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Dangor Z, Benson N, Berkley JA, Bielicki J, Bijsma MW, Broad J, Buurman ET, Cross A, Duffy EM, Holt KE, Iroh Tam PY, Jit M, Karampatsas K, Katwere M, Kwatra G, Laxminarayan R, Le Doare K, Mboizi R, Micoli F, Moore CE, Nakabembe E, Naylor NR, O'Brien S, Olwagen C, Reddy D, Rodrigues C, Rosen DA, Sadarangani M, Srikantiah P, Tennant SM, Hasso-Agopsowicz M, Madhi SA. Vaccine value profile for Klebsiella pneumoniae. Vaccine 2024; 42:S125-S141. [PMID: 38503661 DOI: 10.1016/j.vaccine.2024.02.072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2023] [Revised: 02/07/2024] [Accepted: 02/24/2024] [Indexed: 03/21/2024]
Abstract
Klebsiella pneumoniae causes community- and healthcare-associated infections in children and adults. Globally in 2019, an estimated 1.27 million (95% Uncertainty Interval [UI]: 0.91-1.71) and 4.95 million (95% UI: 3.62-6.57) deaths were attributed to and associated with bacterial antimicrobial resistance (AMR), respectively. K. pneumoniae was the second leading pathogen in deaths attributed to AMR resistant bacteria. Furthermore, the rise of antimicrobial resistance in both community- and hospital-acquired infections is a concern for neonates and infants who are at high risk for invasive bacterial disease. There is a limited antibiotic pipeline for new antibiotics to treat multidrug resistant infections, and vaccines targeted against K. pneumoniae are considered to be of priority by the World Health Organization. Vaccination of pregnant women against K. pneumoniae could reduce the risk of invasive K.pneumoniae disease in their young offspring. In addition, vulnerable children, adolescents and adult populations at risk of K. pneumoniae disease with underlying diseases such as immunosuppression from underlying hematologic malignancy, chemotherapy, patients undergoing abdominal and/or urinary surgical procedures, or prolonged intensive care management are also potential target groups for a K. pneumoniae vaccine. A 'Vaccine Value Profile' (VVP) for K.pneumoniae, which contemplates vaccination of pregnant women to protect their babies from birth through to at least three months of age and other high-risk populations, provides a high-level, holistic assessment of the available information to inform the potential public health, economic and societal value of a pipeline of K. pneumoniae vaccines and other preventatives and therapeutics. This VVP was developed by a working group of subject matter experts from academia, non-profit organizations, public-private partnerships, and multi-lateral organizations, and in collaboration with stakeholders from the WHO. All contributors have extensive expertise on various elements of the K.pneumoniae VVP and collectively aimed to identify current research and knowledge gaps. The VVP was developed using only existing and publicly available information.
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Affiliation(s)
- Ziyaad Dangor
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa.
| | - Nicole Benson
- Global Health Division, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - James A Berkley
- KEMRI/Wellcome Trust Research Programme, Kilifi, Kenya; Centre for Tropical Medicine & Global Health, University of Oxford, UK
| | - Julia Bielicki
- Centre for Neonatal and Paediatric Infection, St George's, University of London, UK; Paediatric Research Centre (PRC), University of Basel Children's Hospital, Basel, Switzerland
| | - Merijn W Bijsma
- Amsterdam UMC, University of Amsterdam, Department of Neurology, Amsterdam Neuroscience, Meibergdreef, Amsterdam, the Netherlands; Amsterdam UMC, University of Amsterdam, Department of Pediatrics, Amsterdam Neuroscience, Meibergdreef, Amsterdam, the Netherlands
| | | | - Ed T Buurman
- CARB-X, Boston University, Boston, MA 02215, USA
| | - Alan Cross
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Erin M Duffy
- CARB-X, Boston University, Boston, MA 02215, USA
| | - Kathryn E Holt
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK; Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Victoria 3004, Australia
| | - Pui-Ying Iroh Tam
- Paediatrics and Child Health Research Group, Malawi-Liverpool Wellcome Programme, Blantyre, Malawi
| | - Mark Jit
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | | | - Michael Katwere
- Makerere University-Johns Hopkins University Research Collaboration, Kampala, Uganda
| | - Gaurav Kwatra
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa; Division of Infectious Diseases, Department of Pediatrics, Cincinnati Children's Hospital Medical Center and University of Cincinnati, Cincinnati, OH, USA; Department of Clinical Microbiology, Christian Medical College, Vellore, India
| | | | - Kirsty Le Doare
- Centre for Neonatal and Paediatric Infection, St George's, University of London, UK; UK Health Security Agency, Porton Down, UK; World Health Organization, Geneva, Switzerland
| | - Robert Mboizi
- Department of Infectious Disease Epidemiology, Faculty of Epidemiology and Population Health, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK
| | | | - Catrin E Moore
- Centre for Neonatal and Paediatric Infection, St George's, University of London, UK
| | - Eve Nakabembe
- Department of Obstetrics and Gynaecology, School of Medicine, Makerere University College of Health Sciences, Upper Mulago Hill Road, P.O. Box 7072 Kampala, Uganda
| | - Nichola R Naylor
- UK Health Security Agency, Porton Down, UK; Department of Health Services Research and Policy, London School of Hygiene & Tropical Medicine, London, UK
| | - Seamus O'Brien
- Global Antibiotic Research & Development Partnership (GARDP), Geneva, Switzerland
| | - Courtney Olwagen
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Denasha Reddy
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
| | - Charlene Rodrigues
- Department of Infection Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene & Tropical Medicine, London WC1E 7HT, UK; Dept of Paediatrics, Imperial College Healthcare NHS Trust, London, UK; Pathogen Genomics Programme, UK Health Security Agency, London, UK
| | - David A Rosen
- Department of Pediatrics and Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, USA
| | - Manish Sadarangani
- Vaccine Evaluation Center, BC Children's Hospital Research Institute, Vancouver, BC, Canada; Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Padmini Srikantiah
- Global Health Division, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Sharon M Tennant
- Center for Vaccine Development and Global Health, University of Maryland School of Medicine, Baltimore, MD, USA
| | - Mateusz Hasso-Agopsowicz
- Department of Immunization, Vaccines & Biologicals, World Health Organization, Geneva, Switzerland
| | - Shabir A Madhi
- South Africa Medical Research Council Vaccines and Infectious Diseases Analytics Research Unit, University of the Witwatersrand, Johannesburg, South Africa
