101
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Antibiotic Sensitivity Screening of Klebsiella spp. and Raoultella spp. Isolated from Marine Bivalve Molluscs Reveal Presence of CTX-M-Producing K. pneumoniae. Microorganisms 2020; 8:microorganisms8121909. [PMID: 33266320 PMCID: PMC7761178 DOI: 10.3390/microorganisms8121909] [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: 10/17/2020] [Revised: 11/25/2020] [Accepted: 11/28/2020] [Indexed: 01/01/2023] Open
Abstract
Klebsiella spp. are a major cause of both nosocomial and community acquired infections, with K. pneumoniae being responsible for most human infections. Although Klebsiella spp. are present in a variety of environments, their distribution in the sea and the associated antibiotic resistance is largely unknown. In order to examine prevalence of K. pneumoniae and related species in the marine environment, we sampled 476 batches of marine bivalve molluscs collected along the Norwegian coast. From these samples, K. pneumoniae (n = 78), K. oxytoca (n = 41), K. variicola (n = 33), K. aerogenes (n = 1), Raoultella ornithinolytica (n = 38) and R. planticola (n = 13) were isolated. The number of positive samples increased with higher levels of faecal contamination. We found low prevalence of acquired resistance in all isolates, with seven K. pneumoniae isolates showing resistance to more than one antibiotic class. The complete genome sequence of cefotaxime-resistant K. pneumoniae sensu stricto isolate 2016-1400 was obtained using Oxford Nanopore and Illumina MiSeq based sequencing. The 2016-1400 genome had two contigs, one chromosome of 5,088,943 bp and one plasmid of 191,744 bp and belonged to ST1035. The β-lactamase genes blaCTX-M-3 and blaTEM-1, as well as the heavy metal resistance genes pco, ars and sil were carried on a plasmid highly similar to one found in K. pneumoniae strain C17KP0055 from South-Korea recovered from a blood stream infection. The present study demonstrates that K. pneumoniae are prevalent in the coastal marine environment and that bivalve molluscs may act as a potential reservoir of extended spectrum β-lactamase (ESBL)-producing K. pneumoniae that may be transmitted through the food chain.
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102
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Hu Y, Anes J, Devineau S, Fanning S. Klebsiella pneumoniae: Prevalence, Reservoirs, Antimicrobial Resistance, Pathogenicity, and Infection: A Hitherto Unrecognized Zoonotic Bacterium. Foodborne Pathog Dis 2020; 18:63-84. [PMID: 33124929 DOI: 10.1089/fpd.2020.2847] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Klebsiella pneumoniae is considered an opportunistic pathogen, constituting an ongoing health concern for immunocompromised patients, the elderly, and neonates. Reports on the isolation of K. pneumoniae from other sources are increasing, many of which express multidrug-resistant (MDR) phenotypes. Three phylogroups were identified based on nucleotide differences. Niche environments, including plants, animals, and humans appear to be colonized by different phylogroups, among which KpI (K. pneumoniae) is commonly associated with human infection. Infections with K. pneumoniae can be transmitted through contaminated food or water and can be associated with community-acquired infections or between persons and animals involved in hospital-acquired infections. Increasing reports are describing detections along the food chain, suggesting the possibility exists that this could be a hitherto unexplored reservoir for this opportunistic bacterial pathogen. Expression of MDR phenotypes elaborated by these bacteria is due to the nature of various plasmids carrying antimicrobial resistance (AMR)-encoding genes, and is a challenge to animal, environmental, and human health alike. Raman spectroscopy has the potential to provide for the rapid identification and screening of antimicrobial susceptibility of Klebsiella isolates. Moreover, hypervirulent isolates linked with extraintestinal infections express phenotypes that may support their niche adaptation. In this review, the prevalence, reservoirs, AMR, Raman spectroscopy detection, and pathogenicity of K. pneumoniae are summarized and various extraintestinal infection pathways are further narrated to extend our understanding of its adaptation and survival ability in reservoirs, and associated disease risks.
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Affiliation(s)
- Yujie Hu
- UCD-Centre for Food Safety, UCD School of Public Health, Physiotherapy and Sports Science, Science Centre South, College of Health and Agricultural Sciences, University College Dublin (UCD), Dublin, Ireland.,Key Laboratory of Food Safety Risk Assessment, Ministry of Health, China National Center for Food Safety Risk Assessment, Beijing, China
| | - João Anes
- UCD-Centre for Food Safety, UCD School of Public Health, Physiotherapy and Sports Science, Science Centre South, College of Health and Agricultural Sciences, University College Dublin (UCD), Dublin, Ireland
| | | | - Séamus Fanning
- UCD-Centre for Food Safety, UCD School of Public Health, Physiotherapy and Sports Science, Science Centre South, College of Health and Agricultural Sciences, University College Dublin (UCD), Dublin, Ireland.,Key Laboratory of Food Safety Risk Assessment, Ministry of Health, China National Center for Food Safety Risk Assessment, Beijing, China.,Institute for Global Food Security, Queen's University Belfast, Belfast, United Kingdom
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103
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Shapiro JT, Leboucher G, Myard-Dury AF, Girardo P, Luzzati A, Mary M, Sauzon JF, Lafay B, Dauwalder O, Laurent F, Lina G, Chidiac C, Couray-Targe S, Vandenesch F, Flandrois JP, Rasigade JP. Metapopulation ecology links antibiotic resistance, consumption, and patient transfers in a network of hospital wards. eLife 2020; 9:54795. [PMID: 33106223 PMCID: PMC7690951 DOI: 10.7554/elife.54795] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2019] [Accepted: 10/12/2020] [Indexed: 02/07/2023] Open
Abstract
Antimicrobial resistance (AMR) is a global threat. A better understanding of how antibiotic use and between-ward patient transfers (or connectivity) impact population-level AMR in hospital networks can help optimize antibiotic stewardship and infection control strategies. Here, we used a metapopulation framework to explain variations in the incidence of infections caused by seven major bacterial species and their drug-resistant variants in a network of 357 hospital wards. We found that ward-level antibiotic consumption volume had a stronger influence on the incidence of the more resistant pathogens, while connectivity had the most influence on hospital-endemic species and carbapenem-resistant pathogens. Piperacillin-tazobactam consumption was the strongest predictor of the cumulative incidence of infections resistant to empirical sepsis therapy. Our data provide evidence that both antibiotic use and connectivity measurably influence hospital AMR. Finally, we provide a ranking of key antibiotics by their estimated population-level impact on AMR that might help inform antimicrobial stewardship strategies.
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Affiliation(s)
- Julie Teresa Shapiro
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France
| | | | - Anne-Florence Myard-Dury
- Pôle de Santé Publique, Département d'Information Médicale, Hospices Civils de Lyon, Lyon, France
| | - Pascale Girardo
- Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Anatole Luzzati
- Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Mélissa Mary
- Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | | | - Bénédicte Lafay
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, University of Lyon, Lyon, France
| | - Olivier Dauwalder
- Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Frédéric Laurent
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France.,Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Gerard Lina
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France.,Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Christian Chidiac
- Service des Maladies Infectieuses et Tropicales, Hospices Civils de Lyon, Lyon, France
| | - Sandrine Couray-Targe
- Pôle de Santé Publique, Département d'Information Médicale, Hospices Civils de Lyon, Lyon, France
| | - François Vandenesch
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France.,Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
| | - Jean-Pierre Flandrois
- Laboratoire de Biométrie et Biologie Evolutive, UMR CNRS 5558, University of Lyon, Lyon, France
| | - Jean-Philippe Rasigade
- CIRI, Centre International de Recherche en Infectiologie, Université de Lyon, Inserm U1111, Ecole Normale Supérieure de Lyon, Université Lyon 1, CNRS, UMR5308, Lyon, France.,Institut des Agents Infectieux, Hospices Civils de Lyon, Lyon, France
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104
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Molecular and Epidemiological Characteristics of Carbapenemase-Producing Klebsiella pneumoniae Clinical Isolates in Japan. mSphere 2020; 5:5/5/e00490-20. [PMID: 33087515 PMCID: PMC7580953 DOI: 10.1128/msphere.00490-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Carbapenems serve as a last resort for the clinical treatment of multidrug-resistant infections. Therefore, the rapid spread of carbapenemase-producing strains represents a serious public health threat, further limiting antibiotic choices. The current findings of hypervirulent carbapenemase-producing Klebsiella pneumoniae clinical isolates in Japan demonstrate the potential broad spread and transfer of these genes, necessitating close surveillance. Carbapenemase-producing Enterobacteriaceae represent a serious public health threat worldwide. Carbapenemase genes, harbored on a transferable plasmid, have been isolated globally with distinct geographical features. Klebsiella pneumoniae, included in Enterobacteriaceae, also produces carbapenemase and often shows hypervirulence. Overlapping carbapenem resistance and hypervirulence in K. pneumoniae have been reported, but such strains have not yet been found in Japan. Here, we screened 104 carbapenemase-producing K. pneumoniae isolates collected from 37 hospitals and outpatient clinics in Japan between September 2014 and July 2015. PCR and DNA sequencing demonstrated IMP-1 in 21 isolates and IMP-6 in 83 isolates, 77 of which coharbored CTX-M-2. Most of the isolates showed low MICs toward imipenem and meropenem but high MICs toward penicillin and cephalosporins. Conjugation experiments with an Escherichia coli J53 recipient showed that most of the plasmids in IMP-6 producers were transferable, whereas only one-half of the plasmids in IMP-1 producers were transferable. PCR-based replicon typing and multiplex PCR identified five isolates belonging to the CG258 non-tonB79 cluster and no isolate belonging to the CG258-tonB79 cluster or sequence type 307 (ST307). Four K1-ST23 isolates, 10 K2-ST65 isolates, and 7 K2-ST86 isolates were detected that harbored virulence genes. The resistance genes in 85 isolates were transferable, but the virulence genes were not transferred. These results demonstrate the acquisition of IMP-type carbapenemase genes and CTX-M-type genes among hypervirulence isolates in Japan, warranting further attention and countermeasures. In this study, we have determined the molecular characteristics and epidemiology of IMP-6 producers that coharbored various CTX-M genes in Japan. IMPORTANCE Carbapenems serve as a last resort for the clinical treatment of multidrug-resistant infections. Therefore, the rapid spread of carbapenemase-producing strains represents a serious public health threat, further limiting antibiotic choices. The current findings of hypervirulent carbapenemase-producing Klebsiella pneumoniae clinical isolates in Japan demonstrate the potential broad spread and transfer of these genes, necessitating close surveillance.
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105
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Hendrickx APA, Landman F, de Haan A, Borst D, Witteveen S, van Santen-Verheuvel MG, van der Heide HGJ, Schouls LM. Plasmid diversity among genetically related Klebsiella pneumoniae bla KPC-2 and bla KPC-3 isolates collected in the Dutch national surveillance. Sci Rep 2020; 10:16778. [PMID: 33033293 PMCID: PMC7546619 DOI: 10.1038/s41598-020-73440-2] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Accepted: 09/10/2020] [Indexed: 12/04/2022] Open
Abstract
Carbapenemase-producing Klebsiella pneumoniae emerged as a nosocomial pathogen causing morbidity and mortality in patients. For infection prevention it is important to track the spread of K. pneumoniae and its plasmids between patients. Therefore, the major aim was to recapitulate the contents and diversity of the plasmids of genetically related K. pneumoniae strains harboring the beta-lactamase gene blaKPC-2 or blaKPC-3 to determine their dissemination in the Netherlands and the former Dutch Caribbean islands from 2014 to 2019. Next-generation sequencing was combined with long-read third-generation sequencing to reconstruct 22 plasmids. wgMLST revealed five genetic clusters comprised of K. pneumoniae blaKPC-2 isolates and four clusters consisted of blaKPC-3 isolates. KpnCluster-019 blaKPC-2 isolates were found both in the Netherlands and the Caribbean islands, while blaKPC-3 cluster isolates only in the Netherlands. Each K. pneumoniae blaKPC-2 or blaKPC-3 cluster was characterized by a distinct resistome and plasmidome. However, the large and medium plasmids contained a variety of antibiotic resistance genes, conjugation machinery, cation transport systems, transposons, toxin/antitoxins, insertion sequences and prophage-related elements. The small plasmids carried genes implicated in virulence. Thus, implementing long-read plasmid sequencing analysis for K. pneumoniae surveillance provided important insights in the transmission of a KpnCluster-019 blaKPC-2 strain between the Netherlands and the Caribbean.
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Affiliation(s)
- Antoni P A Hendrickx
- Center for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands.
| | - Fabian Landman
- Center for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Angela de Haan
- Center for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Dyogo Borst
- Center for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Sandra Witteveen
- Center for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Marga G van Santen-Verheuvel
- Center for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Han G J van der Heide
- Center for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
| | - Leo M Schouls
- Center for Infectious Disease Control (CIb), National Institute for Public Health and the Environment (RIVM), Bilthoven, The Netherlands
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106
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Octavia S, Kalisvar M, Venkatachalam I, Ng OT, Xu W, Sridatta PSR, Ong YF, Wang LD, Chua A, Cheng B, Lin RTP, Teo JWP. Klebsiella pneumoniae and Klebsiella quasipneumoniae define the population structure of blaKPC-2Klebsiella: a 5 year retrospective genomic study in Singapore. J Antimicrob Chemother 2020; 74:3205-3210. [PMID: 31504571 DOI: 10.1093/jac/dkz332] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2019] [Revised: 06/25/2019] [Accepted: 07/04/2019] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVES To describe the population structure, molecular epidemiology and genetic context of blaKPC-2-bearing Klebsiella pneumoniae. METHODS Isolates (n = 157) were retrospective, phenotypically carbapenem-resistant blaKPC-positive K. pneumoniae, collected from public hospitals. WGS was performed on the Illumina platform. Phylogenomic analysis, screening of resistance and virulence genes, and comparison of the genetic environment of blaKPC were carried out. RESULTS Based on core-tree phylogeny, 67.5% of the isolates were K. pneumoniae and the remainder comprised Klebsiella quasipneumoniae. No Klebsiella variicola strains were observed. Only a single K. pneumoniae carbapenemase (KPC) variant type, blaKPC-2, was seen. MLSTs were diverse and did not comprise the 'traditional' KPC clonal group (CG) 258. blaKPC-2 was associated with a non-Tn4401 element (NTE) in >99% of genomes. Screening for four key virulence loci: yersiniabactin (ybt), aerobactin (iuc), salmochelin (iro) and colibactin (clb) as well as ICEKp (virulence-associated integrative conjugative element of K. pneumoniae), revealed the lack of virulence factors and ICEKp within K. quasipneumoniae. Amongst the K. pneumoniae, there were 32 ybt+ isolates (32/106, 30.2%) and, of these, 8 isolates were also clb+ (7.5%). K. pneumoniae serotypes K1 and K2, the majority of capsular serotype seen in patients with invasive liver abscess syndrome, were detected at 4.5% (7/157). CONCLUSIONS Results suggest that dissemination of blaKPC-2 is driven by NTEKPC in non-ST258 isolates. The detection of blaKPC-2K. pneumoniae serotypes K1/K2 carrying virulence factors, albeit in low numbers, reflects the worrisome convergence of carbapenem resistance and hypervirulence in K. pneumoniae.
