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Orel N, Fadeev E, Herndl GJ, Turk V, Tinta T. Recovering high-quality bacterial genomes from cross-contaminated cultures: a case study of marine Vibrio campbellii. BMC Genomics 2024; 25:146. [PMID: 38321410 PMCID: PMC10845552 DOI: 10.1186/s12864-024-10062-2] [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: 01/25/2023] [Accepted: 01/29/2024] [Indexed: 02/08/2024] Open
Abstract
BACKGROUND Environmental monitoring of bacterial pathogens is critical for disease control in coastal marine ecosystems to maintain animal welfare and ecosystem function and to prevent significant economic losses. This requires accurate taxonomic identification of environmental bacterial pathogens, which often cannot be achieved by commonly used genetic markers (e.g., 16S rRNA gene), and an understanding of their pathogenic potential based on the information encoded in their genomes. The decreasing costs of whole genome sequencing (WGS), combined with newly developed bioinformatics tools, now make it possible to unravel the full potential of environmental pathogens, beyond traditional microbiological approaches. However, obtaining a high-quality bacterial genome, requires initial cultivation in an axenic culture, which is a bottleneck in environmental microbiology due to cross-contamination in the laboratory or isolation of non-axenic strains. RESULTS We applied WGS to determine the pathogenic potential of two Vibrio isolates from coastal seawater. During the analysis, we identified cross-contamination of one of the isolates and decided to use this dataset to evaluate the possibility of bioinformatic contaminant removal and recovery of bacterial genomes from a contaminated culture. Despite the contamination, using an appropriate bioinformatics workflow, we were able to obtain high quality and highly identical genomes (Average Nucleotide Identity value 99.98%) of one of the Vibrio isolates from both the axenic and the contaminated culture. Using the assembled genome, we were able to determine that this isolate belongs to a sub-lineage of Vibrio campbellii associated with several diseases in marine organisms. We also found that the genome of the isolate contains a novel Vibrio plasmid associated with bacterial defense mechanisms and horizontal gene transfer, which may offer a competitive advantage to this putative pathogen. CONCLUSIONS Our study shows that, using state-of-the-art bioinformatics tools and a sufficient sequencing effort, it is possible to obtain high quality genomes of the bacteria of interest and perform in-depth genomic analyses even in the case of a contaminated culture. With the new isolate and its complete genome, we are providing new insights into the genomic characteristics and functional potential of this sub-lineage of V. campbellii. The approach described here also highlights the possibility of recovering complete bacterial genomes in the case of non-axenic cultures or obligatory co-cultures.
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Affiliation(s)
- Neža Orel
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia.
| | - Eduard Fadeev
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
| | - Gerhard J Herndl
- Department of Functional and Evolutionary Ecology, Bio-Oceanography and Marine Biology Unit, University of Vienna, Vienna, Austria
- NIOZ, Department of Marine Microbiology and Biogeochemistry, Royal Netherlands Institute for Sea Research, Den Burg, The Netherlands
| | - Valentina Turk
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia
| | - Tinkara Tinta
- Marine Biology Station Piran, National Institute of Biology, Piran, Slovenia.
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Duran-Bedolla J, Rodríguez-Medina N, Dunn M, Mosqueda-García D, Barrios-Camacho H, Aguilar-Vera A, Aguilar-Vera E, Suárez-Rodríguez R, Ramírez-Trujillo JA, Garza-Ramos U. Plasmids of the incompatibility group FIB K occur in Klebsiella variicola from diverse ecological niches. Int Microbiol 2023; 26:917-927. [PMID: 36971854 DOI: 10.1007/s10123-023-00346-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2023] [Revised: 03/08/2023] [Accepted: 03/16/2023] [Indexed: 03/29/2023]
Abstract
Plasmids play a fundamental role in the evolution of bacteria by allowing them to adapt to different environments and acquire, through horizontal transfer, genes that confer resistance to different classes of antibiotics. Using the available in vitro and in silico plasmid typing systems, we analyzed a set of isolates and public genomes of K. variicola to study its plasmid diversity. The resistome, the plasmid multilocus sequence typing (pMLST), and molecular epidemiology using the MLST system were also studied. A high frequency of IncF plasmids from human isolates but lower frequency from plant isolates were found in our strain collection. In silico detection revealed 297 incompatibility (Inc) groups, but the IncFIBK (216/297) predominated in plasmids from human and environmental samples, followed by IncFIIK (89/297) and IncFIA/FIA(HI1) (75/297). These Inc groups were associated with clinically important ESBL (CTX-M-15), carbapenemases (KPC-2 and NDM-1), and colistin-resistant genes which were associated with major sequence types (ST): ST60, ST20, and ST10. In silico MOB typing showed 76% (311/404) of the genomes contained one or more of the six relaxase families with MOBF being most abundant. We identified untypeable plasmids carrying blaKPC-2, blaIMP-1, and blaSHV-187 but for which a relaxase was found; this may suggest that novel plasmid structures could be emerging in this bacterial species. The plasmid content in K. variicola has limited diversity, predominantly composed of IncFIBK plasmids dispersed in different STs. Plasmid detection using the replicon and MOB typing scheme provide a broader context of the plasmids in K. variicola. This study showed that whole-sequence-based typing provides current insights of the prevalence of plasmid types and their association with antimicrobial resistant genes in K. variicola obtained from humans and environmental niches.
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Affiliation(s)
- Josefina Duran-Bedolla
- Laboratorio de Resistencia Bacteriana, Centro de InvestigaciónSobreEnfermedadesInfecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad #655, Col. Sta. Ma. Ahuacatitlán., C.P. 62100, Cuernavaca, Morelos, México
| | - Nadia Rodríguez-Medina
- Laboratorio de Resistencia Bacteriana, Centro de InvestigaciónSobreEnfermedadesInfecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad #655, Col. Sta. Ma. Ahuacatitlán., C.P. 62100, Cuernavaca, Morelos, México
| | - Michael Dunn
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Dalila Mosqueda-García
- Laboratorio de Resistencia Bacteriana, Centro de InvestigaciónSobreEnfermedadesInfecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad #655, Col. Sta. Ma. Ahuacatitlán., C.P. 62100, Cuernavaca, Morelos, México
| | - Humberto Barrios-Camacho
- Laboratorio de Resistencia Bacteriana, Centro de InvestigaciónSobreEnfermedadesInfecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad #655, Col. Sta. Ma. Ahuacatitlán., C.P. 62100, Cuernavaca, Morelos, México
| | - Alejandro Aguilar-Vera
- Programa de Genómica Funcional de Procariotes, Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Morelos, México
| | - Edgar Aguilar-Vera
- Laboratorio de Resistencia Bacteriana, Centro de InvestigaciónSobreEnfermedadesInfecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad #655, Col. Sta. Ma. Ahuacatitlán., C.P. 62100, Cuernavaca, Morelos, México
| | - Ramón Suárez-Rodríguez
- Laboratorio de Fisiología Molecular de Plantas, Centro de Investigación en Biotecnología (CEIB), Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - José Augusto Ramírez-Trujillo
- Laboratorio de Fisiología Molecular de Plantas, Centro de Investigación en Biotecnología (CEIB), Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México
| | - Ulises Garza-Ramos
- Laboratorio de Resistencia Bacteriana, Centro de InvestigaciónSobreEnfermedadesInfecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad #655, Col. Sta. Ma. Ahuacatitlán., C.P. 62100, Cuernavaca, Morelos, México.
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Mr. Saddam, Khan M, Jamal M, Rahman SU, Qadeer A, Khan I, Mahmoud MH, Batiha GES, Shah SH. Nutritional analysis and characterization of carbapenemase producing-Klebsiella pneumoniae resistant genes associated with bovine mastitis infected cow's milk. PLoS One 2023; 18:e0293477. [PMID: 37889925 PMCID: PMC10610456 DOI: 10.1371/journal.pone.0293477] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2023] [Accepted: 10/13/2023] [Indexed: 10/29/2023] Open
Abstract
The current study was designed to analyze nutritional parameters and to characterize carbapenemase producing-Klebsiella pneumoniae isolates from bovine mastitic cow's milk. Out of 700 milk samples K. pneumoniae was identified by phenotypic and molecular techniques along with their antibiogram analysis and nutritional analysis was performed using the procedure of Association of Official Analytical Chemists. Carbapenemase-producing K. pneumoniae was detected by phenotypic CarbaNP test followed by molecular characterization of their associated resistant genes blaVIM, blaKPC, blaOXA-48, blaNDM, and blaIMP along with insertion sequence common region 1 (ISCR1) and integrons (Int1, Int2, and Int3) genes. Among nutritional parameters, fat content was observed (2.99%) followed by protein (2.78%), lactose (4.32%), and total solid (11.34%), respectively. The prevalence of K. pneumoniae among bovine mastitis was found 25.71%. Antibiogram analysis revealed that more effective antibiotics was ceftazidime (80%) followed by amikacin (72%), while highly resistant antibiotics was Fusidic acid (100%). Distribution of carbapenemase producer K. pneumoniae was found 44.4%. Among carbapenem resistant genes blaKPC was found 11.25%, blaVIM 2.75%, blaNDM 17.5%, and blaOXA-48 7.5%, while blaIMP gene was not detected. Furthermore, distribution of ISCR1 was found 40%, while integron 1 was found 61.2% followed by integron 2 (20%), and integron 3 (5%). In conclusion, the recent scenario of carbapenemase resistant K. pneumoniae isolates responsible for mastitis may affect not only the current treatment regime but also possess a serious threat to public health due to its food borne transmission and zoonotic potential.
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Affiliation(s)
- Mr. Saddam
- Department of Microbiology, Abdul Wali Khan University, Marden, Pakistan
| | - Muddasir Khan
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar, Pakistan
| | - Muhsin Jamal
- Department of Microbiology, Abdul Wali Khan University, Marden, Pakistan
| | - Sadeeq Ur Rahman
- College of Veterinary Sciences and Animal Husbandry, Abdul Wali Khan University, Mardan, Pakistan
| | - Abdul Qadeer
- Shanghai Tenth People’s Hospital, Institute for Infectious Diseases and Vaccine Development, Tongji University School of Medicine, Shanghai, China
| | - Imad Khan
- College of Veterinary Sciences and Animal Husbandry, Abdul Wali Khan University, Mardan, Pakistan
| | - Mohamed H. Mahmoud
- Department of Biochemistry, College of Science, King Saud University, Riyadh, Saudi Arabia
| | - Gaber El-Saber Batiha
- Department of Pharmacology, Faculty of Veterinary Medicine, Damanhour University, Damanhour, AlBeheira, Egypt
| | - Syed Hussain Shah
- Department of Health and Biological Sciences, Abasyn University Peshawar, Peshawar, Pakistan
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Nucci A, Janaszkiewicz J, Rocha EPC, Rendueles O. Emergence of novel non-aggregative variants under negative frequency-dependent selection in Klebsiella variicola. MICROLIFE 2023; 4:uqad038. [PMID: 37781688 PMCID: PMC10540941 DOI: 10.1093/femsml/uqad038] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/11/2023] [Revised: 09/05/2023] [Accepted: 09/09/2023] [Indexed: 10/03/2023]
Abstract
Klebsiella variicola is an emergent human pathogen causing diverse infections, some of which in the urinary tract. However, little is known about the evolution and maintenance of genetic diversity in this species, the molecular mechanisms and their population dynamics. Here, we characterized the emergence of a novel rdar-like (rough and dry) morphotype which is contingent both on the genetic background and the environment. We show that mutations in either the nitrogen assimilation control gene (nac) or the type III fimbriae regulator, mrkH, suffice to generate rdar-like colonies. These morphotypes are primarily selected for the reduced inter-cellular aggregation as a result of MrkH loss-of-function which reduces type 3 fimbriae expression. Additionally, these clones also display increased growth rate and reduced biofilm formation. Direct competitions between rdar and wild type clones show that mutations in mrkH provide large fitness advantages. In artificial urine, the morphotype is under strong negative frequency-dependent selection and can socially exploit wild type strains. An exhaustive search for mrkH mutants in public databases revealed that ca 8% of natural isolates analysed had a truncated mrkH gene many of which were due to insertions of IS elements, including a reported clinical isolate with rdar morphology. These strains were rarely hypermucoid and often isolated from human, mostly from urine and blood. The decreased aggregation of these mutants could have important clinical implications as we hypothesize that such clones could better disperse within the host allowing colonisation of other body sites and potentially leading to systemic infections.
