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Bereanu AS, Vintilă BI, Bereanu R, Codru IR, Hașegan A, Olteanu C, Săceleanu V, Sava M. TiO 2 Nanocomposite Coatings and Inactivation of Carbapenemase-Producing Klebsiella Pneumoniae Biofilm-Opportunities and Challenges. Microorganisms 2024; 12:684. [PMID: 38674628 PMCID: PMC11051735 DOI: 10.3390/microorganisms12040684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Revised: 03/26/2024] [Accepted: 03/27/2024] [Indexed: 04/28/2024] Open
Abstract
The worldwide increase of multidrug-resistant Gram-negative bacteria is a global threat. The emergence and global spread of Klebsiella pneumoniae carbapenemase- (KPC-) producing Klebsiella pneumoniae represent a particular concern. This pathogen has increased resistance and abilities to persist in human reservoirs, in hospital environments, on medical devices, and to generate biofilms. Mortality related to this microorganism is high among immunosuppressed oncological patients and those with multiple hospitalizations and an extended stay in intensive care. There is a severe threat posed by the ability of biofilms to grow and resist antibiotics. Various nanotechnology-based strategies have been studied and developed to prevent and combat serious health problems caused by biofilm infections. The aim of this review was to evaluate the implications of nanotechnology in eradicating biofilms with KPC-producing Klebsiella pneumoniae, one of the bacteria most frequently associated with nosocomial infections in intensive care units, including in our department, and to highlight studies presenting the potential applicability of TiO2 nanocomposite materials in hospital practice. We also described the frequency of the presence of bacterial biofilms on medical surfaces, devices, and equipment. TiO2 nanocomposite coatings are one of the best long-term options for antimicrobial efficacy due to their biocompatibility, stability, corrosion resistance, and low cost; they find their applicability in hospital practice due to their critical antimicrobial role for surfaces and orthopedic and dental implants. The International Agency for Research on Cancer has recently classified titanium dioxide nanoparticles (TiO2 NPs) as possibly carcinogenic. Currently, there is an interest in the ecological, non-toxic synthesis of TiO2 nanoparticles via biological methods. Biogenic, non-toxic nanoparticles have remarkable properties due to their biocompatibility, stability, and size. Few studies have mentioned the use of nanoparticle-coated surfaces as antibiofilm agents. A literature review was performed to identify publications related to KPC-producing Klebsiella pneumoniae biofilms and antimicrobial TiO2 photocatalytic nanocomposite coatings. There are few reviews on the antibacterial and antibiofilm applications of TiO2 photocatalytic nanocomposite coatings. TiO2 nanoparticles demonstrated marked antibiofilm activity, but being nano in size, these nanoparticles can penetrate cell membranes and may initiate cellular toxicity and genotoxicity. Biogenic TiO2 nanoparticles obtained via green, ecological technology have less applicability but are actively investigated.
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Affiliation(s)
- Alina-Simona Bereanu
- Faculty of Medicine, Lucian Blaga University of Sibiu, Lucian Blaga Street 2A, 550169 Sibiu, Romania; (A.-S.B.); (R.B.); (A.H.); (V.S.); (M.S.)
- County Clinical Emergency Hospital, Bld. Corneliu Coposu nr. 2-4, 550245 Sibiu, Romania;
| | - Bogdan Ioan Vintilă
- Faculty of Medicine, Lucian Blaga University of Sibiu, Lucian Blaga Street 2A, 550169 Sibiu, Romania; (A.-S.B.); (R.B.); (A.H.); (V.S.); (M.S.)
- County Clinical Emergency Hospital, Bld. Corneliu Coposu nr. 2-4, 550245 Sibiu, Romania;
| | - Rareș Bereanu
- Faculty of Medicine, Lucian Blaga University of Sibiu, Lucian Blaga Street 2A, 550169 Sibiu, Romania; (A.-S.B.); (R.B.); (A.H.); (V.S.); (M.S.)
| | - Ioana Roxana Codru
- Faculty of Medicine, Lucian Blaga University of Sibiu, Lucian Blaga Street 2A, 550169 Sibiu, Romania; (A.-S.B.); (R.B.); (A.H.); (V.S.); (M.S.)
- County Clinical Emergency Hospital, Bld. Corneliu Coposu nr. 2-4, 550245 Sibiu, Romania;
| | - Adrian Hașegan
- Faculty of Medicine, Lucian Blaga University of Sibiu, Lucian Blaga Street 2A, 550169 Sibiu, Romania; (A.-S.B.); (R.B.); (A.H.); (V.S.); (M.S.)
- County Clinical Emergency Hospital, Bld. Corneliu Coposu nr. 2-4, 550245 Sibiu, Romania;
| | - Ciprian Olteanu
- County Clinical Emergency Hospital, Bld. Corneliu Coposu nr. 2-4, 550245 Sibiu, Romania;
| | - Vicențiu Săceleanu
- Faculty of Medicine, Lucian Blaga University of Sibiu, Lucian Blaga Street 2A, 550169 Sibiu, Romania; (A.-S.B.); (R.B.); (A.H.); (V.S.); (M.S.)
- County Clinical Emergency Hospital, Bld. Corneliu Coposu nr. 2-4, 550245 Sibiu, Romania;
| | - Mihai Sava
- Faculty of Medicine, Lucian Blaga University of Sibiu, Lucian Blaga Street 2A, 550169 Sibiu, Romania; (A.-S.B.); (R.B.); (A.H.); (V.S.); (M.S.)
- County Clinical Emergency Hospital, Bld. Corneliu Coposu nr. 2-4, 550245 Sibiu, Romania;
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Pustam A, Jayaraman J, Ramsubhag A. Comparative genomics and virulome analysis reveal unique features associated with clinical strains of Klebsiella pneumoniae and Klebsiella quasipneumoniae from Trinidad, West Indies. PLoS One 2023; 18:e0283583. [PMID: 37428714 DOI: 10.1371/journal.pone.0283583] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 03/12/2023] [Indexed: 07/12/2023] Open
Abstract
Klebsiella pneumoniae and Klebsiella quasipneumoniae are closely related human pathogens of global concern. The more recently described K. quasipneumoniae shares similar morphological characteristics with K. pneumoniae and is commonly misidentified as this species using traditional laboratory techniques. The vast mobilome in these pathogenic bacteria influences the dissemination of virulence factors in high-risk environments and it is, therefore, critical to monitor strains for developing effective clinical management strategies. Herein, this study utilized Illumina sequencing to characterize the whole genomes of nine clinical K. pneumoniae and one K. quasipneumoniae isolate obtained from patients of 3 major hospitals in Trinidad, West Indies. Reconstruction of the assembled genomes and implementation of several bioinformatic tools revealed unique features such as high pathogenicity islands associated with the isolates. The K. pneumoniae isolates were categorized as classical (n = 3), uropathogenic (n = 5), or hypervirulent (n = 1) strains. In silico multilocus sequence typing, and phylogenetic analysis showed that isolates were related to several international high-risk genotypes, including sequence types ST11, ST15, ST86, and ST307. Analysis of the virulome and mobilome of these pathogens showed unique and clinically important features including the presence of genes associated with Type 1 and Type 3 fimbriae, the aerobactin and yersiniabactin siderophore systems, the K2 and O1/2, and the O3 and O5 serotypes. These genes were either on or in close proximity to insertion sequence elements, phage sequences, and plasmids. Several secretion systems including the Type VI system and relevant effector proteins were prevalent in the local isolates. This is the first comprehensive study investigating the genomes of clinical K. pneumoniae and K. quasipneumoniae isolates from Trinidad, West Indies. The data presented illustrate the diversity of Trinidadian clinical K. pneumoniae isolates as well as significant virulence biomarkers and mobile elements associated with these isolates. Additionally, the genomes of the local isolates will add to global databases and thus can be used in future surveillance or genomic studies in this country and the wider Caribbean region.