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Affiliation(s)
- Sophie Octavia
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore
| | - Marimuthu Kalisvar
- Tan Tock Seng Hospital, Department of Infectious Diseases, Singapore.,National Centre for Infectious Diseases, Singapore.,National University of Singapore, Yong Loo Lin School of Medicine, Singapore
| | | | - Oon Tek Ng
- Tan Tock Seng Hospital, Department of Infectious Diseases, Singapore.,National Centre for Infectious Diseases, Singapore.,Nanyang Technological University, Lee Kong Chian School of Medicine, Singapore
| | - Weizhen Xu
- Tan Tock Seng Hospital, Department of Infectious Diseases, Singapore
| | | | - Yi Fa Ong
- Tan Tock Seng Hospital, Department of Infectious Diseases, Singapore
| | - Liang De Wang
- Tan Tock Seng Hospital, Department of Infectious Diseases, Singapore
| | - Amanda Chua
- Tan Tock Seng Hospital, Department of Infectious Diseases, Singapore
| | - Bernadette Cheng
- National University Hospital, Department of Laboratory Medicine, Singapore
| | - Raymond T P Lin
- National Public Health Laboratory, National Centre for Infectious Diseases, Singapore.,National University Hospital, Department of Laboratory Medicine, Singapore
| | - Jeanette W P Teo
- National University Hospital, Department of Laboratory Medicine, Singapore
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107
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Lee M, Choi TJ. Antimicrobial Resistance Caused by KPC-2 Encoded by Promiscuous Plasmids of the Klebsiella pneumoniae ST307 Strain. Ann Lab Med 2020; 41:86-94. [PMID: 32829583 PMCID: PMC7443515 DOI: 10.3343/alm.2021.41.1.86] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Revised: 04/10/2020] [Accepted: 08/06/2020] [Indexed: 12/14/2022] Open
Abstract
Background A lineage of Klebsiella pneumoniae that produces carbapenemase-2 (KPC-2), sequence type (ST) 307, emerged in 2017. We analyzed the complete sequences of plasmids from KPC-2-producing K. pneumoniae (KPC-Kp) ST307, investigated the antimicrobial resistance conferred by this strain, and confirmed the horizontal interspecies transmission of KPC-carbapenemase-producing Enterobacteriaceae (CPE) characteristics among Enterobacteriaceae. Methods We performed antimicrobial susceptibility testing, PCR analysis, multilocus sequence typing, curing tests, and whole-genome sequencing to characterize plasmid-derived KPC-2-producing Enterobacteriaceae clinical isolates. Results Sequence analysis of KPC-Kp strain ST307 revealed novel plasmid-located virulence factors, including a gene cluster for glycogen synthesis. Three Enterobacteriaceae strains were identified in one patient: K. pneumoniae (CPKp1825), Klebsiella aerogenes (CPEa1826), and Escherichia coli (CPEc1827). The blaKPC-2 gene from K. pneumoniae ST307 was horizontally transmitted between these strains. The plasmids could be transferred through conjugation, because all three strains of bacteria contained the type IV secretion system, pilus genes, and tra genes for conjugal transfer. The blaKPC-2 gene was located on a truncated Tn4401 transposon. Plasmids containing the blaKPC-2 gene could not be artificially removed; thus, the three strains could not be cured. Conclusions The ease of horizontal transfer of KPC-Kp ST307 carbapenem resistance has serious public health and epidemiological implications. This study provides a better understanding of the genetic characteristics that can contribute to the growth and spread of KPC-Kp ST307, and their association with antimicrobial resistance genes.
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Affiliation(s)
- Miyoung Lee
- Department of Microbiology, Pukyoung National University, Busan, Korea.,Department of Laboratory Medicine, BHS Hanseo Hospital, Busan, Korea
| | - Tae-Jin Choi
- Department of Microbiology, Pukyoung National University, Busan, Korea
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108
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Maes M, Dyson ZA, Smith SE, Goulding DA, Ludden C, Baker S, Kellam P, Reece ST, Dougan G, Bartholdson Scott J. A novel therapeutic antibody screening method using bacterial high-content imaging reveals functional antibody binding phenotypes of Escherichia coli ST131. Sci Rep 2020; 10:12414. [PMID: 32709982 PMCID: PMC7382476 DOI: 10.1038/s41598-020-69300-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/26/2020] [Indexed: 01/28/2023] Open
Abstract
The increase of antimicrobial resistance (AMR), and lack of new classes of licensed antimicrobials, have made alternative treatment options for AMR pathogens increasingly attractive. Recent studies have demonstrated anti-bacterial efficacy of a humanised monoclonal antibody (mAb) targeting the O25b O-antigen of Escherichia coli ST131. To evaluate the phenotypic effects of antibody binding to diverse clinical E. coli ST131 O25b bacterial isolates in high-throughput, we designed a novel mAb screening method using high-content imaging (HCI) and image-based morphological profiling to screen a mAb targeting the O25b O-antigen. Screening the antibody against a panel of 86 clinical E. coli ST131 O25:H4 isolates revealed 4 binding phenotypes: no binding (18.60%), weak binding (4.65%), strong binding (69.77%) and strong agglutinating binding (6.98%). Impaired antibody binding could be explained by the presence of insertion sequences or mutations in O-antigen or lipopolysaccharide core biosynthesis genes, affecting the amount, structure or chain length of the O-antigen. The agglutinating binding phenotype was linked with lower O-antigen density, enhanced antibody-mediated phagocytosis and increased serum susceptibly. This study highlights the need to screen candidate mAbs against large panels of clinically relevant isolates, and that HCI can be used to evaluate mAb binding affinity and potential functional efficacy against AMR bacteria.
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Affiliation(s)
- Mailis Maes
- Department of Medicine, Cambridge Institute for Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, UK
| | - Zoe A Dyson
- Department of Medicine, Cambridge Institute for Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, UK
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, VIC, 3004, Australia
- London School of Hygiene and Tropical Medicine, London, UK
| | | | | | | | - Stephen Baker
- Department of Medicine, Cambridge Institute for Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, UK
| | - Paul Kellam
- Kymab Ltd, Babraham Research Campus, Cambridge, UK
- Department of Infectious Disease, Imperial College London, London, UK
| | | | - Gordon Dougan
- Department of Medicine, Cambridge Institute for Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, UK
| | - Josefin Bartholdson Scott
- Department of Medicine, Cambridge Institute for Therapeutic Immunology & Infectious Disease, University of Cambridge, Cambridge, UK.
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109
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Cohorting KPC+ Klebsiella pneumoniae (KPC-Kp)-positive patients: A genomic exposé of cross-colonization hazards in a long-term acute-care hospital (LTACH). Infect Control Hosp Epidemiol 2020; 41:1162-1168. [PMID: 32624030 DOI: 10.1017/ice.2020.261] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
OBJECTIVE Cohorting patients who are colonized or infected with multidrug-resistant organisms (MDROs) protects uncolonized patients from acquiring MDROs in healthcare settings. The potential for cross transmission within the cohort and the possibility of colonized patients acquiring secondary isolates with additional antibiotic resistance traits is often neglected. We searched for evidence of cross transmission of KPC+ Klebsiella pneumoniae (KPC-Kp) colonization among cohorted patients in a long-term acute-care hospital (LTACH), and we evaluated the impact of secondary acquisitions on resistance potential. DESIGN Genomic epidemiological investigation. SETTING A high-prevalence LTACH during a bundled intervention that included cohorting KPC-Kp-positive patients. METHODS Whole-genome sequencing (WGS) and location data were analyzed to identify potential cases of cross transmission between cohorted patients. RESULTS Secondary KPC-Kp isolates from 19 of 28 admission-positive patients were more closely related to another patient's isolate than to their own admission isolate. Of these 19 cases, 14 showed strong genomic evidence for cross transmission (<10 single nucleotide variants or SNVs), and most of these patients occupied shared cohort floors (12 patients) or rooms (4 patients) at the same time. Of the 14 patients with strong genomic evidence of acquisition, 12 acquired antibiotic resistance genes not found in their primary isolates. CONCLUSIONS Acquisition of secondary KPC-Kp isolates carrying distinct antibiotic resistance genes was detected in nearly half of cohorted patients. These results highlight the importance of healthcare provider adherence to infection prevention protocols within cohort locations, and they indicate the need for future studies to assess whether multiple-strain acquisition increases risk of adverse patient outcomes.
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110
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De Oliveira DMP, Forde BM, Kidd TJ, Harris PNA, Schembri MA, Beatson SA, Paterson DL, Walker MJ. Antimicrobial Resistance in ESKAPE Pathogens. Clin Microbiol Rev 2020; 23:788-99. [PMID: 32404435 DOI: 10.1111/imb.12124] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023] Open
Abstract
Antimicrobial-resistant ESKAPE ( Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens represent a global threat to human health. The acquisition of antimicrobial resistance genes by ESKAPE pathogens has reduced the treatment options for serious infections, increased the burden of disease, and increased death rates due to treatment failure and requires a coordinated global response for antimicrobial resistance surveillance. This looming health threat has restimulated interest in the development of new antimicrobial therapies, has demanded the need for better patient care, and has facilitated heightened governance over stewardship practices.
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Affiliation(s)
- David M P De Oliveira
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - Brian M Forde
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - Timothy J Kidd
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - Patrick N A Harris
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
- UQ Centre for Clinical Research, The University of Queensland, QLD, Australia
| | - Mark A Schembri
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - David L Paterson
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
- UQ Centre for Clinical Research, The University of Queensland, QLD, Australia
| | - Mark J Walker
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
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111
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De Oliveira DMP, Forde BM, Kidd TJ, Harris PNA, Schembri MA, Beatson SA, Paterson DL, Walker MJ. Antimicrobial Resistance in ESKAPE Pathogens. Clin Microbiol Rev 2020; 33:e00181-19. [PMID: 32404435 PMCID: PMC7227449 DOI: 10.1128/cmr.00181-19] [Citation(s) in RCA: 836] [Impact Index Per Article: 209.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Antimicrobial-resistant ESKAPE ( Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogens represent a global threat to human health. The acquisition of antimicrobial resistance genes by ESKAPE pathogens has reduced the treatment options for serious infections, increased the burden of disease, and increased death rates due to treatment failure and requires a coordinated global response for antimicrobial resistance surveillance. This looming health threat has restimulated interest in the development of new antimicrobial therapies, has demanded the need for better patient care, and has facilitated heightened governance over stewardship practices.
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Affiliation(s)
- David M P De Oliveira
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - Brian M Forde
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - Timothy J Kidd
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - Patrick N A Harris
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
- UQ Centre for Clinical Research, The University of Queensland, QLD, Australia
| | - Mark A Schembri
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - Scott A Beatson
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
| | - David L Paterson
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
- UQ Centre for Clinical Research, The University of Queensland, QLD, Australia
| | - Mark J Walker
- School of Chemistry and Molecular Biosciences, The University of Queensland, QLD, Australia
- Australian Infectious Diseases Research Centre, The University of Queensland, QLD, Australia
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112
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Shamina OV, Kryzhanovskaya OA, Lazareva AV, Alyabieva NM, Mayanskiy NA. Colistin resistance of carbapenem-resistant Klebsiella pneumoniae strains: molecular mechanisms and bacterial fitness. BULLETIN OF RUSSIAN STATE MEDICAL UNIVERSITY 2020. [DOI: 10.24075/brsmu.2020.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The increasing use of colistin in the clinic has led to the emergence and spread of colistin resistance. According to the literature, antibiotic resistance can have a metabolic cost, resulting in poor adaptation and survival, i.e. reduced bacterial fitness. The aim of this study was to investigate molecular mechanisms underlying resistance to colistin and their effect on the bacterial fitness of carbapenem-resistant (carba-R) strains of K. pneumoniae isolated from the patients of Moscow hospitals in 2012–2017. Of 159 analyzed carba-R isolates, 71 (45%) were resistant to colistin (minimum inhibitory concentration over 2 mg/L). By conducting Sanger sequencing, we were able to identify the mechanisms underlying colistin resistance in 26 (37%) isolates. Growth curves were constructed by measuring optical density at 600 nm wavelength for 15 hours. The competitive growth of colistin-resistant (col-R) K. pneumoniae isolates was assessed relative to the colistin-susceptible (col-S) isolate. Col-R and col-S cultures harvested in the exponential phase were combined at the ratio of 1:1, incubated in the Luria-Bertani medium and plated onto Luria-Bertani agar plates with 10 mg/L colistin and without it. The competition index was calculated as the ratio of grown col-R and col-S colonies. Resistance to colistin did not affect the growth kinetics of K. pneumoniae, but did reduce the competitive ability of the bacteria as compared to the col-S isolates. However, some col-R isolates were more competitive than the col-S strains of the same sequence type. Further research is needed to elucidate the effects of colistin resistance on bacterial fitness.
