Methods Based on the whole genome sequencing, species identification was performed by 16S rRNA gene homology and average nucleotide identity (ANI) analysis. STs were determined in accordance with the international MLST schemes for K. pneumoniae and K. variicola. Integron characterization and comparative genomic analysis were performed using various bioinformatic tools. Results Species identification showed that the 167 isolates belonged to four species: K. pneumoniae, K. variicola subsp. variicola, K. quasipneumoniae and K. aerogenes. Thirty-six known and 5 novel STs were identified in K. pneumoniae, and 10 novel STs were identified in K. variicola subsp. variicola. Class 1 integrons were found in 57.49% (96/167) of the isolates, and a total of 169 resistance gene cassettes encoding 19 types of resistance genes, including carbapenem resistance gene (bla IPM-4) and class D β-lactamases gene (bla OXA-1 and bla OXA-10), were identified. Among the 17 complete genomes, 29 class 1 integrons from 12 groups were found, only 1 group was encoded on chromosomes. Interestingly, one plasmid (pKP167-261) carrying two copies of approximately 19-kb IS26-Int1 complex resistance region that contains an integron and a multidrug resistance gene fragment. Conclusion The results of this work demonstrated that the species and STs of the clinical Klebsiella isolates were more complex by the whole genome sequence analysis than by the traditional laboratory methods. Finding of the new structure of MGEs related to the resistance genes indicates the great importance of deeply exploring the molecular mechanisms of bacterial multidrug resistance.
Collapse
Affiliation(s)
- Lan Wang
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Mei Zhu
- Department of Clinical Laboratory, Zhejiang Hospital, Hangzhou, Zhejiang, China
| | - Chunxia Yan
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Yanfang Zhang
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Xuying He
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Lin Wu
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Jiefeng Xu
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Junwan Lu
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
| | - Qiyu Bao
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Yunliang Hu
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
| | - Teng Xu
- Institute of Translational Medicine, Baotou Central Hospital, Baotou, China
- *Correspondence: Teng Xu,
| | - Jialei Liang
- Medical Molecular Biology Laboratory, School of Medicine, Jinhua Polytechnic, Jinhua, China
- The Second Affiliated Hospital and Yuying Children’s Hospital, Wenzhou Medical University, Wenzhou, China
- Jialei Liang,
| |
Collapse
|
22
|
Mahazu S, Prah I, Ota Y, Hayashi T, Nukui Y, Suzuki M, Hoshino Y, Akeda Y, Suzuki T, Ishino T, Ablordey A, Saito R. Klebsiella Species and Enterobacter cloacae Isolates Harboring blaOXA-181 and blaOXA-48: Resistome, Fitness Cost, and Plasmid Stability. Microbiol Spectr 2022; 10:e0332022. [PMID: 36453894 PMCID: PMC9769605 DOI: 10.1128/spectrum.03320-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 11/11/2022] [Indexed: 12/03/2022] Open
Abstract
IncX3 and IncL plasmids have been named as catalysts advancing dissemination of blaOXA-181 and blaOXA-48 genes. However, their impact on the performance of host cells is vastly understudied. Genetic characteristics of blaOXA-48- and blaOXA-181-containing Klebsiella pneumoniae (EFN299), Klebsiella quasipneumoniae (EFN262), and Enterobacter cloacae (EFN743) isolated from clinical samples in a Ghanaian hospital were investigated by whole-genome sequencing. Transfer of plasmids by conjugation and electroporation, plasmid stability, fitness cost, and genetic context of blaOXA-48, blaOXA-181, and blaDHA-1 were assessed. blaOXA-181 was carried on two IncX3 plasmids, an intact 51.5-kb IncX3 plasmid (p262-OXA-181) and a 45.3-kb IncX3 plasmid (p743-OXA-181) without replication protein sequence. The fluoroquinolone-resistant gene qnrS1 region was also excised, and unlike in p262-OXA-181, the blaOXA-181 drug-resistant region was not found on a composite transposon. blaOXA-48 was carried on a 74.6-kb conjugative IncL plasmid with unknown ~10.9-kb sequence insertion. This IncL plasmid proved to be highly transferable, with a conjugation efficiency of 1.8 × 10-2. blaDHA-1 was present on an untypeable 22.2 kb genetic structure. Plasmid stability test revealed plasmid loss rate between 4.3% and 12.4%. The results also demonstrated that carriage of IncX3-blaOXA-181 or IncL-blaOXA-48 plasmids was not associated with any fitness defect, but rather an enhanced competitive ability of host cells. This study underscores the significant contribution of IncX3 and IncL plasmids in the dissemination of resistance genes and their efficient transfer calls for regular monitoring to control the expansion of resistant strains. IMPORTANCE The growing rate of antibiotic resistance is an important global health threat. This threat is exacerbated by the lack of safe and potent alternatives to carbapenems in addition to the slow developmental process of newer and effective antibiotics. Infections by carbapenem-resistant Gram-negative bacteria are becoming almost untreatable, leading to poor clinical outcomes and high mortality rates. OXA-48-like carbapenemases are one of the most widespread carbapenemases accounting for resistance among Enterobacteriaecae. We characterized OXA-48- and OXA-181-producing Enterobacteriaecae to gain insights into the genetic basis and mechanism of resistance to carbapenems. Findings from the study showed that the genes encoding these enzymes were carried on highly transmissible plasmids, one of which had sequences absent in other similar plasmids. This implies that mobile genetic elements are important players in the dissemination of resistance genes. Further characterization of this plasmid is warranted to determine the role of this sequence in the spread of resistance genes.
Collapse
Affiliation(s)
- Samiratu Mahazu
- Department of Molecular Microbiology, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Parasitology and Tropical Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Isaac Prah
- Department of Molecular Microbiology, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Molecular Virology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yusuke Ota
- Department of Molecular Microbiology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Takaya Hayashi
- Department of Molecular Virology, Tokyo Medical and Dental University, Tokyo, Japan
| | - Yoko Nukui
- Department of Infection Control and Prevention, Tokyo Medical and Dental University Hospital, Tokyo, Japan
- Department of Infection Control and Laboratory Medicine, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Masato Suzuki
- Antimicrobial Resistance Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yoshihiko Hoshino
- Department of Mycobacteriology, Leprosy Research Center, National Institute of Infectious Diseases, Tokyo, Japan
| | - Yukihiro Akeda
- Department of Bacteriology I, National Institute of Infectious Diseases, Tokyo, Japan
| | - Toshihiko Suzuki
- Department of Bacterial Pathogenesis, Tokyo Medical and Dental University, Tokyo, Japan
| | - Tomoko Ishino
- Department of Parasitology and Tropical Medicine, Tokyo Medical and Dental University, Tokyo, Japan
| | - Anthony Ablordey
- Department of Bacteriology, Noguchi Memorial Institute for Medical Research, University of Ghana, Accra, Ghana
| | - Ryoichi Saito
- Department of Molecular Microbiology, Tokyo Medical and Dental University, Tokyo, Japan
- Department of Infection Control and Prevention, Tokyo Medical and Dental University Hospital, Tokyo, Japan
| |
Collapse
|
23
|
Accurate Identification of Klebsiella variicola by MALDI-TOF Mass Spectrometry in Clinical Microbiology Laboratories. Microbiol Spectr 2022; 10:e0284422. [PMID: 36125293 PMCID: PMC9603720 DOI: 10.1128/spectrum.02844-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Klebsiella variicola is a pathogen that is increasingly recognized as being associated with human infections, but the methods available to clinical microbiology laboratories for accurate identification are limited. In this study, we assessed the accuracy of identification of K. variicola by matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) mass spectrometry using genetic identification with multiplex PCR as the reference method. Antimicrobial susceptibilities and virulence of K. variicola strains were also investigated. Fifty-five Klebsiella pneumoniae, 26 K. variicola, and 2 Klebsiella quasipneumoniae clinical strains were used for evaluation. Both MALDI Biotyper with library version 9 and Klebsiella MALDI TypeR, a web-based species identification tool using MALDI-TOF data, accurately identified all K. variicola strains. In addition, two strains of K. quasipneumoniae were accurately identified with Klebsiella MALDI TypeR. Whole-genome sequencing confirmed the accurate identification to the subspecies level by Klebsiella MALDI TypeR for four strains (two strains each of K. variicola subsp. variicola and K. quasipneumoniae subsp. similipneumoniae). While 13 strains, 3 strains, and 1 strain of K. pneumoniae showed nonsusceptibility to ampicillin-sulbactam, ceftriaxone, and meropenem, respectively, all strains of K. variicola were susceptible to all tested antimicrobial agents. Although two K. variicola strains were positive for the string test, no K. variicola strains harbored any of the genes associated with hypervirulence of K. pneumoniae. Accurate identification of the K. pneumoniae complex, including K. variicola, by MALDI-TOF in clinical microbiology laboratories is expected to clarify the clinical characteristics of each species in the future. IMPORTANCE Recent widespread use of bacterial whole-genome sequencing analysis has resulted in the proposal of novel bacterial species and reclassification of taxonomy. Accurate methods for identification of bacterial species in clinical microbiology laboratories are essential to accumulate information on the clinical characteristics of each bacterial species. Klebsiella variicola is a member of the Klebsiella pneumoniae complex, and its association with human infections has been increasingly recognized, but accurate identification methods approved for use in clinical microbiology laboratories have been limited thus far. The findings of the present study suggest that K. variicola can be accurately identified by matrix-assisted laser desorption ionization-time of flight mass spectrometry using updated library or web-based identification tools. Accurate identification will promote exploration of clinical characteristics of K. variicola.