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Mohammed R, Nader SM, Hamza DA, Sabry MA. Occurrence of carbapenem-resistant hypervirulent Klebsiella pneumoniae in oysters in Egypt: a significant public health issue. Ann Clin Microbiol Antimicrob 2024; 23:53. [PMID: 38886796 PMCID: PMC11184735 DOI: 10.1186/s12941-024-00711-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 06/02/2024] [Indexed: 06/20/2024] Open
Abstract
BACKGROUND The global dissemination of critical-priority carbapenem-resistant hypervirulent Klebsiella pneumoniae (CR-hvKp) via food sources represents a significant public health concern. Epidemiological data on CR-hvKp in oysters in Egypt is limited. This study aimed to investigate the potential role of oysters sold in Egypt as a source for carbapenem-resistant K. pneumoniae (CRKP), hypervirulent K. pneumoniae (hvKp), and CR-hvKp and assess associated zoonotic risks. METHODS A sample of 330 fresh oysters was randomly purchased from various retail fish markets in Egypt and divided into 33 pools. Bacteriological examination and the identification of Klebsiella pneumoniae were performed. Carbapenem resistance in K. pneumoniae isolates was determined by phenotypic and molecular methods. Additionally, the presence of hypervirulent K. pneumoniae was identified based on virulence gene markers (peg-344, rmpA, rmpA2, iucA, and iroB), followed by a string test. The clustering of CR-hvKp strains was carried out using R with the pheatmap package. RESULTS The overall prevalence of K. pneumoniae was 48.5% (16 out of 33), with 13 isolates displaying carbapenem resistance, one intermediate resistance, and two sensitive. Both carbapenem-resistant K. pneumoniae and carbapenem-intermediate-resistant K. pneumoniae strains exhibited carbapenemase production, predominantly linked to the blaVIM gene (68.8%). HvKp strains were identified at a rate of 62.5% (10/16); notably, peg-344 was the most prevalent gene. Significantly, 10 of the 13 CRKP isolates possessed hypervirulence genes, contributing to the emergence of CR-hvKp. Moreover, cluster analysis revealed the clustering of two CR-hvKp isolates from the same retail fish market. CONCLUSION This study provides the first insight into the emergence of CR-hvKp among oysters in Egypt. It underscores the potential role of oysters as a source for disseminating CR-hvKp within aquatic ecosystems, presenting a possible threat to public health.
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Affiliation(s)
- Rahma Mohammed
- Department of Zoonoses, Faculty of Veterinary Medicine, Cairo University, PO Box 12211, Giza, Egypt
| | - Sara M Nader
- Department of Zoonoses, Faculty of Veterinary Medicine, Cairo University, PO Box 12211, Giza, Egypt
| | - Dalia A Hamza
- Department of Zoonoses, Faculty of Veterinary Medicine, Cairo University, PO Box 12211, Giza, Egypt.
| | - Maha A Sabry
- Department of Zoonoses, Faculty of Veterinary Medicine, Cairo University, PO Box 12211, Giza, Egypt
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Wahl A, Fischer MA, Klaper K, Müller A, Borgmann S, Friesen J, Hunfeld KP, Ilmberger A, Kolbe-Busch S, Kresken M, Lippmann N, Lübbert C, Marschner M, Neumann B, Pfennigwerth N, Probst-Kepper M, Rödel J, Schulze MH, Zautner AE, Werner G, Pfeifer Y. Presence of hypervirulence-associated determinants in Klebsiella pneumoniae from hospitalised patients in Germany. Int J Med Microbiol 2024; 314:151601. [PMID: 38359735 DOI: 10.1016/j.ijmm.2024.151601] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Revised: 12/15/2023] [Accepted: 01/15/2024] [Indexed: 02/17/2024] Open
Abstract
BACKGROUND Klebsiella (K.) pneumoniae is a ubiquitous Gram-negative bacterium and a common coloniser of animals and humans. Today, K. pneumoniae is one of the most persistent nosocomial pathogens worldwide and poses a severe threat/burden to public health by causing urinary tract infections, pneumonia and bloodstream infections. Infections mainly affect immunocompromised individuals and hospitalised patients. In recent years, a new type of K. pneumoniae has emerged associated with community-acquired infections such as pyogenic liver abscess in otherwise healthy individuals and is therefore termed hypervirulent K. pneumoniae (hvKp). The aim of this study was the characterisation of K. pneumoniae isolates with properties of hypervirulence from Germany. METHODS A set of 62 potentially hypervirulent K. pneumoniae isolates from human patients was compiled. Inclusion criteria were the presence of at least one determinant that has been previously associated with hypervirulence: (I) clinical manifestation, (II) a positive string test as a marker for hypermucoviscosity, and (III) presence of virulence associated genes rmpA and/or rmpA2 and/or magA. Phenotypic characterisation of the isolates included antimicrobial resistance testing by broth microdilution. Whole genome sequencing (WGS) was performed using Illumina® MiSeq/NextSeq to investigate the genetic repertoire such as multi-locus sequence types (ST), capsule types (K), further virulence associated genes and resistance genes of the collected isolates. For selected isolates long-read sequencing was applied and plasmid sequences with resistance and virulence determinants were compared. RESULTS WGS analyses confirmed presence of several signature genes for hvKp. Among them, the most prevalent were the siderophore loci iuc and ybt and the capsule regulator genes rmpA and rmpA2. The most dominant ST among the hvKp isolates were ST395 capsule type K2 and ST395 capsule type K5; both have been described previously and were confirmed by our data as multidrug-resistant (MDR) isolates. ST23 capsule type K1 was the second most abundant ST in this study; this ST has been described as commonly associated with hypervirulence. In general, resistance to beta-lactams caused by the production of extended-spectrum beta-lactamases (ESBL) and carbapenemases was observed frequently in our isolates, confirming the threatening rise of MDR-hvKp strains. CONCLUSIONS Our study results show that K. pneumoniae strains that carry several determinants of hypervirulence are present for many years in Germany. The detection of carbapenemase genes and hypervirulence associated genes on the same plasmid is highly problematic and requires intensified screening and molecular surveillance. However, the non-uniform definition of hvKp complicates their detection. Testing for hypermucoviscosity alone is not specific enough to identify hvKp. Thus, we suggest that the classification of hvKp should be applied to isolates that not only fulfil phenotypical criteria (severe clinical manifestations, hypermucoviscosity) but also (I) the presence of at least two virulence loci e.g. iuc and ybt, and (II) the presence of rmpA and/or rmpA2.