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Affiliation(s)
- OV Shamina
- National Medical Research Center for Children's Health, Moscow, Russia
| | - OA Kryzhanovskaya
- National Medical Research Center for Children's Health, Moscow, Russia
| | - AV Lazareva
- National Medical Research Center for Children's Health, Moscow, Russia
| | - NM Alyabieva
- National Medical Research Center for Children's Health, Moscow, Russia
| | - NA Mayanskiy
- Pirogov Russian National Research Medical University, Moscow, Russia
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113
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Rodrigues MX, Yang Y, de Souza Meira EB, do Carmo Silva J, Bicalho RC. Development and evaluation of a new recombinant protein vaccine (YidR) against Klebsiella pneumoniae infection. Vaccine 2020; 38:4640-4648. [PMID: 32444194 DOI: 10.1016/j.vaccine.2020.03.057] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2019] [Revised: 02/24/2020] [Accepted: 03/30/2020] [Indexed: 12/19/2022]
Abstract
Vaccination is a promising approach to prevent Klebsiella infection; however, the high heterogeneity of strains is a limiting factor. The best antigenic target for an anti-Klebsiella vaccine should be expressed by all or most of strains. We previously found YidR protein to be highly conserved among K. pneumoniae strains independently of antigen serotype. Therefore, in the present study, we developed a recombinant YidR protein vaccine and evaluated its protective efficacy against lethal challenge with K. pneumoniae in a mouse model. The yidR gene was cloned in Escherichia coli for recombinant expression. The lethal dose (LD100) of K. pneumoniae was determined and lethal challenge was carried out after immunization with recombinant purified YidR. After immunization, the concentration of total serum IgG was significantly higher in YidR-immunized mice than in non-immunized mice, indicating strong induction of antibodies. Mice were challenged with LD100 of K. pneumoniae, and significantly lower murine sepsis and higher body weight were observed in YidR-immunized mice compared to unvaccinated controls. Moreover, ∼90% of YidR-immunized mice survived beyond 10 days of observation, whereas none of the control mice survived past 48 h. The protective effect of YidR recombinant protein vaccine was demonstrated and YidR may be a promising vaccine candidate to prevent klebsiellosis.
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Affiliation(s)
- Marjory Xavier Rodrigues
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, United States.
| | - Yongqiang Yang
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, United States
| | - Enoch Brandão de Souza Meira
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, United States
| | - Josiane do Carmo Silva
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, United States
| | - Rodrigo Carvalho Bicalho
- Department of Population Medicine and Diagnostic Sciences, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853, United States.
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114
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A Retrospective Whole-Genome Sequencing Analysis of Carbapenem and Colistin-Resistant Klebsiella Pneumoniae Nosocomial Strains Isolated during an MDR Surveillance Program. Antibiotics (Basel) 2020; 9:antibiotics9050246. [PMID: 32408565 PMCID: PMC7277725 DOI: 10.3390/antibiotics9050246] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 05/03/2020] [Accepted: 05/06/2020] [Indexed: 12/02/2022] Open
Abstract
Multidrug-resistant Klebsiella pneumoniae (MDR Kp), in particular carbapenem-resistant Kp (CR-Kp), has become endemic in Italy, where alarming data have been reported on the spread of colistin-resistant CR-Kp (CRCR-Kp). During the period 2013–2014, 27 CRCR-Kp nosocomial strains were isolated within the Modena University Hospital Policlinico (MUHP) multidrug resistance surveillance program. We retrospectively investigated these isolates by whole-genome sequencing (WGS) analysis of the resistome, virulome, plasmid content, and core single nucleotide polymorphisms (cSNPs) in order to gain insights into their molecular epidemiology. The in silico WGS analysis of the resistome revealed the presence of genes, such as blaKPC, related to the phenotypically detected resistances to carbapenems. Concerning colistin resistance, the plasmidic genes mcr1–9 were not detected, while known and new genetic variations in mgrB, phoQ, and pmrB were found. The virulome profile revealed the presence of type-3 fimbriae, capsular polysaccharide, and iron acquisition system genes. The detected plasmid replicons were classified as IncFIB(pQil), IncFIB(K), ColRNAI, IncX3, and IncFII(K) types. The cSNPs genotyping was consistent with the multi locus sequence typing (MLST) and with the distribution of mutations related to colistin resistance genes. In a nosocomial drug resistance surveillance program, WGS proved to be a useful tool for elucidating the spread dynamics of CRCR-Kp nosocomial strains and could help to limit their diffusion.
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115
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Benulič K, Pirš M, Couto N, Chlebowicz M, Rossen JWA, Zorec TM, Seme K, Poljak M, Lejko Zupanc T, Ružić-Sabljić E, Cerar T. Whole genome sequencing characterization of Slovenian carbapenem-resistant Klebsiella pneumoniae, including OXA-48 and NDM-1 producing outbreak isolates. PLoS One 2020; 15:e0231503. [PMID: 32282829 PMCID: PMC7153892 DOI: 10.1371/journal.pone.0231503] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Accepted: 03/24/2020] [Indexed: 11/21/2022] Open
Abstract
Objectives The first hospital outbreak of carbapenemase-producing Enterobacteriaceae in Slovenia occurred in 2014–2016. Whole genome sequencing was used to analyse the population of carbapenem-resistant Klebsiella pneumoniae collected in Slovenia in 2014–2017, including OXA-48 and/or NDM-1 producing strains from the outbreak. Methods A total of 32 K. pneumoniae isolates were analysed using short-read sequencing. Multi-locus sequence typing and core genome multi-locus sequence typing were used to infer genetic relatedness. Antimicrobial resistance markers, virulence factors, plasmid content and wzi types were determined. Long-read sequencing was used for six isolates for detailed analysis of plasmids and their possible transmission. Results Overall, we detected 10 different sequence types (STs), the most common being ST437 (40.6%). Isolates from the initial outbreak belonged to ST437 (12/16) and ST147 (4/16). A second outbreak of four ST15 isolates was discovered. A new ST (ST3390) and two new wzi types (wzi-556, wzi-559) were identified. blaOXA-48 was found in 17 (53.1%) isolates, blaNDM-1 in five (15.6%), and a combination of blaOXA-48/NDM-1 in seven (21.9%) isolates. Identical plasmids carrying blaOXA-48 were found in outbreak isolates sequenced with long-read sequencing technology. Conclusions Whole genome sequencing of Slovenian carbapenem-resistant K. pneumoniae isolates revealed multiple clusters of STs, two of which were involved in the first hospital outbreak of carbapenem producing K. pneumoniae in Slovenia. Transmission of the plasmid carrying blaOXA-48 between two STs was likely to have occurred. A previously unidentified second outbreak was also discovered, highlighting the importance of whole genome sequencing in detection and/or characterization of hospital outbreaks and surveillance of drug-resistant bacterial clones.
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Affiliation(s)
- Katarina Benulič
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
- * E-mail:
| | - Mateja Pirš
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| | - Natacha Couto
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Monika Chlebowicz
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - John W. A. Rossen
- Department of Medical Microbiology and Infection Prevention, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Tomaž Mark Zorec
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| | - Katja Seme
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| | - Mario Poljak
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| | - Tatjana Lejko Zupanc
- Department of Infectious Diseases, University Medical Center Ljubljana, Ljubljana, Slovenia
| | - Eva Ružić-Sabljić
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
| | - Tjaša Cerar
- Faculty of Medicine, Institute of Microbiology and Immunology, University of Ljubljana, Ljubljana, Slovenia
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Coevolution of host-plasmid pairs facilitates the emergence of novel multidrug resistance. Nat Ecol Evol 2020; 4:863-869. [PMID: 32251388 DOI: 10.1038/s41559-020-1170-1] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Accepted: 03/05/2020] [Indexed: 11/08/2022]
Abstract
Multidrug resistance (MDR) of pathogens is an ongoing public health crisis exacerbated by the horizontal transfer of antibiotic resistance genes via conjugative plasmids. Factors that stabilize these plasmids in bacterial communities contribute to an even higher incidence of MDR, given the increased likelihood that a host will already contain a plasmid when it acquires another through conjugation. Here, we show one such stabilizing factor is host-plasmid coevolution under antibiotic selection, which facilitated the emergence of MDR via two distinct plasmids in communities consisting of Escherichia coli and Klebsiella pneumoniae once antibiotics were removed. In our system, evolution promoted greater stability of a plasmid in its coevolved host. Further, pleiotropic effects resulted in greater plasmid persistence in both novel host-plasmid combinations and, in some cases, multi-plasmid hosts. This evolved stability favoured the generation of MDR cells and thwarted their loss within communities with multiple plasmids. By selecting for plasmid persistence, the application of antibiotics may promote MDR well after their original period of use.
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117
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A Front Line on Klebsiella pneumoniae Capsular Polysaccharide Knowledge: Fourier Transform Infrared Spectroscopy as an Accurate and Fast Typing Tool. mSystems 2020; 5:5/2/e00386-19. [PMID: 32209717 PMCID: PMC7093823 DOI: 10.1128/msystems.00386-19] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Klebsiella pneumoniae is nowadays recognized as one of the most defiant human pathogens, whose infections are increasingly more challenging to treat and control. Whole-genome sequencing (WGS) has been key for clarifying the population structure of K. pneumoniae, and it is still instrumental to provide insights into potential pathogenicity and evolutionary markers, such as the capsular locus. However, this information and WGS are still far from being accessible and translated into routine clinical microbiology laboratories as quick and cost-efficient strain diagnostic tools. Here, we propose a biochemical fingerprinting approach based on Fourier transform infrared spectroscopy (FT-IR) and multivariate data analysis tools for K. pneumoniae capsular typing that, because of its high resolution, speed, and low cost, can be an asset to provide enough information to support real-time epidemiology and infection control decisions. Besides, it provides a simple framework for phenotypic/biochemical validation of K. pneumoniae capsular diversity. Genomics-based population analysis of multidrug-resistant (MDR) Klebsiella pneumoniae motivated a renewed interest on the capsule as an evolutionary and virulence marker of clinically relevant strains. Whole-genome sequencing (WGS)-based approaches have provided great insights into the genetic variability of the capsular locus, but genotypic-biochemical capsular (K)-type correlations are lacking, hindering the establishment of a reliable framework for K-type characterization and typing. To fill this gap, we combined molecular, comparative genomics, and multivariate data analysis tools with biochemical data on the capsular locus to support the usefulness of Fourier transform infrared (FT-IR) spectroscopy as a reliable K typing tool. To validate our approach, we used a representative collection of well-defined MDR K. pneumoniae lineages involved in local or nationwide epidemics in multiple countries. With this, we demonstrate a high accuracy and resolution of our FT-IR-based spectroscopy approach for K-type discrimination that is even higher than that provided by WGS. Moreover, the specific associations established between certain K types and specific K. pneumoniae lineages with high clinical relevance, together with the accuracy, simplicity, short time to result, and inexpensive features of the method, support the value of the developed FT-IR-based approach for an easy, fast, and cost-effective strain typing. This fulfills a still unmet need for tools to support real-time monitoring and control of K. pneumoniae infections. In addition, the genotypic-biochemical correlations established provide insights on sugar composition/structure of newly defined K. pneumoniae capsular types. IMPORTANCEKlebsiella pneumoniae is nowadays recognized as one of the most defiant human pathogens, whose infections are increasingly more challenging to treat and control. Whole-genome sequencing (WGS) has been key for clarifying the population structure of K. pneumoniae, and it is still instrumental to provide insights into potential pathogenicity and evolutionary markers, such as the capsular locus. However, this information and WGS are still far from being accessible and translated into routine clinical microbiology laboratories as quick and cost-efficient strain diagnostic tools. Here, we propose a biochemical fingerprinting approach based on Fourier transform infrared spectroscopy (FT-IR) and multivariate data analysis tools for K. pneumoniae capsular typing that, because of its high resolution, speed, and low cost, can be an asset to provide enough information to support real-time epidemiology and infection control decisions. Besides, it provides a simple framework for phenotypic/biochemical validation of K. pneumoniae capsular diversity.
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118
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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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119
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Fursova NK, Astashkin EI, Gabrielyan NI, Novikova TS, Fedyukina GN, Kubanova MK, Esenova NM, Sharapchenko SO, Volozhantsev NV. Emergence of Five Genetic Lines ST395 NDM-1, ST13 OXA-48, ST3346 OXA-48, ST39 CTX-M-14, and Novel ST3551 OXA-48 of Multidrug-Resistant Clinical Klebsiella pneumoniae in Russia. Microb Drug Resist 2020; 26:924-933. [PMID: 32155384 DOI: 10.1089/mdr.2019.0289] [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: 01/13/2023] Open
Abstract
Aims: The objective of this study was phenotypic and genotypic characterization of antibacterial-resistant Klebsiella pneumoniae clinical strains isolated in Moscow Transplantology Intensive Care Unit in 2017-2019. Results: Major strains among K. pneumoniae (n = 63) isolated from 30 patients were recognized as extensive drug-resistant (n = 55) pathogens, and remaining strains were recognized as multidrug-resistant (n = 8) pathogens. The beta-lactamase genes blaSHV-1,-2a,-11,-27,-67,-187 (n = 63), blaCTX-M-14,-15 (n = 61), blaTEM-1 (n = 54), blaOXA-48 (n = 52), and blaNDM-1 (n = 2), as well as class 1 integrons (n = 19) carried gene cassette arrays aacA4 (n = 2), dfrA1-orfC (n = 6), aadB-aadA1 (n = 9), dfrA15-aadA1 (n = 3), and dfrA12-orfF-aadA2 (n = 1) were identified in the strains. All strains carried four virulence genes: wabG, fimH, uge, and allS, but two strains had additionally kfu gene. Six known sequence types (STs) of K. pneumoniae ST395 (n = 44), ST377 (n = 3), ST307 (n = 4), ST13 (n = 2), ST39 (n = 2), ST3346 (n = 1), and a novel sequence-type ST3551 (n = 7) were identified. Phylogenetic analysis showed that ST3551 belonged to the cluster of clonal group CG147, and the remaining six STs to the another cluster consisting of four subgroups. The emergence of K. pneumoniae genetic lines carrying epidemiologically significant beta-lactamase genes ST395NDM-1, ST13OXA-48, ST3346OXA-48/CTX-M-14, ST3551OXA-48, and ST39CTX-M-14 was the first case of detection in Russia. Conclusion: The emergence of novel carbapenemase-producing K. pneumoniae genetic lines in Russia highlights the global negative tendency of multidrug-resistant pathogens spread in high-technological medical centers.