Collapse
|
24
|
Bellini R, Guedes IA, Ciapina LP, de Vasconcelos ATR, Dardenne LE, Nicolás MF. Analysis of a novel class A β-lactamase OKP-B-6 of Klebsiella quasipneumoniae: structural characterisation and interaction with commercially available drugs. Mem Inst Oswaldo Cruz 2022; 117:e220102. [PMID: 36169569 PMCID: PMC9506704 DOI: 10.1590/0074-02760220102] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2022] [Accepted: 08/22/2022] [Indexed: 08/30/2023] Open
Abstract
BACKGROUND Gram-negative and Gram-positive bacteria produce beta-lactamase as factors to overcome beta-lactam antibiotics, causing their hydrolysis and impaired antimicrobial action. Class A beta-lactamase contains the chromosomal sulfhydryl reagent variable (SHV, point mutation variants of SHV-1), LEN (Klebsiella pneumoniae strain LEN-1), and other K. pneumoniae beta-lactamase (OKP) found mostly in Klebsiella’s phylogroups. The SHV known as extended-spectrum β-lactamase can inactivate most beta-lactam antibiotics. Class A also includes the worrisome plasmid-encoded Klebsiella pneumoniae carbapenemase (KPC-2), a carbapenemase that can inactivate most beta-lactam antibiotics, carbapenems, and some beta-lactamase inhibitors. OBJECTIVES So far, there is no 3D crystal structure for OKP-B, so our goal was to perform structural characterisation and molecular docking studies of this new enzyme. METHODS We applied a homology modelling method to build the OKP-B-6 structure, which was compared with SHV-1 and KPC-2 according to their electrostatic potentials at the active site. Using the DockThor-VS, we performed molecular docking of the SHV-1 inhibitors commercially available as sulbactam, tazobactam, and avibactam against the constructed model of OKP-B-6. FINDINGS From the point of view of enzyme inhibition, our results indicate that OKP-B-6 should be an extended-spectrum beta-lactamase (ESBL) susceptible to the same drugs as SHV-1. MAIN CONCLUSIONS This conclusion advantageously impacts the clinical control of the bacterial pathogens encoding OKP-B in their genome by using any effective, broad-spectrum, and multitarget inhibitor against SHV-containing bacteria.
Collapse
Affiliation(s)
- Reinaldo Bellini
- Laboratório Nacional de Computação Científica, Petrópolis, RJ, Brasil
| | | | | | | | | | | |
Collapse
|
25
|
Draft Genome Sequence of a Multidrug-Resistant and Novel Sequence Type 6130 Klebsiella quasipneumoniae Strain C11S11_BCSIR Isolated from Wastewater of a Tertiary Care Hospital in Chattogram, Bangladesh. Microbiol Resour Announc 2022; 11:e0065422. [DOI: 10.1128/mra.00654-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
In this article, we report draft genome sequence and annotation of
Klebsiella quasipneumoniae
from the wastewater source in Bangladesh. Here, we identified
Klebsiella quasipneumoniae
strain C11S11_BCSIR, a multidrug-resistant pathogenic bacterium harboring seven antimicrobial resistance genes of five major antibiotic classes with a novel multilocus sequence type (MLST) (ST6130).
Collapse
|
26
|
Relevance of prokaryotic subspecies in the age of genomics. New Microbes New Infect 2022; 48:101024. [PMID: 36176539 PMCID: PMC9513812 DOI: 10.1016/j.nmni.2022.101024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 08/13/2022] [Accepted: 08/22/2022] [Indexed: 11/20/2022] Open
|
27
|
Hernández-Salmerón JE, Moreno-Hagelsieb G. FastANI, Mash and Dashing equally differentiate between Klebsiella species. PeerJ 2022; 10:e13784. [PMID: 35891643 PMCID: PMC9308963 DOI: 10.7717/peerj.13784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 07/05/2022] [Indexed: 01/17/2023] Open
Abstract
Bacteria of the genus Klebsiella are among the most important multi-drug resistant human pathogens, though they have been isolated from a variety of environments. The importance and ubiquity of these organisms call for quick and accurate methods for their classification. Average Nucleotide Identity (ANI) is becoming a standard for species delimitation based on whole genome sequence comparison. However, much faster genome comparison tools have been appearing in the literature. In this study we tested the quality of different approaches for genome-based species delineation against ANI. To this end, we compared 1,189 Klebsiella genomes using measures calculated with Mash, Dashing, and DNA compositional signatures, all of which run in a fraction of the time required to obtain ANI. Receiver Operating Characteristic (ROC) curve analyses showed equal quality in species discrimination for ANI, Mash and Dashing, with Area Under the Curve (AUC) values above 0.99, followed by DNA signatures (AUC: 0.96). Accordingly, groups obtained at optimized cutoffs largely agree with species designation, with ANI, Mash and Dashing producing 15 species-level groups. DNA signatures broke the dataset into more than 30 groups. Testing Mash to map species after adding draft genomes to the dataset also showed excellent results (AUC above 0.99), producing a total of 26 Klebsiella species-level groups. The ecological niches of Klebsiella strains were found to neither be related to species delimitation, nor to protein functional content, suggesting that a single Klebsiella species can have a wide repertoire of ecological functions.
Collapse
|
28
|
Zhang Z, Wang H, Guo Y, Liu Z, Chang Z. Metagenome Analysis of the Bacterial Characteristics in Invasive Klebsiella Pneumoniae Liver Abscesses. Front Cell Infect Microbiol 2022; 12:812542. [PMID: 35909970 PMCID: PMC9334793 DOI: 10.3389/fcimb.2022.812542] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Accepted: 06/01/2022] [Indexed: 11/17/2022] Open
Abstract
Background Klebsiella pneumoniae liver abscess (KPLA) combined with extrahepatic migratory infection (EMI) is defined as invasive KPLA (IKPLA) and is associated with a poor prognosis. The mechanism of IKPLA formation is yet to be elucidated. In this study, metagenomic sequencing was used to compare the bacterial characteristics between IKPLA and KPLA to explore the underlying mechanism of invasiveness. Methods Clinical details, imaging, and microbial features were retrospectively evaluated by medical record review. Metagenomic sequencing was performed on the pus samples of liver abscesses whose culture results were indicative of monomicrobial Klebsiella pneumoniae (K. pneumoniae). Bacterial diversity and composition in IKPLA and KPLA were comparatively analyzed, and the key pathways and genes that may affect invasiveness were further explored. Results Sixteen patients were included in this study. Five patients with EMI were included in the IKPLA group, and the other eleven patients without EMI were assigned to the KPLA group. There was no statistical difference in the hypermucoviscous phenotype and serotype of K. pneumoniae between the two groups. The bacterial diversity of IKPLA was lower than that of KPLA. The abundant taxa in the IKPLA group were primarily species of unclassified Enterobacteriaceae and K. pneumoniae. The KPLA group had a high abundance of the genera Tetrasphaera and Leuconostoc. Metabolic pathway genes represented most of the enriched genes in IKPLA. Fourteen pathogenic genes with significant differences in abundance were identified between the two groups, including ybtS, fepC, phoQ, acrB, fimK, magA, entC, arnT, iucA, fepG, oqxB, entA, tonB, and entF (p < 0.001). Conclusion The diversity and bacterial composition of IKPLA were significantly different from those of KPLA. Microbiological changes in the abscess, activation of the related metabolic pathways, and the pathogenic gene expression may constitute a novel mechanism that regulates the invasiveness of KPLA.
Collapse
Affiliation(s)
- Zhijie Zhang
- Department of Laboratory Medicine, Shengjing Hospital of China Medical University, Shenyang, China
| | - Hairui Wang
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Yawen Guo
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhaoyu Liu
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, China
| | - Zhihui Chang
- Department of Radiology, Shengjing Hospital of China Medical University, Shenyang, China
- *Correspondence: Zhihui Chang,
| |
Collapse
|
29
|
Sajeev S, Hamza M, Sivaraman GK, Ghatak S, Ojha R, Mendem SK, Murugesan D, Raisen C, Shome BR, Holmes MA. Genomic insights of beta-lactamase producing Klebsiella quasipneumoniae subsp. similipneumoniae belonging to sequence type 1699 from retail market fish, India. Arch Microbiol 2022; 204:454. [PMID: 35781844 DOI: 10.1007/s00203-022-03071-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 06/07/2022] [Accepted: 06/13/2022] [Indexed: 11/25/2022]
Abstract
Klebsiella quasipneumoniae is a recently described species and often misidentified as Klebsiella pneumoniae. Here, we report the genomic characterization of Klebsiella quasipneumoniae subsp. similipneumoniae (India238 strain) isolated from fish. The annotated genome acknowledged the presence of blaCTX-M-15, blaOKP-B-1, fosA5, oqxAB and virulence genes. The strain with ST1699 and serotypes KL52 and OL103 also harboured insertion sequences (ISs): ISKpn26 and ISEc9. Three complete phage genomes were identified in contigs 1 and 6 of the bacterial genome, enhancing the prospects of genome manipulation. The study highlights the pitfall of conventional microbiological identification methods to distinguish K. pneumoniae and K. quasipneumoniae. This is the first Indian study documenting the incidence of extended-spectrum beta-lactamase (ESBL)-producing K. quasipneumoniae subsp. similipneumoniae from a non-clinical environment, equipped with virulomes and associated mobile genetic elements. Given that fish can act as a potential vector for transmission of antimicrobial resistance genes, our findings have paramount importance on human health.