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Affiliation(s)
- Aarti Pustam
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Jayaraj Jayaraman
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
| | - Adesh Ramsubhag
- Department of Life Sciences, Faculty of Science and Technology, The University of the West Indies, St. Augustine, Trinidad and Tobago
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Li S, Wang X, Lu Y, Wang J, Yu D, Zhou Z, Wei J, Liu L, Liu J, Liu F, Su Y, Xu H. Co-infections of Klebsiella pneumoniae and Elizabethkingia miricola in black-spotted frogs (Pelophylax nigromaculatus). Microb Pathog 2023; 180:106150. [PMID: 37196678 DOI: 10.1016/j.micpath.2023.106150] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/07/2023] [Accepted: 05/08/2023] [Indexed: 05/19/2023]
Abstract
Pelophylax nigromaculatus is a common commercial species of frogs that generally cultured throughout China. With the application of high-density culture, P. nigromaculatus can be co-infected by two or more pathogens, which thereby induce synergistic influence on the virulence of the infection. In this study, two bacterial strains were simultaneously isolated from diseased frogs by incubating on Luria-Bertani (LB) agar. Isolates were identified as Klebsiella pneumoniae and Elizabethkingia miricola by morphological, physiological and biochemical features, as well as 16S rRNA sequencing and phylogenetic analysis. The whole genome of K. pneumoniae and E. miricola isolates consist single circular chromosome of 5,419,557 bp and 4,215,349 bp, respectively. The genomic sequence analysis further indicated that K. pneumoniae isolates conserved 172 virulent and 349 antibiotic-resistance genes, whereas E. miricola contained 24 virulent and 168 antibiotic resistance genes. In LB broth, both isolates could grow well at 0%-1% NaCl concentration and pH 5-7. Antibiotic susceptibility testing revealed that both K. pneumoniae and E. miricola were resistant to kanamycin, neomycin, ampicillin, piperacillin, carbenicillin, enrofloxacin, norfloxacin and sulfisoxazole. Histopathological studies showed that co-infection caused considerable lesions in the tissues of brain, eye, muscle, spleen, kidney and liver, including cell degeneration, necrosis, hemorrhage and inflammatory cell infiltration. The LD50 of K. pneumoniae and E. miricola isolates were 6.31 × 105 CFU/g and 3.98 × 105 CFU/g frog weight, respectively. Moreover, experimentally infected frogs exhibited quick and higher mortality under coinfection with K. pneumoniae and E. miricola than those single challenge of each bacterium. To date, no natural co-infection by these two bacteria has been reported from frogs and even amphibians. The results will not only shed light on the feature and pathogenesis of K. pneumoniae and E. miricola, but also highlight that co-infection of these two pathogen is a potential threat to black-spotted frog farming.
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Affiliation(s)
- Shurui Li
- Hubei Key Laboratory of Animal Nutrition and Feed Science, School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Xiaoni Wang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Yulan Lu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Jiahuan Wang
- Hubei Key Laboratory of Animal Nutrition and Feed Science, School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Denghang Yu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Zhigang Zhou
- Hubei Key Laboratory of Animal Nutrition and Feed Science, School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, 430023, China; China-Norway Joint Lab on Fish Gastrointestinal Microbiota, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China; Key Laboratory for Feed Biotechnology of the Ministry of Agriculture, Feed Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Jin Wei
- Hubei Key Laboratory of Animal Nutrition and Feed Science, School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Lihe Liu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Jun Liu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, 430023, China
| | - Fuguo Liu
- Scottish Fish Immunology Research Centre, School of Biological Sciences, University of Aberdeen, Aberdeen, AB242TZ, UK
| | - Yingbing Su
- School of Animal Science, Yangtze University, Jingzhou, 434020, China
| | - Hongsen Xu
- Hubei Key Laboratory of Animal Nutrition and Feed Science, School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan, 430023, China.
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Liu J, Carmichael C, Hasturk H, Shi W, Bor B. Rapid specific detection of oral bacteria using Cas13-based SHERLOCK. J Oral Microbiol 2023; 15:2207336. [PMID: 37187674 PMCID: PMC10177689 DOI: 10.1080/20002297.2023.2207336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2023] [Revised: 04/18/2023] [Accepted: 04/21/2023] [Indexed: 05/17/2023] Open
Abstract
Decades of ongoing research has established that oral microbial communities play a role in oral diseases such as periodontitis and caries. Yet the detection of oral bacteria and the profiling of oral polymicrobial communities currently rely on methods that are costly, slow, and technically complex, such as qPCR or next-generation sequencing. For the widescale screening of oral microorganisms suitable for point-of-care settings, there exists the need for a low-cost, rapid detection technique. Here, we tailored the novel CRISPR-Cas-based assay SHERLOCK for the species-specific detection of oral bacteria. We developed a computational pipeline capable of generating constructs suitable for SHERLOCK and experimentally validated the detection of seven oral bacteria. We achieved detection within the single-molecule range that remained specific in the presence of off-target DNA found within saliva. Further, we adapted the assay for detecting target sequences directly from unprocessed saliva samples. The results of our detection, when tested on 30 healthy human saliva samples, fully aligned with 16S rRNA sequencing. Looking forward, this method of detecting oral bacteria is highly scalable and can be easily optimized for implementation at point-of-care settings.