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Affiliation(s)
- Nadezhda K Fursova
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | - Evgeny I Astashkin
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | - Nina I Gabrielyan
- Academician V.I. Shumakov Federal Research Center of Transplantology and Artificial Organs, Moscow, Russia
| | - Tatiana S Novikova
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | - Galina N Fedyukina
- State Research Center for Applied Microbiology and Biotechnology, Obolensk, Russia
| | - Madina Kh Kubanova
- Academician V.I. Shumakov Federal Research Center of Transplantology and Artificial Organs, Moscow, Russia
| | - Nadezhda M Esenova
- Academician V.I. Shumakov Federal Research Center of Transplantology and Artificial Organs, Moscow, Russia
| | - Sofia O Sharapchenko
- Academician V.I. Shumakov Federal Research Center of Transplantology and Artificial Organs, Moscow, Russia
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120
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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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Leggett RM, Alcon-Giner C, Heavens D, Caim S, Brook TC, Kujawska M, Martin S, Peel N, Acford-Palmer H, Hoyles L, Clarke P, Hall LJ, Clark MD. Rapid MinION profiling of preterm microbiota and antimicrobial-resistant pathogens. Nat Microbiol 2020; 5:430-442. [PMID: 31844297 PMCID: PMC7044117 DOI: 10.1038/s41564-019-0626-z] [Citation(s) in RCA: 86] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 11/01/2019] [Indexed: 12/29/2022]
Abstract
The MinION sequencing platform offers near real-time analysis of DNA sequence; this makes the tool attractive for deployment in fieldwork or clinical settings. We used the MinION platform coupled to the NanoOK RT software package to perform shotgun metagenomic sequencing and profile mock communities and faecal samples from healthy and ill preterm infants. Using Nanopore data, we reliably classified a 20-species mock community and captured the diversity of the immature gut microbiota over time and in response to interventions such as probiotic supplementation, antibiotic treatment or episodes of suspected sepsis. We also performed rapid real-time runs to assess gut-associated microbial communities in critically ill and healthy infants, facilitated by NanoOK RT software package, which analysed sequences as they were generated. Our pipeline reliably identified pathogenic bacteria (that is, Klebsiella pneumoniae and Enterobacter cloacae) and their corresponding antimicrobial resistance gene profiles within as little as 1 h of sequencing. Results were confirmed using pathogen isolation, whole-genome sequencing and antibiotic susceptibility testing, as well as mock communities and clinical samples with known antimicrobial resistance genes. Our results demonstrate that MinION (including cost-effective Flongle flow cells) with NanoOK RT can process metagenomic samples to a rich dataset in < 5 h, which creates a platform for future studies aimed at developing these tools and approaches in clinical settings with a focus on providing tailored patient antimicrobial treatment options.
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Affiliation(s)
| | | | | | - Shabhonam Caim
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK
| | | | | | - Samuel Martin
- Earlham Institute, Norwich Research Park, Norwich, UK
| | - Ned Peel
- Earlham Institute, Norwich Research Park, Norwich, UK
| | | | | | - Paul Clarke
- Norfolk and Norwich University Hospital, Norwich, UK
- Norwich Medical School, University of East Anglia, Norwich, UK
| | - Lindsay J Hall
- Quadram Institute Bioscience, Norwich Research Park, Norwich, UK.
| | - Matthew D Clark
- Earlham Institute, Norwich Research Park, Norwich, UK.
- Natural History Museum, London, UK.
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122
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Lu B, Lin C, Liu H, Zhang X, Tian Y, Huang Y, Yan H, Qu M, Jia L, Wang Q. Molecular Characteristics of Klebsiella pneumoniae Isolates From Outpatients in Sentinel Hospitals, Beijing, China, 2010-2019. Front Cell Infect Microbiol 2020; 10:85. [PMID: 32181161 PMCID: PMC7059253 DOI: 10.3389/fcimb.2020.00085] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/19/2020] [Indexed: 11/13/2022] Open
Abstract
Background: Klebsiella pneumoniae is an opportunistic pathogen associated with community-acquired and nosocomial infections. Since 2010, K. pneumoniae testing has been included into an existing diarrhea-syndrome surveillance system for estimating the prevalence of K. pneumoniae in diarrhea-syndrome patients, assessing antibiotic susceptibility, and investigating molecular characteristics of K. pneumoniae. Methods: Klebsiella pneumoniae strains were isolated from stool specimens from diarrhea-syndrome outpatients in Beijing, China. Isolates were tested for antibiotic susceptibility, and phylogenetic relationships were explored though whole genome sequence analysis. Multi-locus sequence type (MLST) alleles were extracted from the whole genome sequence (WGS) data. A maximum likelihood tree was generated by MEGAX. Genomes were annotated by Prokka; core genes were produced by Roary; a maximum likelihood phylogenetic tree was generated using FastTree. Results: Forty-four K. pnuemoniae strains were isolated from 2010 to July 2019; of these 37 were K. pneumoniae and seven were K. variicola. Antibiotic susceptibility testing showed that all 44 strains were sensitive to gentamicin, imipenem, amikacin, meropenem, kanamycin; 97.73% were sensitive to cefoxitin andlavo-ofloxacin; the highest antibiotic resistance rate was 79.55%, which was to ampicillin. We found three extended-spectrum beta-lactamase (ESBL) producing strains; we identified high-virulence ST types, including ST307 and ST65; and we found that ST23 has been the epidemic clone since 2010. MLST and core genome sequence analysis showed two distinct clusters of 44 K. pnuemoniae; 40 alleles were identified in core genome sequence analysis, while 36 alleles were identified in MLST typing. Conclusions: There is an urgent need for epidemiological and molecular studies to understand the dynamics of antibiotic resistance and virulence gene transmission to guide strategies for K. pneumoniae surveillance. WGS analysis provided high discrimination power and reliable and robust data useful for molecular epidemiology.
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Affiliation(s)
- Bing Lu
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing Research Center for Preventive Medicine, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
| | - Changying Lin
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing Research Center for Preventive Medicine, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
| | - Haican Liu
- State Key Laboratory for Infectious Disease Prevention and Control, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing, China
| | - Xin Zhang
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing Research Center for Preventive Medicine, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
| | - Yi Tian
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing Research Center for Preventive Medicine, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
| | - Ying Huang
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing Research Center for Preventive Medicine, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
| | - Hanqiu Yan
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing Research Center for Preventive Medicine, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
| | - Mei Qu
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing Research Center for Preventive Medicine, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
| | - Lei Jia
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing Research Center for Preventive Medicine, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
| | - Quanyi Wang
- Institute for Infectious Disease and Endemic Disease Control, Beijing Center for Disease Prevention and Control, Beijing Research Center for Preventive Medicine, Beijing Key Laboratory of Diagnostic and Traceability Technologies for Food Poisoning, Beijing, China
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Abstract
Klebsiella pneumoniae is a common cause of antimicrobial-resistant opportunistic infections in hospitalized patients. The species is naturally resistant to penicillins, and members of the population often carry acquired resistance to multiple antimicrobials. However, knowledge of K. pneumoniae ecology, population structure or pathogenicity is relatively limited. Over the past decade, K. pneumoniae has emerged as a major clinical and public health threat owing to increasing prevalence of healthcare-associated infections caused by multidrug-resistant strains producing extended-spectrum β-lactamases and/or carbapenemases. A parallel phenomenon of severe community-acquired infections caused by 'hypervirulent' K. pneumoniae has also emerged, associated with strains expressing acquired virulence factors. These distinct clinical concerns have stimulated renewed interest in K. pneumoniae research and particularly the application of genomics. In this Review, we discuss how genomics approaches have advanced our understanding of K. pneumoniae taxonomy, ecology and evolution as well as the diversity and distribution of clinically relevant determinants of pathogenicity and antimicrobial resistance. A deeper understanding of K. pneumoniae population structure and diversity will be important for the proper design and interpretation of experimental studies, for interpreting clinical and public health surveillance data and for the design and implementation of novel control strategies against this important pathogen.
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124
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Emergence of a ST307 clone carrying a novel insertion element MITEKpn1 in the mgrB gene among carbapenem-resistant Klebsiella pneumoniae from Moscow, Russia. Int J Antimicrob Agents 2020; 55:105850. [DOI: 10.1016/j.ijantimicag.2019.11.007] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/31/2019] [Accepted: 11/13/2019] [Indexed: 01/18/2023]
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125
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Ding L, Yang Z, Lu J, Ma L, Liu Y, Wu X, Yao W, Zhang X, Zhu K. Characterization of Phenotypic and Genotypic Traits of Klebsiella pneumoniae from Lung Cancer Patients with Respiratory Infection. Infect Drug Resist 2020; 13:237-245. [PMID: 32099416 PMCID: PMC6996219 DOI: 10.2147/idr.s229085] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Accepted: 12/17/2019] [Indexed: 12/24/2022] Open
Abstract
Background Klebsiella pneumoniae has been a leading healthcare-acquired infection (HAI) agent worldwide for decades. However, the epidemiological characteristics of K. pneumoniae in lung cancer patients with respiratory infection are unclear. Here, we characterized the frequency of K. pneumoniae in lung cancer patients with respiratory infection in a cancer hospital in China and determined the antibiotic resistance profile, virulence phenotype and clonal relationships among these K. pneumoniae strains. Methods The clinical data of lung cancer patients with respiratory infection from September 2017 to October 2018 were retrospectively evaluated. Microbiological methods, antimicrobial susceptibility tests, pulsed-field gel electrophoresis (PFGE), polymerase chain reaction (PCR) assays, Sanger sequencing and Galleria mellonella larvae infection model were used in this study. Results During the study period, a total of 47 lung cancer patients with respiratory infection caused by bacteria were identified, among 27 patients were identified as positive for K. pneumoniae and the positive rate was 57.45%. Among 37 nonduplicate K. pneumoniae strains from these 27 patients, 19 isolates (51.4%) were classified as multidrug resistant (MDR) with high-level resistance to, at least one agent in three or more antibiotic categories, including polymyxin B and tigecycline. Sixteen of the 37 strains (43.2%) were hypermucoviscous isolates. Extended spectrum β-lactamases-producing K. pneumoniae strains consisted of two dominant PFGE types. Furthermore, the assessment of virulence potential using a G. mellonella larvae infection model showed that K. pneumoniae isolated from these patients exhibited a high virulence level. Conclusion Our data showed that K. pneumoniae is the most critical cause of lung infection in patients with lung cancer in this hospital. The various drug resistance and virulence backgrounds of K. pneumoniae may make this clinical center a breeding ground for superbugs. It is paramount to enhance surveillance of K. pneumoniae strains and take control measures.
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Affiliation(s)
- Lingchi Ding
- Oncology Department, Nantong Tumor Hospital, Nantong 226361, People's Republic of China
| | - Zhiqiang Yang
- Oncology Department, Nantong Tumor Hospital, Nantong 226361, People's Republic of China.,Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, People's Republic of China
| | - Junguo Lu
- Oncology Department, Nantong Tumor Hospital, Nantong 226361, People's Republic of China
| | - Lichao Ma
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, People's Republic of China
| | - Ying Liu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, People's Republic of China
| | - Xiaoyan Wu
- Clinical Laboratory, Nantong Tumor Hospital, Nantong 226361, People's Republic of China
| | - Weidong Yao
- Oncology Department, Nantong Tumor Hospital, Nantong 226361, People's Republic of China
| | - Xiaodong Zhang
- Oncology Department, Nantong Tumor Hospital, Nantong 226361, People's Republic of China
| | - Kui Zhu
- Beijing Advanced Innovation Center for Food Nutrition and Human Health, College of Veterinary Medicine, China Agricultural University, Beijing 100193, People's Republic of China
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126
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Isolation of Four Lytic Phages Infecting Klebsiella pneumoniae K22 Clinical Isolates from Spain. Int J Mol Sci 2020; 21:ijms21020425. [PMID: 31936552 PMCID: PMC7013548 DOI: 10.3390/ijms21020425] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2019] [Revised: 12/28/2019] [Accepted: 01/07/2020] [Indexed: 01/15/2023] Open
Abstract
The emergence of multi-drug-resistant bacteria represents a major public-health threat. Phages constitute a promising alternative to chemical antibiotics due to their high host specificity, abundance in nature, and evolvability. However, phage host specificity means that highly diverse bacterial species are particularly difficult to target for phage therapy. This is the case of Klebsiella pneumoniae, which presents a hypervariable extracellular matrix capsule exhibiting dozens of variants. Here, we report four novel phages infecting K. pneumoniae capsular type K22 which were isolated from environmental samples in Valencia, Spain. Full genome sequencing showed that these phages belong to the Podoviridae family and encode putative depolymerases that allow digestion of specific K22 K. pneumoniae capsules. Our results confirm the capsular type-specificity of K. pneumoniae phages, as indicated by their narrow infectivity in a panel of K. pneumoniae clinical isolates. Nonetheless, this work represents a step forward in the characterization of phage diversity, which may culminate in the future use of large panels of phages for typing and/or for combating multi-drug-resistant K. pneumoniae.