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Affiliation(s)
- Amandine Nucci
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, F-75015, Paris, France
| | - Juliette Janaszkiewicz
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, F-75015, Paris, France
| | - Eduardo P C Rocha
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, F-75015, Paris, France
| | - Olaya Rendueles
- Institut Pasteur, Université Paris Cité, CNRS, UMR3525, Microbial Evolutionary Genomics, F-75015, Paris, France
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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.
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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.
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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.
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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
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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.
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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.
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Pyelonephritis and Bacteremia Caused by Klebsiella variicola following Renal Transplantation. Case Rep Infect Dis 2021; 2021:9988396. [PMID: 34603805 PMCID: PMC8481055 DOI: 10.1155/2021/9988396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2021] [Accepted: 09/14/2021] [Indexed: 12/03/2022] Open
Abstract
Klebsiella variicola (K. variicola) is a Gram-negative organism genetically similar to Klebsiella pneumoniae (K. pneumoniae) that can cause a variety of diseases in humans. Bacteremia due to K. variicola is associated with a higher mortality rate than bacteremia with K. pneumoniae. Here, we describe a 65-year-old woman who developed pyelonephritis 2 months after receiving a renal transplantation following a longstanding history of end-stage renal disease secondary to polycystic kidney disease. Her creatinine on admission was unchanged from her posttransplant baseline, and an abdominal CT scan showed inflammatory changes around the transplanted kidney that were suggestive of an infection rather than allograft rejection. She was initially treated empirically with meropenem given a history of extended-spectrum beta-lactamase- (ESBL-) producing E. coli bacteriuria. After a day of therapy with meropenem, her therapy was streamlined based on culture results to ceftriaxone. She continued to improve, her kidney function remained stable, and she was prescribed oral ciprofloxacin to complete a 14-day total course of antibiotics. This case is the first reported instance of K. variicola bacteremia associated with pyelonephritis in a renal transplant recipient. Hospitalization with acute pyelonephritis within the first year following kidney transplant is common and is associated with increased risk of graft loss and mortality. However, K. variicola is not a commonly known organism to cause this infection. Despite the risk of allograft failure in this circumstance, this patient was successfully treated with a 14-day course of antibiotic therapy.
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Kiley JL, Mende K, Beckius ML, Kaiser SJ, Carson ML, Lu D, Whitman TJ, Petfield JL, Tribble DR, Blyth DM. Resistance patterns and clinical outcomes of Klebsiella pneumoniae and invasive Klebsiella variicola in trauma patients. PLoS One 2021; 16:e0255636. [PMID: 34339473 PMCID: PMC8328492 DOI: 10.1371/journal.pone.0255636] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Accepted: 07/20/2021] [Indexed: 12/20/2022] Open
Abstract
Recent reclassification of the Klebsiella genus to include Klebsiella variicola, and its association with bacteremia and mortality, has raised concerns. We examined Klebsiella spp. infections among battlefield trauma patients, including occurrence of invasive K. variicola disease. Klebsiella isolates collected from 51 wounded military personnel (2009-2014) through the Trauma Infectious Disease Outcomes Study were examined using polymerase chain reaction (PCR) and pulsed-field gel electrophoresis. K. variicola isolates were evaluated for hypermucoviscosity phenotype by the string test. Patients were severely injured, largely from blast injuries, and all received antibiotics prior to Klebsiella isolation. Multidrug-resistant Klebsiella isolates were identified in 23 (45%) patients; however, there were no significant differences when patients with and without multidrug-resistant Klebsiella were compared. A total of 237 isolates initially identified as K. pneumoniae were analyzed, with 141 clinical isolates associated with infections (remaining were colonizing isolates collected through surveillance groin swabs). Using PCR sequencing, 221 (93%) isolates were confirmed as K. pneumoniae, 10 (4%) were K. variicola, and 6 (3%) were K. quasipneumoniae. Five K. variicola isolates were associated with infections. Compared to K. pneumoniae, infecting K. variicola isolates were more likely to be from blood (4/5 versus 24/134, p = 0.04), and less likely to be multidrug-resistant (0/5 versus 99/134, p<0.01). No K. variicola isolates demonstrated the hypermucoviscosity phenotype. Although K. variicola isolates were frequently isolated from bloodstream infections, they were less likely to be multidrug-resistant. Further work is needed to facilitate diagnosis of K. variicola and clarify its clinical significance in larger prospective studies.
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Affiliation(s)
- John L. Kiley
- Brooke Army Medical Center, JBSA Fort Sam Houston, San Antonio, Texas, United States of America
| | - Katrin Mende
- Brooke Army Medical Center, JBSA Fort Sam Houston, San Antonio, Texas, United States of America
- Department of Preventive Medicine and Biostatistics, Infectious Disease Clinical Research Program, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
| | - Miriam L. Beckius
- Brooke Army Medical Center, JBSA Fort Sam Houston, San Antonio, Texas, United States of America
| | - Susan J. Kaiser
- Brooke Army Medical Center, JBSA Fort Sam Houston, San Antonio, Texas, United States of America
- Department of Preventive Medicine and Biostatistics, Infectious Disease Clinical Research Program, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
| | - M. Leigh Carson
- Department of Preventive Medicine and Biostatistics, Infectious Disease Clinical Research Program, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
| | - Dan Lu
- Department of Preventive Medicine and Biostatistics, Infectious Disease Clinical Research Program, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
- Henry M. Jackson Foundation for the Advancement of Military Medicine, Inc., Bethesda, Maryland, United States of America
| | - Timothy J. Whitman
- Walter Reed National Military Medical Center, Bethesda, Maryland, United States of America
| | | | - David R. Tribble
- Department of Preventive Medicine and Biostatistics, Infectious Disease Clinical Research Program, Uniformed Services University of the Health Sciences, Bethesda, Maryland, United States of America
| | - Dana M. Blyth
- Brooke Army Medical Center, JBSA Fort Sam Houston, San Antonio, Texas, United States of America
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11
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Lim HJ, Kang ER, Park MY, Kim BK, Kim MJ, Jung S, Roh KH, Sung N, Yang JH, Lee MW, Lee SH, Yang YJ. Development of a multiplex real-time PCR assay for the simultaneous detection of four bacterial pathogens causing pneumonia. PLoS One 2021; 16:e0253402. [PMID: 34138947 PMCID: PMC8211157 DOI: 10.1371/journal.pone.0253402] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 06/03/2021] [Indexed: 12/18/2022] Open
Abstract
Classification of clinical symptoms and diagnostic microbiology are essential to effectively employ antimicrobial therapy for lower respiratory tract infections (LRTIs) in a timely manner. Empirical antibiotic treatment without microbial identification hinders the selective use of narrow-spectrum antibiotics and effective patient treatment. Thus, the development of rapid and accurate diagnostic procedures that can be readily adopted by the clinic is necessary to minimize non-essential or excessive use of antibiotics and accelerate patient recovery from LRTI-induced damage. We developed and validated a multiplex real-time polymerase chain reaction (mRT-PCR) assay with good analytical performance and high specificity to simultaneously detect four bacterial pathogens causing pneumonia: Klebsiella pneumoniae, Pseudomonas aeruginosa, Staphylococcus aureus, and Moraxella catarrhalis. The analytical performance of mRT-PCR against target pathogens was evaluated by the limit of detection (LOD), specificity, and repeatability. Two hundred and ten clinical specimens from pneumonia patients were processed using an automatic nucleic acid extraction system for the “respiratory bacteria four” (RB4) mRT-PCR assay, and the results were directly compared to references from bacterial culture and/or Sanger sequencing. The RB4 mRT-PCR assay detected all target pathogens from sputum specimens with a coefficient of variation ranging from 0.29 to 1.71 and conservative LOD of DNA corresponding to 5 × 102 copies/reaction. The concordance of the assay with reference-positive specimens was 100%, and additional bacterial infections were detected from reference-negative specimens. Overall, the RB4 mRT-PCR assay showed a more rapid turnaround time and higher performance that those of reference assays. The RB4 mRT-PCR assay is a high-throughput and reliable tool that assists decision-making assessment and outperforms other standard methods. This tool supports patient management by considerably reducing the inappropriate use of antibiotics.
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Affiliation(s)
- Ho Jae Lim
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
- Department of Integrative Biological Sciences, Chosun University, Gwangju, Republic of Korea
| | - Eun-Rim Kang
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Min Young Park
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Bo Kyung Kim
- Department of Laboratory Medicine, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Min Jin Kim
- Department of Laboratory Medicine, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Sunkyung Jung
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Kyoung Ho Roh
- Department of Laboratory Medicine, National Health Insurance Service Ilsan Hospital, Goyang, Gyeonggi, Republic of Korea
| | - Nackmoon Sung
- Clinical Research Institute, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Jae-Hyun Yang
- Paul F. Glenn Center for Biology of Aging Research, Department of Genetics, Blavatnik Institute, Harvard Medical School, Boston, MA, United States of America
| | - Min-Woo Lee
- Soonchunhyang Institute of Medi-bio Science (SIMS) and Department of Integrated Biomedical Science, Soonchunhyang University, Cheonan-si, Republic of Korea
| | - Sun-Hwa Lee
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
- Department of Laboratory Medicine, Seegene Medical Foundation, Seoul, Republic of Korea
| | - Yong-Jin Yang
- Department of Molecular Diagnostics, Seegene Medical Foundation, Seoul, Republic of Korea
- * E-mail:
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12
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Saxenborn P, Baxter J, Tilevik A, Fagerlind M, Dyrkell F, Pernestig AK, Enroth H, Tilevik D. Genotypic Characterization of Clinical Klebsiella spp. Isolates Collected From Patients With Suspected Community-Onset Sepsis, Sweden. Front Microbiol 2021; 12:640408. [PMID: 33995300 PMCID: PMC8120268 DOI: 10.3389/fmicb.2021.640408] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 04/13/2021] [Indexed: 02/02/2023] Open
Abstract
Klebsiella is a genus of Gram-negative bacteria known to be opportunistic pathogens that may cause a variety of infections in humans. Highly drug-resistant Klebsiella species, especially K. pneumoniae, have emerged rapidly and are becoming a major concern in clinical management. Although K. pneumoniae is considered the most important pathogen within the genus, the true clinical significance of the other species is likely underrecognized due to the inability of conventional microbiological methods to distinguish between the species leading to high rates of misidentification. Bacterial whole-genome sequencing (WGS) enables precise species identification and characterization that other technologies do not allow. Herein, we have characterized the diversity and traits of Klebsiella spp. in community-onset infections by WGS of clinical isolates (n = 105) collected during a prospective sepsis study in Sweden. The sequencing revealed that 32 of the 82 isolates (39.0%) initially identified as K. pneumoniae with routine microbiological methods based on cultures followed by matrix-assisted laser desorption-time of flight mass spectrometry (MALDI-TOF MS) had been misidentified. Of these, 23 were identified as Klebsiella variicola and nine as other members of the K. pneumoniae complex. Comparisons of the number of resistance genes showed that significantly fewer resistance genes were detected in Klebsiella oxytoca compared to K. pneumoniae and K. variicola (both values of p < 0.001). Moreover, a high proportion of the isolates within the K. pneumoniae complex were predicted to be genotypically multidrug-resistant (MDR; 79/84, 94.0%) in contrast to K. oxytoca (3/16, 18.8%) and Klebsiella michiganensis (0/4, 0.0%). All isolates predicted as genotypically MDR were found to harbor the combination of β-lactam, fosfomycin, and quinolone resistance markers. Multi-locus sequence typing (MLST) revealed a high diversity of sequence types among the Klebsiella spp. with ST14 (10.0%) and ST5429 (10.0%) as the most prevalent ones for K. pneumoniae, ST146 for K. variicola (12.0%), and ST176 for K. oxytoca (25.0%). In conclusion, the results from this study highlight the importance of using high-resolution genotypic methods for identification and characterization of clinical Klebsiella spp. isolates. Our findings indicate that infections caused by other members of the K. pneumoniae complex than K. pneumoniae are a more common clinical problem than previously described, mainly due to high rates of misidentifications.