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Affiliation(s)
- Jett Liu
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
| | - Camden Carmichael
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
| | - Hatice Hasturk
- Center for Clinical and Translational Research, The Forsyth Institute, Cambridge, MA, USA
| | - Wenyuan Shi
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
| | - Batbileg Bor
- Department of Microbiology, The Forsyth Institute, Cambridge, MA, USA
- Department of Oral Medicine, Infection and Immunity, Harvard School of Dental Medicine, Boston, MA, USA
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Alemán-Duarte MI, Aguilar-Uscanga BR, García-Robles G, Ramírez-Salazar FDJ, Benítez-García I, Balcázar-López E, Solís-Pacheco JR. Improvement and Validation of a Genomic DNA Extraction Method for Human Breastmilk. Methods Protoc 2023; 6:mps6020034. [PMID: 37104016 PMCID: PMC10144544 DOI: 10.3390/mps6020034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/08/2023] [Accepted: 03/09/2023] [Indexed: 03/29/2023] Open
Abstract
The human milk microbiota (HMM) of healthy women can vary substantially, as demonstrated by recent advances in DNA sequencing technology. However, the method used to extract genomic DNA (gDNA) from these samples may impact the observed variations and potentially bias the microbiological reconstruction. Therefore, it is important to use a DNA extraction method that is able to effectively isolate gDNA from a diverse range of microorganisms. In this study, we improved and compared a DNA extraction method for gDNA isolation from human milk (HM) samples to commercial and standard protocols. We evaluated the extracted gDNA using spectrophotometric measurements, gel electrophoresis, and PCR amplifications to assess its quantity, quality, and amplifiability. Additionally, we tested the improved method’s ability to isolate amplifiable gDNA from fungi, Gram-positive and Gram-negative bacteria to validate its potential for reconstructing microbiological profiles. The improved DNA extraction method resulted in a higher quality and quantity of the extracted gDNA compared to the commercial and standard protocols and allowed for polymerase chain reaction (PCR) amplification of the V3–V4 regions of the 16S ribosomal gene in all the samples and the ITS-1 region of the fungal 18S ribosomal gene in 95% of the samples. These results suggest that the improved DNA extraction method demonstrates better performance for gDNA extraction from complex samples such as HM.
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Affiliation(s)
- Mario Iván Alemán-Duarte
- Laboratorio de Microbiología Industrial, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Blvd, Gral, Marcelino García Barragán 1421, Olímpica, Guadalajara 44430, Mexico
| | - Blanca Rosa Aguilar-Uscanga
- Laboratorio de Microbiología Industrial, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Blvd, Gral, Marcelino García Barragán 1421, Olímpica, Guadalajara 44430, Mexico
| | - Guadalupe García-Robles
- Laboratorio de Microbiología Industrial, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Blvd, Gral, Marcelino García Barragán 1421, Olímpica, Guadalajara 44430, Mexico
| | - Felipe de Jesús Ramírez-Salazar
- Laboratorio de Microbiología Industrial, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Blvd, Gral, Marcelino García Barragán 1421, Olímpica, Guadalajara 44430, Mexico
| | - Israel Benítez-García
- Unidad Académica de Ingeniería en Biotecnología, Universidad Politécnica de Sinaloa (UPSIN), Carretera Municipal Libre Mazatlán Higueras Km 3 Col. Genaro Estrada, Mazatlán 82199, Mexico
| | - Edgar Balcázar-López
- Laboratorio de Microbiología Industrial, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Blvd, Gral, Marcelino García Barragán 1421, Olímpica, Guadalajara 44430, Mexico
- Correspondence: (E.B.-L.); (J.R.S.-P.); Tel.: +52-(33)-1378-59000 (ext. 27648) (J.R.S.-P.)
| | - Josué Raymundo Solís-Pacheco
- Laboratorio de Microbiología Industrial, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Blvd, Gral, Marcelino García Barragán 1421, Olímpica, Guadalajara 44430, Mexico
- Correspondence: (E.B.-L.); (J.R.S.-P.); Tel.: +52-(33)-1378-59000 (ext. 27648) (J.R.S.-P.)
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Hennequin C, Forestier C, Traore O, Debroas D, Bricheux G. Plasmidome analysis of a hospital effluent biofilm: Status of antibiotic resistance. Plasmid 2022; 122:102638. [PMID: 35691511 DOI: 10.1016/j.plasmid.2022.102638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 06/01/2022] [Accepted: 06/06/2022] [Indexed: 11/30/2022]
Abstract
Plasmids are widely involved in the dissemination of characteristics within bacterial communities. Their genomic content can be assessed by high-throughput sequencing of the whole plasmid fraction of an environment, the plasmidome. In this study, we analyzed the plasmidome of a biofilm formed in the effluents of the teaching hospital of Clermont-Ferrand (France). Our analysis discovered >350 new complete plasmids, with a length ranging from 1219 to 40,193 bp. Forty-two plasmid incompatibility (Inc) groups were found among all the plasmid contigs. Ten large plasmids, described here in detail, were reconstructed from plasmid contigs, seven of which carried antibiotic resistance genes. Four plasmids potentially confer resistance to numerous families of antibiotics, including carbapenems, aminoglycosides, colistin, and chloramphenicol. Most of these plasmids were affiliated to Proteobacteria, a phylum of Gram-negative bacteria. This study therefore illustrates the composition of an environmental mixed biofilm in terms of plasmids and antibiotic resistance genes.
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Affiliation(s)
- Claire Hennequin
- CHU Clermont-Ferrand, Service de Bactériologie Clinique, 58 rue Montalembert, 63000 Clermont-Ferrand, France; Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, F-63000 Clermont-Ferrand, France; Laboratoire Microorganismes: Génome et Environnement, Campus Universitaire des Cézeaux, TSA 60026 - CS 60026, 1, impasse Amélie Murat, 63178 Aubière, France
| | - Christiane Forestier
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, F-63000 Clermont-Ferrand, France
| | - Ousmane Traore
- Université Clermont Auvergne, CNRS, Laboratoire Microorganismes: Génome et Environnement, F-63000 Clermont-Ferrand, France
| | - Didier Debroas
- Laboratoire Microorganismes: Génome et Environnement, Campus Universitaire des Cézeaux, TSA 60026 - CS 60026, 1, impasse Amélie Murat, 63178 Aubière, France
| | - Geneviève Bricheux
- Laboratoire Microorganismes: Génome et Environnement, Campus Universitaire des Cézeaux, TSA 60026 - CS 60026, 1, impasse Amélie Murat, 63178 Aubière, France.
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Whole genome sequencing of Klebsiella pneumoniae clinical isolates sequence type 627 isolated from Egyptian patients. PLoS One 2022; 17:e0265884. [PMID: 35320327 PMCID: PMC8942217 DOI: 10.1371/journal.pone.0265884] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 03/09/2022] [Indexed: 12/13/2022] Open
Abstract
Klebsiella pneumoniae is considered a threat to public health especially due to multidrug resistance emergence. It is largely oligoclonal based on multi-locus sequence typing (MLST); in Egypt, ST 627 was recently detected. Despites the global dissemination of this ST, there is still paucity of information about it. Herein, we used 4 K. pneumoniae ST627 for whole genome sequencing utilizing an Illumina MiSeq platform. Genome sequences were examined for resistance and virulence determinants, capsular types, plasmids, insertion sequences, phage regions, and Clustered Regularly Interspaced Palindromic Repeats (CRISPR) regions using bioinformatic analysis. The molecular characterization revealed 15 and 65 antimicrobial resistance and virulence genes, respectively. Resistance genes such as tet(D), aph(3’’)-Ib, aph(6)-Id, blaTEM-234, fosA, and fosA6; were mainly responsible for tetracycline, aminoglycoside, and fosfomycin resistance; respectively. The capsular typing revealed that the four strains are KL-24 and O1v1. One plasmid was found in all samples known as pC17KP0052-1 and another plasmid with accession no. NZ_CP032191.1 was found only in K90. IncFIB(K) and IncFII(K) are two replicons found in all samples, while ColRNAI replicon was found only in K90. Entero P88, Salmon SEN5, and Klebsi phiKO2 intact phage regions were identified. All samples harbored CRISPR arrays including CRISPR1 and CRISPR2. Our results shed light on critical tasks of mobile genetic elements in ST 627 in antibiotic resistance spreading.