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127
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Zhang X, Wang W, Yu H, Wang M, Zhang H, Lv J, Tang YW, Kreiswirth BN, Du H, Chen L. New Delhi Metallo-β-Lactamase 5-Producing Klebsiella pneumoniae Sequence Type 258, Southwest China, 2017. Emerg Infect Dis 2020; 25:1209-1213. [PMID: 31107227 PMCID: PMC6537745 DOI: 10.3201/eid2506.181939] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
We isolated a New Delhi metallo-β-lactamase 5 (NDM-5)–producing Klebsiella pneumoniae sequence type (ST) 258 strain in southwest China during 2017. The blaNDM-5 gene was acquired by horizontal plasmid transfer from NDM-5–producing Escherichia coli. We identified genomic characteristics in ST258 strains that differed from those of global K. pneumoniae carbapenemase–producing strains.
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128
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Ludden C, Moradigaravand D, Jamrozy D, Gouliouris T, Blane B, Naydenova P, Hernandez-Garcia J, Wood P, Hadjirin N, Radakovic M, Crawley C, Brown NM, Holmes M, Parkhill J, Peacock SJ. A One Health Study of the Genetic Relatedness of Klebsiella pneumoniae and Their Mobile Elements in the East of England. Clin Infect Dis 2020; 70:219-226. [PMID: 30840764 PMCID: PMC6938978 DOI: 10.1093/cid/ciz174] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2018] [Accepted: 02/27/2019] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Klebsiella pneumoniae is a human, animal, and environmental commensal and a leading cause of nosocomial infections, which are often caused by multiresistant strains. We evaluate putative sources of K. pneumoniae that are carried by and infect hospital patients. METHODS We conducted a 6-month survey on 2 hematology wards at Addenbrooke's Hospital, Cambridge, United Kingdom, in 2015 to isolate K. pneumoniae from stool, blood, and the environment. We conducted cross-sectional surveys of K. pneumoniae from 29 livestock farms, 97 meat products, the hospital sewer, and 20 municipal wastewater treatment plants in the East of England between 2014 and 2015. Isolates were sequenced and their genomes compared. RESULTS Klebsiella pneumoniae was isolated from stool of 17/149 (11%) patients and 18/922 swabs of their environment, together with 1 bloodstream infection during the study and 4 others over a 24-month period. Each patient carried 1 or more lineages that was unique to them, but 2 broad environmental contamination events and patient-environment transmission were identified. Klebsiella pneumoniae was isolated from cattle, poultry, hospital sewage, and 12/20 wastewater treatment plants. There was low genetic relatedness between isolates from patients/their hospital environment vs isolates from elsewhere. Identical genes encoding cephalosporin resistance were carried by isolates from humans/environment and elsewhere but were carried on different plasmids. CONCLUSION We identified no patient-to-patient transmission and no evidence for livestock as a source of K. pneumoniae infecting humans. However, our findings reaffirm the importance of the hospital environment as a source of K. pneumoniae associated with serious human infection.
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Affiliation(s)
- Catherine Ludden
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, Hinxton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton
| | - Danesh Moradigaravand
- Center for Computational Biology, Institute of Cancer and Genomic Sciences, University of Birmingham, Cambridge
| | - Dorota Jamrozy
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton
| | - Theodore Gouliouris
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge
- Cambridge University Hospitals National Health Service Foundation Trust, Cambridge
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge
| | - Beth Blane
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge
| | - Plamena Naydenova
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge
| | | | - Paul Wood
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, United Kingdom
| | - Nazreen Hadjirin
- Department of Veterinary Medicine, University of Cambridge, United Kingdom
| | - Milorad Radakovic
- Department of Veterinary Medicine, University of Cambridge, United Kingdom
| | - Charles Crawley
- Cambridge University Hospitals National Health Service Foundation Trust, Cambridge
| | - Nicholas M Brown
- Cambridge University Hospitals National Health Service Foundation Trust, Cambridge
- Clinical Microbiology and Public Health Laboratory, Public Health England, Cambridge
| | - Mark Holmes
- Department of Veterinary Medicine, University of Cambridge, United Kingdom
| | - Julian Parkhill
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton
| | - Sharon J Peacock
- Department of Pathogen Molecular Biology, London School of Hygiene & Tropical Medicine, Hinxton
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton
- Department of Medicine, University of Cambridge, Addenbrooke’s Hospital, Cambridge
- Cambridge University Hospitals National Health Service Foundation Trust, Cambridge
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129
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Prophages contribute to genome plasticity of Klebsiella pneumoniae and may involve the chromosomal integration of ARGs in CG258. Genomics 2020; 112:998-1010. [DOI: 10.1016/j.ygeno.2019.06.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2018] [Revised: 04/21/2019] [Accepted: 06/15/2019] [Indexed: 12/31/2022]
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130
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Abd El Ghany M, Fouz N, Hill-Cawthorne GA. Human Movement and Transmission of Antimicrobial-Resistant Bacteria. THE HANDBOOK OF ENVIRONMENTAL CHEMISTRY 2020:311-344. [DOI: 10.1007/698_2020_560] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/02/2023]
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131
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Garcia-Fulgueiras V, Zapata Y, Papa-Ezdra R, Ávila P, Caiata L, Seija V, Rojas Rodriguez AE, Magallanes C, Márquez Villalba C, Vignoli R. First characterization of K. pneumoniae ST11 clinical isolates harboring bla KPC-3 in Latin America. Rev Argent Microbiol 2019; 52:211-216. [PMID: 31874719 DOI: 10.1016/j.ram.2019.10.003] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2019] [Revised: 09/02/2019] [Accepted: 10/25/2019] [Indexed: 12/01/2022] Open
Abstract
Antimicrobial resistance due to carbapenemase production in Enterobacteriaceae clinical isolates is a global threat. Klebsiellapneumoniae harboring the blaKPC gene is one of the major concerns in hospital settings in Latin America. The aim of this study was to characterize the antibiotic resistance mechanisms and to typify four carbapenem-resistant K. pneumoniae clinical isolates from the city of Manizales, Colombia. We identified blaKPC-3 in all four isolates by polymerase chain reaction and subsequent sequencing. The plasmid-mediated quinolone resistance genes qnrB19-like and aac(6')Ib-cr; fosfomycin resistance gene fosA and an insertion sequence IS5-like in mgrB (colistin resistance) were also detected. Sequence types ST11 with capsular type wzi75, and ST258 with wzi154, were characterized. The blaKPC-3 gene was mobilized in a 100-kb IncFIB conjugative plasmid with vagCD toxin-antitoxin system. This work reports multiple resistance genes in blaKPC-producing K. pneumoniae and the first occurrence of ST11 clinical isolates harboring blaKPC-3 in Latin America.
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Affiliation(s)
- Virginia Garcia-Fulgueiras
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Yuliana Zapata
- Grupo de Investigación en Enfermedades Infecciosas, Universidad Católica de Manizales, Caldas, Colombia
| | - Romina Papa-Ezdra
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Pablo Ávila
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Leticia Caiata
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Verónica Seija
- Departamento de Laboratorio Clínico, Área Microbiología, Hospital de Clínicas, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Ana E Rojas Rodriguez
- Grupo de Investigación en Enfermedades Infecciosas, Universidad Católica de Manizales, Caldas, Colombia
| | - Carmen Magallanes
- Cátedra de Microbiología, Instituto de Química Biológica, Facultad de Ciencias y de Química, Universidad de la República, Montevideo, Uruguay
| | - Carolina Márquez Villalba
- Cátedra de Microbiología, Instituto de Química Biológica, Facultad de Ciencias y de Química, Universidad de la República, Montevideo, Uruguay
| | - Rafael Vignoli
- Departamento de Bacteriología y Virología, Instituto de Higiene, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay.
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Hala S, Antony CP, Alshehri M, Althaqafi AO, Alsaedi A, Mufti A, Kaaki M, Alhaj-Hussein BT, Zowawi HM, Al-Amri A, Pain A. First report of Klebsiella quasipneumoniae harboring bla KPC-2 in Saudi Arabia. Antimicrob Resist Infect Control 2019; 8:203. [PMID: 31890159 PMCID: PMC6923860 DOI: 10.1186/s13756-019-0653-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 11/14/2019] [Indexed: 12/20/2022] Open
Abstract
Background Nosocomial infections caused by multi-drug resistant Enterobacteriaceae are a global public health threat that ought to be promptly identified, reported, and addressed accurately. Many carbapenem-resistant Enterobacteriaceae-associated genes have been identified in Saudi Arabia but not the endemic Klebsiella pneumoniae carbapenemases (KPCs), which are encoded by blaKPC-type genes. KPCs are known for their exceptional spreading potential. Methods We collected n = 286 multi-drug resistant (MDR) Klebsiella spp. isolates as part of screening for resistant patterns from a tertiary hospital in Saudi Arabia between 2014 and 2018. Antimicrobial susceptibility testing was carried out using both VITEK II and the broth microdilution of all collected isolates. Detection of resistance-conferring genes was carried out using Illumina whole-genome shotgun sequencing and PacBio SMRT sequencing protocols. Results A Carbapenem-resistant Enterobacteriaceae (CRE) Klebsiella quasipneumoniae subsp. similipneumoniae strain was identified as a novel ST-3510 carrying a blaKPC-2 carbapenemase encoding gene. The isolate, designated as NGKPC-421, was obtained from shotgun Whole Genome Sequencing (WGS) surveillance of 286 MDR Klebsiella spp. clinical isolates. The NGKPC-421 isolate was collected from a septic patient in late 2017 and was initially misidentified as K. pneumoniae. The sequencing and assembly of the NGKPC-421 genome resulted in the identification of a putative ~ 39.4 kb IncX6 plasmid harboring a blaKPC-2 gene, flanked by transposable elements (ISKpn6-blaKPC-2–ISKpn27). Conclusion This is the first identification of a KPC-2-producing CRE in the Gulf region. The impact on this finding is of major concern to the public health in Saudi Arabia, considering that it is the religious epicenter with a continuous mass influx of pilgrims from across the world. Our study strongly highlights the importance of implementing rapid sequencing-based technologies in clinical microbiology for precise taxonomic classification and monitoring of antimicrobial resistance patterns.
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Affiliation(s)
- Sharif Hala
- 1Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,Clinical Microbiology Department, King Abdullah International Medical Research Centre - Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia.,3King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Chakkiath Paul Antony
- 1Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,7Red Sea Research Center, Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia
| | - Mohammed Alshehri
- Clinical Microbiology Department, King Abdullah International Medical Research Centre - Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia.,3King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Abdulhakeem O Althaqafi
- 3King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia.,WHO Collaborating Centre for Infection Prevention and Control, and GCC Center for Infection Control, Riyadh, Saudi Arabia
| | - Asim Alsaedi
- 3King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia.,WHO Collaborating Centre for Infection Prevention and Control, and GCC Center for Infection Control, Riyadh, Saudi Arabia
| | - Areej Mufti
- 3King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Mai Kaaki
- 3King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | | | - Hosam M Zowawi
- Clinical Microbiology Department, King Abdullah International Medical Research Centre - Ministry of National Guard Health Affairs, Jeddah, Saudi Arabia.,3King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia.,WHO Collaborating Centre for Infection Prevention and Control, and GCC Center for Infection Control, Riyadh, Saudi Arabia.,5UQ Centre for Clinical Research, Herston, Queensland, The University of Queensland, Queensland, Australia
| | - Abdulfattah Al-Amri
- 3King Saud bin Abdulaziz University for Health Sciences, Jeddah, Saudi Arabia
| | - Arnab Pain
- 1Pathogen Genomics Laboratory, Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal, Saudi Arabia.,6Global Station for Zoonosis Control, Global Institution for Collaborative Research and Education (GI-CoRE), Hokkaido University, Thuwal, Japan
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133
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Wang F, Wang D, Hou W, Jin Q, Feng J, Zhou D. Evolutionary Diversity of Prophage DNA in Klebsiella pneumoniae Chromosomes. Front Microbiol 2019; 10:2840. [PMID: 31866991 PMCID: PMC6908951 DOI: 10.3389/fmicb.2019.02840] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 11/22/2019] [Indexed: 12/20/2022] Open
Abstract
Mobile gene elements play an important role in the continuous evolution of the prophage DNA of bacteria, promoting the emergence of new gene structures. This study explored the evolution of four strains of Klebsiella pneumoniae harboring prophages, 19051, 721005, 911021, and 675920, and 16 genomes of K. pneumoniae from GenBank. The results revealed a wide range of genetic variation in the prophage DNA inserted into the sap sites of K. pneumoniae chromosomes. From analysis and comparison of the sequences of the 20 prophage DNAs determined from the four strains and the 16 GenBank genomes of K. pneumoniae using high-throughput sequencing and antimicrobial susceptibility tests, we identified a novel transposon, Tn6556. We also identified at least nine large genetic structures with massive genetic acquisitions or losses and five hotspot sites showing a tendency to undergo insertion of gene elements such as IS1T, IS1R, IS26, ISKpn26, ISKpn28, Tn6556, MDR, and In27-related regions as variable regions; however, the only highly conserved core genes were int and umuCD among the 20 prophage DNAs. These findings provide important insights into the evolutionary diversity of bacteriophage DNA contained in K. pneumoniae.