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Affiliation(s)
- Anika Wahl
- Robert Koch Institute, Division of Infectious Diseases, Department of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Martin A Fischer
- Robert Koch Institute, Division of Infectious Diseases, Department of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Kathleen Klaper
- Robert Koch Institute, Department of Sexually transmitted bacterial Pathogens (STI) and HIV, Berlin, Germany
| | - Annelie Müller
- Robert Koch Institute, Division of Infectious Diseases, Department of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Stefan Borgmann
- Klinikum Ingolstadt, Department of Infectious Diseases and Infection Control, Ingolstadt, Germany
| | | | - Klaus-Peter Hunfeld
- Institute for Laboratory Medicine, Microbiology & Infection Control, Northwest Medical Centre, Medical Faculty, Goethe University, Frankfurt am Main, Germany
| | | | - Susanne Kolbe-Busch
- Institute of Hygiene, Hospital Epidemiology and Environmental Medicine, Leipzig University Medical Center, Leipzig, Germany; Interdisciplinary Center for Infectious Diseases, Leipzig University Medical Center, Leipzig, Germany
| | - Michael Kresken
- Paul-Ehrlich-Gesellschaft für Infektionstherapie e. V., Cologne, Germany
| | - Norman Lippmann
- Institute for Medical Microbiology and Virology, University Hospital of Leipzig, Leipzig, Germany
| | - Christoph Lübbert
- Interdisciplinary Center for Infectious Diseases, Leipzig University Medical Center, Leipzig, Germany; Division of Infectious Diseases and Tropical Medicine, Department of Medicine I, Leipzig University Medical Center, Leipzig, Germany
| | | | - Bernd Neumann
- Institute of Clinical Microbiology, Infectious Diseases and Infection Control, Paracelsus Medical University, Nuremberg General Hospital, Nuremberg, Germany
| | - Niels Pfennigwerth
- German National Reference Centre for Multidrug-Resistant Gram-Negative Bacteria, Department of Medical Microbiology, Ruhr-University Bochum, Bochum, Germany
| | | | - Jürgen Rödel
- Institute of Medical Microbiology, Jena University Hospital, Friedrich Schiller University, Jena, Germany
| | - Marco H Schulze
- Department for Infection Control and Infectious Diseases, University Medical Center Goettingen, Goettingen, Germany
| | - Andreas E Zautner
- Institute of Medical Microbiology and Hospital Hygiene, Faculty of Medicine, Otto-von-Guericke-University, Magdeburg, Germany; Center for Health and Medical Prevention (CHaMP), Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Guido Werner
- Robert Koch Institute, Division of Infectious Diseases, Department of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany
| | - Yvonne Pfeifer
- Robert Koch Institute, Division of Infectious Diseases, Department of Nosocomial Pathogens and Antibiotic Resistances, Wernigerode, Germany.
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Li K, Yang M, Tian M, Jia L, Wu Y, Du J, Yuan L, Li L, Ma Y. The preventive effects of Lactobacillus casei 03 on Escherichia coli-induced mastitis in vitro and in vivo. J Inflamm (Lond) 2024; 21:5. [PMID: 38395896 PMCID: PMC10893599 DOI: 10.1186/s12950-024-00378-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/12/2024] [Indexed: 02/25/2024] Open
Abstract
BACKGROUND Lactobacillus casei possesses many kinds of bioactivities, such as anti-inflammation and anti-oxidant, and has been applied to treating multiple inflammatory diseases. However, its role in mastitis prevention has remained ambiguous. METHODS This study aimed to examine the mechanisms underlying the preventive effects of L. casei 03 against E. coli- mastitis utilizing bovine mammary epithelial cells (BMECs) and a mouse model. RESULTS In vitro assays revealed pretreatment with L. casei 03 reduced the apoptotic ratio and the mRNA expression levels of IL1β, IL6 and TNFα and suppressed phosphorylation of p65, IκBα, p38, JNK and ERK in the NF-κB signaling pathway and MAPK signaling pathway. Furthermore, in vivo tests indicated that intramammary infusion of L. casei 03 relieved pathological changes, reduced the secretion of IL1β, IL6 and TNFα and MPO activity in the mouse mastitis model. CONCLUSIONS These data suggest that L. casei 03 exerts protective effects against E. coli-induced mastitis in vitro and in vivo and may hold promise as a novel agent for the prevention and treatment of mastitis.
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Affiliation(s)
- Ke Li
- College of Veterinary Medicine, Shandong Agricultural University, 271018, Taian, Shandong, China
- College of Veterinary Medicine, Hebei Agricultural University, 2596 Lekai South Street, 071001, Baoding, Hebei, China
| | - Ming Yang
- College of Veterinary Medicine, Hebei Agricultural University, 2596 Lekai South Street, 071001, Baoding, Hebei, China
| | - Mengyue Tian
- College of Life Science and Food Engineering, Hebei University of Engineering, 056038, Handan, Hebei, China
| | - Li Jia
- College of Veterinary Medicine, Hebei Agricultural University, 2596 Lekai South Street, 071001, Baoding, Hebei, China
| | - Yinghao Wu
- College of Veterinary Medicine, Hebei Agricultural University, 2596 Lekai South Street, 071001, Baoding, Hebei, China
| | - Jinliang Du
- College of Veterinary Medicine, Hebei Agricultural University, 2596 Lekai South Street, 071001, Baoding, Hebei, China
- Key Laboratory of Freshwater Fisheries and Germplasm Resources Utilization, Freshwater Fisheries Research Center, Ministry of Agriculture, Chinese Academy of Fishery Sciences, 214081, Wuxi, China
| | - Lining Yuan
- College of Veterinary Medicine, Hebei Agricultural University, 2596 Lekai South Street, 071001, Baoding, Hebei, China
| | - Lianmin Li
- College of Veterinary Medicine, Hebei Agricultural University, 2596 Lekai South Street, 071001, Baoding, Hebei, China
| | - Yuzhong Ma
- College of Veterinary Medicine, Hebei Agricultural University, 2596 Lekai South Street, 071001, Baoding, Hebei, China.