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A global perspective on the convergence of hypervirulence and carbapenem resistance in Klebsiella pneumoniae. J Glob Antimicrob Resist 2021; 25:26-34. [PMID: 33667703 DOI: 10.1016/j.jgar.2021.02.020] [Citation(s) in RCA: 111] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Revised: 02/03/2021] [Accepted: 02/19/2021] [Indexed: 12/31/2022] Open
Abstract
Hypervirulence and carbapenem resistance have emerged as two distinct evolutionary directions for Klebsiella pneumoniae, which pose a great threat in clinical settings. Multiple virulence factors contribute to hypervirulence, and the mechanisms of carbapenem resistance are complicated. However, more and more K. pneumoniae strains have been identified in recent years integrating both phenotypes, resulting in devastating clinical outcomes. Hypervirulent and carbapenem-resistant K. pneumoniae (CR-hvKP) emerged in the early 2010s and thereafter have become increasingly prevalent. CR-hvKP are primarily prevalent in Asia, especially China, but are reported all over the world. Mechanisms for the emergence of CR-hvKP can be summarised by three patterns: (i) carbapenem-resistant K. pneumoniae (CRKP) acquiring a hypervirulent phenotype; (ii) hypervirulent K. pneumoniae (hvKP) acquiring a carbapenem-resistant phenotype; and (iii) K. pneumoniae acquiring both a carbapenem resistance and hypervirulence hybrid plasmid. With their global dissemination, continued surveillance of the emergence of CR-hvKP should be more highly prioritised.
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Tang M, Kong X, Hao J, Liu J. Epidemiological Characteristics and Formation Mechanisms of Multidrug-Resistant Hypervirulent Klebsiella pneumoniae. Front Microbiol 2020; 11:581543. [PMID: 33329444 PMCID: PMC7714786 DOI: 10.3389/fmicb.2020.581543] [Citation(s) in RCA: 55] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 10/14/2020] [Indexed: 12/18/2022] Open
Abstract
Multi-drug resistance (MDR) and hypervirulence (hv) were exhibited by different well-separated Klebsiella pneumoniae lineages in the past, but their convergence clones—MDR-hypervirulent K. pneumoniae (HvKPs)—both highly pathogenic and resistant to most available antibiotics, have increasingly been reported. In light of the clonal lineages and molecular characteristics of the studied MDR-HvKP strains found in the literature since 2014, this review discusses the epidemiology of MDR-HvKPs, in particular summarizing the three general aspects of plasmids-associated mechanisms underlying the formation of MDR-HvKPs clones: MDR-classic K. pneumoniae (cKPs) acquiring hv plasmids, hvKPs obtaining MDR plasmids, and the acquisition of hybrid plasmids harboring virulence and resistance determinants. A deeper understanding of epidemiological characteristics and possible formation mechanisms of MDR-HvKPs is greatly needed for the proper surveillance and management of this potential threat.
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Affiliation(s)
- Miran Tang
- Clinical Laboratory Department, Santai People's Hospital, Mianyang, China
| | - Xin Kong
- Department of Laboratory Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jingchen Hao
- Department of Laboratory Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
| | - Jinbo Liu
- Department of Laboratory Medicine, Affiliated Hospital of Southwest Medical University, Luzhou, China
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Liu Z, Chu W, Li X, Tang W, Ye J, Zhou Q, Guan S. Genomic Features and Virulence Characteristics of a Community-Acquired Bloodstream Infection-Causing Hypervirulent Klebsiella pneumoniae ST86 Strain Harboring KPC-2-Encoding IncX6 Plasmid. Microb Drug Resist 2020; 27:360-368. [PMID: 32716252 DOI: 10.1089/mdr.2019.0394] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
The emergence and spread of carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKP) is causing worldwide concern. Sequence type (ST) 86 K. pneumoniae, a major hvKP clone, is rarely resistant to carbapenem. In this study, we report the genomic features and virulence characteristics of a community-acquired bloodstream infection (CA-BSI)-causing CR-hvKP ST86 strain (KPN55602). This strain is resistant to carbapenem but sensitive to amikacin, gentamicin, tigecycline, and colistin. According to in vitro and in vivo virulence assessments, it was classified as hypervirulent. Whole-genome sequencing revealed that KPN55602 has a single 5.13 Mb chromosome and two plasmids. The chromosome of KPN55602 is phylogenetically similar to those of other sequenced ST86 strains. The incompatibility (Inc) group HI1B plasmid pK55602_1, harboring a set of virulence genes, was classified as a virulence plasmid. The IncX6 plasmid pK55602_2, carrying blaKPC-2, was transferable through conjugation and is highly homologous to all five sequenced blaKPC-bearing IncX6 plasmids. In conclusion, to our knowledge, this is the first report of a CA-BSI-causing CR-hvKP ST86 strain harboring an exogenous blaKPC-2-bearing IncX6 plasmid, supplementing existing knowledge on the CR-hvKP evolutionary scenario. The IncX6 plasmid may be an important vehicle for blaKPC, and its horizontal transfer may have led to CR-hvKP evolution in the community setting.