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Affiliation(s)
- Patricia Saxenborn
- Systems Biology Research Centre, School of Bioscience, University of Skövde, Skövde, Sweden
| | - John Baxter
- Systems Biology Research Centre, School of Bioscience, University of Skövde, Skövde, Sweden
| | - Andreas Tilevik
- Systems Biology Research Centre, School of Bioscience, University of Skövde, Skövde, Sweden
| | - Magnus Fagerlind
- Systems Biology Research Centre, School of Bioscience, University of Skövde, Skövde, Sweden
| | | | - Anna-Karin Pernestig
- Systems Biology Research Centre, School of Bioscience, University of Skövde, Skövde, Sweden
| | - Helena Enroth
- Systems Biology Research Centre, School of Bioscience, University of Skövde, Skövde, Sweden.,Molecular Microbiology, Laboratory Medicine, Unilabs AB, Skövde, Sweden
| | - Diana Tilevik
- Systems Biology Research Centre, School of Bioscience, University of Skövde, Skövde, Sweden
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13
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Silva-Sanchez J, Barrios-Camacho H, Hernández-Rodriguez E, Duran-Bedolla J, Sanchez-Perez A, Martínez-Chavarría LC, Xicohtencatl-Cortes J, Hernández-Castro R, Garza-Ramos U. Molecular characterization of KPC-2-producing Klebsiella pneumoniae ST258 isolated from bovine mastitis. Braz J Microbiol 2021; 52:1029-1036. [PMID: 33580865 DOI: 10.1007/s42770-021-00445-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2020] [Accepted: 02/02/2021] [Indexed: 11/30/2022] Open
Abstract
Bovine mastitis, an inflammation of the mammary gland of dairy cattle, is the most prevalent disease causing economically important losses, reduced milk production, early culling, veterinary expenses, and higher death rates. Bovine mastitis infections are the main cause for the use of antibiotics; however, the emergence of multidrug-resistant bacteria and the poor or nil response to antibiotics has become a critical global health problem. The goal of this study was the characterization of bacterial infections associated with clinical bovine mastitis. All the isolates were multidrug-resistant and were negative for the production of extended spectrum β-lactamases. However, all isolates were identified as carbapenemase-producing organisms by the Carba NP test. The carbapenemase identified was the product of the KPC-2 gene. The isolates were identified as Klebsiella pneumoniae and contained virulence genes for fimbriae, lipopolysaccharides, nitrogen starvation genes, and siderophores. Sixty-nine percent of the KPC-2-producing isolates had the same plasmid profile, although the genetic mobilization of resistance by bacterial conjugation was unsuccessful. The carbapenemase corresponded to the plasmid-borne KPC-2 gene identified by Southern blot hybridization. The assay showed a positive signal in the 90 kb (69% of the isolates), 165 kb (31% of the isolates), and 130 kb (6% of the isolates) plasmids. The IncFIIy and IncFIIk replicons were detected among these K. pneumoniae isolates. The PFGE and MLST analysis showed that all of the isolates are comprised by two clones (A and B) belonging to Sequence Type 258. This is the first report of K. pneumoniae producing carbapenemase KPC-2 isolated from bovine mastitis.
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Affiliation(s)
- Jesús Silva-Sanchez
- Laboratorio de Resistencia Bacteriana, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Santa María Ahuacatitlán. C.P, 62100, Cuernavaca, Morelos, México
| | - Humberto Barrios-Camacho
- Laboratorio de Resistencia Bacteriana, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Santa María Ahuacatitlán. C.P, 62100, Cuernavaca, Morelos, México
| | - Emmanuel Hernández-Rodriguez
- Laboratorio de Resistencia Bacteriana, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Santa María Ahuacatitlán. C.P, 62100, Cuernavaca, Morelos, México
| | - Josefina Duran-Bedolla
- Laboratorio de Resistencia Bacteriana, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Santa María Ahuacatitlán. C.P, 62100, Cuernavaca, Morelos, México
| | - Alejandro Sanchez-Perez
- Laboratorio de Resistencia Bacteriana, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Santa María Ahuacatitlán. C.P, 62100, Cuernavaca, Morelos, México
| | - Luary C Martínez-Chavarría
- Departamento de Patología, Facultad de Medicina Veterinaria y Zootecnia, Universidad Nacional Autónoma de México, Coyoacán, 04510, Ciudad de México, México
| | - Juan Xicohtencatl-Cortes
- Laboratorio de Bacteriología Intestinal, Hospital Infantil de México, Dr. Federico Gómez, Cuauhtémoc, 06720, Ciudad de México, México
| | - Rigoberto Hernández-Castro
- Departamento Ecología de Agentes Patógenos, Hospital General "Dr. Manuel Gea González", Calzada de Tlalpan 4800, 14080. Tlalpan, Cd de Mexico, Mexico.
| | - Ulises Garza-Ramos
- Laboratorio de Resistencia Bacteriana, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Av. Universidad # 655, Col. Santa María Ahuacatitlán. C.P, 62100, Cuernavaca, Morelos, México.
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14
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Shen X, Yin L, Ma H, Pan X, Zhang D, Zhao R, Dai Y, Hou H, Hu X. Comprehensive genomic analysis and characterization of a new ST 174 type Klebsiella variicola strain isolated from chicken embryos. INFECTION GENETICS AND EVOLUTION 2021; 90:104768. [PMID: 33588064 DOI: 10.1016/j.meegid.2021.104768] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2020] [Revised: 12/31/2020] [Accepted: 02/10/2021] [Indexed: 10/22/2022]
Abstract
Klebsiella variicola is a widespread opportunistic pathogen that causes infections in humans and animals. Herein a novel Klebsiella strain, AHKv-S01, was isolated and identified from dead chicken embryos in Anhui, China. Its genome contained a circular chromosome of 5,505,304 bp, with 5244 protein-coding genes, and an integrative conjugative element region containing 79 ORF sequences. AHKv-S01 was given a new sequence type number-174. Phylogenetic analyses showed that rpoB partial nucleotide sequences were highly reliable for identifying Klebsiella spp. Most of the 340 unique genes of AHKv-S01 were involved in cell envelop biogenesis, transcription, transport, and metabolic processes. Moreover, AHKv-S01 was sensitive to several antibiotics, but it showed strong resistance to penicillins, macrolides, and lincosamide. The genome contained three drug efflux pump superfamilies, β-lactamase genes, and fosfomycin resistance-related genes. Most drug resistance genes showed amino acid mutations. Multiple virulence and pathogenic factors were also identified, and they were mainly related to adhesion, secretion, iron acquisition, and immune evasion. Chicken embryo lethality assay results revealed that the 7-day chicken embryo lethality rate was 80%, 40%, and 50% for AHKv-S01, K. pneumoniae ATCC10031, and K. pneumoniae CICC24714, respectively. The median lethal dose of AHKv-S01 was 39.9 CFU/embryo. Even low infection levels of AHKv-S01 caused a significant reduction in chicken embryo hatchability. Severe pathological changes to the liver, heart, and brain tissues of embryos infected with AHKv-S01 were observed, and these changes appeared earlier in the heart and brain than in the liver. To conclude, our results provide a foundation for further studies aiming to assess the potential risk of K. variicola to poultry populations and production yields.
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Affiliation(s)
- Xuehuai Shen
- Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Anhui, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Anhui, China
| | - Lei Yin
- Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Anhui, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Anhui, China
| | - Haitian Ma
- Key Laboratory of Animal Physiology and Biochemistry, College of Veterinary Medicine, Nanjing Agricultural University, Nanjing, China
| | - Xiaocheng Pan
- Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Anhui, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Anhui, China.
| | - Danjun Zhang
- Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Anhui, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Anhui, China.
| | - Ruihong Zhao
- Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Anhui, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Anhui, China
| | - Yin Dai
- Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Anhui, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Anhui, China
| | - Hongyan Hou
- Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Anhui, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Anhui, China
| | - Xiaomiao Hu
- Institute of Animal Husbandry and Veterinary Science, Anhui Academy of Agricultural Sciences, Livestock and Poultry Epidemic Diseases Research Center of Anhui Province, Anhui, China; Anhui Province Key Laboratory of Livestock and Poultry Product Safety Engineering, Anhui, China
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15
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Mondo E, Rinnovati R, Spadari A, Giacometti F, Serraino A, Savini F, Piva S. First isolation of Klebsiella variicola from a horse pleural effusion. BMC Vet Res 2021; 17:75. [PMID: 33579291 PMCID: PMC7881548 DOI: 10.1186/s12917-021-02776-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2020] [Accepted: 01/26/2021] [Indexed: 11/23/2022] Open
Abstract
Background Respiratory diseases are the second most common cause of illnesses in horses, their etiology can be viral, bacterial, immune-mediated, or mechanical (Racklyeft and Love DN, Aust Vet J 78:549–59, 2000; Austin et al., J Am Vet Med Assoc 207:325–328, 1995; Arroyo et al., J Vet Intern Med 31:894–900, 2017). Klebsiella variicola is a Gram-negative bacterium that was initially identified as an endophyte in soil and plants such as bananas, rice, sugar cane and maize but recent studies have identified this microorganism as an emerging pathogen in humans (Rodríguez-Medina et al., Emerg Microbes Infect 8:973–988, 2019; Fontana et al., J Clin Microbiol 57:e00825–18, 2019; Rosenblueth et al., Syst Appl Microbiol 27:27–35, 2004). This paper describes, for the first time to our knowledge, the isolation of K. variicola from pleural effusion in a male adult horse. Case presentation 17-years Italian Saddle Horse with respiratory distress and fever was admitted to the Veterinary Teaching Hospital of the Department of Veterinary Medical Sciences, University of Bologna. At home, the patient had undergone antibiotic therapy without clinical improvement. Vital signs on admission revealed an increased respiratory rate, tachycardia, pyrexia and weight loss. The animal was submitted for collateral examination including thoracic radiology and ultrasound and thoracoscopy that showed bilateral pleural effusion associated with multifocal pulmonary atelectasis. During the thoracoscopic examination, that confirmed the presence of a seropurulent pleural effusion, a sample of pleural fluid was collected and Gram-negative bacteria were isolated and subjected to matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF MS) that allowed the identification of K. variicola. The isolate was sensitive to amikacin, cefazolin, enrofloxacin, marbofloxacin, tetracycline, and trimethoprim-sulfamethoxazole;the horse was treated with Oxytetracycline and amikacin. Despite a general health improvement of the subject, the pleural effusion did not resolve after treatment. Conclusions This paper describes, for the first time, the isolation of K. variicola in a horse with respiratory disease. The misidentification between K. variicola and K. pneumoniae has caused unawareness about significant aspects of this bacterial species. In fact, even though in animals the role of this bacterium is not clear, in humans it has been recognized as an emerging pathogen. The use of new methods for bacterial identification will probably lead to the isolation of a greater number of strains which will have to be studied to acquire knowledge that will be useful to clarify the clinical importance and relevance of K. variicola also in animals.
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Affiliation(s)
- Elisabetta Mondo
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, Bologna, 40064, Italy
| | - Riccardo Rinnovati
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, Bologna, 40064, Italy
| | - Alessandro Spadari
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, Bologna, 40064, Italy
| | - Federica Giacometti
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, Bologna, 40064, Italy.
| | - Andrea Serraino
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, Bologna, 40064, Italy
| | - Federica Savini
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, Bologna, 40064, Italy
| | - Silvia Piva
- Department of Veterinary Medical Sciences, University of Bologna, Via Tolara di Sopra 50, Bologna, 40064, Italy
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16
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Morales-León F, Opazo-Capurro A, Caro C, Lincopan N, Cardenas-Arias A, Esposito F, Illesca V, Rioseco ML, Domínguez-Yévenes M, Lima CA, Bello-Toledo H, González-Rocha G. Hypervirulent and hypermucoviscous extended-spectrum β-lactamase-producing Klebsiella pneumoniae and Klebsiella variicola in Chile. Virulence 2020; 12:35-44. [PMID: 33372844 PMCID: PMC7781644 DOI: 10.1080/21505594.2020.1859274] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Convergence of virulence and antibiotic-resistance has been reported in Klebsiella pneumoniae, but not in Klebsiella variicola. We, hereby, report the detection and genomic characterization of hypervirulent and hypermucoviscous K. pneumoniae and K.variicola recovered in Chile from health-care associated infections, which displayed resistance to broad-spectrum cephalosporins. One hundred forty-six K. pneumoniae complex isolates were screened by hypermucoviscosity by the “string test.” Two hypermucoid isolates, one hypermucoviscous K. pneumoniae (hmKp) and one K. variicola (hmKv), were further investigated by whole-genome sequencing. In vivo virulence was analyzed by the Galleria mellonella killing assay. In silico analysis of hmKp UCO-494 and hmKv UCO-495 revealed the presence of multiple antibiotic-resistance genes, such as blaCTX-M-1, blaDHA-1 and blaLEN-25 among others clinically relevant resistance determinants, including mutations in a two-component regulatory system related to colistin resistance. These genetic features confer a multidrug-resistant (MDR) phenotype in both strains. Moreover, virulome in silico analysis confirmed the presence of the aerobactin gene iutA, in addition to yersiniabactin and/or colicin V encoding genes, which are normally associated to high virulence in humans. Furthermore, both isolates were able to kill G. mellonella and displayed higher virulence in comparison with the control strain. In summary, the convergence of virulence and the MDR-phenotype in K. pneumoniae complex members is reported for the first time in Chile, denoting a clinical problem that deserves special attention and continuous surveillance in South America.