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Affiliation(s)
- Fengling Wang
- Department of Infectious Disease, Taizhou Municipal Hospital, Taizhou University, Taizhou, China
| | - Dongguo Wang
- Department of Clinical Laboratory Medicine, Taizhou Municipal Hospital, Taizhou University, Taizhou, China
| | - Wei Hou
- Department of Infectious Disease, Taizhou Municipal Hospital, Taizhou University, Taizhou, China
| | - Qian Jin
- Department of Infectious Disease, Taizhou Municipal Hospital, Taizhou University, Taizhou, China
| | - Jiao Feng
- Institute of Biomedical Sciences, Shanxi University, Taiyuan, China
| | - Dongsheng Zhou
- State Key Laboratory of Pathogens and Biosecurity, Beijing Institute of Microbiology and Epidemiology, Beijing, China
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134
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Crellen T, Turner P, Pol S, Baker S, Nguyen Thi Nguyen T, Stoesser N, Day NPJ, Turner C, Cooper BS. Transmission dynamics and control of multidrug-resistant Klebsiella pneumoniae in neonates in a developing country. eLife 2019; 8:e50468. [PMID: 31793878 PMCID: PMC6977969 DOI: 10.7554/elife.50468] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 11/26/2019] [Indexed: 12/11/2022] Open
Abstract
Multidrug-resistant Klebsiella pneumoniae is an increasing cause of infant mortality in developing countries. We aimed to develop a quantitative understanding of the drivers of this epidemic by estimating the effects of antibiotics on nosocomial transmission risk, comparing competing hypotheses about mechanisms of spread, and quantifying the impact of potential interventions. Using a sequence of dynamic models, we analysed data from a one-year prospective carriage study in a Cambodian neonatal intensive care unit with hyperendemic third-generation cephalosporin-resistant K. pneumoniae. All widely-used antibiotics except imipenem were associated with an increased daily acquisition risk, with an odds ratio for the most common combination (ampicillin + gentamicin) of 1.96 (95% CrI 1.18, 3.36). Models incorporating genomic data found that colonisation pressure was associated with a higher transmission risk, indicated sequence type heterogeneity in transmissibility, and showed that within-ward transmission was insufficient to maintain endemicity. Simulations indicated that increasing the nurse-patient ratio could be an effective intervention.
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Affiliation(s)
- Thomas Crellen
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical MedicineMahidol UniversityBangkokThailand
- Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Paul Turner
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical MedicineMahidol UniversityBangkokThailand
- Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
- Cambodia-Oxford Medical Research UnitAngkor Hospital for ChildrenSiem ReapCambodia
| | - Sreymom Pol
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical MedicineMahidol UniversityBangkokThailand
- Cambodia-Oxford Medical Research UnitAngkor Hospital for ChildrenSiem ReapCambodia
| | - Stephen Baker
- Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
- Oxford University Clinical Research UnitCentre for Tropical MedicineHo Chi Minh CityViet Nam
| | - To Nguyen Thi Nguyen
- Oxford University Clinical Research UnitCentre for Tropical MedicineHo Chi Minh CityViet Nam
| | - Nicole Stoesser
- Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Nicholas PJ Day
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical MedicineMahidol UniversityBangkokThailand
- Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
| | - Claudia Turner
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical MedicineMahidol UniversityBangkokThailand
- Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
- Cambodia-Oxford Medical Research UnitAngkor Hospital for ChildrenSiem ReapCambodia
| | - Ben S Cooper
- Mahidol-Oxford Tropical Medicine Research Unit, Faculty of Tropical MedicineMahidol UniversityBangkokThailand
- Nuffield Department of MedicineUniversity of OxfordOxfordUnited Kingdom
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135
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Clonal Confinement of a Highly Mobile Resistance Element Driven by Combination Therapy in Rhodococcus equi. mBio 2019; 10:mBio.02260-19. [PMID: 31615959 PMCID: PMC6794481 DOI: 10.1128/mbio.02260-19] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
MDR clades arise upon acquisition of resistance traits, but the determinants of their clonal expansion remain largely undefined. Taking advantage of the unique features of Rhodococcus equi infection control in equine farms, involving the same dual antibiotic treatment since the 1980s (a macrolide and rifampin), this study sheds light into the determinants of multiresistance clonality and the importance of combination therapy in limiting the dissemination of mobile resistance elements. Clinically effective therapeutic alternatives against R. equi foal pneumonia are currently lacking, and the identified macrolide-rifampin MDR clone 2287 has serious implications. Still at early stages of evolution and local spread, R. equi 2287 may disseminate globally, posing a significant threat to the equine industry and, also, public health due to the risk of zoonotic transmission. The characterization of the 2287 clone and its resistance determinants will enable targeted surveillance and control interventions to tackle the emergence of MDR R. equi. Antibiotic use has been linked to changes in the population structure of human pathogens and the clonal expansion of multidrug-resistant (MDR) strains among healthcare- and community-acquired infections. Here we present a compelling example in a veterinary pathogen, Rhodococcus equi, the causative agent of a severe pulmonary infection affecting foals worldwide. We show that the erm(46) gene responsible for emerging macrolide resistance among equine R. equi isolates in the United States is part of a 6.9-kb transposable element, TnRErm46, actively mobilized by an IS481 family transposase. TnRErm46 is carried on an 87-kb conjugative plasmid, pRErm46, transferable between R. equi strains at frequencies up to 10−3. The erm(46) gene becomes stabilized in R. equi by pRErm46’s apparent fitness neutrality and wholesale TnRErm46 transposition onto the host genome. This includes the conjugally exchangeable pVAPA virulence plasmid, enabling the possibility of cotransfer of two essential traits for survival in macrolide-treated foals in a single mating event. Despite its high horizontal transfer potential, phylogenomic analyses show that erm(46) is paradoxically confined to a specific R. equi clone, 2287. R. equi 2287 also carries a unique rpoBS531F mutation conferring high-level resistance to rifampin, systematically administered together with macrolides against rhodococcal pneumonia on equine farms. Our data illustrate that under sustained combination therapy, several independent “founder” genetic events are concurrently required for resistance, limiting not only its emergence but also, crucially, horizontal spread, ultimately determining multiresistance clonality.
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136
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Volozhantsev NV, Shpirt AM, Kislichkina AA, Shashkov AS, Verevkin VV, Fursova NK, Knirel YA. Structure and gene cluster of the capsular polysaccharide of multidrug resistant carbapenemase OXA-48-producing Klebsiella pneumoniae strain KPB536 of the genetic line ST147. Res Microbiol 2019; 171:74-79. [PMID: 31606486 DOI: 10.1016/j.resmic.2019.10.001] [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] [Received: 07/01/2019] [Revised: 09/13/2019] [Accepted: 10/01/2019] [Indexed: 01/09/2023]
Abstract
The Gram-negative opportunistic pathogen Klebsiella pneumoniae is a significant cause of community-acquired and healthcare-associated infections for which multidrug resistance is a concern worldwide. A major virulence determinant of K. pneumoniae is a polysaccharide capsule (CPS) which forms a barrier around the bacterial cell wall, providing protection from environmental pressures and immune responses of eukaryotic organisms. More than 70 chemical capsule structures of serologically typeable K. pneumoniae strains are known. However, there are little data on the CPS structure and cps gene cluster organization of clinical multidrug resistant K. pneumoniae strains. Our investigation of multidrug resistant carbapenemase OXA-48-producing K. pneumoniae strain KPB536 identified a capsular type that was structurally similar to K. pneumoniae K10 but different from any K. pneumoniae CPS reported so far. The content and organization of the cps gene cluster in K. pneumoniae KPB536 also was determined. The catalytic functions of glycosyltransferases coded by the cps_KPB536 gene cluster were assigned by comparison with those responsible for the synthesis of glycoside linkages in the CPSs of K. pneumoniae types K10 and K61.
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Affiliation(s)
- Nikolay V Volozhantsev
- State Research Center for Applied Microbiology and Biotechnology, 142279, Obolensk, Moscow Region, Russia.
| | - Anna M Shpirt
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, 119991, Moscow, Russia.
| | - Angelina A Kislichkina
- State Research Center for Applied Microbiology and Biotechnology, 142279, Obolensk, Moscow Region, Russia.
| | - Alexander S Shashkov
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, 119991, Moscow, Russia.
| | - Vladimir V Verevkin
- State Research Center for Applied Microbiology and Biotechnology, 142279, Obolensk, Moscow Region, Russia.
| | - Nadezhda K Fursova
- State Research Center for Applied Microbiology and Biotechnology, 142279, Obolensk, Moscow Region, Russia.
| | - Yuriy A Knirel
- N.D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, Leninsky Prospekt 47, 119991, Moscow, Russia.
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Song JE, Jeong H, Lim YS, Ha EJ, Jung IY, Jeong W, Choi H, Jeong SJ, Ku NS, Park ES, Yong D, Lee K, Kim JM, Choi JY. An Outbreak of KPC-Producing Klebsiella pneumoniae Linked with an Index Case of Community-Acquired KPC-Producing Isolate: Epidemiological Investigation and Whole Genome Sequencing Analysis. Microb Drug Resist 2019; 25:1475-1483. [PMID: 31334673 DOI: 10.1089/mdr.2018.0475] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Aims: A hospital outbreak of Klebsiella pneumoniae carbapenemase (KPC)-producing Klebsiella pneumoniae (KPN) linked with an index case of community-acquired infection occurred in an urban tertiary care hospital in Seoul, South Korea. Therefore, we performed an outbreak investigation and whole genome sequencing (WGS) analysis to trace the outbreak and investigate the molecular characteristics of the isolates. Results: From October 2014 to January 2015, we identified a cluster of three patients in the neurosurgery ward with sputum cultures positive for carbapenem-resistant KPN. An epidemiological investigation, including pulsed-field gel electrophoresis analysis was performed to trace the origins of this outbreak. The index patient's infection was community acquired. Active surveillance cultures using perirectal swabbing from exposed patients, identified one additional patient with KPC-producing KPN colonization. WGS analyses using PacBio RSII instruments were performed for four linked isolates. WGS revealed a genetic linkage of the four isolates belonging to the same sequence type (ST307). All KPN isolates harbored conjugative resistance plasmids, which has blaKPC-2 carbapenemase genes contained within the Tn4401 "a" isoform and other resistance genes. However, WGS showed only three isolates among four KPC-producing KPN were originated from a common origin. Conclusions: This report demonstrates the challenge that KPC-2-producing KPN with the conjugative resistance plasmid may spread not only in hospitals but also in community, and WGS can help to accurately characterize the outbreak.
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Affiliation(s)
- Je Eun Song
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea.,Department of Internal Medicine, Inje University Ilsan Paik Hospital, Goyang, South Korea
| | - Haeyoung Jeong
- Infectious Disease Research Center, Korea Research Institute of Bioscience and Biotechnology (KRIBB), Daejeon, South Korea
| | - Young Sun Lim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea.,AIDS Research Institute, Yonsei University College of Medicine, Seoul, South Korea
| | - Eun Jin Ha
- Infection Control Unit, Yonsei University College of Medicine, Seoul, South Korea
| | - In Young Jung
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Wooyong Jeong
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Heun Choi
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Su Jin Jeong
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea
| | - Nam Su Ku
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea.,AIDS Research Institute, Yonsei University College of Medicine, Seoul, South Korea
| | - Eun Suk Park
- Infection Control Unit, Yonsei University College of Medicine, Seoul, South Korea
| | - Dongeun Yong
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - Kyungwon Lee
- Department of Laboratory Medicine, Research Institute of Bacterial Resistance, Yonsei University College of Medicine, Seoul, South Korea
| | - June Myung Kim
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea.,AIDS Research Institute, Yonsei University College of Medicine, Seoul, South Korea
| | - Jun Yong Choi
- Department of Internal Medicine, Yonsei University College of Medicine, Seoul, South Korea.,AIDS Research Institute, Yonsei University College of Medicine, Seoul, South Korea
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138
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Next-Generation-Sequencing-Based Hospital Outbreak Investigation Yields Insight into Klebsiella aerogenes Population Structure and Determinants of Carbapenem Resistance and Pathogenicity. Antimicrob Agents Chemother 2019; 63:AAC.02577-18. [PMID: 30910904 DOI: 10.1128/aac.02577-18] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Accepted: 03/21/2019] [Indexed: 02/08/2023] Open
Abstract
Klebsiella aerogenes is a nosocomial pathogen associated with drug resistance and outbreaks in intensive care units. In a 5-month period in 2017, we experienced an increased incidence of cultures for carbapenem-resistant K. aerogenes (CR-KA) from an adult cardiothoracic intensive care unit (CICU) involving 15 patients. Phylogenomic analysis following whole-genome sequencing (WGS) identified the outbreak CR-KA isolates to group together as a tight monoclonal cluster (with no more than six single nucleotide polymorphisms [SNPs]), suggestive of a protracted intraward transmission event. No clonal relationships were identified between the CICU CR-KA strains and additional hospital CR-KA patient isolates from different wards and/or previous years. Carbapenemase-encoding genes and drug-resistant plasmids were absent in the outbreak strains, and carbapenem resistance was attributed to mutations impacting AmpD activity and membrane permeability. The CICU outbreak strains harbored an integrative conjugative element (ICE) which has been associated with pathogenic Klebsiella pneumoniae lineages (ICEKp10). Comparative genomics with global K. aerogenes genomes showed our outbreak strains to group closely with global sequence type 4 (ST4) strains, which, along with ST93, likely represent dominant K. aerogenes lineages associated with human infections. For poorly characterized pathogens, scaling analyses to include sequenced genomes from public databases offer the opportunity to identify emerging trends and dominant clones associated with specific attributes, syndromes, and geographical locations.