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Affiliation(s)
- Zhou Liu
- Department of Laboratory Medicine and The Second Hospital of Anhui Medical University, Hefei, China
| | - Wenwen Chu
- Department of Laboratory Medicine and The Second Hospital of Anhui Medical University, Hefei, China
| | - Xin Li
- Department of Laboratory Medicine and The Second Hospital of Anhui Medical University, Hefei, China
| | - Wei Tang
- Department of Laboratory Medicine and The Second Hospital of Anhui Medical University, Hefei, China
| | - Jun Ye
- Department of Infectious Disease, The Second Hospital of Anhui Medical University, Hefei, China
| | - Qiang Zhou
- Department of Laboratory Medicine and The Second Hospital of Anhui Medical University, Hefei, China
| | - Shihe Guan
- Department of Laboratory Medicine and The Second Hospital of Anhui Medical University, Hefei, China
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11
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Choby JE, Howard-Anderson J, Weiss DS. Hypervirulent Klebsiella pneumoniae - clinical and molecular perspectives. J Intern Med 2020; 287:283-300. [PMID: 31677303 PMCID: PMC7057273 DOI: 10.1111/joim.13007] [Citation(s) in RCA: 270] [Impact Index Per Article: 67.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/19/2019] [Revised: 09/24/2019] [Accepted: 10/01/2019] [Indexed: 12/29/2022]
Abstract
Hypervirulent Klebsiella pneumoniae (hvKp) has emerged as a concerning global pathogen. hvKp is more virulent than classical K. pneumoniae (cKp) and capable of causing community-acquired infections, often in healthy individuals. hvKp is carried in the gastrointestinal tract, which contributes to its spread in the community and healthcare settings. First recognized in Asia, hvKp arose as a leading cause of pyogenic liver abscesses. In the decades since, hvKp has spread globally and causes a variety of infections. In addition to liver abscesses, hvKp is distinct from cKp in its ability to metastasize to distant sites, including most commonly the eye, lung and central nervous system (CNS). hvKp has also been implicated in primary extrahepatic infections including bacteremia, pneumonia and soft tissue infections. The genetic determinants of hypervirulence are often found on large virulence plasmids as well as chromosomal mobile genetic elements which can be used as biomarkers to distinguish hvKp from cKp clinical isolates. These distinct virulence determinants of hvKp include up to four siderophore systems for iron acquisition, increased capsule production, K1 and K2 capsule types, and the colibactin toxin. Additionally, hvKp strains demonstrate hypermucoviscosity, a phenotypic description of hvKp in laboratory conditions that has become a distinguishing feature of many hypervirulent isolates. Alarmingly, multidrug-resistant hypervirulent strains have emerged, creating a new challenge in combating this already dangerous pathogen.
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Affiliation(s)
- J E Choby
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA.,Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, USA.,Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, GA, USA
| | - J Howard-Anderson
- Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA
| | - D S Weiss
- Emory Vaccine Center, Emory University School of Medicine, Atlanta, GA, USA.,Emory Antibiotic Resistance Center, Emory University School of Medicine, Atlanta, GA, USA.,Yerkes National Primate Research Center, Emory University School of Medicine, Atlanta, GA, USA.,Division of Infectious Diseases, Department of Medicine, Emory University School of Medicine, Atlanta, GA, USA.,Research Service, Atlanta VA Medical Center, Decatur, GA, USA
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12
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A Nationwide Screen of Carbapenem-Resistant Klebsiella pneumoniae Reveals an Isolate with Enhanced Virulence and Clinically Undetected Colistin Heteroresistance. Antimicrob Agents Chemother 2019; 63:AAC.00107-19. [PMID: 30803966 DOI: 10.1128/aac.00107-19] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2019] [Accepted: 02/13/2019] [Indexed: 02/06/2023] Open
Abstract
The convergence of hypervirulence and multidrug resistance in Klebsiella pneumoniae is a significant concern. Here, we report the first screen for hypermucoviscosity, a trait associated with increased virulence, using a U.S. surveillance collection of carbapenem-resistant (CR) K. pneumoniae isolates. We identified one hypermucoviscous isolate, which carried a gene encoding the KPC-3 carbapenemase, among numerous resistance genes. The strain further exhibited colistin heteroresistance undetected by diagnostics. This convergence of diverse resistance mechanisms and increased virulence underscores the need for enhanced K. pneumoniae surveillance.
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13
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Li J, Zhang H, Ning J, Sajid A, Cheng G, Yuan Z, Hao H. The nature and epidemiology of OqxAB, a multidrug efflux pump. Antimicrob Resist Infect Control 2019; 8:44. [PMID: 30834112 PMCID: PMC6387526 DOI: 10.1186/s13756-019-0489-3] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 02/03/2019] [Indexed: 01/03/2023] Open
Abstract
Background OqxAB efflux pump has been found to mediate multidrug resistance (MDR) in various bacteria over the past decades. The updates on the nature and epidemiology of OqxAB efflux pump need to be fully reviewed to broaden our understanding of this MDR determinant. Methods A literature search using the keyword of "oqxAB" was conducted in the online databases of Pubmed and ISI Web of Science with no restriction on the date of publication. The 87 publications were included into this review as references due to their close relevance to the nature and/or epidemiology of OqxAB efflux pump. Results The oqxAB gene generally locates on chromosome and/or plasmids flanked by IS26-like elements in clinical isolates of Enterobacteriaceae and Klebsiella pneumoniae, conferring low to intermediated resistance to quinoxalines, quinolones tigecycline, nitrofurantoin, several detergents and disinfectants (benzalkonium chloride, triclosan and SDS). It could co-spread with other antimicrobial resistance genes (bla CTX-M, rmtB and aac(6')-Ib etc.), virulence genes and heavy metal resistance genes (pco and sil operons). Both RarA (activator) and OqxR (repressor) play important roles on regulation of the expression of OqxAB. Conclusions The dissemination of oqxAB gene may pose a great risk on food safety and public health. Further investigation and understanding of the natural functions, horizontal transfer, and regulation mechanism of the OqxAB efflux pump will aid in future strategies of antimicrobial usage.