Collapse
Affiliation(s)
- Sudha Sajeev
- Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology, Cochin, Kerala, India
| | - Muneeb Hamza
- Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology, Cochin, Kerala, India
| | - Gopalan Krishnan Sivaraman
- Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology, Cochin, Kerala, India.
| | - Sandeep Ghatak
- Division of Animal Health, ICAR Research Complex for NEH Region, Umiam, India.
| | - Rakshit Ojha
- Department of Disease Investigation, ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | - Suresh Kumar Mendem
- Department of Disease Investigation, ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | - Devi Murugesan
- Department of Disease Investigation, ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | - Claire Raisen
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Bibek R Shome
- Department of Disease Investigation, ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| |
Collapse
|
30
|
Prevalence, molecular characterization, and drug susceptibility of extended-spectrum β-lactamase-producing Klebsiella pneumoniae, K. quasipneumoniae, and K. variicola in Japan. Microb Pathog 2022; 169:105663. [PMID: 35779789 DOI: 10.1016/j.micpath.2022.105663] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 11/20/2022]
Abstract
Klebsiella pneumoniae is an extended-spectrum β-lactamase (ESBL)-producing bacterium (ESBL-KP). Recently, K. quasipneumoniae and K. variicola were reclassified from K. pneumoniae based on genome sequencing. However, the molecular characteristics and antimicrobial susceptibility patterns of ESBL-producing K. quasipneumoniae (ESBL-KQ) and ESBL-producing K. variicola (ESBL-KV) remain unclear. Here, we aimed to distinguish ESBL-KQ and ESBL-KV from ESBL-KP in terms of frequency, genomic characteristics, and antimicrobial susceptibility patterns. Of the 74 ESBL-KP isolates, 12 (16.2%) were reclassified as ESBL-KQ and 1 (1.4%) as ESBL-KV. Patients with ESBL-KP and ESBL-KQ infections were of similar age; ESBL-KQ infection was more frequent in men. Infection-associated mortality seemed to be similar in patients with ESBL-KQ and ESBL-KP infections, without a statistically significant difference (p = 0.99). Genetic analysis revealed that 19.1% of ESBL-producing Klebsiella isolates harbored AmpC. The prevalence of AmpC was higher with ESBL-KP (31.1%) than with ESBL-KQ (8.3%), although this difference was not statistically significant (p = 0.52). The frequency of ESBL-KQ with AmpC and quinolone-resistance-associated genes in clinical samples increased annually (p = 0.04). The prevalence of Klebsiella with fluoroquinolone-resistance genes did not differ significantly between species (p > 0.99). The gene profiles of ESBL-KQ and ESBL-KP differed, and the prevalence of antimicrobial resistance via AmpC and fluoroquinolone-resistance genes increased. Further studies are required to distinguish ESBL-KP and ESBL-KQ and determine the mechanism underlying the spread of AmpC and quinolone-resistance genes to prevent further spread of these genes.
Collapse
|
31
|
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.
Collapse
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
| |
Collapse
|
32
|
Xie M, Chen K, Chan EWC, Zhang R, Chen S. Characterization of clinical carbapenem-resistant K1 Klebsiella quasipneumoniae subsp. similipneumoniae strains harboring virulence plasmid. Int J Antimicrob Agents 2022; 60:106628. [PMID: 35760224 DOI: 10.1016/j.ijantimicag.2022.106628] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2021] [Revised: 06/16/2022] [Accepted: 06/19/2022] [Indexed: 11/05/2022]
Abstract
The continuous emergence of carbapenem-resistant and hypervirulent Klebsiella pneumoniae (CR-HvKP) poses great challenges to human health due to the extremely high morbidity and mortality. Klebsiella quasipneumoniae is a newly described bacterial species and often mis-identified as Klebsiella pneumoniae. Clinical K. quasipneumoniae strains have been reported worldwide, in which multidrug-resistant lineages have become a severe health problem, while less has been understood on this important pathogen. In this study, we characterized three clinical carbapenem-resistant K. quasipneumoniae subsp. similipneumoniae isolates, which belonged to sequence type (ST) ST367 and capsular type K1 and contained several virulence genes, including salmochelin (iroBCDN), aerobactin (iucABCDiutA), regulator of mucoid phenotype (rmpA/A2), as well as some resistance genes, including blaKPC-2, blaOKP-B-9, and oqxAB. These carbapenem-resistant K. quasipneumoniae subsp. similipneumoniae strains that containing virulence genes exhibited higher level of virulence and serum resistance than classical K. pneumoniae strain, while their virulence levels were slightly lower when compared with typical ST11 CR-HvKP and ST23 K1 HvKP strains. This study reported for the first time the genetic and virulence characterization of clinical K. quasipneumoniae subsp. similipneumoniae strains that simultaneously contained blaKPC-2 gene and virulence genes, which contributed to a better understanding of their resistance and pathogenicity as well as for epidemic surveillance worldwide.
Collapse
Affiliation(s)
- Miaomiao Xie
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Kaichao Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Edward Wai-Chi Chan
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong
| | - Rong Zhang
- Department of Clinical Laboratory, Second Affiliated Hospital of Zhejiang University, School of Medicine, Zhejiang, Hangzhou, China.
| | - Sheng Chen
- Department of Infectious Diseases and Public Health, Jockey Club College of Veterinary Medicine and Life Sciences, City University of Hong Kong, Kowloon, Hong Kong.
| |
Collapse
|
33
|
Rocha J, Henriques I, Gomila M, Manaia CM. Common and distinctive genomic features of Klebsiella pneumoniae thriving in the natural environment or in clinical settings. Sci Rep 2022; 12:10441. [PMID: 35729190 PMCID: PMC9213442 DOI: 10.1038/s41598-022-14547-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Accepted: 06/08/2022] [Indexed: 01/17/2023] Open
Abstract
The Klebsiella pneumoniae complex is comprised of ubiquitous bacteria that can be found in soils, plants or water, and as humans' opportunistic pathogens. This study aimed at inferring common and distinctive features in clinical and environmental K. pneumoniae. Whole genome sequences of members of the K. pneumoniae complex (including K. variicola, n = 6; and K. quasipneumoniae, n = 7), of clinical (n = 78) and environmental (n = 61) origin from 21 countries were accessed from the GenBank. These genomes were compared based on phylogeny, pangenome and selected clinically relevant traits. Phylogenetic analysis based on 2704 genes of the core genome showed close relatedness between clinical and environmental strains, in agreement with the multi-locus sequence typing. Eight out of the 62 sequence types (STs) identified, included both clinical and environmental genomes (ST11, ST14, ST15, ST37, ST45, ST147, ST348, ST437). Pangenome-wide association studies did not evidence significant differences between clinical and environmental genomes. However, the genomes of clinical isolates presented significantly more exclusive genes related to antibiotic resistance/plasmids, while the environmental isolates yielded significantly higher allelic diversity of genes related with functions such as efflux or oxidative stress. The study suggests that K. pneumoniae can circulate among the natural environment and clinical settings, probably under distinct adaptation pressures.
Collapse
Affiliation(s)
- Jaqueline Rocha
- Universidade Católica Portuguesa, CBQF-Centro de Biotecnologia e Química Fina-Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal
| | - Isabel Henriques
- Department of Life Sciences, Faculty of Science and Technology, University of Coimbra, Coimbra, Portugal.,CESAM, University of Aveiro, Aveiro, Portugal
| | - Margarita Gomila
- Microbiologia, Departament de Biologia, Universitat de les Illes Balears, Palma de Mallorca, Spain
| | - Célia M Manaia
- Universidade Católica Portuguesa, CBQF-Centro de Biotecnologia e Química Fina-Laboratório Associado, Escola Superior de Biotecnologia, Rua Diogo Botelho 1327, 4169-005, Porto, Portugal.
| |
Collapse
|
34
|
Watanabe N, Watari T, Otsuka Y, Yamagata K, Fujioka M. Clinical characteristics and antimicrobial susceptibility of Klebsiella pneumoniae, Klebsiella variicola and Klebsiella quasipneumoniae isolated from human urine in Japan. J Med Microbiol 2022; 71. [PMID: 35699119 DOI: 10.1099/jmm.0.001546] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Introduction. The three Klebsiella species K. pneumoniae, K. variicola and K. quasipneumoniae are difficult to distinguish, owing to their similar biochemical properties, and are often confused in medical practice.Gap statement. There is a scarcity of data comparing the clinical characteristics and antimicrobial susceptibility of K. pneumoniae, K. variicola and K. quasipneumoniae. We believe that knowledge of the characteristics of each species will help in their better identification. Further, knowing the antimicrobial susceptibility of the species will help physicians in prescribing an effective treatment course for Klebsiella infections.Aim. This study aimed to determine the clinical characteristics and antimicrobial resistance of K. pneumoniae, K. variicola and K. quasipneumoniae isolated from human urine samples.Methodology. This study included 125 K. pneumoniae strains isolated from human urine samples. Multiplex polymerase chain reaction was performed to identify K. pneumoniae, K. variicola and K. quasipneumoniae. We retrospectively investigated the patient background, complications of bacteraemia, antimicrobial susceptibility and extended-spectrum β-lactamase (ESBL).Results. We identified 84 (67.2 %), 31 (24.8 %) and 10 strains (8 .0%) of K. pneumoniae, K. variicola and K. quasipneumoniae, respectively. There was no difference in patient background and frequency of bacteraemia complications among these species. K. pneumoniae was significantly less susceptible than K. variicola to ampicillin/sulbactam (P=0.03) and piperacillin (P<0.01). Furthermore, K. pneumoniae (79.8 %) was less susceptible to trimethoprim/sulfamethoxazole than K. variicola (96.8 %) and K. quasipneumoniae (100 %). There were nine ESBL-producing strains (7.2 %), all of which were K. pneumoniae.Conclusion. There was no difference in patient background and frequency of bacteraemia complications between K. pneumoniae, K. variicola and K. quasipneumoniae isolated from urine. The three Klebsiella species showed a varying extent of antimicrobial susceptibility and ESBL production, and accurate identification is needed to understand the epidemiology of these species.