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139
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Musicha P, Msefula CL, Mather AE, Chaguza C, Cain AK, Peno C, Kallonen T, Khonga M, Denis B, Gray KJ, Heyderman RS, Thomson NR, Everett DB, Feasey NA. Genomic analysis of Klebsiella pneumoniae isolates from Malawi reveals acquisition of multiple ESBL determinants across diverse lineages. J Antimicrob Chemother 2019; 74:1223-1232. [PMID: 30778540 PMCID: PMC6477993 DOI: 10.1093/jac/dkz032] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 12/27/2018] [Accepted: 01/08/2019] [Indexed: 12/15/2022] Open
Abstract
OBJECTIVES ESBL-producing Klebsiella pneumoniae (KPN) pose a major threat to human health globally. We carried out a WGS study to understand the genetic background of ESBL-producing KPN in Malawi and place them in the context of other global isolates. METHODS We sequenced genomes of 72 invasive and carriage KPN isolates collected from patients admitted to Queen Elizabeth Central Hospital, Blantyre, Malawi. We performed phylogenetic and population structure analyses on these and previously published genomes from Kenya (n = 66) and from outside sub-Saharan Africa (n = 67). We screened for presence of antimicrobial resistance (AMR) genetic determinants and carried out association analyses by genomic sequence cluster, AMR phenotype and time. RESULTS Malawian isolates fit within the global population structure of KPN, clustering into the major lineages of KpI, KpII and KpIII. KpI isolates from Malawi were more related to those from Kenya, with both collections exhibiting more clonality than isolates from the rest of the world. We identified multiple ESBL genes, including blaCTX-M-15, several blaSHV, blaTEM-63 and blaOXA-10, and other AMR genes, across diverse lineages of the KPN isolates from Malawi. No carbapenem resistance genes were detected; however, we detected IncFII and IncFIB plasmids that were similar to the carbapenem resistance-associated plasmid pNDM-mar. CONCLUSIONS There are multiple ESBL genes across diverse KPN lineages in Malawi and plasmids in circulation that are capable of carrying carbapenem resistance. Unless appropriate interventions are rapidly put in place, these may lead to a high burden of locally untreatable infection in vulnerable populations.
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Affiliation(s)
- Patrick Musicha
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Centre for Tropical Medicine and Global Health, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Mahidol-Oxford Tropical Medicine Research Unit, Bangkok, Thailand
| | - Chisomo L Msefula
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- College of Medicine, University of Malawi, Blantyre, Malawi
| | | | - Chrispin Chaguza
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Wellcome Sanger Institute, Hinxton, Cambridge, UK
| | - Amy K Cain
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Liverpool School of Tropical Medicine, Liverpool, UK
| | - Chikondi Peno
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | | | | | - Brigitte Denis
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Katherine J Gray
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
| | - Robert S Heyderman
- Division of Infection and Immunity, University College London, London, UK
| | - Nicholas R Thomson
- Quadram Institute Bioscience, Norwich, UK
- London School of Tropical Medicine, London, UK
| | - Dean B Everett
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- University of Edinburgh, Edinburgh, UK
| | - Nicholas A Feasey
- Malawi-Liverpool-Wellcome Trust Clinical Research Programme, Blantyre, Malawi
- Liverpool School of Tropical Medicine, Liverpool, UK
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140
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Lam MMC, Wyres KL, Wick RR, Judd LM, Fostervold A, Holt KE, Löhr IH. Convergence of virulence and MDR in a single plasmid vector in MDR Klebsiella pneumoniae ST15. J Antimicrob Chemother 2019; 74:1218-1222. [PMID: 30770708 PMCID: PMC6477991 DOI: 10.1093/jac/dkz028] [Citation(s) in RCA: 82] [Impact Index Per Article: 16.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Revised: 12/14/2018] [Accepted: 01/08/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND MDR and hypervirulence (hv) are typically observed in separate Klebsiella pneumoniae populations. However, convergent strains with both properties have been documented and potentially pose a high risk to public health in the form of invasive infections with limited treatment options. OBJECTIVES Our aim was to characterize the genetic determinants of virulence and antimicrobial resistance (AMR) in two ESBL-producing K. pneumoniae isolates belonging to the international MDR clone ST15. METHODS The complete genome sequences of both isolates, including their plasmids, were resolved using Illumina and Oxford Nanopore sequencing. RESULTS Both isolates carried large mosaic plasmids in which AMR and virulence loci have converged within the same vector. These closely related mosaic hv-MDR plasmids include sequences typical of the K. pneumoniae virulence plasmid 1 (KpVP-1; including aerobactin synthesis locus iuc) fused with sequences typical of IncFIIK conjugative AMR plasmids. One hv-MDR plasmid carried three MDR elements encoding the ESBL gene blaCTX-M-15 and seven other AMR genes (blaTEM, aac3'-IIa, dfrA1, satA2, blaSHV, sul1 and aadA1). The other carried remnants of these elements encoding blaTEM and aac3'-IIa, and blaCTX-M-15 was located in a second plasmid in this isolate. The two isolates originated from patients hospitalized in Norway but have epidemiological and genomic links to Romania. CONCLUSIONS The presence of both virulence and AMR determinants on a single vector enables simultaneous transfer in a single event and potentially rapid emergence of hv-MDR K. pneumoniae clones. This highlights the importance of monitoring for such convergence events with stringent genomic surveillance.
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Affiliation(s)
- Margaret M C Lam
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Kelly L Wyres
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Ryan R Wick
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Louise M Judd
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Aasmund Fostervold
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
- Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Kathryn E Holt
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
- London School of Hygiene and Tropical Medicine, London, UK
| | - Iren Høyland Löhr
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
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141
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Muthuirulandi Sethuvel DP, Devanga Ragupathi NK, Bakthavatchalam YD, Vijayakumar S, Varghese R, Shankar C, Jacob JJ, Vasudevan K, Elangovan D, Balaji V. Current strategy for local- to global-level molecular epidemiological characterisation of global antimicrobial resistance surveillance system pathogens. Indian J Med Microbiol 2019; 37:147-162. [PMID: 31745014 DOI: 10.4103/ijmm.ijmm_19_396] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
The prime goal of molecular epidemiology is to identify the origin and evolution of pathogens, which can potentially influence the public health worldwide. Traditional methods provide limited information which is not sufficient for outbreak investigation and studying transmission dynamics. The recent advancement of next-generation sequencing had a major impact on molecular epidemiological studies. Currently, whole-genome sequencing (WGS) has become the gold standard typing method, especially for clinically significant pathogens. Here, we aimed to describe the application of appropriate molecular typing methods for global antimicrobial resistance surveillance system pathogens based on the level of discrimination and epidemiological settings. This shows that sequence-based methods such as multi-locus sequence typing (MLST) are widely used due to cost-effectiveness and database accessibility. However, WGS is the only method of choice for studying Escherichia coli and Shigella spp. WGS is shown to have higher discrimination than other methods in typing Klebsiella pneumoniae, Acinetobacter baumannii and Salmonella spp. due to its changing accessory genome content. For Gram positives such as Streptococcus pneumoniae, WGS would be preferable to understand the evolution of the strains. Similarly, for Staphylococcus aureus, combination of MLST, staphylococcal protein A or SCCmec typing along with WGS could be the choice for epidemiological typing of hospital- and community-acquired strains. This review highlights that combinations of different typing methods should be used to get complete information since no one standalone method is sufficient to study the varying genome diversity.
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Affiliation(s)
| | | | | | - Saranya Vijayakumar
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Rosemol Varghese
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Chaitra Shankar
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Jobin John Jacob
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Karthick Vasudevan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Divyaa Elangovan
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
| | - Veeraraghavan Balaji
- Department of Clinical Microbiology, Christian Medical College, Vellore, Tamil Nadu, India
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142
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Wyres KL, Wick RR, Judd LM, Froumine R, Tokolyi A, Gorrie CL, Lam MMC, Duchêne S, Jenney A, Holt KE. Distinct evolutionary dynamics of horizontal gene transfer in drug resistant and virulent clones of Klebsiella pneumoniae. PLoS Genet 2019; 15:e1008114. [PMID: 30986243 PMCID: PMC6483277 DOI: 10.1371/journal.pgen.1008114] [Citation(s) in RCA: 191] [Impact Index Per Article: 38.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Revised: 04/25/2019] [Accepted: 03/29/2019] [Indexed: 11/19/2022] Open
Abstract
Klebsiella pneumoniae has emerged as an important cause of two distinct public health threats: multi-drug resistant (MDR) healthcare-associated infections and drug susceptible community-acquired invasive infections. These pathotypes are generally associated with two distinct subsets of K. pneumoniae lineages or 'clones' that are distinguished by the presence of acquired resistance genes and several key virulence loci. Genomic evolutionary analyses of the most notorious MDR and invasive community-associated ('hypervirulent') clones indicate differences in terms of chromosomal recombination dynamics and capsule polysaccharide diversity, but it remains unclear if these differences represent generalised trends. Here we leverage a collection of >2200 K. pneumoniae genomes to identify 28 common clones (n ≥ 10 genomes each), and perform the first genomic evolutionary comparison. Eight MDR and 6 hypervirulent clones were identified on the basis of acquired resistance and virulence gene prevalence. Chromosomal recombination, surface polysaccharide locus diversity, pan-genome, plasmid and phage dynamics were characterised and compared. The data showed that MDR clones were highly diverse, with frequent chromosomal recombination generating extensive surface polysaccharide locus diversity. Additional pan-genome diversity was driven by frequent acquisition/loss of both plasmids and phage. In contrast, chromosomal recombination was rare in the hypervirulent clones, which also showed a significant reduction in pan-genome diversity, largely driven by a reduction in plasmid diversity. Hence the data indicate that hypervirulent clones may be subject to some sort of constraint for horizontal gene transfer that does not apply to the MDR clones. Our findings are relevant for understanding the risk of emergence of individual K. pneumoniae strains carrying both virulence and acquired resistance genes, which have been increasingly reported and cause highly virulent infections that are extremely difficult to treat. Specifically, our data indicate that MDR clones pose the greatest risk, because they are more likely to acquire virulence genes than hypervirulent clones are to acquire resistance genes.
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Affiliation(s)
- Kelly L. Wyres
- Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia
| | - Ryan R. Wick
- Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia
| | - Louise M. Judd
- Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia
| | - Roni Froumine
- Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia
| | - Alex Tokolyi
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Claire L. Gorrie
- Department of Infectious Diseases and Microbiology Unit, The Alfred Hospital, Melbourne, Victoria, Australia
| | - Margaret M. C. Lam
- Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia
| | - Sebastián Duchêne
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
| | - Adam Jenney
- Microbiological Diagnostic Unit Public Health Laboratory, Department of Microbiology and Immunology, University of Melbourne, Peter Doherty Institute for Infection and Immunity, Melbourne, Victoria, Australia
| | - Kathryn E. Holt
- Department of Infectious Diseases, Monash University, Melbourne, Victoria, Australia
- Department of Biochemistry and Molecular Biology, Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Parkville, Victoria, Australia
- London School of Hygiene and Tropical Medicine, London, United Kingdom
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143
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Heinz E, Ejaz H, Bartholdson Scott J, Wang N, Gujaran S, Pickard D, Wilksch J, Cao H, Haq IU, Dougan G, Strugnell RA. Resistance mechanisms and population structure of highly drug resistant Klebsiella in Pakistan during the introduction of the carbapenemase NDM-1. Sci Rep 2019; 9:2392. [PMID: 30787414 PMCID: PMC6382945 DOI: 10.1038/s41598-019-38943-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2018] [Accepted: 01/11/2019] [Indexed: 11/25/2022] Open
Abstract
Klebsiella pneumoniae is a major threat to public health with the emergence of isolates resistant to most, if not all, useful antibiotics. We present an in-depth analysis of 178 extended-spectrum beta-lactamase (ESBL)-producing K. pneumoniae collected from patients resident in a region of Pakistan, during the period 2010-2012, when the now globally-distributed carbapenemase bla-NDM-1 was being acquired by Klebsiella. We observed two dominant lineages, but neither the overall resistance profile nor virulence-associated factors, explain their evolutionary success. Phenotypic analysis of resistance shows few differences between the acquisition of resistance genes and the phenotypic resistance profile, including beta-lactam antibiotics that were used to treat ESBL-positive strains. Resistance against these drugs could be explained by inhibitor-resistant beta-lactamase enzymes, carbapenemases or ampC type beta-lactamases, at least one of which was detected in most, but not all relevant strains analysed. Complete genomes for six selected strains are reported, these provide detailed insights into the mobile elements present in these isolates during the initial spread of NDM-1. The unexplained success of some lineages within this pool of highly resistant strains, and the discontinuity between phenotypic resistance and genotype at the macro level, indicate that intrinsic mechanisms contribute to competitive advantage and/or resistance.
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Affiliation(s)
- Eva Heinz
- Parasites and Microbes, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.
| | - Hasan Ejaz
- Department of Clinical Laboratory Sciences, CAMS, Jouf University, Al-Jouf, Saudi Arabia
- Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
- Department of Microbiology, The Children's Hospital & The Institute of Child Health, Lahore, Pakistan
| | | | - Nancy Wang
- Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Shruti Gujaran
- Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Derek Pickard
- Parasites and Microbes, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Jonathan Wilksch
- Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Hanwei Cao
- Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Australia
| | - Ikram-Ul Haq
- Institute of Industrial Biotechnology, GC University, Lahore, Pakistan
| | - Gordon Dougan
- Parasites and Microbes, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
- Department of Medicine, University of Cambridge, Cambridge, UK
| | - Richard A Strugnell
- Department of Microbiology and Immunology, The University of Melbourne, at Peter Doherty Institute for Infection and Immunity, Melbourne, Australia.