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Affiliation(s)
- Jun Li
- 1National Reference Laboratory of Veterinary Drug Residues (HZAU) and Key Laboratory of the Detection for Veterinary Drug Residues, Wuhan, 430070 Hubei China.,2Institute of Veterinary Medicine, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014 Jiangsu China
| | - Heying Zhang
- 1National Reference Laboratory of Veterinary Drug Residues (HZAU) and Key Laboratory of the Detection for Veterinary Drug Residues, Wuhan, 430070 Hubei China
| | - Jianan Ning
- 1National Reference Laboratory of Veterinary Drug Residues (HZAU) and Key Laboratory of the Detection for Veterinary Drug Residues, Wuhan, 430070 Hubei China
| | - Abdul Sajid
- 1National Reference Laboratory of Veterinary Drug Residues (HZAU) and Key Laboratory of the Detection for Veterinary Drug Residues, Wuhan, 430070 Hubei China.,4College of Veterinary Sciences and Animal Husbandry, Abdul Wali Khan University Mardan, Mardan, KP Pakistan
| | - Guyue Cheng
- 3Laboratory of Quality & Safety Risk Assessment for Livestock and Poultry Products (Wuhan), Ministry of Agriculture, P.R China, Wuhan, 430070 Hubei China
| | - Zonghui Yuan
- 1National Reference Laboratory of Veterinary Drug Residues (HZAU) and Key Laboratory of the Detection for Veterinary Drug Residues, Wuhan, 430070 Hubei China.,3Laboratory of Quality & Safety Risk Assessment for Livestock and Poultry Products (Wuhan), Ministry of Agriculture, P.R China, Wuhan, 430070 Hubei China
| | - Haihong Hao
- 1National Reference Laboratory of Veterinary Drug Residues (HZAU) and Key Laboratory of the Detection for Veterinary Drug Residues, Wuhan, 430070 Hubei China.,3Laboratory of Quality & Safety Risk Assessment for Livestock and Poultry Products (Wuhan), Ministry of Agriculture, P.R China, Wuhan, 430070 Hubei China
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14
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Fu Y, Xu M, Liu Y, Li A, Zhou J. Virulence and genomic features of a bla CTX-M-3 and bla CTX-M-14 coharboring hypermucoviscous Klebsiella pneumoniae of serotype K2 and ST65. Infect Drug Resist 2019; 12:145-159. [PMID: 30655681 PMCID: PMC6322562 DOI: 10.2147/idr.s187289] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Abstract
Background Capsular serotype K2 Klebsiella pneumoniae of sequence type (ST) 65 has been recognized as a hypervirulent clone. Simultaneous presence of different blaCTX-M genes has never been reported in this clone. In the present study, the genetic characteristics and virulence phenotype of a CTX-M-3 and CTX-M-14 coproducing ST65 K. pneumoniae human isolate, KP_06, that caused an intracranial infection, are evaluated. Methods The potential virulence of KP_06 was assayed by in vitro and in vivo methods. The molecular biology and whole-genome sequencing technology were used to analyze the genomic features associated with the virulence of this strain. Results The KP_06 exhibited typical features of hypervirulent K. pneumoniae (hvKP), showing hypermucoviscosity phenotype and belonging to K2 and ST65. Apart from virulence genes linked to hvKP, including rmpA, rmpA2, and clb cluster and genes encoding siderophores, it was found to harbor a ~170 kb pLVPK-like virulence plasmid. In contrast to most hvKP, KP_06 was resistant to cephalosporins and the coexistence of blaCTX-M-3 and blaCTX-M-14 was detected. Further experiments demonstrated that this strain was classified as a nonbiofilm producer and serum sensitivity (grade 1) and killed only 30% of Galleria mellonella inoculated with 1×106 colony-forming unit of the specimen within 48 hours, suggesting relatively low virulence. Comparative genomic analysis of KP_06 with five K2 hypermucoviscous K. pneumoniae (HMKP) revealed seven unique orthologies with varied function in this strain. Intriguingly, the virulence genes identified in KP-06 were unexpectedly more diverse than those observed in five other K2 HMKP strains. Conclusion Our data support the notion that neither virulence-associated genes (clusters) nor the pLVPK-like virulence plasmid is sufficient for the hypervirulence of K. pneumoniae. Future studies aiming to explore the virulence of K. pneumoniae should take genome-based profile together with experimental work. The detailed mechanism involving in the impaired virulence of KP_06 remains to be further explored.
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Affiliation(s)
- Yiqi Fu
- Department of Respiratory Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China,
| | - Min Xu
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Center of Clinical Laboratory, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Yanchao Liu
- Key Laboratory of Clinical In Vitro Diagnostic Techniques of Zhejiang Province, Center of Clinical Laboratory, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China
| | - Ang Li
- Department of Precision Medicine Center, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Jianying Zhou
- Department of Respiratory Diseases, The First Affiliated Hospital, College of Medicine, Zhejiang University, Hangzhou, China,
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15
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Huang YT, Chuang WY, Ho BC, Wu ZY, Kuo RC, Ko M, Liu PY. Comparative genomics reveals diverse capsular polysaccharide synthesis gene clusters in emerging Raoultella planticola. Mem Inst Oswaldo Cruz 2018; 113:e180192. [PMID: 30204830 PMCID: PMC6135345 DOI: 10.1590/0074-02760180192] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2018] [Accepted: 08/15/2018] [Indexed: 12/11/2022] Open
Abstract
Raoultella planticola is an emerging zoonotic pathogen that is associated with rare but life-threatening cases of bacteremia, biliary tract infections, and urinary tract infections. Moreover, increasing antimicrobial resistance in the organism poses a potential threat to public health. In spite of its importance as a human pathogen, the genome of R. planticola remains largely unexplored and little is known about its virulence factors. Although lipopolysaccharides has been detected in R. planticola and implicated in the virulence in earlier studies, the genetic background is unknown. Here, we report the complete genome and comparative analysis of the multidrug-resistant clinical isolate R. planticola GODA. The complete genome sequence of R. planticola GODA was sequenced using single-molecule real-time DNA sequencing. Comparative genomic analysis reveals distinct capsular polysaccharide synthesis gene clusters in R. planticola GODA. In addition, we found blaTEM-57 and multiple transporters related to multidrug resistance. The availability of genomic data in open databases of this emerging zoonotic pathogen, in tandem with our comparative study, provides better understanding of R. planticola and the basis for future work.
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Affiliation(s)
- Yao-Ting Huang
- National Chung Cheng University, Department of Computer Science and Information Engineering, Chia-Yi, Taiwan
| | - Wei-Yao Chuang
- National Chung Cheng University, Department of Computer Science and Information Engineering, Chia-Yi, Taiwan
| | - Bing-Ching Ho
- National Taiwan University Hospital, Department of Clinical Laboratory Sciences and Medical Biotechnology, Taipei, Taiwan
| | - Zong-Yen Wu
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA.,National Chung Hsing University, Department of Veterinary Medicine, Taichung, Taiwan
| | - Rita C Kuo
- US Department of Energy Joint Genome Institute, Walnut Creek, CA, USA
| | - Mengwei Ko
- University of California, Division of Oral Biology and Oral Medicine, School of Dentistry and Medicine, The Jane and Jerry Weintraub Center for Reconstructive Biotechnology, Los Angeles, CA, USA
| | - Po-Yu Liu
- Shu-Zen Junior College of Medicine and Management, Department of Nursing, Kaohsiung City, Taiwan.,National Chung Hsing University, College of Life Sciences, Rong Hsing Research Center for Translational Medicine, Taichung, Taiwan.,National Chung Hsing University, PhD Program in Translational Medicine, Taichung, Taiwan.,Taichung Veterans General Hospital, Department of Internal Medicine, Division of Infectious Diseases, Taichung, Taiwan
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16
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Founou LL, Founou RC, Allam M, Ismail A, Djoko CF, Essack SY. Genome Sequencing of Extended-Spectrum β-Lactamase (ESBL)-Producing Klebsiella pneumoniae Isolated from Pigs and Abattoir Workers in Cameroon. Front Microbiol 2018; 9:188. [PMID: 29479347 PMCID: PMC5811526 DOI: 10.3389/fmicb.2018.00188] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 01/26/2018] [Indexed: 11/26/2022] Open
Abstract
Background and objectives: Extended-spectrum β-lactamase (ESBL)-producing Klebsiella pneumoniae is a serious public health issue globally. In this study, the antibiotic resistance genes, virulence factors, mobile genetic elements, and genetic lineages of circulating ESBL-producing K. pneumoniae strains isolated from pigs and humans in Cameroonian abattoirs were investigated using whole genome sequencing (WGS), in order to ascertain zoonotic transmission (viz. from animals to humans and/or vice-versa) in the food chain. Methods: During March–October 2016, 288 nasal and rectal pooled samples from 432 pigs as well as nasal and hand swabs from 82 humans were collected from Cameroon and South Africa. Seven ESBL-producing K. pneumoniae circulating in Cameroonian pig abattoirs were selected and their genomic DNA sequenced using an Illumina MiSeq platform. Generated reads were de novo assembled using the Qiagen CLC Genomics Workbench and SPAdes. The assembled contigs were annotated using RAST and antibiotic resistance genes, virulence factors, plasmids, and bacteriophages were identified with ResFinder, Virulence Finder, PlasmidFinder, and PHAST, respectively. Results: ESBL-producing K. pneumoniae were detected in pigs (34/158; 21.52%) and exposed workers (8/71; 11.26%) in Cameroon only. The circulating K. pneumoniae strains were dominated principally by the sequence type (ST) 14 and 39. In addition, the “high-risk” ST307 clone and two novel STs assigned ST2958 and ST2959 were detected. Genomic analysis identified various antibiotic resistance genes associated with resistance to β-lactams, aminoglycosides, fluoroquinolones, macrolide, lincosamide and streptogramins, rifampicin, sulfonamides, trimethoprim, phenicols and tetracycline. None of the ESBL-producing K. pneumoniae harbored virulence genes. Intermingled K. pneumoniae populations were observed between pig- and human-source within and across abattoirs in the country. Conclusion: Our study shows that ESBL-producing K. pneumoniae is actively disseminating in pigs and occupationally exposed workers in Cameroonian pig abattoirs and is probably underestimated in the absence of molecular epidemiological studies. It suggests pigs, abattoir workers and food products as potential reservoirs and sources of zoonotic transmission in Cameroon. Our findings underline the existence of a potential unheeded food safety and public health threat associated with these resistant strains and reinforce the crucial importance of implementing appropriate food safety measures and promoting rational antibiotic use.