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Bello OO, Akinpeloye BO, Bello TK, Oluwafemi YD, Osungbemiro BW. Evaluation of the physicochemical properties and bacterial loads of selected rivers in Ondo State, Nigeria. IRANIAN JOURNAL OF MICROBIOLOGY 2023; 15:788-795. [PMID: 38156303 PMCID: PMC10751605 DOI: 10.18502/ijm.v15i6.14159] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/30/2023]
Abstract
Background and Objectives Water is crucial to human existence but may be contaminated with microorganisms, thus making it unfit for consumption. This study aimed to evaluate the physicochemical properties and bacterial loads of selected river waters in Ondo State, Nigeria. Materials and Methods Ten major rivers were sampled between April and August, 2021. The pH, temperature, total alkalinity, colour, turbidity, electrical conductivity, dissolved oxygen, ammonium, aluminium, organic matters, nitrate levels including the microbial loads were determined according to standard procedures. Confirmation of identified isolates was achieved by API 20E and API 20NE. Results The turbidity, colour, conductivity, ammonium, and aluminium ranged from 4.3 to 15.2 NTU, 4 to 20 NTU, 123.5 to 580.2 mgL-1, 0 to 3.5 mgL-1, and 0.05 to 1.7, respectively. Most physicochemical parameters showed no significant differences from the WHO permissible limits for drinking water (p > 0.05). The total viable bacterial count in the rivers ranged from 1.5 × 105 to 6.3 × 105 CFUmL-1, while the total coliform count ranged from 1.3 × 103 to 4.8 × 103 CFUmL-1. The predominant bacteria were Escherichia coli and Pseudomonas aeruginosa. Conclusion This study revealed that the physiochemical properties of the waters were majorly within the WHO permissible standards but with significantly higher bacterial loads.
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Affiliation(s)
- Olorunjuwon O Bello
- Department of Microbiology, Faculty of Science, University of Medical Sciences, Ondo, Ondo State, Nigeria
| | - Bridget O Akinpeloye
- Department of Microbiology, Faculty of Science, University of Medical Sciences, Ondo, Ondo State, Nigeria
| | - Temitope K Bello
- Department of Biological Sciences, Faculty of Basic and Applied Sciences, Elizade University, Ilara-Mokin, Ondo State, Nigeria
| | - Yinka D Oluwafemi
- Department of Microbiology, Faculty of Science, University of Medical Sciences, Ondo, Ondo State, Nigeria
| | - Bamikole W. Osungbemiro
- Department of Chemistry, Faculty of Science, University of Medical Sciences, Ondo, Ondo State, Nigeria
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Mario E, Hamza D, Abdel-Moein K. Hypervirulent Klebsiella pneumoniae among diarrheic farm animals: A serious public health concern. Comp Immunol Microbiol Infect Dis 2023; 102:102077. [PMID: 37844369 DOI: 10.1016/j.cimid.2023.102077] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Revised: 09/30/2023] [Accepted: 10/03/2023] [Indexed: 10/18/2023]
Abstract
Hypervirulent Klebsiella pneumoniae (hvKp) is an emerging pathogen and it has more virulence factors than classical Klebsiella pneumoniae strains. Carbapenem-resistant hvKp (CR-hvKp) is a dangerous bacteria that has both high virulence and antibiotic resistance and poses a global public health problem worldwide. The current study was carried out to investigate the occurrence of hvKp as well as carbapenem-resistant Klebsiella pneumoniae (CRKP) and CR-hvKp among diarrheic farm animals. For this purpose, rectal swabs from 165 farm animals (45 cattle, 66 sheep, and 54 goats) were collected. Samples were processed for the isolation and identification of Klebsiella pneumoniae. Moreover, hvKp was detected using molecular techniques by amplification of biomarker virulence genes (rmpA, rmpA2, iucA, iroB, and peg-344), followed by a string test. On the other hand, all K. pneumoniae isolates were examined for carbapenem resistance by both phenotypic and molecular methods. The phylogenetic analysis of peg-344 sequences was carried out. The overall prevalence rates of K. pneumoniae, hvKp, CRKP, and CR-hvKp were 24.2%, 7.9%, 16.4%, and 6.1% respectively. HvKp and CR-hvKp were detected among all examined farm animal species. On a Molecular basis, all biomarker virulence genes were identified except iroB, but rmpA is the most prevalent one. The phylogenetic analysis of peg-344 sequences obtained from the study points out their genetic relatedness to those circulated among humans. In conclusion, the emergence of hvKp and CR-hvKp among diarrheic farm animals confers a great public health implication and thus, the possible animal reservoirs for such hypervirulent-antimicrobial resistant strains cannot be ruled out.
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Affiliation(s)
- Esiri Mario
- Department of Zoonoses, Faculty of Veterinary Medicine, Cairo University, Egypt
| | - Dalia Hamza
- Department of Zoonoses, Faculty of Veterinary Medicine, Cairo University, Egypt.
| | - Khaled Abdel-Moein
- Department of Zoonoses, Faculty of Veterinary Medicine, Cairo University, Egypt
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Crippa C, Pasquali F, Rodrigues C, De Cesare A, Lucchi A, Gambi L, Manfreda G, Brisse S, Palma F. Genomic features of Klebsiella isolates from artisanal ready-to-eat food production facilities. Sci Rep 2023; 13:10957. [PMID: 37414963 PMCID: PMC10326032 DOI: 10.1038/s41598-023-37821-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Accepted: 06/27/2023] [Indexed: 07/08/2023] Open
Abstract
Increasing reports on K. pneumoniae strains with antimicrobial resistance and virulence traits from food and farm animals are raising concerns about the potential role of Klebsiella spp. as a foodborne pathogen. This study aimed to report and characterize Klebsiella spp. isolates from two artisanal ready-to-eat food (soft cheese and salami) producing facilities, and to track similar genotypes in different ecological niches. Over 1170 samples were collected during the whole production chain of different food batches. The overall Klebsiella prevalence was 6%. Strains were classified into the three Klebsiella species complexes: K. pneumoniae (KpSC, n = 17), K. oxytoca (KoSC, n = 38) and K. planticola (KplaSC, n = 18). Despite high genetic diversity we found in terms of known and new sequence types (STs), core genome phylogeny revealed clonal strains persisting in the same processing setting for over 14 months, isolated from the environment, raw materials and end-products. Strains showed a natural antimicrobial resistance phenotype-genotype. K. pneumoniae strains showed the highest virulence potential, with sequence types ST4242 and ST107 strains carrying yersiniabactin ybt16 and aerobactin iuc3. The latter was detected in all K. pneumoniae from salami and was located on a large conjugative plasmid highly similar (97% identity) to iuc3+ plasmids from human and pig strains circulating in nearby regions of Italy. While identical genotypes may persist along the whole food production process, different genotypes from distinct sources in the same facility shared an iuc3-plasmid. Surveillance in the food chain will be crucial to obtain a more comprehensive picture of the circulation of Klebsiella strains with pathogenic potential.