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Affiliation(s)
- F Morales-León
- Laboratorio de Investigación en Agentes Antibacterianos, Facultad de Ciencias Biológicas, Universidad de Concepción , Concepción, Chile.,Millennium Nucleus for Collaborative Research on Bacterial Resistance , Chile.,Departamento de Farmacia, Universidad de Concepción, Concepción , Chile
| | - A Opazo-Capurro
- Laboratorio de Investigación en Agentes Antibacterianos, Facultad de Ciencias Biológicas, Universidad de Concepción , Concepción, Chile.,Millennium Nucleus for Collaborative Research on Bacterial Resistance , Chile
| | - C Caro
- Laboratorio de Investigación en Agentes Antibacterianos, Facultad de Ciencias Biológicas, Universidad de Concepción , Concepción, Chile.,Departamento de Farmacia, Universidad de Concepción, Concepción , Chile
| | - N Lincopan
- Department of Microbiology, Institute of Biomedical Sciences, Universidade de São Paulo , São Paulo, Brazil.,Department of Clinical Analysis, School of Pharmacy, Universidade de São Paulo , São Paulo, Brazil
| | - A Cardenas-Arias
- Department of Microbiology, Institute of Biomedical Sciences, Universidade de São Paulo , São Paulo, Brazil
| | - F Esposito
- Department of Microbiology, Institute of Biomedical Sciences, Universidade de São Paulo , São Paulo, Brazil.,Department of Clinical Analysis, School of Pharmacy, Universidade de São Paulo , São Paulo, Brazil
| | - V Illesca
- Unidad de Microbiología, Hospital Dr. Hernan Henriquez Aravena , Temuco, Chile
| | - M L Rioseco
- Laboratorio de Microbiologia, Hospital de Puerto Montt , Puerto Montt, Chile
| | - M Domínguez-Yévenes
- Laboratorio de Investigación en Agentes Antibacterianos, Facultad de Ciencias Biológicas, Universidad de Concepción , Concepción, Chile
| | - C A Lima
- Laboratorio de Investigación en Agentes Antibacterianos, Facultad de Ciencias Biológicas, Universidad de Concepción , Concepción, Chile.,Millennium Nucleus for Collaborative Research on Bacterial Resistance , Chile
| | - H Bello-Toledo
- Laboratorio de Investigación en Agentes Antibacterianos, Facultad de Ciencias Biológicas, Universidad de Concepción , Concepción, Chile.,Millennium Nucleus for Collaborative Research on Bacterial Resistance , Chile
| | - Gerardo González-Rocha
- Laboratorio de Investigación en Agentes Antibacterianos, Facultad de Ciencias Biológicas, Universidad de Concepción , Concepción, Chile.,Millennium Nucleus for Collaborative Research on Bacterial Resistance , Chile
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17
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The ZKIR Assay, a Real-Time PCR Method for the Detection of Klebsiella pneumoniae and Closely Related Species in Environmental Samples. Appl Environ Microbiol 2020; 86:AEM.02711-19. [PMID: 32005732 PMCID: PMC7082575 DOI: 10.1128/aem.02711-19] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 01/21/2020] [Indexed: 11/20/2022] Open
Abstract
The Klebsiella pneumoniae species complex Kp includes human and animal pathogens, some of which are emerging as hypervirulent and/or antibiotic-resistant strains. These pathogens are diverse and classified into seven phylogroups, which may differ in their reservoirs and epidemiology. Proper management of this public health hazard requires a better understanding of Kp ecology and routes of transmission to humans. So far, detection of these microorganisms in complex matrices such as food or the environment has been difficult due to a lack of accurate and sensitive methods. Here, we describe a novel method based on real-time PCR which enables detection of all Kp phylogroups with high sensitivity and specificity. We used this method to detect Kp isolates from environmental samples, and we show based on genomic sequencing that they differ in antimicrobial resistance and virulence gene content from human clinical Kp isolates. The ZKIR PCR assay will enable rapid screening of multiple samples for Kp presence and will thereby facilitate tracking the dispersal patterns of these pathogenic strains across environmental, food, animal and human sources. Klebsiella pneumoniae is of growing public health concern due to the emergence of strains that are multidrug resistant, virulent, or both. Taxonomically, the K. pneumoniae complex (“Kp”) includes seven phylogroups, with Kp1 (K. pneumoniaesensu stricto) being medically prominent. Kp can be present in environmental sources such as soils and vegetation, which could act as reservoirs of animal and human infections. However, the current lack of screening methods to detect Kp in complex matrices limits research on Kp ecology. Here, we analyzed 1,001 genome sequences and found that existing molecular detection targets lack specificity for Kp. A novel real-time PCR method, the ZKIR (zur-khe intergenic region) assay, was developed and used to detect Kp in 96 environmental samples. The results were compared to a culture-based method using Simmons citrate agar with 1% inositol medium coupled to matrix-assisted laser desorption ionization–time of flight mass spectrometry identification. Whole-genome sequencing of environmental Kp was performed. The ZKIR assay was positive for the 48 tested Kp reference strains, whereas 88 non-Kp strains were negative. The limit of detection of Kp in spiked soil microcosms was 1.5 × 10−1 CFU g−1 after enrichment for 24 h in lysogeny broth supplemented with ampicillin, and it was 1.5 × 103 to 1.5 × 104 CFU g−1 directly after soil DNA extraction. The ZKIR assay was more sensitive than the culture method. Kp was detected in 43% of environmental samples. Genomic analysis of the isolates revealed a predominance of phylogroups Kp1 (65%) and Kp3 (32%), a high genetic diversity (23 multilocus sequence types), a quasi-absence of antibiotic resistance or virulence genes, and a high frequency (50%) of O-antigen type 3. This study shows that the ZKIR assay is an accurate, specific, and sensitive novel method to detect the presence of Kp in complex matrices and indicates that Kp isolates from environmental samples differ from clinical isolates. IMPORTANCE The Klebsiella pneumoniae species complex Kp includes human and animal pathogens, some of which are emerging as hypervirulent and/or antibiotic-resistant strains. These pathogens are diverse and classified into seven phylogroups, which may differ in their reservoirs and epidemiology. Proper management of this public health hazard requires a better understanding of Kp ecology and routes of transmission to humans. So far, detection of these microorganisms in complex matrices such as food or the environment has been difficult due to a lack of accurate and sensitive methods. Here, we describe a novel method based on real-time PCR which enables detection of all Kp phylogroups with high sensitivity and specificity. We used this method to detect Kp isolates from environmental samples, and we show based on genomic sequencing that they differ in antimicrobial resistance and virulence gene content from human clinical Kp isolates. The ZKIR PCR assay will enable rapid screening of multiple samples for Kp presence and will thereby facilitate tracking the dispersal patterns of these pathogenic strains across environmental, food, animal and human sources.
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18
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Geng BY, Cao LY, Li F, Song H, Liu CG, Zhao XQ, Bai FW. Potential of Zymomonas mobilis as an electricity producer in ethanol production. BIOTECHNOLOGY FOR BIOFUELS 2020; 13:36. [PMID: 32158500 PMCID: PMC7057670 DOI: 10.1186/s13068-020-01672-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 02/01/2020] [Indexed: 06/10/2023]
Abstract
BACKGROUND Microbial fuel cell (MFC) convokes microorganism to convert biomass into electricity. However, most well-known electrogenic strains cannot directly use glucose to produce valuable products. Zymomonas mobilis, a promising bacterium for ethanol production, owns special Entner-Doudoroff pathway with less ATP and biomass produced and the low-energy coupling respiration, making Z. mobilis a potential exoelectrogen. RESULTS A glucose-consuming MFC is constructed by inoculating Z. mobilis. The electricity with power density 2.0 mW/m2 is derived from the difference of oxidation-reduction potential (ORP) between anode and cathode chambers. Besides, two-type electricity generation is observed as glucose-independent process and glucose-dependent process. For the sake of enhancing MFC efficiency, extracellular and intracellular strategies are implemented. Biofilm removal and addition of c-type cytochrome benefit electricity performance and Tween 80 accelerates the electricity generation. Perturbation of cellular redox balance compromises the electricity output, indicating that redox homeostasis is the principal requirement to reach ideal voltage. CONCLUSION This study identifies potential feature of electricity activity for Z. mobilis and provides multiple strategies to enhance the electricity output. Therefore, additional electricity generation will benefit the techno-economic viability of the commercial bulk production for biochemicals or biofuels in an efficient and environmentally sustainable manner.
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Affiliation(s)
- Bo-Yu Geng
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences of Ministry of Education, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Lian-Ying Cao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences of Ministry of Education, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Feng Li
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
| | - Hao Song
- Key Laboratory of Systems Bioengineering (Ministry of Education), School of Chemical Engineering and Technology, Tianjin University, Tianjin, 300072 China
| | - Chen-Guang Liu
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences of Ministry of Education, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Xin-Qing Zhao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences of Ministry of Education, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
| | - Feng-Wu Bai
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic & Developmental Sciences of Ministry of Education, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, 200240 China
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19
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Cesa-Luna C, Baez A, Quintero-Hernández V, De la Cruz-Enríquez J, Castañeda-Antonio MD, Muñoz-Rojas J. The importance of antimicrobial compounds produced by beneficial bacteria on the biocontrol of phytopathogens. ACTA BIOLÓGICA COLOMBIANA 2020. [DOI: 10.15446/abc.v25n1.76867] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Bacteria produce antimicrobial compounds to compete for nutrients and space in a particular habitat. Antagonistic interactions can be evaluated by several methodologies including the double-layer agar and simultaneous inhibition assays. Among the well-known inhibitory substances produced by bacteria are the broad-spectrum antibiotics, organic acids, siderophores, antifungal, and bacteriocins. The most studied bacterial genera able to produce these inhibitory substances are Enterococcus, Lactococcus, Streptomyces, Bacillus, Pseudomonas, Klebsiella, Escherichia, and Burkholderia. Some beneficial bacteria can promote plant growth and degrade toxic compounds in the environment representing an attractive solution to diverse issues in agriculture and soil pollution, particularly in fields with damaged soils where pesticides and fertilizers have been indiscriminately used. Beneficial bacteria may increase plant health by inhibiting pathogenic microorganisms; some examples include Gluconacetobacter diazotrophicus, Azospirullum brasilense, Pseudomonas fluorescens, Pseudomonas protegens, and Burkholderia tropica. However, most studies showing the antagonistic potential of these bacteria have been performed in vitro, and just a few of them have been evaluated in association with plants. Several inhibitory substances involved in pathogen antagonism have not been elucidated yet; in fact, we know only 1 % of the bacterial diversity in a natural environment leading us to assume that many other inhibitory substances remain unexplored. In this review, we will describe the characteristics of some antimicrobial compounds produced by beneficial bacteria, the principal methodologies performed to evaluate their production, modes of action, and their importance for biotechnological purposes.
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20
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Molecular epidemiology of Klebsiella variicola obtained from different sources. Sci Rep 2019; 9:10610. [PMID: 31337792 PMCID: PMC6650414 DOI: 10.1038/s41598-019-46998-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Accepted: 07/09/2019] [Indexed: 12/24/2022] Open
Abstract
Klebsiella variicola is considered an emerging pathogen in humans and has been described in different environments. K. variicola belongs to Klebsiella pneumoniae complex, which has expanded the taxonomic classification and hindered epidemiological and evolutionary studies. The present work describes the molecular epidemiology of K. variicola based on MultiLocus Sequence Typing (MLST) developed for this purpose. In total, 226 genomes obtained from public data bases and 28 isolates were evaluated, which were mainly obtained from humans, followed by plants, various animals, the environment and insects. A total 166 distinct sequence types (STs) were identified, with 39 STs comprising at least two isolates. The molecular epidemiology of K. variicola showed a global distribution for some STs was observed, and in some cases, isolates obtained from different sources belong to the same ST. Several examples of isolates corresponding to kingdom-crossing bacteria from plants to humans were identified, establishing this as a possible route of transmission. goeBURST analysis identified Clonal Complex 1 (CC1) as the clone with the greatest distribution. Whole-genome sequencing of K. variicola isolates revealed extended-spectrum β-lactamase- and carbapenemase-producing strains with an increase in pathogenicity. MLST of K. variicola is a strong molecular epidemiological tool that allows following the evolution of this bacterial species obtained from different environments.