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Affiliation(s)
- Luria L Founou
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,Department of Food Safety and Environmental Microbiology, Centre of Expertise and Biological Diagnostic of Cameroon, Yaoundé, Cameroon
| | - Raspail C Founou
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa.,Department of Clinical Microbiology, Centre of Expertise and Biological Diagnostic of Cameroon, Yaoundé, Cameroon
| | - Mushal Allam
- Sequencing Core Facility, National Health Laboratory Service, Johannesburg, South Africa
| | - Arshad Ismail
- Sequencing Core Facility, National Health Laboratory Service, Johannesburg, South Africa
| | - Cyrille F Djoko
- Centre for Research and Doctoral Training in Life Science, Health and Environment, The Biotechnology Centre, University of Yaoundé I, Yaoundé, Cameroon.,Metabiota Inc., Yaoundé, Cameroon
| | - Sabiha Y Essack
- Antimicrobial Research Unit, College of Health Sciences, University of KwaZulu-Natal, Durban, South Africa
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17
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Genomic insights of aromatic hydrocarbon degrading Klebsiella pneumoniae AWD5 with plant growth promoting attributes: a paradigm of soil isolate with elements of biodegradation. 3 Biotech 2018; 8:118. [PMID: 29430379 PMCID: PMC5803133 DOI: 10.1007/s13205-018-1134-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2017] [Accepted: 01/23/2018] [Indexed: 12/13/2022] Open
Abstract
This research employs draft genome sequence data of Klebsiella pneumoniae AWD5 to explore genes that contribute to the degradation of polyaromatic hydrocarbon (PAH) and stimulate plant growth, for rhizosphere-mediated bioremediation. Annotation analysis suggests that the strain AWD5 not only possess gene clusters for PAH utilization, but also for utilization of benzoate, fluorobenzoate, phenylacetate (paa), hydroxyphenylacetic acid (hpa), 3-hydroxyphenyl propionate (mhp). A comparative genome analysis revealed that the genome of AWD5 was highly similar with genomes of environmental as well as clinical K. pneumoniae isolates. The artemis output confirmed that there are 139 different genes present in AWD5 which were absent in genome of clinical strain K. pneumoniae ATCC BAA-2146, and 25 genes were identified to be present in AWD5 genome but absent in genome of environmental strain K. pneumoniae KP-1. Pathway analyzed using Kyoto Encyclopedia of Genes and Genomes enzyme database revealed the presence of gene clusters that code for enzymes to initiate the opening of aromatic rings. The polyaromatic hydrocarbon and benzoate degradation were found to be metabolized through ortho-cleavage pathway, mineralizing the compounds to TCA cycle intermediates. Genes for plant growth promoting attributes such as Indole acetic acid (IAA) synthesis, siderophore production, and phosphate solubilization were detected in the genome. These attributes were verified in vitro, including IAA (14.75 µg/ml), siderophore production (13.56%), phosphate solubilization (198.28 ng/ml), and ACC deaminase (0.118 mM α-ketobutyrate/mg) in the presence of pyrene, and also compared with results obtained in glucose amended medium. K. pneumoniae AWD5 enhanced the growth of Jatropha curcas in the presence of pyrene-contaminated soil. Moreover, AWD5 harbors heavy metal resistance genes indicating adaptation to contaminants. The study revealed the genomic attributes of K. pneumoniae AWD5 for its catabolic characteristics for different aromatic compounds, which makes it suitable for rhizoremediation of PAH-contaminated soil.
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18
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Babouee Flury B, Donà V, Buetti N, Furrer H, Endimiani A. First two cases of severe multifocal infections caused by Klebsiella pneumoniae in Switzerland: characterization of an atypical non-K1/K2-serotype strain causing liver abscess and endocarditis. J Glob Antimicrob Resist 2017; 10:165-170. [PMID: 28729207 DOI: 10.1016/j.jgar.2017.04.006] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2017] [Revised: 03/24/2017] [Accepted: 04/03/2017] [Indexed: 10/19/2022] Open
Abstract
BACKGROUND We describe the first two multifocal invasive infections due to Klebsiella pneumoniae recently observed in Switzerland. METHODS Phenotypic (MIC assays and string test) and molecular analyses (PCR/Sequencing for bla, virulence factor genes and whole genome sequencing for one strain) were performed to characterize the causative K. pneumoniae isolates. RESULTS Both K. pneumoniae isolates (Kp1 and Kp2) were pan-susceptible to antibiotics and produced narrow-spectrum SHV β-lactamases. However, only Kp1 was string test positive. Kp1 was of ST380 and caused liver abscess as well as pneumonia and orbital phlegmon in an Eritrean patient. It belonged to the hypervirulent capsular serotype K2 and harboured the classic virulence-associated rmpA and aerobactin genes, fulfilling both the clinical and microbiological definitions for an invasive K. pneumoniae syndrome. Kp2 was of ST1043 and caused both liver abscess and endocarditis in a Swiss patient. Moreover, it did not possess the classic virulence-associated genes. Whole genome sequencing identified less well-known virulence factors in Kp2 that might have contributed to its virulence. Among these there were genes important for intestinal colonization and/or invasion, such as genes involved in adhesion (e.g., fimABCD and mrkABCD), regulation of capsule polysaccharide biosynthesis (e.g., evgS-evgA), as well as iron uptake (iroN), energy conversion, and metabolism. DISCUSSION This report confirms the continuous dissemination of hypervirulent K. pneumoniae strains among patients of non-Asian descent in Europe. Moreover, it highlights the genetic background of an atypical hypervirulent K. pneumoniae causing a severe invasive infection despite not possessing the classical virulence characteristics of hypermucoviscous strains.