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Schweizer C, Bischoff P, Bender J, Kola A, Gastmeier P, Hummel M, Klefisch FR, Schoenrath F, Frühauf A, Pfeifer Y. Plasmid-Mediated Transmission of KPC-2 Carbapenemase in Enterobacteriaceae in Critically Ill Patients. Front Microbiol 2019; 10:276. [PMID: 30837980 PMCID: PMC6390000 DOI: 10.3389/fmicb.2019.00276] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2018] [Accepted: 02/01/2019] [Indexed: 11/25/2022] Open
Abstract
Carbapenem-resistant Enterobacteriaceae (CRE) cause health care-associated infections worldwide, and they are of severe concern due to limited treatment options. We report an outbreak of KPC-2-producing CRE that was caused by horizontal transmission of a promiscuous plasmid across different genera of bacteria and hospitals in Germany. Eleven isolates (8 Citrobacter freundii, 2 Klebsiella oxytoca, and 1 Escherichia coli) were obtained from seven critically ill patients during the six months of the outbreak in 2016. One patient developed a CRE infection while the other six patients were CRE-colonized. Three patients died in the course of the hospital stay. Six of the seven patients carried the same C. freundii clone; one K. oxytoca clone was found in two patients, and one patient carried E. coli and C. freundii. Molecular analysis confirmed the presence of a conjugative, blaKPC-2-carrying 70 kb-IncN plasmid in C. freundii and E. coli and an 80 kb-IncN plasmid in K. oxytoca. All transconjugants harbored either the 70 or 80 kb plasmid with blaKPC-2, embedded within transposon variant Tn4401g. Whole genome sequencing and downstream bioinformatics analyses of all plasmid sequences showed an almost perfect match when compared to a blaKPC-2-carrying plasmid of a large outbreak in another German hospital two years earlier. Differences in plasmid sizes and open reading frames point to the presence of inserted mobile genetic elements. There are few outbreak reports worldwide on the transmission of blaKPC-2-carrying plasmids across different bacterial genera. Our data suggest a regional and supraregional spread of blaKPC-2-carrying IncN-plasmids harboring the Tn4401g isoform in Germany.
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Affiliation(s)
- Christian Schweizer
- Department of Infection Control/Internal Medicine, Paulinenkrankenhaus, Berlin, Germany.,Department of Infection Control, German Heart Center Berlin, Berlin, Germany
| | - Peter Bischoff
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Jennifer Bender
- Robert Koch Institute, FG13 Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Axel Kola
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Petra Gastmeier
- Institute of Hygiene and Environmental Medicine, Charité - Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin and Berlin Institute of Health, Berlin, Germany
| | - Manfred Hummel
- Department of Infection Control/Internal Medicine, Paulinenkrankenhaus, Berlin, Germany
| | - Frank-Rainer Klefisch
- Department of Infection Control/Internal Medicine, Paulinenkrankenhaus, Berlin, Germany
| | - Felix Schoenrath
- Department of Cardiothoracic and Vascular Surgery, German Heart Center Berlin, Berlin, Germany.,Partner Site Berlin, DZHK: German Centre for Cardiovascular Research, Berlin, Germany
| | - Andre Frühauf
- Robert Koch Institute, FG13 Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Yvonne Pfeifer
- Robert Koch Institute, FG13 Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
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145
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Bocanegra-Ibarias P, Garza-González E, Padilla-Orozco M, Mendoza-Olazarán S, Pérez-Alba E, Flores-Treviño S, Garza-Ramos U, Silva-Sánchez J, Camacho-Ortiz A. The successful containment of a hospital outbreak caused by NDM-1-producing Klebsiella pneumoniae ST307 using active surveillance. PLoS One 2019; 14:e0209609. [PMID: 30759100 PMCID: PMC6373926 DOI: 10.1371/journal.pone.0209609] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2018] [Accepted: 12/07/2018] [Indexed: 12/29/2022] Open
Abstract
The worldwide dissemination of high-risk carbapenemase-producing Klebsiella pneumoniae clones has become a major threat to healthcare facilities. This study describes the successful containment of a hospital outbreak caused by NDM-1-producing K. pneumoniae Sequence Type (ST) 307 using active surveillance. The outbreak began when a patient was transferred from a local hospital. After 48 hours in our hospital, a tracheal aspirate was positive for a meropenem resistant and carbapenemase-producing K. pneumoniae. All patients in the medical intensive care unit (ICU) and the neurology wards were subject to contact precautions. The hospital surfaces and devices, healthcare workers, and patients from these wards were screened by cultures. Fecal swabs were placed into broth and PCR for blaKPC, blaOXA-48, blaIMP, blaVIM, and blaNDM, which were performed directly from the broth after 12 hours. PCRs were also performed on DNA extracted from carbapenemase-producing species from subcultured broths. Five and nine days later, two more patients' rectal swabs tested positive. Molecular assays identified K. pneumoniae blaNDM-1 onto a 130-kb conjugative plasmid (IncY, IncFIIs, and IncFIIY), ST307. After the three patients were discharged, monitoring continued, and after three weeks with negative results, rectal swabbing ended. In conclusion, it was possible to contain a hospital outbreak caused by NDM-1-producing K. pneumoniae ST307 through epidemiological and microbiological surveillance. With the methodology used, the detection of NDM-type genes in fecal samples was obtained in approximately 15 hours after obtaining the fecal sample.
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Affiliation(s)
- Paola Bocanegra-Ibarias
- Hospital Universitario Dr. José Eleuterio González, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
| | - Elvira Garza-González
- Hospital Universitario Dr. José Eleuterio González, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
| | - Magaly Padilla-Orozco
- Hospital Universitario Dr. José Eleuterio González, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
| | - Soraya Mendoza-Olazarán
- Hospital Universitario Dr. José Eleuterio González, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
| | - Eduardo Pérez-Alba
- Hospital Universitario Dr. José Eleuterio González, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
| | - Samantha Flores-Treviño
- Hospital Universitario Dr. José Eleuterio González, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
| | - Ulises Garza-Ramos
- Laboratorio de Resistencia Bacteriana; Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico
| | - Jesus Silva-Sánchez
- Laboratorio de Resistencia Bacteriana; Centro de Investigación Sobre Enfermedades Infecciosas, Instituto Nacional de Salud Pública, Cuernavaca, Morelos, Mexico
| | - Adrián Camacho-Ortiz
- Hospital Universitario Dr. José Eleuterio González, Universidad Autónoma de Nuevo León, Monterrey, Nuevo León, Mexico
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146
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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: 121] [Impact Index Per Article: 24.2] [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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147
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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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148
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Liu S, Zhang P, Liu Y, Gao X, Hua J, Li W. Metabolic regulation protects mice against Klebsiella pneumoniae lung infection. Exp Lung Res 2018; 44:302-311. [PMID: 30513234 DOI: 10.1080/01902148.2018.1538396] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
PURPOSE Klebsiella pneumoniae-caused pneumonia is a risk factor for development of lung injury. However, the current clinical isolates of K. pneumoniae are mostly multidrug-resistance and thus must be addressed with new treatments. One ideal approach is to enhance the innate immunity of the infected host through metabolic modulators. MATERIALS AND METHODS We used GC/MS-based metabolomics to profile the metabolomes among Control, Dead and Survival groups. The key metabolites were administrated in mice, and the bacterial loads in lung and survival were measured. The effect of the key metabolites on macrophage phagocytosis was determined by flow cytometry. RESULTS Compared with the mice that compromised from K. pneumoniae lung infection, mice that survived the infection displayed the varied metabolomic profile. The differential analysis of metabolome showed D-Glucose, Glutamine, L-Serine, Myo-inositol, Ethanedioic acid and Lactic acid related to the host surviving a K. pneumoniae lung infection. Further pathway enrichment analysis proposed that valine, leucine and isoleucine biosynthesis involved in outcome of lung infection. The follow-up data showed that exogenous L-Serine, L-Valine and L-Leucine could decline the load of K. pneumoniae in infected lung and increases the mouse survival. More interestingly, L-Serine, L-Valine and L-Leucine also were able to promote macrophage phagocytosis that is the natural way to promote hosts to clear lung pathogens. CONCLUSIONS Our study establishes a novel strategy of identifying metabolic modulator from surviving host and emphasizes the feasibility of employing the metabolic modulator as a therapy for K. pneumoniae lung infection.
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Affiliation(s)
- Sunan Liu
- a Emergency department , Affiliated Union Hospital of Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Pan Zhang
- b Department of Infectious Diseases , Affiliated Union Hospital of Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Yanan Liu
- b Department of Infectious Diseases , Affiliated Union Hospital of Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Xiaoyan Gao
- b Department of Infectious Diseases , Affiliated Union Hospital of Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Juan Hua
- b Department of Infectious Diseases , Affiliated Union Hospital of Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
| | - Wei Li
- b Department of Infectious Diseases , Affiliated Union Hospital of Tongji Medical College, Huazhong University of Science and Technology , Wuhan , Hubei , China
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149
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Pérez-Losada M, Arenas M, Castro-Nallar E. Microbial sequence typing in the genomic era. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2018; 63:346-359. [PMID: 28943406 PMCID: PMC5908768 DOI: 10.1016/j.meegid.2017.09.022] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Revised: 09/18/2017] [Accepted: 09/19/2017] [Indexed: 12/18/2022]
Abstract
Next-generation sequencing (NGS), also known as high-throughput sequencing, is changing the field of microbial genomics research. NGS allows for a more comprehensive analysis of the diversity, structure and composition of microbial genes and genomes compared to the traditional automated Sanger capillary sequencing at a lower cost. NGS strategies have expanded the versatility of standard and widely used typing approaches based on nucleotide variation in several hundred DNA sequences and a few gene fragments (MLST, MLVA, rMLST and cgMLST). NGS can now accommodate variation in thousands or millions of sequences from selected amplicons to full genomes (WGS, NGMLST and HiMLST). To extract signals from high-dimensional NGS data and make valid statistical inferences, novel analytic and statistical techniques are needed. In this review, we describe standard and new approaches for microbial sequence typing at gene and genome levels and guidelines for subsequent analysis, including methods and computational frameworks. We also present several applications of these approaches to some disciplines, namely genotyping, phylogenetics and molecular epidemiology.
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Affiliation(s)
- Marcos Pérez-Losada
- Computational Biology Institute, Milken Institute School of Public Health, George Washington University, Ashburn, VA 20147, USA; CIBIO-InBIO, Centro de Investigação em Biodiversidade e Recursos Genéticos, Universidade do Porto, Campus Agrário de Vairão, Vairão 4485-661, Portugal; Children's National Medical Center, Washington, DC 20010, USA.
| | - Miguel Arenas
- Department of Biochemistry, Genetics and Immunology, University of Vigo, Vigo, Spain
| | - Eduardo Castro-Nallar
- Universidad Andrés Bello, Center for Bioinformatics and Integrative Biology, Facultad de Ciencias Biológicas, Santiago 8370146, Chile
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150
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Ravichandran A, Subramanian P, Manoharan V, Muthu T, Periyannan R, Thangapandi M, Ponnuchamy K, Pandi B, Marimuthu PN. Phyto-mediated synthesis of silver nanoparticles using fucoidan isolated from Spatoglossum asperum and assessment of antibacterial activities. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY. B, BIOLOGY 2018; 185:117-125. [PMID: 29886330 DOI: 10.1016/j.jphotobiol.2018.05.031] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2018] [Revised: 05/24/2018] [Accepted: 05/30/2018] [Indexed: 12/17/2022]
Abstract
The present study was aimed to investigate the antibacterial efficacy of fucoidan mediated silver nanoparticles (Fu-AgNPs) synthesized from Spatoglossum asperum. The synthesized Fu-AgNPs were characterized by UV-visible, Field emission - scanning electron microscope (FE-SEM), Tranmission electron microscope (TEM), X-ray diffraction (XRD), Selected area electron diffraction (SAED) pattern, Energy-dispersive X-ray spectroscopy (EDAX), Fourier transform infrared spectroscopy (FT-IR), Dynamic light scattering (DLS) and Zeta potential analysis. The UV-visible spectrum of Fu-AgNPs exhibited a characteristic surface plasmon resonance (SPR) peak at 440 nm. The electron microscopic results revealed that the nanoparticles were spherical to oval in shape and are found to be 20 to 46 nm. Altogether the X-ray diffraction analysis showed that the Fu-AgNPs were crystalline in nature. The FT-IR spectrum confirmed the existence of CC stretching vibration of aromatic compounds and sulfated groups of fucoidan plays a major role in the synthesis of Fu-AgNPs. The biosynthesized Fu-AgNPs shows potential antibacterial activity against Klebsiella pneumoniae in agar bioassay, disk diffusion, reactive oxygen species, protein leakage and confocal laser scanning microscopy assays. Furthermore, Artemia toxicity assay results showed less mortality (3.3 ± 0.8%) even at higher concentration of Fu-AgNPs. Therefore, Fu-AgNPs can be effectively used as an antibacterial agent in the pharmaceutical fields.
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Affiliation(s)
- Anjali Ravichandran
- Disease Control and Prevention Lab, Department of Animal Health and Management, Science Campus, Alagappa University, Karaikudi 630 003, India
| | - Palanisamy Subramanian
- Disease Control and Prevention Lab, Department of Animal Health and Management, Science Campus, Alagappa University, Karaikudi 630 003, India
| | - Vinosha Manoharan
- Disease Control and Prevention Lab, Department of Animal Health and Management, Science Campus, Alagappa University, Karaikudi 630 003, India
| | - Thenmozhi Muthu
- Disease Control and Prevention Lab, Department of Animal Health and Management, Science Campus, Alagappa University, Karaikudi 630 003, India
| | - Rajasekar Periyannan
- Disease Control and Prevention Lab, Department of Animal Health and Management, Science Campus, Alagappa University, Karaikudi 630 003, India
| | - Marudhupandi Thangapandi
- Biomaterials and Biotechnology in Animal Health Lab, Department of Animal Health and Management, Science Campus, Alagappa University, Karaikudi 630 003, India
| | - Kumar Ponnuchamy
- Food Chemistry and Molecular Cancer Biology Lab, Department of Animal Health and Management, Science Campus, Alagappa University, Karaikudi 630 003, India
| | - Boomi Pandi
- Department of Bioinformatics, Science Campus, Alagappa University, Karaikudi 630 003, India
| | - Prabhu Narayanasamy Marimuthu
- Disease Control and Prevention Lab, Department of Animal Health and Management, Science Campus, Alagappa University, Karaikudi 630 003, India.
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