Collapse
Affiliation(s)
- Naoki Watanabe
- Department of Clinical Laboratory, Kameda Medical Center, Higashi-cho 929, Kamogawa-shi, Chiba, 296-8602, Japan.,Hirosaki University, Graduate School of Health Sciences, Hon-cho 66-1, Hirosaki-shi, Aomori, 036-8564, Japan
| | - Tomohisa Watari
- Department of Clinical Laboratory, Kameda Medical Center, Higashi-cho 929, Kamogawa-shi, Chiba, 296-8602, Japan
| | - Yoshihito Otsuka
- Department of Clinical Laboratory, Kameda Medical Center, Higashi-cho 929, Kamogawa-shi, Chiba, 296-8602, Japan
| | - Kazufumi Yamagata
- Hirosaki University, Graduate School of Health Sciences, Hon-cho 66-1, Hirosaki-shi, Aomori, 036-8564, Japan
| | - Miyuki Fujioka
- Hirosaki University, Graduate School of Health Sciences, Hon-cho 66-1, Hirosaki-shi, Aomori, 036-8564, Japan
| |
Collapse
|
35
|
Gorrie CL, Mirčeta M, Wick RR, Judd LM, Lam MMC, Gomi R, Abbott IJ, Thomson NR, Strugnell RA, Pratt NF, Garlick JS, Watson KM, Hunter PC, Pilcher DV, McGloughlin SA, Spelman DW, Wyres KL, Jenney AWJ, Holt KE. Genomic dissection of Klebsiella pneumoniae infections in hospital patients reveals insights into an opportunistic pathogen. Nat Commun 2022; 13:3017. [PMID: 35641522 PMCID: PMC9156735 DOI: 10.1038/s41467-022-30717-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 05/04/2022] [Indexed: 12/11/2022] Open
Abstract
Klebsiella pneumoniae is a major cause of opportunistic healthcare-associated infections, which are increasingly complicated by the presence of extended-spectrum beta-lactamases (ESBLs) and carbapenem resistance. We conducted a year-long prospective surveillance study of K. pneumoniae clinical isolates in hospital patients. Whole-genome sequence (WGS) data reveals a diverse pathogen population, including other species within the K. pneumoniae species complex (18%). Several infections were caused by K. variicola/K. pneumoniae hybrids, one of which shows evidence of nosocomial transmission. A wide range of antimicrobial resistance (AMR) phenotypes are observed, and diverse genetic mechanisms identified (mainly plasmid-borne genes). ESBLs are correlated with presence of other acquired AMR genes (median n = 10). Bacterial genomic features associated with nosocomial onset are ESBLs (OR 2.34, p = 0.015) and rhamnose-positive capsules (OR 3.12, p < 0.001). Virulence plasmid-encoded features (aerobactin, hypermucoidy) are observed at low-prevalence (<3%), mostly in community-onset cases. WGS-confirmed nosocomial transmission is implicated in just 10% of cases, but strongly associated with ESBLs (OR 21, p < 1 × 10−11). We estimate 28% risk of onward nosocomial transmission for ESBL-positive strains vs 1.7% for ESBL-negative strains. These data indicate that K. pneumoniae infections in hospitalised patients are due largely to opportunistic infections with diverse strains, with an additional burden from nosocomially-transmitted AMR strains and community-acquired hypervirulent strains. Klebsiella pneumoniae is an opportunistic pathogen of increasing public health concern due to the prevalence of antimicrobial resistance. Here, the authors provide insight into the resistance profiles, bacterial genome features and virulence genes, in a year-long prospective study of K. pneumoniae clinical isolates.
Collapse
Affiliation(s)
- Claire L Gorrie
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Vic, Australia.
| | - Mirjana Mirčeta
- Microbiology Unit, Alfred Pathology Service, The Alfred Hospital, Melbourne, Vic, Australia
| | - Ryan R Wick
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia
| | - Louise M Judd
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia.,Doherty Applied Microbial Genomics (DAMG), Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Vic, Australia
| | - Margaret M C Lam
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia
| | - Ryota Gomi
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia.,Department of Environmental Engineering, Graduate School of Engineering, Kyoto University, Kyoto, Japan
| | - Iain J Abbott
- Microbiology Unit, Alfred Pathology Service, The Alfred Hospital, Melbourne, Vic, Australia.,Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia
| | - Nicholas R Thomson
- Wellcome Sanger Institute, Hinxton, Cambs, UK.,Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK
| | - Richard A Strugnell
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Vic, Australia
| | - Nigel F Pratt
- Infectious Diseases Clinical Research Unit, The Alfred Hospital, Melbourne, Vic, Australia
| | - Jill S Garlick
- Infectious Diseases Clinical Research Unit, The Alfred Hospital, Melbourne, Vic, Australia
| | - Kerrie M Watson
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia
| | - Peter C Hunter
- Aged Care, Caulfield Hospital, Alfred Health, Melbourne, Vic, Australia
| | - David V Pilcher
- Intensive Care Unit, The Alfred Hospital, Melbourne, Vic, Australia.,Australian and New Zealand Intensive Care Research Centre, School of Public Health and Preventative Medicine, Monash University, Melbourne, Vic, Australia
| | - Steve A McGloughlin
- Intensive Care Unit, The Alfred Hospital, Melbourne, Vic, Australia.,Australian and New Zealand Intensive Care Research Centre, School of Public Health and Preventative Medicine, Monash University, Melbourne, Vic, Australia
| | - Denis W Spelman
- Microbiology Unit, Alfred Pathology Service, The Alfred Hospital, Melbourne, Vic, Australia.,Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia
| | - Kelly L Wyres
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia
| | - Adam W J Jenney
- Department of Microbiology and Immunology at the Peter Doherty Institute for Infection and Immunity, The University of Melbourne, Melbourne, Vic, Australia.,Microbiology Unit, Alfred Pathology Service, The Alfred Hospital, Melbourne, Vic, Australia.,Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia
| | - Kathryn E Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Vic, Australia. .,Department of Infection Biology, London School of Hygiene & Tropical Medicine, London, UK.
| |
Collapse
|
36
|
Karaliute I, Ramonaite R, Bernatoniene J, Petrikaite V, Misiunas A, Denkovskiene E, Razanskiene A, Gleba Y, Kupcinskas J, Skieceviciene J. Reduction of gastrointestinal tract colonization by Klebsiella quasipneumoniae using antimicrobial protein KvarIa. Gut Pathog 2022; 14:17. [PMID: 35473598 PMCID: PMC9040220 DOI: 10.1186/s13099-022-00492-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Accepted: 04/09/2022] [Indexed: 12/03/2022] Open
Abstract
Background Klebsiella quasipneumoniae is an opportunistic pathogen causing antibiotic-resistant infections of the gastrointestinal tract in many clinical cases. Orally delivered bioactive Klebsiella-specific antimicrobial proteins, klebicins, could be a promising method to eradicate Klebsiella species infecting the gut. Methods Mouse infection model was established based on infection of antibiotic-treated BALB/C mice with K. quasipneumoniae strain DSM28212. Four study groups were used (3 animals/group) to test the antimicrobial efficacy of orally delivered klebicin KvarIa: vehicle-only group (control, phosphate-buffered saline), and other three groups with bacteria, antibiotic therapy and 100 µg of uncoated Kvarla, 100 µg coated KvarIa, 1000 µg coated-KvarIa. Because of the general sensitivity of bacteriocins to gastroduodenal proteases, Kvarla doses were coated with Eudragit®, a GMP-certified formulation agent that releases the protein at certain pH. The coating treatment was selected based on measurements of mouse GI tract pH. The quantity of Klebsiella haemolysin gene (khe) in faecal samples of the study animals was used to quantify the presence of Klebsiella. Results GI colonization of K. quasipneumoniae was achieved only in the antibiotic-treated mice groups. Significant changes in khe marker quantification were found after the use of Eudragit® S100 formulated klebicin KvarIa, at both doses, with a significant reduction of K. quasipneumoniae colonization compared to the vehicle-only control group. Conclusions Mouse GI tract colonization with K. quasipneumoniae can be achieved if natural gut microbiota is suppressed by prior antibiotic treatment. The study demonstrates that GI infection caused by K. quasipneumoniae can be significantly reduced using Eudragit®-protected klebicin KvarIa.
Collapse
Affiliation(s)
- Indre Karaliute
- Institute for Digestive Research, Laboratory of Clinical and Molecular Gastroenterology, Lithuanian University of Health Sciences, Mickeviciaus st. 9, 44307, Kaunas, Lithuania
| | - Rima Ramonaite
- Institute for Digestive Research, Laboratory of Clinical and Molecular Gastroenterology, Lithuanian University of Health Sciences, Mickeviciaus st. 9, 44307, Kaunas, Lithuania
| | - Jurga Bernatoniene
- Department of Drug Technology and Social Pharmacy, Lithuanian University of Health Sciences, Sukileliu Pr. 13, 50161, Kaunas, Lithuania
| | - Vilma Petrikaite
- Laboratory of Drug Targets Histopathology, Institute of Cardiology, Lithuanian University of Health Sciences, 50162, Kaunas, Lithuania
| | | | | | | | - Yuri Gleba
- Nomad Bioscience GmbH, Biozentrum Halle, Weinbergweg 22, 06120, Halle (Saale), Germany
| | - Juozas Kupcinskas
- Institute for Digestive Research, Laboratory of Clinical and Molecular Gastroenterology, Lithuanian University of Health Sciences, Mickeviciaus st. 9, 44307, Kaunas, Lithuania.,Department of Gastroenterology, Lithuanian University of Health Sciences, 44307, Kaunas, Lithuania
| | - Jurgita Skieceviciene
- Institute for Digestive Research, Laboratory of Clinical and Molecular Gastroenterology, Lithuanian University of Health Sciences, Mickeviciaus st. 9, 44307, Kaunas, Lithuania.