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21
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Gomez-Gamboa L, Barrios-Camacho H, Duran-Bedolla J, Sánchez-Perez A, Reyna-Flores F, Perozo-Mena A, Zabala I, Rodriguez-Medina N, Martínez-Barnetche J, Téllez-Sosa J, Valdovinos-Torres H, Garza-Ramos U. Molecular and genetic characterization of carbapenemase-producing bacteria in Venezuela. J Chemother 2019; 31:349-353. [PMID: 31046636 DOI: 10.1080/1120009x.2019.1607452] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Carbapenem-resistant Gram-negative bacteria isolated in Venezuela have been poorly characterized. The present study characterized a total of 34 isolates obtained from 27 patients; five of these patients were multi-infected. The bacterial species identified were Klebsiella pneumoniae (17), Pseudomonas aeruginosa (9), and Acinetobacter baumannii (8). From these isolates, 85% were identified as carbapenemase-producing bacteria, and the identified carbapenemase genes were blaKPC-2 (10/29 [34.4%]), blaVIM-type (7/29 [24.1%]), blaOXA-23 (7/29 [24.1%]), blaNDM-1 (8/29 [27.5%]), and the coexistence of blaOXA-23/blaNDM-1 (2/29 [6.8%]). Patient 1 was multi-infected by K. pneumoniae ST11 and ST2413 isolates harbouring the blaNDM-1 and blaKPC-2 genes, respectively. The other patients were multi-infected by two or three different bacterial species such as ESBL-producing K. pneumoniae isolates, P. aeruginosa harbouring the blaVIM-type gene, K. pneumoniae ST147 harbouring the blaKPC-2 gene and by A. baumannii harbouring the blaOXA-23 gene. The blaNDM-1 gene in A. baumannii is flanked by an uncommon genetic structure, whereas blaNDM-1 gene in K. pneumoniae revealed a common structure described in different plasmids from Enterobacteriaceae isolates. This study provides new information about the epidemiology of carbapenemase-producing bacteria in clinical setting in Venezuela.
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Affiliation(s)
- Liliana Gomez-Gamboa
- Department of Tropical and Infectious Diseases School of Medicine, University of Zulia , Maracaibo , Venezuela
| | - Humberto Barrios-Camacho
- Instituto Nacional de Salud Pública (INSP), CISEI Laboratorio de Resistencia Bacteriana , Cuernavaca , Morelos , Mexico
| | - Josefina Duran-Bedolla
- Instituto Nacional de Salud Pública (INSP), CISEI Laboratorio de Resistencia Bacteriana , Cuernavaca , Morelos , Mexico
| | - Alejandro Sánchez-Perez
- Instituto Nacional de Salud Pública (INSP), CISEI Laboratorio de Resistencia Bacteriana , Cuernavaca , Morelos , Mexico
| | - Fernando Reyna-Flores
- Instituto Nacional de Salud Pública (INSP), CISEI Laboratorio de Resistencia Bacteriana , Cuernavaca , Morelos , Mexico
| | - Armindo Perozo-Mena
- Laboratory of Bacteriology Department of Microbiology Faculty of Medicine. University of Zulia, Maracaibo , Venezuela
| | - Irene Zabala
- Genetics and Molecular Biology Laboratory Faculty of Science, University of Zulia , Maracaibo , Venezuela
| | - Nadia Rodriguez-Medina
- Instituto Nacional de Salud Pública (INSP), CISEI Laboratorio de Resistencia Bacteriana , Cuernavaca , Morelos , Mexico
| | - Jesús Martínez-Barnetche
- Instituto Nacional de Salud Pública (INSP), CISEI, Departamento de Inmunología , Cuernavaca , Morelos , Mexico
| | - Juan Téllez-Sosa
- Instituto Nacional de Salud Pública (INSP), CISEI, Departamento de Inmunología , Cuernavaca , Morelos , Mexico
| | - Humberto Valdovinos-Torres
- Instituto Nacional de Salud Pública (INSP), CISEI, Departamento de Inmunología , Cuernavaca , Morelos , Mexico
| | - Ulises Garza-Ramos
- Instituto Nacional de Salud Pública (INSP), CISEI Laboratorio de Resistencia Bacteriana , Cuernavaca , Morelos , Mexico
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22
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Catalán-Nájera JC, Barrios-Camacho H, Duran-Bedolla J, Sagal-Prado A, Hernández-Castro R, García-Méndez J, Morfín-OteroMorfín-Otero R, Velázquez-Larios MDR, Ortíz-Navarrete V, Gutierrez-Xicotencatl L, Alpuche-Aranda C, Silva-Sánchez J, Garza-Ramos U. Molecular characterization and pathogenicity determination of hypervirulent Klebsiella pneumoniae clinical isolates serotype K2 in Mexico. Diagn Microbiol Infect Dis 2019; 94:316-319. [PMID: 30857917 DOI: 10.1016/j.diagmicrobio.2019.01.013] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 01/11/2019] [Accepted: 01/18/2019] [Indexed: 01/20/2023]
Abstract
Hypervirulent Klebsiella pneumoniae have been rarely described in Latin America. This work describes the characterization of hypervirulent K. pneumoniae isolates capsular serotype K2 belonging to sequence types 86 and 380. The assays showed the hypervirulent K. pneumoniae highly virulent, which is determined by the plasmid borne virulence genes. At this time, the hypervirulent K. pneumoniae clinical isolates in Mexico are extensively susceptible to antibiotics.
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Affiliation(s)
- Juan Carlos Catalán-Nájera
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca, Morelos, México
| | - Humberto Barrios-Camacho
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca, Morelos, México
| | - Josefina Duran-Bedolla
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca, Morelos, México
| | - Alan Sagal-Prado
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca, Morelos, México
| | - Rigoberto Hernández-Castro
- Departamento Ecología de Agentes Patógenos, Hospital General "Dr. Manuel Gea González", Ciudad de México, México
| | - Jorge García-Méndez
- Departamento de Posgrado y Educación Médica Continua, Instituto Nacional de Cancerología, Ciudad de México, México
| | - Rayo Morfín-OteroMorfín-Otero
- Instituto de Patología Infecciosa y Experimental, Centro Universitario de Ciencias de la Salud, Hospital Civil de Guadalajara "Fray Antonio Alcalde", Universidad de Guadalajara, Guadalajara, Jalisco, México
| | | | - Vianney Ortíz-Navarrete
- Departamento de Biomedicina Molecular, Centro de Investigación y Estudios Avanzados (CINVESTAV), Ciudad de México, México
| | - Lourdes Gutierrez-Xicotencatl
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca, Morelos, México
| | - Celia Alpuche-Aranda
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca, Morelos, México
| | - Jesús Silva-Sánchez
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca, Morelos, México.
| | - Ulises Garza-Ramos
- Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Instituto Nacional de Salud Pública (INSP), Cuernavaca, Morelos, México.
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The Brief Case: Klebsiella variicola-Identifying the Misidentified. J Clin Microbiol 2019; 57:57/1/e00826-18. [PMID: 30602547 DOI: 10.1128/jcm.00826-18] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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24
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Rodríguez-Medina N, Barrios-Camacho H, Duran-Bedolla J, Garza-Ramos U. Klebsiella variicola: an emerging pathogen in humans. Emerg Microbes Infect 2019; 8:973-988. [PMID: 31259664 PMCID: PMC6609320 DOI: 10.1080/22221751.2019.1634981] [Citation(s) in RCA: 111] [Impact Index Per Article: 22.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2019] [Revised: 06/13/2019] [Accepted: 06/16/2019] [Indexed: 12/13/2022]
Abstract
The Klebsiella pneumoniae complex comprises seven K. pneumoniae-related species, including K. variicola. K. variicola is a versatile bacterium capable of colonizing different hosts such as plants, humans, insects and animals. Currently, K. variicola is gaining recognition as a cause of several human infections; nevertheless, its virulence profile is not fully characterized. The clinical significance of K. variicola infection is hidden by imprecise detection methods that underestimate its real prevalence; however, several methods have been developed to correctly identify this species. Recent studies of carbapenemase-producing and colistin-resistant strains demonstrate a potential reservoir of multidrug-resistant genes. This finding presents an imminent scenario for spreading antimicrobial resistant genes among close relatives and, more concerningly, in clinical and environmental settings. Since K. variicola was identified as a novel bacterial species, different research groups have contributed findings elucidating this pathogen; however, important details about its epidemiology, pathogenesis and ecology are still missing. This review highlights the most significant aspects of K. variicola, discussing its different phenotypes, mechanisms of resistance, and virulence traits, as well as the types of infections associated with this pathogen.
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Affiliation(s)
- Nadia Rodríguez-Medina
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Cuernavaca, México
| | - Humberto Barrios-Camacho
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Cuernavaca, México
| | - Josefina Duran-Bedolla
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Cuernavaca, México
| | - Ulises Garza-Ramos
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana, Cuernavaca, México
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25
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Rodrigues C, Passet V, Rakotondrasoa A, Brisse S. Identification of Klebsiella pneumoniae, Klebsiella quasipneumoniae, Klebsiella variicola and Related Phylogroups by MALDI-TOF Mass Spectrometry. Front Microbiol 2018; 9:3000. [PMID: 30581423 PMCID: PMC6294014 DOI: 10.3389/fmicb.2018.03000] [Citation(s) in RCA: 75] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2018] [Accepted: 11/20/2018] [Indexed: 12/13/2022] Open
Abstract
Klebsiella pneumoniae (phylogroup Kp1), one of the most problematic pathogens associated with antibiotic resistance worldwide, is phylogenetically closely related to K. quasipneumoniae [subsp. quasipneumoniae (Kp2) and subsp. similipneumoniae (Kp4)], K. variicola (Kp3) and two unnamed phylogroups (Kp5 and Kp6). Together, Kp1 to Kp6 make-up the K. pneumoniae complex. Currently, the phylogroups can be reliably identified only based on gene (or genome) sequencing. Misidentification using standard laboratory methods is common and consequently, the clinical significance of K. pneumoniae complex members is imprecisely defined. Here, we evaluated and validated the potential of MALDI-TOF mass spectrometry (MS) to discriminate K. pneumoniae complex members. We detected mass spectrometry biomarkers associated with the phylogroups, with a sensitivity and specificity ranging between 80-100% and 97-100%, respectively. Strains within phylogroups Kp1, Kp2, Kp4, and Kp5 each shared two specific peaks not observed in other phylogroups. Kp3 strains shared a peak that was only observed otherwise in Kp5. Finally, Kp6 had a diagnostic peak shared only with Kp1. Kp3 and Kp6 could therefore be identified by exclusion criteria (lacking Kp5 and Kp1-specific peaks, respectively). Further, ranked Pearson correlation clustering of spectra grouped strains according to their phylogroup. The model was tested and successfully validated using different culture media. These results demonstrate the potential of MALDI-TOF MS for precise identification of K. pneumoniae complex members. Incorporation of spectra of all K. pneumoniae complex members into reference MALDI-TOF spectra databases, in which they are currently lacking, is desirable. MALDI-TOF MS may thereby enable a better understanding of the epidemiology, ecology, and pathogenesis of members of the K. pneumoniae complex.
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Affiliation(s)
- Carla Rodrigues
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
| | - Virginie Passet
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
| | - Andriniaina Rakotondrasoa
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
- Institut Pasteur Madagascar, Madagascar, Africa
| | - Sylvain Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Paris, France
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Martínez-Romero E, Rodríguez-Medina N, Beltrán-Rojel M, Silva-Sánchez J, Barrios-Camacho H, Pérez-Rueda E, Garza-Ramos U. Genome misclassification of Klebsiella variicola and Klebsiella quasipneumoniae isolated from plants, animals and humans. SALUD PUBLICA DE MEXICO 2018; 60:56-62. [PMID: 29689657 DOI: 10.21149/8149] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 06/13/2017] [Indexed: 11/06/2022] Open
Abstract
OBJECTIVE Due to the fact that K. variicola, K. quasipneumoniae and K. pneumoniae are closely related bacterial species, misclassification can occur due to mistakes either in normal biochemical tests or during submission to public databases. The objective of this work was to identify K. variicola and K. quasipneumoniae genomes misclassified in GenBank database. MATERIALS AND METHODS Both rpoB phylogenies and average nucleotide identity (ANI) were used to identify a significant number of misclassified Klebsiella spp. genomes. RESULTS Here we report an update of K. variicola and K. Quasipneumoniae genomes correctly classified and a list of isolated genomes obtained from humans, plants, animals and insects, described originally as K. pneumoniae or K. variicola, but known now to be misclassified. CONCLUSIONS This work contributes to recognize the extensive presence of K. variicola and K. quasipneumoniae isolates in diverse sites and samples.