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Affiliation(s)
- Cecilia Crippa
- Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, Ozzano dell'Emilia, 40064, Bologna, Italy.
| | - Frédérique Pasquali
- Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Carla Rodrigues
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Alessandra De Cesare
- Department of Veterinary Medical Sciences, Alma Mater Studiorum-University of Bologna, Ozzano Dell'Emilia, 40064, Bologna, Italy
| | - Alex Lucchi
- Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Lucia Gambi
- Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Gerardo Manfreda
- Department of Agricultural and Food Sciences, Alma Mater Studiorum-University of Bologna, Ozzano dell'Emilia, 40064, Bologna, Italy
| | - Sylvain Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens, Institut Pasteur, Université Paris Cité, 75015, Paris, France
- Biological Resource Center of Institut Pasteur, Institut Pasteur, Université Paris Cité, 75015, Paris, France
| | - Federica Palma
- Biological Resource Center of Institut Pasteur, Institut Pasteur, Université Paris Cité, 75015, Paris, France
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Martin MJ, Stribling W, Ong AC, Maybank R, Kwak YI, Rosado-Mendez JA, Preston LN, Lane KF, Julius M, Jones AR, Hinkle M, Waterman PE, Lesho EP, Lebreton F, Bennett JW, Mc Gann PT. A panel of diverse Klebsiella pneumoniae clinical isolates for research and development. Microb Genom 2023; 9. [PMID: 37141116 DOI: 10.1099/mgen.0.000967] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/05/2023] Open
Abstract
Klebsiella pneumoniae are a leading cause of healthcare-associated infections worldwide. In particular, strains expressing extended-spectrum β-lactamases (ESBLs) and carbapenemases pose serious treatment challenges, leading the World Health Organization (WHO) to designate ESBL and carbapenem-resistant Enterobacteriaceae as 'critical' threats to human health. Research efforts to combat these pathogens can be supported by accessibility to diverse and clinically relevant isolates for testing novel therapeutics. Here, we describe a panel of 100 diverse K. pneumoniae isolates that are publicly available to assist the research community in this endeavour. Whole-genome sequencing (WGS) was performed on 3878 K. pneumoniae clinical isolates housed at the Multidrug-Resistant Organism Repository and Surveillance Network. The isolates were cultured from 63 facilities in 19 countries between 2001 and 2020. Core-genome multilocus sequence typing and high-resolution single-nucleotide polymorphism-based phylogenetic analyses captured the genetic diversity of the collection and were used to select the final panel of 100 isolates. In addition to known multidrug-resistant (MDR) pandemic lineages, the final panel includes hypervirulent lineages and isolates with specific and diverse resistance genes and virulence biomarkers. A broad range of antibiotic susceptibilities, ranging from pan-sensitive to extensively drug-resistant isolates, are described. The panel collection, and all associated metadata and genome sequences, are available at no additional cost and will be an important resource for the research community and for the design and development of novel antimicrobial agents and diagnostics against this important pathogen.
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Affiliation(s)
- Melissa J Martin
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - William Stribling
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Ana C Ong
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Rosslyn Maybank
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Yoon I Kwak
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Joshua A Rosado-Mendez
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Lan N Preston
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Katharine F Lane
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Michael Julius
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Anthony R Jones
- Department of Virology, Armed Forces Research Institute of Medical Sciences, Bangkok, Thailand
| | - Mary Hinkle
- Infectious Diseases Unit, Rochester General Hospital, Rochester, New York, USA
| | - Paige E Waterman
- Department of Medicine, Uniformed Services University of the Health Sciences, Bethesda, Maryland, USA
| | - Emil P Lesho
- Infectious Diseases Unit, Rochester General Hospital, Rochester, New York, USA
| | - Francois Lebreton
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Jason W Bennett
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
| | - Patrick T Mc Gann
- Multidrug-Resistant Organism Repository and Surveillance Network, Walter Reed Army Institute of Research, Silver Spring, Maryland, USA
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9
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Thompson C, Garcia G, Masi BP, Freitas T, Paz PHC, Leal CV, Otsuki K, Tschoeke D, Salazar V, Soares M, Lopes G, Bacha L, Cosenza C, Vieira VV, Botelho ACN, de Oliveira BCV, de Rezende CE, Teixeira L, Thompson F. Brumadinho dam collapse induces changes in the microbiome and the antibiotic resistance of the Paraopeba River (Minas Gerais, Brazil). THE SCIENCE OF THE TOTAL ENVIRONMENT 2023; 865:161278. [PMID: 36592904 DOI: 10.1016/j.scitotenv.2022.161278] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/14/2022] [Accepted: 12/26/2022] [Indexed: 06/17/2023]
Abstract
The rupture of the Córrego do Feijão dam in Brumadinho (January 25, 2019) caused serious damage to the Paraopeba River and compromised the quality of its waters for human consumption. However, the possible effects of the dam collapse on the river microbiome and its antibiotic resistance profiles are unknown. The present study aims to analyse the possible shifts in microbial diversity and enhancement of antibiotic resistance in the Paraopeba River. To this end, two sampling campaigns (February and May 2019) were performed to obtain water across the entire Paraopeba River (eight sampling locations: Moeda, Brumadinho, Igarapé, Juatuba, Varginha, Angueretá, Retiro Baixo and Três Marias; ~464 km). This sampling scheme enabled determining the effects of the disaster on the river microbiome. Total DNA and microbial isolation were performed with these water samples. The 16S rRNA-based microbiome analyses (n = 24; 2.05 million 16S rRNA reads) showed changes in microbial diversity immediately after the disaster with the presence of metal-indicating bacteria (Acinetobacter, Bacillus, Novosphingobium, and Sediminibacterium). Matrix-assisted laser desorption ionization-time of flight (MALDI-TOF) identification of bacterial isolates (n = 170) also disclosed possible indicators of faecal contamination across the Paraopeba (Cloacibacterium, Bacteroides, Feaecalibacterium, Bifidobacterium, Citrobacter, Enterobacter, Enterococcus and Escherichia). Antibiotic resistance increased significantly to ampicillin, ampicillin/sulbactam, amoxicillin/clavulanate, ceftriaxone, and cefalotin among isolates obtained in May after the disaster. The effects of toxic mud on microbiomes were felt at all points sampled up to Anguereta. The ore mud may have exacerbated the growth of different antibiotic-resistant, metal-resistant, and faecal-indicating bacteria in the Paraopeba River.