| |
Collapse
|
37
|
Liu S, Chen L, Wang L, Zhou B, Ye D, Zheng X, Lin Y, Zeng W, Zhou T, Ye J. Cluster Differences in Antibiotic Resistance, Biofilm Formation, Mobility, and Virulence of Clinical Enterobacter cloacae Complex. Front Microbiol 2022; 13:814831. [PMID: 35464993 PMCID: PMC9019753 DOI: 10.3389/fmicb.2022.814831] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Accepted: 02/24/2022] [Indexed: 12/03/2022] Open
Abstract
Due to the lack of research on the characteristics of different clusters of Enterobacter cloacae complex (ECC), this study aimed to characterize and explore the differences among species of the ECC. An analysis based on hsp60 showed that Enterobacter hormaechei was predominant in ECC. Interestingly, the antibiotic resistance rates of clusters were different, among which E. hormaechei subsp. steigerwaltii (cluster VIII) and Enterobacter cloacae IX (cluster IX) possessed high resistant rates to ciprofloxacin and levofloxacin, but cluster II (Enterobacter kobei) had low resistant rates. Cluster II exhibited a strong biofilm formation ability. Different motility and protease production ability were shown for distinct clusters. A PCR analysis showed that clusters I, III, VI, VIII, and IX carried more virulence genes, while cluster II had fewer. Clusters I, VIII, and IX with high pathogenicity were evaluated using the Galleria mellonella infection model. Thus, the characteristics of resistance, biofilm-forming ability, mobility, and virulence differed among the clusters. The strains were divided into 12 subgroups based on hsp60. The main clusters of ECC clinical strains were I, II, III, VI, VIII, and IX, among which IX, VIII, and I were predominant with high resistance and pathogenicity, and cluster II (E. kobei) was a special taxon with a strong biofilm formation ability under nutrient deficiency, but was associated with low resistance, virulence, and pathogenicity. Hence, clinical classification methods to identify ECC subgroups are an urgent requirement to guide the treatment of clinical infections.
Collapse
Affiliation(s)
- Shixing Liu
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Liqiong Chen
- School of Laboratory Medicine and Life Science, Wenzhou Medical University, Wenzhou, China
| | - Lingbo Wang
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Beibei Zhou
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Dandan Ye
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Xiangkuo Zheng
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Yishuai Lin
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Weiliang Zeng
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Tieli Zhou
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| | - Jianzhong Ye
- Key Laboratory of Clinical Laboratory Diagnosis and Translational Research of Zhejiang Province, Department of Clinical Laboratory, The First Affiliated Hospital of Wenzhou Medical University, Wenzhou, China
| |
Collapse
|
38
|
Multidrug-Resistant Klebsiella variicola Isolated in the Urine of Healthy Bovine Heifers, a Potential Risk as an Emerging Human Pathogen. Appl Environ Microbiol 2022; 88:e0004422. [PMID: 35416681 DOI: 10.1128/aem.00044-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Klebsiella variicola, a member of Klebsiella pneumoniae complex, is found to infect plants, insects, and animals and is considered an emerging pathogen in humans. While antibiotic resistance is often prevalent among K. variicola isolates from humans, this has not been thoroughly investigated in isolates from nonhuman sources. Prior evidence suggests that K. variicola can be transmitted between agricultural products as well as between animals, and the use of antibiotics in agriculture has increased antibiotic resistance in other emerging pathogens. Furthermore, in animals that contain K. variicola as a normal member of the rumen microbiota, the same bacteria can also cause infections, such as clinical mastitis in dairy cows. Here, we describe K. variicola UFMG-H9 and UFMG-H10, both isolated from the urine of healthy Gyr heifers. These two genomes represent the first isolates from the urine of cattle and exhibit greater similarity with strains from the human urinary tract than isolates from bovine fecal or milk samples. Unique to the UFMG-H9 genome is the presence of flagellar genes, the first such observation for K. variicola. Neither of the sampled animals had symptoms associated with K. variicola infection, even though genes associated with virulence and antibiotic resistance were identified in both strains. Both strains were resistant to amoxicillin, erythromycin, and vancomycin, and UFMG-H10 is resistant to fosfomycin. The observed resistances emphasize the concern regarding the emergence of this species as a human pathogen given its circulation in healthy livestock animals. IMPORTANCE Klebsiella variicola is an opportunistic pathogen in humans. It also has been associated with bovine mastitis, which can have significant economic effects. While numerous isolates have been sequenced from human infections, only 12 have been sequenced from cattle (fecal and milk samples) to date. Recently, we discovered the presence of K. variicola in the urine of two healthy heifers, the first identification of K. variicola in the bovine urinary tract and the first confirmed K. variicola isolate encoding for flagella-mediated motility. Here, we present the genome sequences and analysis of these isolates. The bovine urinary genomes are more similar to isolates from the human urinary tract than they are to other isolates from cattle, suggesting niche specialization. The presence of antibiotic resistance genes is concerning, as prior studies have found transmission between animals. These findings are important to understand the circulation of K. variicola in healthy livestock animals.
Collapse
|
39
|
Avershina E, Frye SA, Ali J, Taxt AM, Ahmad R. Ultrafast and Cost-Effective Pathogen Identification and Resistance Gene Detection in a Clinical Setting Using Nanopore Flongle Sequencing. Front Microbiol 2022; 13:822402. [PMID: 35369431 PMCID: PMC8970966 DOI: 10.3389/fmicb.2022.822402] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/27/2022] [Indexed: 02/04/2023] Open
Abstract
Rapid bacterial identification and antimicrobial resistance gene (ARG) detection are crucial for fast optimization of antibiotic treatment, especially for septic patients where each hour of delayed antibiotic prescription might have lethal consequences. This work investigates whether the Oxford Nanopore Technology’s (ONT) Flongle sequencing platform is suitable for real-time sequencing directly from blood cultures to identify bacteria and detect resistance-encoding genes. For the analysis, we used pure bacterial cultures of four clinical isolates of Escherichia coli and Klebsiella pneumoniae and two blood samples spiked with either E. coli or K. pneumoniae that had been cultured overnight. We sequenced both the whole genome and plasmids isolated from these bacteria using two different sequencing kits. Generally, Flongle data allow rapid bacterial ID and resistome detection based on the first 1,000–3,000 generated sequences (10 min to 3 h from the sequencing start), albeit ARG variant identification did not always correspond to ONT MinION and Illumina sequencing-based data. Flongle data are sufficient for 99.9% genome coverage within at most 20,000 (clinical isolates) or 50,000 (positive blood cultures) sequences generated. The SQK-LSK110 Ligation kit resulted in higher genome coverage and more accurate bacterial identification than the SQK-RBK004 Rapid Barcode kit.
Collapse
Affiliation(s)
- Ekaterina Avershina
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Stephan A Frye
- Division of Laboratory Medicine, Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Jawad Ali
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway
| | - Arne M Taxt
- Division of Laboratory Medicine, Department of Microbiology, Oslo University Hospital, Oslo, Norway
| | - Rafi Ahmad
- Department of Biotechnology, Inland Norway University of Applied Sciences, Hamar, Norway.,Faculty of Health Sciences, Institute of Clinical Medicine, UiT - The Arctic University of Norway, Tromsø, Norway
| |
Collapse
|
40
|
Zhang JQ, He CC, Yuan B, Liu R, Qi YJ, Wang ZX, He XN, Li YM. Fatal systemic emphysematous infection caused by Klebsiella pneumoniae: A case report. World J Clin Cases 2022; 10:2610-2615. [PMID: 35434061 PMCID: PMC8968611 DOI: 10.12998/wjcc.v10.i8.2610] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 12/26/2021] [Accepted: 02/10/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Systemic emphysematous infection caused by Klebsiella pneumoniae (K. pneumoniae) is a rare but severe infection which can be lethal if the diagnosis is delayed.
CASE SUMMARY We report a rare case of systemic emphysematous infection via hematogenous dissemination from a liver abscess caused by K. pneumoniae, complicated by multiple organ dysfunction syndrome, septic shock, bacteremia, emphysematous cystitis, prostate and left seminal vesicle abscesses in a diabetic patient. The patient simultaneously presented with spontaneous pneumoperitoneum secondary to rupture of the emphysematous liver abscess. His condition after admission deteriorated rapidly and he died within a short period. This disease is a great challenge for the clinician as K. pneumoniae can cause multifocal emphysematous infections and fulminant septic shock. Pneumoperitoneum following spontaneous rupture of the liver abscess can result in intra-abdominal sepsis that further increases mortality rate. Moreover, appropriate site-specific intervention and adequate drainage of numerous emphysematous liver lesions are difficult.
CONCLUSION Early diagnosis followed by efficient antibiotic therapy and surgical management are essential for systemic emphysematous infection.