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Affiliation(s)
| | - Nadia Rodríguez-Medina
- Grupo de Resistencia Bacteriana, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública. Cuernavaca, Morelos, México
| | - Marilu Beltrán-Rojel
- Grupo de Resistencia Bacteriana, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública. Cuernavaca, Morelos, México
| | - Jesús Silva-Sánchez
- Grupo de Resistencia Bacteriana, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública. Cuernavaca, Morelos, México
| | - Humberto Barrios-Camacho
- Grupo de Resistencia Bacteriana, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública. Cuernavaca, Morelos, México
| | - Ernesto Pérez-Rueda
- Departamento de Ingeniería Celular y Biocatálisis, Instituto de Biotecnología, Universidad Nacional Autónoma de México. México.,Instituto de Investigaciones en Matemáticas Aplicadas y en Sistemas, Universidad Nacional Autónoma de México. Mérida, Yucatán, México
| | - Ulises Garza-Ramos
- Grupo de Resistencia Bacteriana, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública. Cuernavaca, Morelos, México
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27
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Martínez-Romero E, Rodríguez-Medina N, Beltrán-Rojel M, Toribio-Jiménez J, Garza-Ramos U. Klebsiella variicola and Klebsiella quasipneumoniae with capacity to adapt to clinical and plant settings. SALUD PUBLICA DE MEXICO 2018; 60:29-40. [PMID: 29689654 DOI: 10.21149/8156] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 02/24/2017] [Indexed: 11/06/2022] Open
Abstract
OBJECTIVE To compare the genetic determinants involved in plant colonization or virulence in the reported genomes of K. variicola, K. quasipneumoniae and K. pneumoniae. MATERIALS AND METHODS In silico comparisons and Jaccard analysis of genomic data were used. Fimbrial genes were detected by PCR. Biological assays were performed with plant and clinical isolates. RESULTS Plant colonization genes such as cellulases, catalases and hemagglutinins were mainly present in K. variicola genomes. Chromosomal β-lactamases were characteristic of this species and had been previously misclassified. K. variicola and K. pneumoniae isolates produced plant hormones. CONCLUSIONS A mosaic distribution of different virulence- and plant-associated genes was found in K. variicola and in K. quasipneumoniae genomes. Some plant colonizing genes were found mainly in K. variicola genomes. The term plantanosis is proposed for plant-borne human infections.
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Affiliation(s)
| | - Nadia Rodríguez-Medina
- Laboratorio de Resistencia Bacteriana, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública. Cuernavaca, Morelos, México
| | - Marilú Beltrán-Rojel
- Laboratorio de Resistencia Bacteriana, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública. Cuernavaca, Morelos, México
| | - Jeiry Toribio-Jiménez
- Laboratorio de Biotecnología y Genética Microbiana, Unidad Académica de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero. Chilpancingo, Guerrero, México
| | - Ulises Garza-Ramos
- Laboratorio de Resistencia Bacteriana, Centro de Investigación sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública. Cuernavaca, Morelos, México
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28
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Guo Y, Zhai Y, Zhang Z, Li D, Wang Z, Li J, He Z, Hu S, Kang Y, Gao Z. Complete Genomic Analysis of a Kingdom-Crossing Klebsiella variicola Isolate. Front Microbiol 2018; 9:2428. [PMID: 30356723 PMCID: PMC6189331 DOI: 10.3389/fmicb.2018.02428] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/21/2018] [Indexed: 01/21/2023] Open
Abstract
Bacterial isolate X39 was isolated from a community-acquired pneumonia patient in Beijing, China. A phylogenetic tree based on rpoB genes and average nucleotide identity data confirmed that isolate X39 belonged to Klebsiella variicola. The genome of K. variicola X39 contained one circular chromosome and nine plasmids. Comparative genomic analyses with other K. variicola isolates revealed that K. variicola X39 contained the most unique genes. Of these unique genes, many were prophages and transposases. Many virulence factors were shared between K. variicola X39 and Klebsiella pneumoniae F1. The pathogenicity of K. variicola X39 was compared with that of K. pneumoniae F1 in an abdominal infection model. The results indicated that K. variicola X39 was less virulent than typical clinical K. pneumoniae F1. The genome of K. variicola X39 also contained some genes involved in plant colonization, nitrogen fixation, and defense against oxidative stress. GFP-labeled K. variicola X39 could colonize maize as an endophytic bacterium. We concluded that K. variicola X39 was a kingdom-crossing strain.
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Affiliation(s)
- Yatao Guo
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Yao Zhai
- University of Technology Sydney, Ultimo, NSW, Australia
| | - Zhao Zhang
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Daixi Li
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
| | - Zhanwei Wang
- Laboratory Medicine, Peking University People's Hospital, Beijing, China
| | - Jingquan Li
- Institute of Botany, Chinese Academy of Sciences, Beijing, China
| | - Zilong He
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Songnian Hu
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Yu Kang
- Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China
| | - Zhancheng Gao
- Department of Respiratory and Critical Care Medicine, Peking University People's Hospital, Beijing, China
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29
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Draft Genome Sequences of Endophytic Isolates of Klebsiella variicola and Klebsiella pneumoniae Obtained from the Same Sugarcane Plant. GENOME ANNOUNCEMENTS 2018; 6:6/12/e00147-18. [PMID: 29567733 PMCID: PMC5864947 DOI: 10.1128/genomea.00147-18] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Endophytic Klebsiella variicola KvMx2 and Klebsiella pneumoniae KpMx1 isolates obtained from the same sugarcane stem were used for whole-genome sequencing. The genomes revealed clear differences in essential genes for plant growth, development, and detoxification, as well as nitrogen fixation, catalases, cellulases, and shared virulence factors described in the K. pneumoniae pathogen.
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30
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Becker L, Fuchs S, Pfeifer Y, Semmler T, Eckmanns T, Korr G, Sissolak D, Friedrichs M, Zill E, Tung ML, Dohle C, Kaase M, Gatermann S, Rüssmann H, Steglich M, Haller S, Werner G. Whole Genome Sequence Analysis of CTX-M-15 Producing Klebsiella Isolates Allowed Dissecting a Polyclonal Outbreak Scenario. Front Microbiol 2018. [PMID: 29527200 PMCID: PMC5829066 DOI: 10.3389/fmicb.2018.00322] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022] Open
Abstract
Extended-spectrum β-lactamase (ESBL) producing Klebsiella pneumoniae pose an important threat of infection with increased morbidity and mortality, especially for immunocompromised patients. Here, we use the rise of multidrug-resistant K. pneumoniae in a German neurorehabilitation center from April 2015 to April 2016 to dissect the benefit of whole genome sequencing (WGS) for outbreak analyses. In total, 53 isolates were obtained from 52 patients and examined using WGS. Two independent analysis strategies (reference-based and -free) revealed the same distinct clusters of two CTX-M-15 producing K. pneumoniae clones (ST15, n = 31; ST405, n = 7) and one CTX-M-15 producing Klebsiella quasipneumoniae strain (ST414, n = 8). Additionally, we determined sequence variations associated with antimicrobial resistance phenotypes in single isolates expressing carbapenem and colistin resistance, respectively. For rapid detection of the major K. pneumoniae outbreak clone (ST15), a selective triplex PCR was deduced from WGS data of the major outbreak strain and K. pneumoniae genome data deposited in central databases. Moreover, we introduce two novel open-source applications supporting reference genome selection (refRank; https://gitlab.com/s.fuchs/refRank) and alignment-based SNP-filtering (SNPfilter; https://gitlab.com/s.fuchs/snpfilter) in NGS analyses.
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Affiliation(s)
- Laura Becker
- Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Stephan Fuchs
- Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Yvonne Pfeifer
- Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Torsten Semmler
- Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Tim Eckmanns
- Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Gerit Korr
- Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany.,Postgraduate Training for Applied Epidemiology, Robert Koch Institute, Affiliated to the European Programme for Intervention Epidemiology Training, European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | - Dagmar Sissolak
- Department of Infection Control, Medical Disaster Control and Environmental Health Control, Department of Public Health, Berlin, Germany
| | | | - Edith Zill
- Medical Care Centre Labor 28 GmbH, Berlin, Germany
| | | | | | - Martin Kaase
- National Reference Centre for Multidrug-Resistant Gram-Negative Bacteria, Department for Medical Microbiology, Ruhr-University Bochum, Berlin, Germany
| | - Sören Gatermann
- National Reference Centre for Multidrug-Resistant Gram-Negative Bacteria, Department for Medical Microbiology, Ruhr-University Bochum, Berlin, Germany
| | - Holger Rüssmann
- Immunology and Laboratory Medicine, Institute for Microbiology, HELIOS Klinikum Emil von Behring, Berlin, Germany
| | - Matthias Steglich
- Leibniz Institute DSMZ, German Collection of Microorganisms and Cell Culture, Braunschweig, Germany
| | - Sebastian Haller
- Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
| | - Guido Werner
- Department of Infectious Diseases, Robert Koch Institute, Berlin, Germany
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31
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Garza-Ramos U, Barrios-Camacho H, Moreno-Domínguez S, Toribio-Jiménez J, Jardón-Pineda D, Cuevas-Peña J, Sánchez-Pérez A, Duran-Bedolla J, Olguín-Rodriguez J, Román-Román A. Phenotypic and molecular characterization of Klebsiella spp. isolates causing community-acquired infections. New Microbes New Infect 2018; 23:17-27. [PMID: 29692906 PMCID: PMC5913063 DOI: 10.1016/j.nmni.2018.02.002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2017] [Revised: 02/03/2018] [Accepted: 02/09/2018] [Indexed: 12/19/2022] Open
Abstract
Klebsiella spp. isolates from community-acquired infections were characterized. A total of 39 Klebsiella spp. isolates were obtained from outpatients at four rural hospitals in Mexico (2013–2014). The biochemical tests identified all as being K. pneumoniae. The molecular multiplex-PCR test identified 36 (92.4%) K. pneumoniae isolates and one (2.5%) K. variicola isolate, and phylogenetic analysis of the rpoB gene identified two isolates (5.1%) belonging to K. quasipneumoniae subsp. quasipneumoniae and K. quasivariicola. The last one was confirmed by phylogenetic analysis of six-loci concatenated genes. Mostly the isolates were multidrug resistant; however, a minority were extended-spectrum β-lactamase producing (10.2%). The extended-spectrum β-lactamase CTX-M-15 gene was identified in these isolates. Analysis of biofilm production and the hypermucoviscosity phenotype showed a total of 35 (92.3%) and seven (17.9%) of the isolates were positive for these phenotypes respectively. The K2 (4/39, 10.2%), K5 (2/39, 5.1%) and K54 (1/39, 2.5%) serotypes were identified in seven (17.9%) of the isolates, and only 28.5% (2/7) hypermucoviscous isolates were positive for the K2 and K5 serotypes. In general, the sequence type (ST) analysis and phylogenetic analysis of seven multilocus sequence typing loci were heterogeneous; however, ST29 was the most prevalent ST in the analysed isolates, accounting for 19% (4/21) of the total isolates. Two of the four ST29 isolates had the hypermucoviscosity phenotype. The virulence factors for fimbriae were the most prevalent, followed by siderophores. Community-acquired infections are caused by various species from Klebsiella genus, with different profiles of antibiotic resistance and heterogeneous virulence factors.