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Affiliation(s)
- Cristiane Thompson
- Institute of Biology and SAGE/COPPE, Centro de Gestão Tecnológica-CT2, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.
| | - Gizele Garcia
- Institute of Biology and SAGE/COPPE, Centro de Gestão Tecnológica-CT2, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; State UniversityDarcy Ribeiro (UENF), Centro de Biociências e Biotecnologia, Laboratório de Ciências Ambientais, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Bruno P Masi
- Laboratório de Ecologia Marinha e Oceanografia Pesqueira da Amazônia (LEMOPA), Instituto Socioambiental e dos Recursos Hídricos (ISARH), Universidade Federal Rural da Amazônia (UFRA), Belém, PA 66077-830, Brazil
| | - Thamyres Freitas
- Institute of Biology and SAGE/COPPE, Centro de Gestão Tecnológica-CT2, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Pedro H C Paz
- Institute of Biology and SAGE/COPPE, Centro de Gestão Tecnológica-CT2, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Camille V Leal
- Institute of Biology and SAGE/COPPE, Centro de Gestão Tecnológica-CT2, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Koko Otsuki
- Institute of Biology and SAGE/COPPE, Centro de Gestão Tecnológica-CT2, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Diogo Tschoeke
- Institute of Biology and SAGE/COPPE, Centro de Gestão Tecnológica-CT2, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil; Health Systems Engineering Laboratory, Alberto Luiz Coimbra Institute of Graduate Studies and Engineering Research (COPPE), Federal University of Rio de Janeiro, Rio de Janeiro, Brazil
| | - Vinicius Salazar
- Institute of Biology and SAGE/COPPE, Centro de Gestão Tecnológica-CT2, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Maria Soares
- Institute of Biology and SAGE/COPPE, Centro de Gestão Tecnológica-CT2, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Grasiele Lopes
- Institute of Biology and SAGE/COPPE, Centro de Gestão Tecnológica-CT2, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Leonardo Bacha
- Institute of Biology and SAGE/COPPE, Centro de Gestão Tecnológica-CT2, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Carlos Cosenza
- Institute of Biology and SAGE/COPPE, Centro de Gestão Tecnológica-CT2, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil
| | - Veronica V Vieira
- Interdisciplinary Laboratory of Medical Research, Oswaldo Cruz Institute, Oswaldo Cruz Foundation, Rio de Janeiro, RJ, Brazil
| | - Ana Caroline N Botelho
- Institute of Microbiology Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | | | - Carlos E de Rezende
- State UniversityDarcy Ribeiro (UENF), Centro de Biociências e Biotecnologia, Laboratório de Ciências Ambientais, Campos dos Goytacazes, Rio de Janeiro, Brazil
| | - Lucia Teixeira
- Institute of Microbiology Paulo de Góes, Universidade Federal do Rio de Janeiro, Rio de Janeiro, Brazil
| | - Fabiano Thompson
- Institute of Biology and SAGE/COPPE, Centro de Gestão Tecnológica-CT2, Universidade Federal do Rio de Janeiro (UFRJ), Rio de Janeiro, RJ, Brazil.
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10
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Kaspersen H, Franklin-Alming FV, Hetland MAK, Bernhoff E, Löhr IH, Jiwakanon J, Urdahl AM, Leangapichart T, Sunde M. Highly conserved composite transposon harbouring aerobactin iuc3 in Klebsiella pneumoniae from pigs. Microb Genom 2023; 9:mgen000960. [PMID: 36820818 PMCID: PMC9997749 DOI: 10.1099/mgen.0.000960] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023] Open
Abstract
Klebsiella pneumoniae is an important opportunistic pathogen associated with severe invasive disease in humans. Hypervirulent K. pneumoniae, which are K. pneumoniae with several acquired virulence determinants such as the siderophore aerobactin and others, are more prominent in countries in South and South-East Asia compared to European countries. This Klebsiella pathotype is capable of causing liver abscesses in immunocompetent persons in the community. K. pneumoniae has not been extensively studied in non-human niches. In the present study, K. pneumoniae isolated from caecal samples (n=299) from healthy fattening pigs in Norway were characterized with regard to population structure and virulence determinants. These data were compared to data from a previous study on K. pneumoniae from healthy pigs in Thailand. Lastly, an in-depth plasmid study on K. pneumoniae with aerobactin was performed. Culturing and whole-genome sequencing was applied to detect, confirm and characterize K. pneumoniae isolates. Phylogenetic analysis described the evolutionary relationship and diversity of the isolates, while virulence determinants and sequence types were detected with Kleborate. Long-read sequencing was applied to obtain the complete sequence of virulence plasmids harbouring aerobactin. A total of 48.8 % of the investigated Norwegian pig caecal samples (n=299) were positive for K. pneumoniae. Acquired virulence determinants were detected in 72.6 % of the isolates, the most prominent being aerobactin (69.2 %), all of which were iuc3. In contrast, only 4.6 % of the isolates from Thailand harboured aerobactin. The aerobactin operon was located on potentially conjugative IncFIBK/FIIK plasmids of varying sizes in isolates from both countries. A putative, highly conserved composite transposon with a mean length of 16.2 kb flanked by truncated IS3-family IS407-group insertion sequences was detected on these plasmids, harbouring the aerobactin operon as well as several genes that may confer increased fitness in mammalian hosts. This putative composite transposon was also detected in plasmids harboured by K. pneumoniae from several countries and sources, such as human clinical samples. The high occurrence of K. pneumoniae harbouring aerobactin in Norwegian pigs, taken together with international data, suggest that pigs are a reservoir for K. pneumoniae with iuc3. Truncation of the flanking ISKpn78-element suggest that the putative composite transposon has been permanently integrated into the plasmid, and that it is no longer mobilizable.