Collapse
Affiliation(s)
- Jun-Qiang Zhang
- Department of General Surgery, Lanzhou University Second Hospital, Lanzhou 730030, Gansu Province, China
| | - Chan-Chan He
- Department of General Surgery, Lanzhou University Second Hospital, Lanzhou 730030, Gansu Province, China
| | - Bo Yuan
- Department of General Surgery, Lanzhou University Second Hospital, Lanzhou 730030, Gansu Province, China
| | - Rui Liu
- Department of General Surgery, Lanzhou University Second Hospital, Lanzhou 730030, Gansu Province, China
| | - Yu-Jing Qi
- Department of General Surgery, Lanzhou University Second Hospital, Lanzhou 730030, Gansu Province, China
| | - Zi-Xia Wang
- Department of General Surgery, Lanzhou University Second Hospital, Lanzhou 730030, Gansu Province, China
| | - Xiao-Na He
- Department of General Surgery, Lanzhou University Second Hospital, Lanzhou 730030, Gansu Province, China
| | - Yu-Min Li
- Department of General Surgery, Lanzhou University Second Hospital, Lanzhou 730030, Gansu Province, China
| |
Collapse
|
41
|
Zhang Z, Zhang L, Dai H, Zhang H, Song Y, An Q, Wang J, Xia Z. Multidrug-Resistant Klebsiella pneumoniae Complex From Clinical Dogs and Cats in China: Molecular Characteristics, Phylogroups, and Hypervirulence-Associated Determinants. Front Vet Sci 2022; 9:816415. [PMID: 35359688 PMCID: PMC8960377 DOI: 10.3389/fvets.2022.816415] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Accepted: 01/31/2022] [Indexed: 12/15/2022] Open
Abstract
Klebsiella pneumoniae complex is an increasingly important bacterial pathogen that is capable of causing severe organs and life-threatening disease. This study aimed to investigate the multidrug resistance, phylogroups, molecular characterization, and hypervirulence-associated determinants of the complex, which were isolated from clinical diseased dogs and cats. A total of 35 K. pneumoniae complex (2.3%; 95% confidence interval, 1.6–3.2) isolates were identified from 1,500 samples, all of which were collected randomly from veterinary hospitals in the 12 regions across China. Antimicrobial susceptibility testing showed that isolates were extremely resistant to amoxicillin–clavulanate (82.9%) and trimethoprim–sulfamethoxazole (77.1%). The rate of multidrug-resistant reached an astonishing 82.9% and found a carbapenemase-producing strain carrying IncX3-blaNDM−5 derived a cat from Zhejiang. The prevalence rates of extended-spectrum β-lactamase gene blaCTX−M and plasmid-mediated quinolone resistance gene aac(6')Ib-cr were 51.4% and 45.7%, respectively. The resistance gene aph(3')-Ia of isolates from cats was more significantly (p < 0.05) prevalent than that from dogs. Likewise, K. pneumoniae complex harbored hypervirulence-associated genes ybt (11.4%), iuc (5.7%), and iroB (2.9%). Three (8.6%) of the 35 isolates were determined as hypermucoviscous by the string test. Lipopolysaccharide serotype O1v2 had the highest percentage of 25.7%, but capsular serotypes presented diversity distribution among the isolates. The core–genome phylogenetic tree demonstrated most of the isolates belonged to the KpI phylogroup (91.4%). Multilocus sequence typing analysis identified 25 different STs; ST15 and ST37 were the most abundant accounting for isolates, followed by ST307, ST656, ST1408, and ST4566. In addition, the prevalence of IncFIB-type plasmid for cat isolates was significantly higher (p < 0.05) than that for dogs. Sequences of IncX3 in blaNDM−5-positive strain contained regions showing >99% nucleotide sequence identity to the reference plasmid pNDM-MGR194 from the human.
Collapse
Affiliation(s)
- Zhenbiao Zhang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Liu Zhang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Hegen Dai
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Haixia Zhang
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yu Song
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Qi An
- College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jianzhong Wang
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
- *Correspondence: Jianzhong Wang ;
| | - Zhaofei Xia
- College of Veterinary Medicine, China Agricultural University, Beijing, China
- Zhaofei Xia
| |
Collapse
|
42
|
Yin L, Shen X, Zhang D, Zhao R, Dai Y, Hu X, Wang J, Hou H, Pan X, Qi K. Transcriptome response of a new serotype of avian type Klebsiella varicella strain to chicken sera. Res Vet Sci 2022; 145:222-228. [PMID: 35278892 DOI: 10.1016/j.rvsc.2022.03.001] [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: 11/16/2021] [Revised: 02/16/2022] [Accepted: 03/03/2022] [Indexed: 11/17/2022]
Abstract
Klebsiella variicola is a newly discovered pathogen of zoonotic importance, commonly causing serious systemic infection via the bloodstream route. However, the mechanism by which K. variicola survives and grows in the bloodstream is poorly understood. In a previous study, a strain of Klebsiella causing chicken bloodstream infection was obtained, and whole genome sequencing showed that it was a new ST174 type K. variicola. Therefore, the present study aimed to determine the molecular mechanism underlying the survival and development of K. variicola in host serum. First, we compared the transcriptomes of K. variicola grown in Luria-Bertani broth and chicken serum. We sequenced six RNA libraries from the two groups, each library had three repeats. A total of 1046 differentially expressed genes were identified. Functional annotation analysis showed that the differentially expressed genes are mainly involved in adaptive metabolism, biosynthesis pathways (including biosynthesis of siderophore group nonribosomal peptides and lipopolysaccharide (LPS) biosynthesis), stress resistance, and several known virulence regulatory systems (including the ABC transporter system, the two-component signal transduction system and the quorum sensing system). These genes are expected to contribute to the adaptation and growth of K. variicola in host birds. This analysis provides a new insight into the pathogenesis of K. variicola.
Collapse
Affiliation(s)
- Lei Yin
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, Anhui 230031, China
| | - Xuehuai Shen
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, Anhui 230031, China
| | - Danjun Zhang
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, Anhui 230031, China
| | - Ruihong Zhao
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, Anhui 230031, China
| | - Yin Dai
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, Anhui 230031, China
| | - Xiaomiao Hu
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, Anhui 230031, China
| | - Jieru Wang
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, Anhui 230031, China
| | - Hongyan Hou
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, Anhui 230031, China
| | - Xiaocheng Pan
- Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Hefei, Anhui 230031, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Hefei, Anhui 230031, China.
| | - Kezong Qi
- Anhui Province Key Laboratory of Veterinary Pathobiology and Disease Control, College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, PR China.
| |
Collapse
|
43
|
Rodrigues C, Hauser K, Cahill N, Ligowska-Marzęta M, Centorotola G, Cornacchia A, Garcia Fierro R, Haenni M, Nielsen EM, Piveteau P, Barbier E, Morris D, Pomilio F, Brisse S. High Prevalence of Klebsiella pneumoniae in European Food Products: a Multicentric Study Comparing Culture and Molecular Detection Methods. Microbiol Spectr 2022; 10:e0237621. [PMID: 35196810 PMCID: PMC8865463 DOI: 10.1128/spectrum.02376-21] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2021] [Accepted: 01/20/2022] [Indexed: 12/20/2022] Open
Abstract
The Klebsiella pneumoniae species complex (KpSC) is a leading cause of multidrug-resistant human infections. To better understand the potential contribution of food as a vehicle of KpSC, we conducted a multicentric study to define an optimal culture method for its recovery from food matrices and to characterize food isolates phenotypically and genotypically. Chicken meat (n = 160) and salad (n = 145) samples were collected in five European countries and screened for the presence of KpSC using culture-based and zur-khe intergenic region (ZKIR) quantitative PCR (qPCR) methods. Enrichment using buffered peptone water followed by streaking on Simmons citrate agar with inositol (44°C for 48 h) was defined as the most suitable selective culture method for KpSC recovery. A high prevalence of KpSC was found in chicken meat (60% and 52% by ZKIR qPCR and the culture approach, respectively) and salad (30% and 21%, respectively) samples. Genomic analyses revealed high genetic diversity with the dominance of phylogroups Kp1 (91%) and Kp3 (6%). A total of 82% of isolates presented a natural antimicrobial susceptibility phenotype and genotype, with only four CTX-M-15-producing isolates detected. Notably, identical genotypes were found across samples-same food type and same country (15 cases), different food types and same country (1), and same food type and two countries (1)-suggesting high rates of transmission of KpSC within the food sector. Our study provides a novel isolation strategy for KpSC from food matrices and reinforces the view of food as a potential source of KpSC colonization in humans. IMPORTANCE Bacteria of the Klebsiella pneumoniae species complex (KpSC) are ubiquitous, and K. pneumoniae is a leading cause of antibiotic-resistant infections in humans. Despite the urgent public health threat represented by K. pneumoniae, there is a lack of knowledge of the contribution of food sources to colonization and subsequent infection in humans. This is partly due to the absence of standardized methods for characterizing the presence of KpSC in food matrices. Our multicentric study provides and implements a novel isolation strategy for KpSC from food matrices and shows that KpSC members are highly prevalent in salads and chicken meat, reinforcing the view of food as a potential source of KpSC colonization in humans. Despite the large genetic diversity and the low levels of resistance detected, the occurrence of identical genotypes across samples suggests high rates of transmission of KpSC within the food sector, which need to be further explored to define possible control strategies.
Collapse
Affiliation(s)
- Carla Rodrigues
- Institut Pasteur, Université de Paris, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Kathrin Hauser
- Institute for Medical Microbiology and Hygiene, Austrian Agency for Health and Food Safety, Vienna/Graz, Austria
| | - Niamh Cahill
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland
| | | | - Gabriella Centorotola
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Alessandra Cornacchia
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Raquel Garcia Fierro
- Unité Antibiorésistance et Virulence Bactériennes, Université Claude Bernard Lyon 1 - ANSES, Lyon, France
| | - Marisa Haenni
- Unité Antibiorésistance et Virulence Bactériennes, Université Claude Bernard Lyon 1 - ANSES, Lyon, France
| | | | | | - Elodie Barbier
- Agroécologie, AgroSup Dijon, INRAE, Université Bourgogne Franche-Comté, Dijon, France
| | - Dearbháile Morris
- Antimicrobial Resistance and Microbial Ecology Group, School of Medicine, National University of Ireland, Galway, Ireland
| | - Francesco Pomilio
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Teramo, Italy
| | - Sylvain Brisse
- Institut Pasteur, Université de Paris, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| |
Collapse
|
44
|
Barrios-Camacho H, Silva-Sánchez J, Cercas-Ayala E, Lozano-Aguirre L, Duran-Bedolla J, Aguilar-Vera A, Garza-González E, Bocanegra-Ibarias P, Morfín-Otero R, Hernández-Castro R, Garza-Ramos U. PCR system for the correct differentiation of the main bacterial species of the Klebsiella pneumoniae complex. Arch Microbiol 2021; 204:73. [PMID: 34951665 DOI: 10.1007/s00203-021-02668-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 10/15/2021] [Accepted: 10/17/2021] [Indexed: 12/27/2022]
Abstract
Accurate recognition of the closely related species Klebsiella pneumoniae, Klebsiella quasipneumoniae and Klebsiella variicola by phenotypic, biochemical and automated tests is notoriously unreliable in hospitals' diagnostic laboratories. A comparative genomics approach was conducted for the correct differentiation of the main bacterial species in the K. pneumoniae complex. Analysis of the deduced proteomes of 87 unique genomes of the Klebsiella in public databases, was used for the identification of unique protein family members. This allowed the design of a multiplex-PCR assay for the correct differentiation of these three species from different origins. This system allowed us to determine the prevalence of K. pneumoniae, K. quasipneumoniae and K. variicola among a collection of 552 clinical isolates. Of these, 87.3% (482/552) isolates corresponded to K. pneumoniae, 6.7% (33/552) to K. quasipneumoniae and 5.9% (33/552) to K. variicola. The multiplex-PCR results showed a 100% accuracy for the correct identification of the three species evaluated, which was validated with rpoB phylogenetic sequence analysis.