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Affiliation(s)
- Baharak Babouee Flury
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland; Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Valentina Donà
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Niccolò Buetti
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Hansjakob Furrer
- Department of Infectious Diseases, Bern University Hospital, University of Bern, Bern, Switzerland
| | - Andrea Endimiani
- Institute for Infectious Diseases, University of Bern, Bern, Switzerland.
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19
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Salloum T, Arabaghian H, Alousi S, Abboud E, Tokajian S. Genome sequencing and comparative analysis of an NDM-1-producing Klebsiella pneumoniae ST15 isolated from a refugee patient. Pathog Glob Health 2017; 111:166-175. [PMID: 28395597 DOI: 10.1080/20477724.2017.1314069] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The escalating problem of antibiotic resistance, specifically cabarpenemase and extended-spectrum β-lacatamase (ESBL) producing K. pneumoniae strains, is directly correlated with increased patient morbidity and mortality and prolonged hospitalization and costs. In this study, a comprehensive genomic analysis encompassing the resistomics, virulence repertoire and mobile genetic elements of an NDM-1 positive ESBL-producing K. pneumoniae EA-MEH ST15 isolated from a urine sample collected from a Syrian refugee was conducted. Illumina paired-end libraries were prepared and sequenced resulting in 892,300 high-quality reads. The initial assembly produced 329 contigs with a combined 5,954,825 bp and a 56.5% G+C content. Resistome analysis revealed the presence of several β-lactamases including NDM-1, SHV-28, CTX-M-15 and OXA-1 in addition to 18 other genes encoding for resistance, among which are aph(3')-Ia, aac(6')Ib-cr, armA, strB, strA and aadA2 genes. Additionally, five plasmids IncFIB(Mar), IncHI1B, IncFIB(pKPHS1), IncFIB(K) and IncFII(K) and four integrated phages were detected. In silico MLST analysis revealed that the isolate was of sequence type ST15. To our knowledge this is the first in-depth genomic analysis of a NDM-1 positive K. pneumoniae ST15 in Lebanon associated with the recent population migration. The potential dissemination of such MDR strains is an important public health concern.
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Affiliation(s)
- Tamara Salloum
- a Department of Natural Sciences, School of Arts and Sciences , Lebanese American University , Byblos , Lebanon
| | - Harout Arabaghian
- a Department of Natural Sciences, School of Arts and Sciences , Lebanese American University , Byblos , Lebanon
| | - Sahar Alousi
- a Department of Natural Sciences, School of Arts and Sciences , Lebanese American University , Byblos , Lebanon
| | - Edmond Abboud
- b Clinical Laboratory , The Middle East Institute of Health , Bsalim , Lebanon
| | - Sima Tokajian
- a Department of Natural Sciences, School of Arts and Sciences , Lebanese American University , Byblos , Lebanon
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20
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Arena F, Henrici De Angelis L, D'Andrea MM, Cannatelli A, Fossati L, Di Pilato V, Giani T, Cavallo R, Rossolini GM. Infections caused by carbapenem-resistant Klebsiella pneumoniae with hypermucoviscous phenotype: A case report and literature review. Virulence 2017; 8:1900-1908. [PMID: 28276993 PMCID: PMC5810476 DOI: 10.1080/21505594.2017.1286439] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Fabio Arena
- a Department of Medical Biotechnologies , University of Siena , Siena , Italy
| | | | - Marco Maria D'Andrea
- b Department of Experimental and Clinical Medicine , University of Florence , Florence , Italy
| | - Antonio Cannatelli
- a Department of Medical Biotechnologies , University of Siena , Siena , Italy
| | - Lucina Fossati
- c Department of Public Health and Pediatric Sciences , AOU, City of Health and Sciences, University of Turin , Turin , Italy
| | - Vincenzo Di Pilato
- d Department of Surgery and Translational Medicine , University of Florence , Florence , Italy
| | - Tommaso Giani
- a Department of Medical Biotechnologies , University of Siena , Siena , Italy
| | - Rossana Cavallo
- c Department of Public Health and Pediatric Sciences , AOU, City of Health and Sciences, University of Turin , Turin , Italy
| | - Gian Maria Rossolini
- a Department of Medical Biotechnologies , University of Siena , Siena , Italy.,b Department of Experimental and Clinical Medicine , University of Florence , Florence , Italy.,e Clinical Microbiology and Virology Unit , Florence Careggi University Hospital , Florence , Italy.,f Don Carlo Gnocchi Foundation , Florence , Italy
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21
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Dsouza R, Pinto NA, Hwang I, Cho Y, Yong D, Choi J, Lee K, Chong Y. Panel strain of Klebsiella pneumoniae for beta-lactam antibiotic evaluation: their phenotypic and genotypic characterization. PeerJ 2017; 5:e2896. [PMID: 28133574 PMCID: PMC5251932 DOI: 10.7717/peerj.2896] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2016] [Accepted: 12/10/2016] [Indexed: 01/21/2023] Open
Abstract
Klebsiella pneumoniae is responsible for numerous infections caused in hospitals, leading to mortality and morbidity. It has been evolving as a multi-drug resistant pathogen, acquiring multiple resistances such as such as horizontal gene transfer, transposon-mediated insertions or change in outer membrane permeability. Therefore, constant efforts are being carried out to control the infections using various antibiotic therapies. Considering the severity of the acquired resistance, we developed a panel of strains of K. pneumoniae expressing different resistance profiles such as high-level penicillinase and AmpC production, extended spectrum beta-lactamases and carbapenemases. Bacterial strains expressing different resistance phenotypes were collected and examined for resistance genes, mutations and porin alterations contributing to the detected phenotypes. Using the Massive parallel sequencing (MPS) technology we have constructed and genotypically characterized the panel strains to elucidate the multidrug resistance. These panel strains can be used in the clinical laboratory as standard reference strains. In addition, these strains could be significant in the field of pharmaceuticals for the antibiotic drug testing to verify its efficiency on pathogens expressing various resistances.
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Affiliation(s)
- Roshan Dsouza
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine , Seoul , South Korea
| | - Naina Adren Pinto
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea; Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, South Korea
| | - InSik Hwang
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea; Brain Korea 21 PLUS Project for Medical Science, Yonsei University, Seoul, South Korea
| | | | - Dongeun Yong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine , Seoul , South Korea
| | - Jongrak Choi
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine , Seoul , South Korea
| | - Kyungwon Lee
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine , Seoul , South Korea
| | - Yunsop Chong
- Department of Laboratory Medicine and Research Institute of Bacterial Resistance, Yonsei University College of Medicine , Seoul , South Korea
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