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Affiliation(s)
- U Garza-Ramos
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana y Genómica de Bacterias, Cuernavaca, Morelos, Mexico
| | - H Barrios-Camacho
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana y Genómica de Bacterias, Cuernavaca, Morelos, Mexico
| | - S Moreno-Domínguez
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana y Genómica de Bacterias, Cuernavaca, Morelos, Mexico
| | - J Toribio-Jiménez
- Laboratorio de Biotecnología y Genética Microbiana, Unidad Académica de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo, Guerrero, Mexico
| | - D Jardón-Pineda
- Laboratorio de Biotecnología y Genética Microbiana, Unidad Académica de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo, Guerrero, Mexico
| | - J Cuevas-Peña
- Laboratorio de Biotecnología y Genética Microbiana, Unidad Académica de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo, Guerrero, Mexico
| | - A Sánchez-Pérez
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana y Genómica de Bacterias, Cuernavaca, Morelos, Mexico
| | - J Duran-Bedolla
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana y Genómica de Bacterias, Cuernavaca, Morelos, Mexico
| | - J Olguín-Rodriguez
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Laboratorio de Resistencia Bacteriana y Genómica de Bacterias, Cuernavaca, Morelos, Mexico
| | - A Román-Román
- Laboratorio de Biotecnología y Genética Microbiana, Unidad Académica de Ciencias Químico Biológicas, Universidad Autónoma de Guerrero, Chilpancingo, Guerrero, Mexico
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32
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Nicolás MF, Ramos PIP, Marques de Carvalho F, Camargo DRA, de Fátima Morais Alves C, Loss de Morais G, Almeida LGP, Souza RC, Ciapina LP, Vicente ACP, Coimbra RS, Ribeiro de Vasconcelos AT. Comparative Genomic Analysis of a Clinical Isolate of Klebsiella quasipneumoniae subsp. similipneumoniae, a KPC-2 and OKP-B-6 Beta-Lactamases Producer Harboring Two Drug-Resistance Plasmids from Southeast Brazil. Front Microbiol 2018; 9:220. [PMID: 29503635 PMCID: PMC5820359 DOI: 10.3389/fmicb.2018.00220] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 01/30/2018] [Indexed: 12/19/2022] Open
Abstract
The aim of this study was to unravel the genetic determinants responsible for multidrug (including carbapenems) resistance and virulence in a clinical isolate of Klebsiella quasipneumoniae subsp. similipneumoniae by whole-genome sequencing and comparative analyses. Eighty-three clinical isolates initially identified as carbapenem-resistant K. pneumoniae were collected from nosocomial infections in southeast Brazil. After RAPD screening, the KPC-142 isolate, showing the most divergent DNA pattern, was selected for complete genome sequencing in an Illumina HiSeq 2500 instrument. Reads were assembled into scaffolds, gaps between scaffolds were resolved by in silico gap filling and extensive bioinformatics analyses were performed, using multiple comparative analysis tools and databases. Genome sequencing allowed to correct the classification of the KPC-142 isolate as K. quasipneumoniae subsp. similipneumoniae. To the best of our knowledge this is the first complete genome reported to date of a clinical isolate of this subspecies harboring both class A beta-lactamases KPC-2 and OKP-B-6 from South America. KPC-142 has one 5.2 Mbp chromosome (57.8% G+C) and two plasmids: 190 Kbp pKQPS142a (50.7% G+C) and 11 Kbp pKQPS142b (57.3% G+C). The 3 Kbp region in pKQPS142b containing the blaKPC−2 was found highly similar to that of pKp13d of K. pneumoniae Kp13 isolated in Southern Brazil in 2009, suggesting the horizontal transfer of this resistance gene between different species of Klebsiella. KPC-142 additionally harbors an integrative conjugative element ICEPm1 that could be involved in the mobilization of pKQPS142b and determinants of resistance to other classes of antimicrobials, including aminoglycoside and silver. We present the completely assembled genome sequence of a clinical isolate of K. quasipneumoniae subsp. similipneumoniae, a KPC-2 and OKP-B-6 beta-lactamases producer and discuss the most relevant genomic features of this important resistant pathogen in comparison to several strains belonging to K. quasipneumoniae subsp. similipneumoniae (phylogroup II-B), K. quasipneumoniae subsp. quasipneumoniae (phylogroup II-A), K. pneumoniae (phylogroup I), and K. variicola (phylogroup III). Our study contributes to the description of the characteristics of a novel K. quasipneumoniae subsp. similipneumoniae strain circulating in South America that currently represent a serious potential risk for nosocomial settings.
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Affiliation(s)
- Marisa F Nicolás
- Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | | | | | | | | | | | - Luiz G P Almeida
- Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | - Rangel C Souza
- Laboratório Nacional de Computação Científica, Petrópolis, Brazil
| | | | - Ana C P Vicente
- Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Roney S Coimbra
- Neurogenômica, Fiocruz Institute Renê Rachou, Belo Horizonte, Brazil
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33
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Atypical Klebsiella Species in a Third Level Hospital as Cause of Neonatal Infection. Jundishapur J Microbiol 2018. [DOI: 10.5812/jjm.62393] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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34
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Whole-Genome Sequencing of Human Clinical Klebsiella pneumoniae Isolates Reveals Misidentification and Misunderstandings of Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae. mSphere 2017; 2:mSphere00290-17. [PMID: 28776045 PMCID: PMC5541162 DOI: 10.1128/mspheredirect.00290-17] [Citation(s) in RCA: 106] [Impact Index Per Article: 15.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2017] [Accepted: 07/03/2017] [Indexed: 12/13/2022] Open
Abstract
Klebsiella pneumoniae is a serious human pathogen associated with resistance to multiple antibiotics and high mortality. K. variicola and K. quasipneumoniae are closely related organisms that are generally considered to be less-virulent opportunistic pathogens. We used a large, comprehensive, population-based strain collection and whole-genome sequencing to investigate infections caused by these organisms in our hospital system. We discovered that K. variicola and K. quasipneumoniae isolates are often misidentified as K. pneumoniae by routine clinical microbiology diagnostics and frequently cause severe life-threatening infections similar to K. pneumoniae. The presence of KPC in K. variicola and K. quasipneumoniae strains as well as NDM-1 metallo-beta-lactamase in one K. variicola strain is particularly concerning because these genes confer resistance to many different beta-lactam antibiotics. The sharing of plasmids, as well as evidence of homologous recombination, between these three species of Klebsiella is cause for additional concern. Klebsiella pneumoniae is a major threat to public health, causing significant morbidity and mortality worldwide. The emergence of highly drug-resistant strains is particularly concerning. There has been a recognition and division of Klebsiella pneumoniae into three distinct phylogenetic groups: Klebsiella pneumoniae, Klebsiella variicola, and Klebsiella quasipneumoniae. K. variicola and K. quasipneumoniae have often been described as opportunistic pathogens that have less virulence in humans than K. pneumoniae does. We recently sequenced the genomes of 1,777 extended-spectrum-beta-lactamase (ESBL)-producing K. pneumoniae isolates recovered from human infections and discovered that 28 strains were phylogenetically related to K. variicola and K. quasipneumoniae. Whole-genome sequencing of 95 additional non-ESBL-producing K. pneumoniae isolates recovered from patients found 12 K. quasipneumoniae strains. Matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS) analysis initially identified all patient isolates as K. pneumoniae, suggesting a potential pitfall in conventional clinical microbiology laboratory identification methods. Whole-genome sequence analysis revealed extensive sharing of core gene content and plasmid replicons among the Klebsiella species. For the first time, strains of both K. variicola and K. quasipneumoniae were found to carry the Klebsiella pneumoniae carbapenemase (KPC) gene, while another K. variicola strain was found to carry the New Delhi metallo-beta-lactamase 1 (NDM-1) gene. K. variicola and K. quasipneumoniae infections were not less virulent than K. pneumoniae infections, as assessed by in-hospital mortality and infection type. We also discovered evidence of homologous recombination in one K. variicola strain, as well as one strain from a novel Klebsiella species, which challenge the current understanding of interrelationships between clades of Klebsiella. IMPORTANCEKlebsiella pneumoniae is a serious human pathogen associated with resistance to multiple antibiotics and high mortality. K. variicola and K. quasipneumoniae are closely related organisms that are generally considered to be less-virulent opportunistic pathogens. We used a large, comprehensive, population-based strain collection and whole-genome sequencing to investigate infections caused by these organisms in our hospital system. We discovered that K. variicola and K. quasipneumoniae isolates are often misidentified as K. pneumoniae by routine clinical microbiology diagnostics and frequently cause severe life-threatening infections similar to K. pneumoniae. The presence of KPC in K. variicola and K. quasipneumoniae strains as well as NDM-1 metallo-beta-lactamase in one K. variicola strain is particularly concerning because these genes confer resistance to many different beta-lactam antibiotics. The sharing of plasmids, as well as evidence of homologous recombination, between these three species of Klebsiella is cause for additional concern.
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35
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Blin C, Passet V, Touchon M, Rocha EPC, Brisse S. Metabolic diversity of the emerging pathogenic lineages of Klebsiella pneumoniae. Environ Microbiol 2017; 19:1881-1898. [PMID: 28181409 DOI: 10.1111/1462-2920.13689] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2016] [Revised: 02/01/2017] [Accepted: 02/01/2017] [Indexed: 11/30/2022]
Abstract
Multidrug resistant and hypervirulent clones of Klebsiella pneumoniae are emerging pathogens. To understand the association between genotypic and phenotypic diversity in this process, we combined genomic, phylogenomic and phenotypic analysis of a diverse set of K. pneumoniae and closely related species. These species were able to use an unusually large panel of metabolic substrates for growth, many of which were shared between all strains. We analysed the substrates used by only a fraction of the strains, identified some of their genetic basis, and found that many could not be explained by the phylogeny of the strains. Puzzlingly, few traits were associated with the ecological origin of the strains. One noticeable exception was the ability to use D-arabinose, which was much more frequent in hypervirulent strains. The broad carbon and nitrogen core metabolism of K. pneumoniae might contribute to its ability to thrive in diverse environments. Accordingly, even the hypervirulent and multidrug resistant clones have the metabolic signature of ubiquitous bacteria. The apparent few metabolic differences between hypervirulent, multi-resistant and environmental strains may favour the emergence of dual-risk strains that combine resistance and hypervirulence.
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Affiliation(s)
- Camille Blin
- UPMC Univ Paris06, IFD, 4 Place Jussieu, Sorbonne Universités, 75252 PARIS cedex 05, France.,Institut Pasteur, Microbial Evolutionary Genomics, Paris, France.,UMR3525, Paris, CNRS, France
| | - Virginie Passet
- Institut Pasteur, Microbial Evolutionary Genomics, Paris, France.,UMR3525, Paris, CNRS, France
| | - Marie Touchon
- Institut Pasteur, Microbial Evolutionary Genomics, Paris, France.,UMR3525, Paris, CNRS, France
| | - Eduardo P C Rocha
- Institut Pasteur, Microbial Evolutionary Genomics, Paris, France.,UMR3525, Paris, CNRS, France
| | - Sylvain Brisse
- Institut Pasteur, Microbial Evolutionary Genomics, Paris, France.,UMR3525, Paris, CNRS, France.,Institut Pasteur, Molecular Prevention and Therapy of Human Diseases, Paris, France
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36
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Islam MA, Karim A, Woon CW, Ethiraj B, Cheng CK, Yousuf A, Rahman Khan MM. Augmentation of air cathode microbial fuel cell performance using wild type Klebsiella variicola. RSC Adv 2017. [DOI: 10.1039/c6ra24835g] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Simultaneous power generation and wastewater treatment in the single chamber air cathode microbial fuel cell have been enhanced by introducing wild-type Klebsiella variicola as an efficient inoculum for the anode operated with palm oil mill effluent.
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Affiliation(s)
- M. Amirul Islam
- Chemical and Natural Resources Engineering
- University Malaysia Pahang
- Pahang
- Malaysia
| | - Ahasanul Karim
- Faculty of Engineering Technology
- University Malaysia Pahang
- Pahang
- Malaysia
| | - Chee Wai Woon
- Chemical and Natural Resources Engineering
- University Malaysia Pahang
- Pahang
- Malaysia
| | - Baranitharan Ethiraj
- Chemical and Natural Resources Engineering
- University Malaysia Pahang
- Pahang
- Malaysia
| | - Chin Kui Cheng
- Chemical and Natural Resources Engineering
- University Malaysia Pahang
- Pahang
- Malaysia
- Centre of Excellence for Advanced Research in Fluid Flow (CARIFF)
| | - Abu Yousuf
- Faculty of Engineering Technology
- University Malaysia Pahang
- Pahang
- Malaysia
| | - Md Maksudur Rahman Khan
- Chemical and Natural Resources Engineering
- University Malaysia Pahang
- Pahang
- Malaysia
- Centre of Excellence for Advanced Research in Fluid Flow (CARIFF)
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37
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Xue G, Li J, Feng Y, Xu W, Li S, Yan C, Zhao H, Sun H. High Prevalence of Plasmid-Mediated Quinolone Resistance Determinants in Escherichia coli and Klebsiella pneumoniae Isolates from Pediatric Patients in China. Microb Drug Resist 2017; 23:107-114. [PMID: 27167505 DOI: 10.1089/mdr.2016.0004] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Guanhua Xue
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Jing Li
- Affiliated Children's Hospital, Capital Institute of Pediatrics, Beijing, China
| | - Yanling Feng
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Wenjian Xu
- Affiliated Children's Hospital, Capital Institute of Pediatrics, Beijing, China
| | - Shaoli Li
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Chao Yan
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Hanqing Zhao
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
| | - Hongmei Sun
- Department of Bacteriology, Capital Institute of Pediatrics, Beijing, China
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38
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Draft Genome Sequence of a Hypermucoviscous Extended-Spectrum-β-Lactamase-Producing Klebsiella quasipneumoniae subsp. similipneumoniae Clinical Isolate. GENOME ANNOUNCEMENTS 2016; 4:4/4/e00475-16. [PMID: 27389261 PMCID: PMC4939778 DOI: 10.1128/genomea.00475-16] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A clinical isolate of extended-spectrum-β-lactamase-producing Klebsiella quasipneumoniae subsp. similipneumoniae 06-219 with hypermucoviscosity phenotypes obtained from a urine culture of an adult patient was used for whole-genome sequencing. Here, we report the draft genome sequences of this strain, consisting of 53 contigs with an ~5.6-Mb genome size and an average G+C content of 57.36%. The annotation revealed 6,622 coding DNA sequences and 77 tRNA genes.