Collapse
Affiliation(s)
- Humberto Barrios-Camacho
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Sta. Ma. Ahuacatitlán, C.P. 62100, Cuernavaca, Morelos, Mexico
| | - Jesús Silva-Sánchez
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Sta. Ma. Ahuacatitlán, C.P. 62100, Cuernavaca, Morelos, Mexico
| | - Elena Cercas-Ayala
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Sta. Ma. Ahuacatitlán, C.P. 62100, Cuernavaca, Morelos, Mexico
| | - Luis Lozano-Aguirre
- Programa de Genómica Evolutiva, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Josefina Duran-Bedolla
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Sta. Ma. Ahuacatitlán, C.P. 62100, Cuernavaca, Morelos, Mexico
| | - Alejandro Aguilar-Vera
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, Mexico
| | - Elvira Garza-González
- Hospital Universitario Dr. José Eleuterio González, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
| | - Paola Bocanegra-Ibarias
- Hospital Universitario Dr. José Eleuterio González, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
| | - Rayo Morfín-Otero
- Hospital Civil de Guadalajara Fray Antonio Alcalde, Universidad de Guadalajara, Guadalajara, Jalisco, Mexico
| | | | - Ulises Garza-Ramos
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Sta. Ma. Ahuacatitlán, C.P. 62100, Cuernavaca, Morelos, Mexico.
| |
Collapse
|
45
|
Wen A, Havens KL, Bloch SE, Shah N, Higgins DA, Davis-Richardson AG, Sharon J, Rezaei F, Mohiti-Asli M, Johnson A, Abud G, Ane JM, Maeda J, Infante V, Gottlieb SS, Lorigan JG, Williams L, Horton A, McKellar M, Soriano D, Caron Z, Elzinga H, Graham A, Clark R, Mak SM, Stupin L, Robinson A, Hubbard N, Broglie R, Tamsir A, Temme K. Enabling Biological Nitrogen Fixation for Cereal Crops in Fertilized Fields. ACS Synth Biol 2021; 10:3264-3277. [PMID: 34851109 DOI: 10.1021/acssynbio.1c00049] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Agricultural productivity relies on synthetic nitrogen fertilizers, yet half of that reactive nitrogen is lost to the environment. There is an urgent need for alternative nitrogen solutions to reduce the water pollution, ozone depletion, atmospheric particulate formation, and global greenhouse gas emissions associated with synthetic nitrogen fertilizer use. One such solution is biological nitrogen fixation (BNF), a component of the complex natural nitrogen cycle. BNF application to commercial agriculture is currently limited by fertilizer use and plant type. This paper describes the identification, development, and deployment of the first microbial product optimized using synthetic biology tools to enable BNF for corn (Zea mays) in fertilized fields, demonstrating the successful, safe commercialization of root-associated diazotrophs and realizing the potential of BNF to replace and reduce synthetic nitrogen fertilizer use in production agriculture. Derived from a wild nitrogen-fixing microbe isolated from agricultural soils, Klebsiella variicola 137-1036 ("Kv137-1036") retains the capacity of the parent strain to colonize corn roots while increasing nitrogen fixation activity 122-fold in nitrogen-rich environments. This technical milestone was then commercialized in less than half of the time of a traditional biological product, with robust biosafety evaluations and product formulations contributing to consumer confidence and ease of use. Tested in multi-year, multi-site field trial experiments throughout the U.S. Corn Belt, fields grown with Kv137-1036 exhibited both higher yields (0.35 ± 0.092 t/ha ± SE or 5.2 ± 1.4 bushels/acre ± SE) and reduced within-field yield variance by 25% in 2018 and 8% in 2019 compared to fields fertilized with synthetic nitrogen fertilizers alone. These results demonstrate the capacity of a broad-acre BNF product to fix nitrogen for corn in field conditions with reliable agronomic benefits.
Collapse
Affiliation(s)
- Amy Wen
- Pivot Bio, Berkeley, California 94710, United States
| | | | - Sarah E. Bloch
- Morrison & Foerster LLP, San Francisco, California 94105, United States
| | - Neal Shah
- Pivot Bio, Berkeley, California 94710, United States
| | | | | | - Judee Sharon
- University of Minnesota─Twin Cities, Minneapolis, Minnesota 55401, United States
| | | | | | | | - Gabriel Abud
- Tempo Automation, San Francisco, California 94103, United States
| | - Jean-Michel Ane
- University of Minnesota─Twin Cities, Minneapolis, Minnesota 55401, United States
| | - Junko Maeda
- University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | - Valentina Infante
- University of Wisconsin−Madison, Madison, Wisconsin 53706, United States
| | | | | | | | - Alana Horton
- Pivot Bio, Berkeley, California 94710, United States
| | | | | | - Zoe Caron
- Pivot Bio, Berkeley, California 94710, United States
| | | | - Ashley Graham
- Olema Oncology, San Francisco, California 94107, United States
| | | | - San-Ming Mak
- Pivot Bio, Berkeley, California 94710, United States
| | - Laura Stupin
- Pivot Bio, Berkeley, California 94710, United States
| | | | | | | | - Alvin Tamsir
- Pivot Bio, Berkeley, California 94710, United States
| | - Karsten Temme
- Pivot Bio, Berkeley, California 94710, United States
| |
Collapse
|
46
|
Carlos CC, Masim MAL, Lagrada ML, Gayeta JM, Macaranas PKV, Sia SB, Facun MAM, Palarca JFC, Olorosa AM, Cueno GAC, Abrudan M, Abudahab K, Argimón S, Kekre M, Underwood A, Stelling J, Aanensen DM. Genome Sequencing Identifies Previously Unrecognized Klebsiella pneumoniae Outbreaks in Neonatal Intensive Care Units in the Philippines. Clin Infect Dis 2021; 73:S316-S324. [PMID: 34850834 PMCID: PMC8634409 DOI: 10.1093/cid/ciab776] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Klebsiella pneumoniae is a critically important pathogen in the Philippines. Isolates are commonly resistant to at least 2 classes of antibiotics, yet mechanisms and spread of its resistance are not well studied. METHODS A retrospective sequencing survey was performed on carbapenem-, extended spectrum beta-lactam-, and cephalosporin-resistant Klebsiella pneumoniae isolated at 20 antimicrobial resistance (AMR) surveillance sentinel sites from 2015 through 2017. We characterized 259 isolates using biochemical methods, antimicrobial susceptibility testing, and whole-genome sequencing (WGS). Known AMR mechanisms were identified. Potential outbreaks were investigated by detecting clusters from epidemiologic, phenotypic, and genome-derived data. RESULTS Prevalent AMR mechanisms detected include blaCTX-M-15 (76.8%) and blaNDM-1 (37.5%). An epidemic IncFII(Yp) plasmid carrying blaNDM-1 was also detected in 46 isolates from 6 sentinel sites and 14 different sequence types (STs). This plasmid was also identified as the main vehicle of carbapenem resistance in 2 previously unrecognized local outbreaks of ST348 and ST283 at 2 different sentinel sites. A third local outbreak of ST397 was also identified but without the IncFII(Yp) plasmid. Isolates in each outbreak site showed identical STs and K- and O-loci, and similar resistance profiles and AMR genes. All outbreak isolates were collected from blood of children aged < 1 year. CONCLUSION WGS provided a better understanding of the epidemiology of multidrug resistant Klebsiella in the Philippines, which was not possible with only phenotypic and epidemiologic data. The identification of 3 previously unrecognized Klebsiella outbreaks highlights the utility of WGS in outbreak detection, as well as its importance in public health and in implementing infection control programs.
Collapse
Affiliation(s)
- Celia C Carlos
- Research Institute for Tropic al Medicine, Muntinlupa, the Philippines
| | | | | | - June M Gayeta
- Research Institute for Tropic al Medicine, Muntinlupa, the Philippines
| | | | - Sonia B Sia
- Research Institute for Tropic al Medicine, Muntinlupa, the Philippines
| | | | | | | | | | - Monica Abrudan
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Khalil Abudahab
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Mihir Kekre
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | - Anthony Underwood
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Brigham and Women’s Hospital, Boston, MA, USA
| | | | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Centre for Genomic Pathogen Surveillance, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Oxford, UK
| |
Collapse
|
47
|
Argimón S, David S, Underwood A, Abrudan M, Wheeler NE, Kekre M, Abudahab K, Yeats CA, Goater R, Taylor B, Harste H, Muddyman D, Feil EJ, Brisse S, Holt K, Donado-Godoy P, Ravikumar KL, Okeke IN, Carlos C, Aanensen DM. Rapid Genomic Characterization and Global Surveillance of Klebsiella Using Pathogenwatch. Clin Infect Dis 2021; 73:S325-S335. [PMID: 34850838 PMCID: PMC8634497 DOI: 10.1093/cid/ciab784] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Klebsiella species, including the notable pathogen K. pneumoniae, are increasingly associated with antimicrobial resistance (AMR). Genome-based surveillance can inform interventions aimed at controlling AMR. However, its widespread implementation requires tools to streamline bioinformatic analyses and public health reporting. METHODS We developed the web application Pathogenwatch, which implements analytics tailored to Klebsiella species for integration and visualization of genomic and epidemiological data. We populated Pathogenwatch with 16 537 public Klebsiella genomes to enable contextualization of user genomes. We demonstrated its features with 1636 genomes from 4 low- and middle-income countries (LMICs) participating in the NIHR Global Health Research Unit (GHRU) on AMR. RESULTS Using Pathogenwatch, we found that GHRU genomes were dominated by a small number of epidemic drug-resistant clones of K. pneumoniae. However, differences in their distribution were observed (eg, ST258/512 dominated in Colombia, ST231 in India, ST307 in Nigeria, ST147 in the Philippines). Phylogenetic analyses including public genomes for contextualization enabled retrospective monitoring of their spread. In particular, we identified hospital outbreaks, detected introductions from abroad, and uncovered clonal expansions associated with resistance and virulence genes. Assessment of loci encoding O-antigens and capsule in K. pneumoniae, which represent possible vaccine candidates, showed that 3 O-types (O1-O3) represented 88.9% of all genomes, whereas capsule types were much more diverse. CONCLUSIONS Pathogenwatch provides a free, accessible platform for real-time analysis of Klebsiella genomes to aid surveillance at local, national, and global levels. We have improved representation of genomes from GHRU participant countries, further facilitating ongoing surveillance.