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Affiliation(s)
| | | | - Marit A K Hetland
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway.,Department of Biological Sciences, Faculty of Mathematics and Natural Sciences, University of Bergen, Bergen, Norway
| | - Eva Bernhoff
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway
| | - Iren H Löhr
- Department of Medical Microbiology, Stavanger University Hospital, Stavanger, Norway.,Department of Clinical Science, Faculty of Medicine, University of Bergen, Bergen, Norway
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11
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Dereeper A, Gruel G, Pot M, Couvin D, Barbier E, Bastian S, Bambou JC, Gelu-Simeon M, Ferdinand S, Guyomard-Rabenirina S, Passet V, Martino F, Piveteau P, Reynaud Y, Rodrigues C, Roger PM, Roy X, Talarmin A, Tressieres B, Valette M, Brisse S, Breurec S. Limited Transmission of Klebsiella pneumoniae among Humans, Animals, and the Environment in a Caribbean Island, Guadeloupe (French West Indies). Microbiol Spectr 2022; 10:e0124222. [PMID: 36094181 PMCID: PMC9603589 DOI: 10.1128/spectrum.01242-22] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2022] [Accepted: 08/08/2022] [Indexed: 12/30/2022] Open
Abstract
Guadeloupe (French West Indies), a Caribbean island, is an ideal place to study the reservoirs of the Klebsiella pneumoniae species complex (KpSC) and identify the routes of transmission between human and nonhuman sources due to its insularity, small population size, and small area. Here, we report an analysis of 590 biological samples, 546 KpSC isolates, and 331 genome sequences collected between January 2018 and May 2019. The KpSC appears to be common whatever the source. Extended-spectrum-β-lactamase (ESBL)-producing isolates (21.4%) belonged to K. pneumoniae sensu stricto (phylogroup Kp1), and all but one were recovered from the hospital setting. The distribution of species and phylogroups across the different niches was clearly nonrandom, with a distinct separation of Kp1 and Klebsiella variicola (Kp3). The most frequent sequence types (STs) (≥5 isolates) were previously recognized as high-risk multidrug-resistant (MDR) clones, namely, ST17, ST307, ST11, ST147, ST152, and ST45. Only 8 out of the 63 STs (12.7%) associated with human isolates were also found in nonhuman sources. A total of 22 KpSC isolates were defined as hypervirulent: 15 associated with human infections (9.8% of all human isolates), 4 (8.9%) associated with dogs, and 3 (15%) associated with pigs. Most of the human isolates (33.3%) belonged to the globally successful sublineage CG23-I. ST86 was the only clone shared by a human and a nonhuman (dog) source. Our work shows the limited transmission of KpSC isolates between human and nonhuman sources and points to the hospital setting as a cornerstone of the spread of MDR clones and antibiotic resistance genes. IMPORTANCE In this study, we characterized the presence and genomic features of isolates of the Klebsiella pneumoniae species complex (KpSC) from human and nonhuman sources in Guadeloupe (French West Indies) in order to identify the reservoirs and routes of transmission. This is the first study in an island environment, an ideal setting that limits the contribution of external imports. Our data showed the limited transmission of KpSC isolates between the different compartments. In contrast, we identified the hospital setting as the epicenter of antibiotic resistance due to the nosocomial spread of successful multidrug-resistant (MDR) K. pneumoniae clones and antibiotic resistance genes. Ecological barriers and/or limited exposure may restrict spread from the hospital setting to other reservoirs and vice versa. These results highlight the need for control strategies focused on health care centers, using genomic surveillance to limit the spread, particularly of high-risk clones, of this important group of MDR pathogens.
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Affiliation(s)
- Alexis Dereeper
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | - Gaëlle Gruel
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | - Matthieu Pot
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | - David Couvin
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | - Elodie Barbier
- UMR AgroEcologie, INRAE, Bourgogne Franche-Comté University, Dijon, France
| | - Sylvaine Bastian
- Laboratory of Clinical Microbiology, University Hospital Center of Guadeloupe, Pointe-à-Pitre/Les Abymes, France
| | | | - Moana Gelu-Simeon
- Hepato-Gastroenterology Department, University Hospital Center of Guadeloupe, Pointe-à-Pitre/Les Abymes, France
| | - Séverine Ferdinand
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | | | - Virginie Passet
- Institut Pasteur, University Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Frederic Martino
- Intensive Care Department, University Hospital Center of Guadeloupe, Pointe-à-Pitre/Les Abymes, France
| | | | - Yann Reynaud
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | - Carla Rodrigues
- Institut Pasteur, University Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Pierre-Marie Roger
- Infectious Disease Department, University Hospital Center of Guadeloupe, Pointe-à-Pitre/Les Abymes, France
- Faculty of Medecine Hyacinthe Bastaraud, University of the Antilles, Pointe-à-Pitre, France
| | - Xavier Roy
- Veterinary Clinic, Baie-Mahault, Guadeloupe
| | - Antoine Talarmin
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
| | - Benoit Tressieres
- INSERM Center for Clinical Investigation 1424, Pointe-à-Pitre/Les Abymes, France
| | - Marc Valette
- Intensive Care Department, University Hospital Center of Guadeloupe, Pointe-à-Pitre/Les Abymes, France
| | - Sylvain Brisse
- Institut Pasteur, University Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Sébastien Breurec
- Transmission, Reservoir and Diversity of Pathogens Unit, Pasteur Institute of Guadeloupe, Pointe-à-Pitre, France
- Laboratory of Clinical Microbiology, University Hospital Center of Guadeloupe, Pointe-à-Pitre/Les Abymes, France
- Faculty of Medecine Hyacinthe Bastaraud, University of the Antilles, Pointe-à-Pitre, France
- INSERM Center for Clinical Investigation 1424, Pointe-à-Pitre/Les Abymes, France
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12
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First Belgian Report of Ertapenem Resistance in an ST11 Klebsiella Pneumoniae Strain Isolated from a Dog Carrying blaSCO-1 and blaDHA-1 Combined with Permeability Defects. Antibiotics (Basel) 2022; 11:antibiotics11091253. [PMID: 36140031 PMCID: PMC9495147 DOI: 10.3390/antibiotics11091253] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/17/2022] Open
Abstract
Klebsiella pneumoniae of sequence type (ST) 11 is a hyper-epidemic nosocomial clone, which is spreading worldwide among humans and emerging in pets. This is the first report, to the best of our knowledge, of multidrug-resistant (MDR) K. pneumoniae ST11 carrying blaSCO-1 and blaDHA-1, isolated from a four-month-old dog in Belgium. Antimicrobial susceptibility testing (AST) of the isolate, performed via broth microdilution following the European Committee on Antimicrobial Susceptibility Testing (EUCAST) guidelines, revealed resistance to eight different classes of antimicrobials, including carbapenems, in particular ertapenem, third-generation cephalosporins and fluoroquinolones. A hybrid approach, combining long- and short-read sequencing, was employed for in silico plasmid characterization, multi-locus sequence typing (MLST) and the identification and localization of antimicrobial resistance (AMR) and virulence-associated genes. Three plasmids were reconstructed from the whole-genome sequence (WGS) data: the conjugative IncFIB(K), the non-mobilizable IncR and the mobilizable but unconjugative ColRNAI. The IncFIB(K) plasmid carried the blaSCO-1 gene, whereas IncR carried blaDHA-1, both alongside several other antimicrobial resistance genes (ARGs). No virulence genes could be detected. Here, we suggest that the resistance to ertapenem associated with susceptibility to imipenem and meropenem in K. pneumoniae could be related to the presence of blaSCO-1 and blaDHA-1, combined with permeability defects caused by point mutations in an outer membrane porin (OmpK37). The presence of the blaSCO-1 gene on a conjugative IncFIB(K) plasmid is worrisome as it can increase the risk of transmission to humans, to animals and to the environment.