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Liu W, Wang Q, Hou J, Tu C, Luo Y, Christie P. Whole genome analysis of halotolerant and alkalotolerant plant growth-promoting rhizobacterium Klebsiella sp. D5A. Sci Rep 2016; 6:26710. [PMID: 27216548 PMCID: PMC4877636 DOI: 10.1038/srep26710] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2016] [Accepted: 05/09/2016] [Indexed: 11/09/2022] Open
Abstract
This research undertook the systematic analysis of the Klebsiella sp. D5A genome and identification of genes that contribute to plant growth-promoting (PGP) traits, especially genes related to salt tolerance and wide pH adaptability. The genome sequence of isolate D5A was obtained using an Illumina HiSeq 2000 sequencing system with average coverages of 174.7× and 200.1× using the paired-end and mate-pair sequencing, respectively. Predicted and annotated gene sequences were analyzed for similarity with the Kyoto Encyclopedia of Genes and Genomes (KEGG) enzyme database followed by assignment of each gene into the KEGG pathway charts. The results show that the Klebsiella sp. D5A genome has a total of 5,540,009 bp with 57.15% G + C content. PGP conferring genes such as indole-3-acetic acid (IAA) biosynthesis, phosphate solubilization, siderophore production, acetoin and 2,3-butanediol synthesis, and N2 fixation were determined. Moreover, genes putatively responsible for resistance to high salinity including glycine-betaine synthesis, trehalose synthesis and a number of osmoregulation receptors and transport systems were also observed in the D5A genome together with numerous genes that contribute to pH homeostasis. These genes reveal the genetic adaptation of D5A to versatile environmental conditions and the effectiveness of the isolate to serve as a plant growth stimulator.
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Affiliation(s)
- Wuxing Liu
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Qingling Wang
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Jinyu Hou
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
| | - Chen Tu
- Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Yongming Luo
- Institute of Coastal Zone Research, Chinese Academy of Sciences, Yantai 264003, China
| | - Peter Christie
- Key Laboratory of Soil Environment and Pollution Remediation, Institute of Soil Science, Chinese Academy of Sciences, Nanjing 210008, China
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Garza-Ramos U, Silva-Sánchez J, Martínez-Romero E, Tinoco P, Pina-Gonzales M, Barrios H, Martínez-Barnetche J, Gómez-Barreto RE, Tellez-Sosa J. Erratum to: Development of a Multiplex-PCR probe system for the proper identification of Klebsiella variicola. BMC Microbiol 2016; 16:43. [PMID: 26984789 PMCID: PMC4794917 DOI: 10.1186/s12866-016-0652-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2016] [Accepted: 03/02/2016] [Indexed: 11/23/2022] Open
Affiliation(s)
- Ulises Garza-Ramos
- Departamento de Diagnóstico Epidemiológico, Av. Universidad # 655, Col. Sta. Ma. Ahuacatitlán, C.P. 62100, Cuernavaca, Morelos, Mexico.
| | - Jesús Silva-Sánchez
- Departamento de Diagnóstico Epidemiológico, Av. Universidad # 655, Col. Sta. Ma. Ahuacatitlán, C.P. 62100, Cuernavaca, Morelos, Mexico
| | - Esperanza Martínez-Romero
- Centro de Ciencias Genómicas (CCG), Universidad Nacional Autónoma de México (UNAM), Cuernavaca, Morelos, Mexico
| | - Perla Tinoco
- Departamento de Diagnóstico Epidemiológico, Av. Universidad # 655, Col. Sta. Ma. Ahuacatitlán, C.P. 62100, Cuernavaca, Morelos, Mexico
| | - Marisol Pina-Gonzales
- Departamento de Diagnóstico Epidemiológico, Av. Universidad # 655, Col. Sta. Ma. Ahuacatitlán, C.P. 62100, Cuernavaca, Morelos, Mexico
| | - Humberto Barrios
- Departamento de Diagnóstico Epidemiológico, Av. Universidad # 655, Col. Sta. Ma. Ahuacatitlán, C.P. 62100, Cuernavaca, Morelos, Mexico
| | - Jesús Martínez-Barnetche
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Departamento de Inmunología, Cuernavaca, México
| | - Rosa Elena Gómez-Barreto
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Departamento de Inmunología, Cuernavaca, México
| | - Juan Tellez-Sosa
- Instituto Nacional de Salud Pública (INSP), Centro de Investigación Sobre Enfermedades Infecciosas (CISEI), Departamento de Inmunología, Cuernavaca, México
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Garza-Ramos U, Moreno-Dominguez S, Hernández-Castro R, Silva-Sanchez J, Barrios H, Reyna-Flores F, Sanchez-Perez A, Carrillo-Casas EM, Sanchez-León MC, Moncada-Barron D. Identification and Characterization of Imipenem-Resistant Klebsiella pneumoniae and Susceptible Klebsiella variicola Isolates Obtained from the Same Patient. Microb Drug Resist 2015; 22:179-84. [PMID: 26571390 DOI: 10.1089/mdr.2015.0181] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
Klebsiella variicola, a bacterium closely genetically related to Klebsiella pneumoniae, is commonly misidentified as K. pneumoniae by biochemical tests. To distinguish between the two bacteria, phylogenetic analysis of the rpoB gene and the identification of unique genes in both bacterial species by multiplex-polymerase chain reaction (PCR) provide the means to reliably identify and genotype K. variicola. In recent years, K. variicola has been described both as the cause of an intrahospital outbreak in a pediatric hospital, which resulted in sepsis in inpatients, and as a frequent cause of bloodstream infections. In the present study, K. pneumoniae and K. variicola were isolated from a unique patient displaying different antimicrobial susceptibility phenotypes and different genotypes of virulence determinants. Eight clinical isolates were obtained at different time intervals; all during a 5-month period. The isolates were identified as K. pneumoniae by an automated identification system. The clinical (biochemical test) and molecular (multiplex-PCR and rpoB gene) characterization identified imipenem resistance in the first six K. pneumoniae ST258 isolates, which encode the SHV-12 cephalosporinase and KPC-3 carbapenemase genes. The two last remaining isolates corresponded to susceptible K. variicola. The bacterial species showed a specific profile of virulence-associated determinants, specifically the fimA, fimH, and ecpRAB fimbrial-encoding genes identified only in K. pneumoniae isolates. However, the entb (enterobactin), mrkD (fimbrial adhesin), uge (epimerase), ureA (urease), and wabG (transferase) genes were shared between both bacterial species. Recent studies attribute a higher mortality rate to K. variicola than to K. pneumonia. This work highlights the identification of K. pneumoniae and the closely related K. variicola isolated from the same patient. The value of distinguishing between these two bacterial species is in their clinical significance, their different phenotypes and genotypes, and the fact that they can be isolated from the same patient.
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Affiliation(s)
- Ulises Garza-Ramos
- 1 Departamento de Diagnóstico Epidemiológico, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI) , Instituto Nacional de Salud Pública (INSP), Cuernavaca, México
| | - Stephania Moreno-Dominguez
- 1 Departamento de Diagnóstico Epidemiológico, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI) , Instituto Nacional de Salud Pública (INSP), Cuernavaca, México
| | - Rigoberto Hernández-Castro
- 2 Departamento Ecología de Agentes Patógenos, Hospital General "Dr. Manuel Gea González," México, México
| | - Jesús Silva-Sanchez
- 1 Departamento de Diagnóstico Epidemiológico, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI) , Instituto Nacional de Salud Pública (INSP), Cuernavaca, México
| | - Humberto Barrios
- 1 Departamento de Diagnóstico Epidemiológico, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI) , Instituto Nacional de Salud Pública (INSP), Cuernavaca, México
| | - Fernando Reyna-Flores
- 1 Departamento de Diagnóstico Epidemiológico, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI) , Instituto Nacional de Salud Pública (INSP), Cuernavaca, México
| | - Alejandro Sanchez-Perez
- 1 Departamento de Diagnóstico Epidemiológico, Centro de Investigación Sobre Enfermedades Infecciosas (CISEI) , Instituto Nacional de Salud Pública (INSP), Cuernavaca, México
| | - Erika M Carrillo-Casas
- 3 Departamento Biología Molecular e Histocompatibilidad, Hospital General "Dr. Manuel Gea González," México, México
| | - María Carmen Sanchez-León
- 2 Departamento Ecología de Agentes Patógenos, Hospital General "Dr. Manuel Gea González," México, México
| | - David Moncada-Barron
- 4 Laboratorio Clínico, Hospital General "Dr. Manuel Gea González," México, México
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Chen M, Li Y, Li S, Tang L, Zheng J, An Q. Genomic identification of nitrogen-fixing Klebsiella variicola, K. pneumoniae and K. quasipneumoniae. J Basic Microbiol 2015; 56:78-84. [PMID: 26471769 DOI: 10.1002/jobm.201500415] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Accepted: 10/06/2015] [Indexed: 11/09/2022]
Abstract
It was difficult to differentiate Klebsiella pneumoniae, K. quasipneumoniae and K. variicola by biochemical and phenotypic tests. Genomics increase the resolution and credibility of taxonomy for closely-related species. Here, we obtained the complete genome sequence of the K. variicola type strain DSM 15968(T) (=F2R9(T)). The genome of the type strain is a circular chromosome of 5,521,203 bp with 57.56% GC content. From 540 Klebsiella strains whose genomes had been publicly available as at 3 March 2015, we identified 21 strains belonging to K. variicola and 8 strains belonging to K. quasipneumoniae based on the genome average nucleotide identities (ANI). All the K. variicola strains, one K. pneumoniae strain and five K. quasipneumoniae strains contained nitrogen-fixing genes. A phylogenomic analysis showed clear species demarcations for these nitrogen-fixing bacteria. In accordance with the key biochemical characteristics of K. variicola, the idnO gene encoding 5-keto-D-gluconate 5-reductase for utilization of 5-keto-D-gluconate and the sorCDFBAME operon for catabolism of L-sorbose were present whereas the rbtRDKT operon for catabolism of adonitol was absent in the genomes of K. variicola strains. Therefore, the genomic analyses supported the ANI-based species delineation; the genome sequence of the K. variicola type strain provides the reference genome for genomic identification of K. variicola, which is a nitrogen-fixing species.
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Affiliation(s)
- Mingyue Chen
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Yuanyuan Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Shuying Li
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Lie Tang
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Jingwu Zheng
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Qianli An
- State Key Laboratory of Rice Biology, Institute of Biotechnology, Zhejiang University, Hangzhou, China
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Abstract
Three endophytic Klebsiella variicola isolates—T29A, 3, and 6A2, obtained from sugar cane stem, maize shoots, and banana leaves, respectively—were used for whole-genome sequencing. Here, we report the draft genome sequences of circular chromosomes and plasmids. The genomes contain plant colonization and cellulases genes. This study will help toward understanding the genomic basis of K. variicola interaction with plant hosts.
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Draft Genome Sequence of the First Hypermucoviscous Klebsiella variicola Clinical Isolate. GENOME ANNOUNCEMENTS 2015; 3:3/2/e01352-14. [PMID: 25858850 PMCID: PMC4392162 DOI: 10.1128/genomea.01352-14] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
An antibiotic-susceptible and hypermucoviscous clinical isolate of Klebsiella variicola (K. variicola 8917) was obtained from the sputum of an adult patient. This work reports the complete draft genome sequence of K. variicola 8917 with 103 contigs and an annotation that revealed a 5,686,491-bp circular chromosome containing a total of 5,621 coding DNA sequences, 65 tRNA genes, and an average G+C content of 56.98%.
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