Collapse
Affiliation(s)
- Silvia Argimón
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Sophia David
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Anthony Underwood
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Monica Abrudan
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Nicole E Wheeler
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Mihir Kekre
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Khalil Abudahab
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Corin A Yeats
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Centre for Genomic Pathogen Surveillance, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Old Road Campus, Oxford, United Kingdom
| | - Richard Goater
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Ben Taylor
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Centre for Genomic Pathogen Surveillance, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Old Road Campus, Oxford, United Kingdom
| | - Harry Harste
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Dawn Muddyman
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Edward J Feil
- Milner Centre for Evolution, University of Bath, Bath, United Kingdom
| | - Sylvain Brisse
- Institut Pasteur, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Kathryn Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria, Australia
- London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Pilar Donado-Godoy
- Colombian Integrated Program for Antimicrobial Resistance Surveillance (Coipars), CI Tibaitatá, Corporación Colombiana de Investigación Agropecuaria (AGROSAVIA), Tibaitatá–Mosquera, Cundinamarca, Colombia
| | - K L Ravikumar
- Central Research Laboratory, Kempegowda Institute of Medical Sciences, Bengaluru, India
| | - Iruka N Okeke
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, University of Ibadan, Oyo State, Nigeria
| | - Celia Carlos
- Antimicrobial Resistance Surveillance Reference Laboratory, Research Institute for Tropical Medicine, Muntinlupa, The Philippines
| | - David M Aanensen
- Centre for Genomic Pathogen Surveillance, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
- Centre for Genomic Pathogen Surveillance, Li Ka Shing Centre for Health Information and Discovery, University of Oxford, Old Road Campus, Oxford, United Kingdom
| |
Collapse
|
48
|
The Association of the Phylogenetic Typing of the Klebsiella pneumoniae Isolates with Antibiotic Resistance. Emerg Med Int 2021; 2021:1316992. [PMID: 34777863 PMCID: PMC8589475 DOI: 10.1155/2021/1316992] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Revised: 10/09/2021] [Accepted: 10/22/2021] [Indexed: 11/17/2022] Open
Abstract
Klebsiella pneumoniae complex (KPC) accounts for approximately one-third of all Gram-negative infections. Moreover, it is highly resistant and can taxonomically be distributed into KpI, KpII, and KpIII phylogroups. This study aimed to investigate the distribution of phylogenetic groups and the relationship between them and antibiotic resistance patterns. For this purpose, we collected KPC isolates from Tabriz, Iran, between 2018 and 2020. Antimicrobial susceptibility testing was performed by disk diffusion agar, and phylogenetic groups were then examined using gyrA restriction fragment length polymorphism (RFLP) and parC PCR methods. A total of 100 KPC isolates were obtained from the clinical specimens (urine, respiratory secretion, blood, wounds, and trachea). The enrolled patients included 47 men and 53 women aged from 1 to 91 years old. The highest sensitivity was found related to fosfomycin as 85%, followed by amikacin as 66%. The three phylogenetically groups by the RFLP-PCR method were found in KPC, 96% (96 isolates) as KpI, 3% (3 isolates) as KpII, and 1% (1isolate) as KpIII. The highest antibiotic resistance was observed in KpI. It was shown that a valid identification of three phylogenetic groups of KPC can be done by combining both gyrA PCR-RFLP and parC PCR. Of note, the KpI group was also observed as the dominant phylogenetic group with the highest resistance to antibiotics.
Collapse
|
49
|
Gómez M, Valverde A, del Campo R, Rodríguez JM, Maldonado-Barragán A. Phenotypic and Molecular Characterization of Commensal, Community-Acquired and Nosocomial Klebsiella spp. Microorganisms 2021; 9:2344. [PMID: 34835469 PMCID: PMC8625991 DOI: 10.3390/microorganisms9112344] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 11/09/2021] [Accepted: 11/09/2021] [Indexed: 11/17/2022] Open
Abstract
Klebsiella spp. is a relevant pathogen that can present acquired resistance to almost all available antibiotics, thus representing a serious threat for public health. While most studies have been focused on isolates causing community-acquired and nosocomial infections, little is known about the commensal isolates colonizing healthy subjects. We describe the molecular identification and the phenotypic characterization of commensal Klebsiella spp. from breast milk of healthy women and faeces from healthy breast-fed infants, which were compared with isolates from community-acquired infections and from a nosocomial NICU outbreak. The phylogenetic analysis of a 454-bp sequence of the rpoB gene was useful for species identification (K. pneumoniae, K. variicola, K. quasipneumoniae, K. oxytoca, K. grimontii, K. michiganensis, Raoultella planticola and R. ornithinolytica), previously misidentified as K. pneumoniae or K. oxytoca by biochemical methods. Globally, we report that commensal strains present virulence traits (virulence genes, siderophores and biofilms) comparable to community-acquired and NICU-infective isolates, thus suggesting that the human microbiota could constitute a reservoir for infection. Isolates causing NICU outbreak were multi-drug resistant (MDR) and ESBLs producers, although an imipenem-resistant commensal MDR K. quasipneumoniae isolate was also found. A commensal K. pneumoniae strain showed a potent bacteriocin-like inhibitory activity against MDR Klebsiella isolates, thus highlighting the potential role of commensal Klebsiella spp. in health and disease.
Collapse
Affiliation(s)
- Marta Gómez
- Department of Nutrition and Food Science, Complutense University of Madrid, 28040 Madrid, Spain; (M.G.); (J.M.R.)
| | - Arancha Valverde
- Department of Microbiology, Hospital Universitario Ramón y Cajal IRYCIS, 28034 Madrid, Spain; (A.V.); (R.d.C.)
| | - Rosa del Campo
- Department of Microbiology, Hospital Universitario Ramón y Cajal IRYCIS, 28034 Madrid, Spain; (A.V.); (R.d.C.)
| | - Juan Miguel Rodríguez
- Department of Nutrition and Food Science, Complutense University of Madrid, 28040 Madrid, Spain; (M.G.); (J.M.R.)
| | - Antonio Maldonado-Barragán
- Department of Nutrition and Food Science, Complutense University of Madrid, 28040 Madrid, Spain; (M.G.); (J.M.R.)
- Infection and Global Health Research Division, School of Medicine, University of St. Andrews, North Haugh, St Andrews KY16 9TF, UK
| |
Collapse
|
50
|
Within patient genetic diversity of bla KPC harboring Klebsiella pneumoniae in a Colombian hospital and identification of a new NTE KPC platform. Sci Rep 2021; 11:21409. [PMID: 34725422 PMCID: PMC8560879 DOI: 10.1038/s41598-021-00887-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 10/19/2021] [Indexed: 11/30/2022] Open
Abstract
Resistance to carbapenems in Klebsiellapneumoniae has been mostly related with the worldwide dissemination of KPC, largely due to the pandemic clones belonging to the complex clonal (CC) 258. To unravel blaKPC post-endemic clinical impact, here we describe clinical characteristics of 68 patients from a high complexity hospital, and the molecular and genetic characteristics of their 139 blaKPC—K.pneumoniae (KPC-Kp) isolates. Of the 26 patients that presented relapses or reinfections, 16 had changes in the resistance profiles of the isolates recovered from the recurrent episodes. In respect to the genetic diversity of KPC-Kp isolates, PFGE revealed 45 different clonal complexes (CC). MLST for 12 representative clones showed ST258 was present in the most frequent CC (23.0%), however, remaining 11 representative clones belonged to non-CC258 STs (77.0%). Interestingly, 16 patients presented within-patient genetic diversity of KPC-Kp clones. In one of these, three unrelated KPC-Kp clones (ST258, ST504, and ST846) and a blaKPC—K.variicola isolate (ST182) were identified. For this patient, complete genome sequence of one representative isolate of each clone was determined. In K.pneumoniae isolates blaKPC was mobilized by two Tn3-like unrelated platforms: Tn4401b (ST258) and Tn6454 (ST504 and ST846), a new NTEKPC-IIe transposon for first time characterized also determined in the K.variicola isolate of this study. Genome analysis showed these transposons were harbored in different unrelated but previously reported plasmids and in the chromosome of a K.pneumoniae (for Tn4401b). In conclusion, in the blaKPC post-endemic dissemination in Colombia, different KPC-Kp clones (mostly non-CC258) have emerged due to integration of the single blaKPC gene in new genetic platforms. This work also shows the intra-patient resistant and genetic diversity of KPC-Kp isolates. This circulation dynamic could impact the effectiveness of long-term treatments.
Collapse
|