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13
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Smith-Zaitlik T, Shibu P, McCartney AL, Foster G, Hoyles L, Negus D. Extended genomic analyses of the broad-host-range phages vB_KmiM-2Di and vB_KmiM-4Dii reveal slopekviruses have highly conserved genomes. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 36156193 DOI: 10.1099/mic.0.001247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
High levels of antimicrobial resistance among members of the Klebsiella oxytoca complex (KoC) have led to renewed interest in the use of bacteriophage (phage) therapy to tackle infections caused by these bacteria. In this study we characterized two lytic phages, vB_KmiM-2Di and vB_KmiM-4Dii, that were isolated from sewage water against two GES-5-positive Klebsiella michiganensis strains (PS_Koxy2 and PS_Koxy4, respectively). ViPTree analysis showed both phages belonged to the genus Slopekvirus. rpoB gene-based sequence analysis of 108 presumptive K. oxytoca isolates (n=59 clinical, n=49 veterinary) found K. michiganensis to be more prevalent (46 % clinical and 43 % veterinary, respectively) than K. oxytoca (40 % clinical and 6 % veterinary, respectively). Host range analysis against these 108 isolates found both vB_KmiM-2Di and vB_KmiM-4Dii showed broad lytic activity against KoC species. Several hypothetical homing endonuclease genes were encoded within the genomes of both phages, which may contribute to their broad host range. Differences in the tail fibre protein may explain the non-identical host range of the two phages. Pangenome analysis of 24 slopekviruses found that genomes within this genus are highly conserved, with more than 50 % of all predicted coding sequences representing core genes at ≥95 % identity and ≥70 % coverage. Given their broad host ranges, our results suggest vB_KmiM-2Di and vB_KmiM-4Dii represent attractive potential therapeutics. In addition, current recommendations for phage-based pangenome analyses may require revision.
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Affiliation(s)
| | - Preetha Shibu
- Life Sciences, University of Westminster, London, UK.,Present address: Berkshire and Surrey Pathology Services, Frimley Health NHS Trust, Wexham Park Hospital, Slough, UK
| | - Anne L McCartney
- Department of Food and Nutritional Sciences, University of Reading, Reading, UK
| | | | - Lesley Hoyles
- Department of Biosciences, Nottingham Trent University, Nottingham NG1 4FQ, UK
| | - David Negus
- Department of Biosciences, Nottingham Trent University, Nottingham NG1 4FQ, UK
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14
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Sajeev S, Hamza M, Sivaraman GK, Ghatak S, Ojha R, Mendem SK, Murugesan D, Raisen C, Shome BR, Holmes MA. Genomic insights of beta-lactamase producing Klebsiella quasipneumoniae subsp. similipneumoniae belonging to sequence type 1699 from retail market fish, India. Arch Microbiol 2022; 204:454. [PMID: 35781844 DOI: 10.1007/s00203-022-03071-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Revised: 06/07/2022] [Accepted: 06/13/2022] [Indexed: 11/25/2022]
Abstract
Klebsiella quasipneumoniae is a recently described species and often misidentified as Klebsiella pneumoniae. Here, we report the genomic characterization of Klebsiella quasipneumoniae subsp. similipneumoniae (India238 strain) isolated from fish. The annotated genome acknowledged the presence of blaCTX-M-15, blaOKP-B-1, fosA5, oqxAB and virulence genes. The strain with ST1699 and serotypes KL52 and OL103 also harboured insertion sequences (ISs): ISKpn26 and ISEc9. Three complete phage genomes were identified in contigs 1 and 6 of the bacterial genome, enhancing the prospects of genome manipulation. The study highlights the pitfall of conventional microbiological identification methods to distinguish K. pneumoniae and K. quasipneumoniae. This is the first Indian study documenting the incidence of extended-spectrum beta-lactamase (ESBL)-producing K. quasipneumoniae subsp. similipneumoniae from a non-clinical environment, equipped with virulomes and associated mobile genetic elements. Given that fish can act as a potential vector for transmission of antimicrobial resistance genes, our findings have paramount importance on human health.
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Affiliation(s)
- Sudha Sajeev
- Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology, Cochin, Kerala, India
| | - Muneeb Hamza
- Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology, Cochin, Kerala, India
| | - Gopalan Krishnan Sivaraman
- Microbiology, Fermentation and Biotechnology Division, ICAR-Central Institute of Fisheries Technology, Cochin, Kerala, India.
| | - Sandeep Ghatak
- Division of Animal Health, ICAR Research Complex for NEH Region, Umiam, India.
| | - Rakshit Ojha
- Department of Disease Investigation, ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | - Suresh Kumar Mendem
- Department of Disease Investigation, ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | - Devi Murugesan
- Department of Disease Investigation, ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | - Claire Raisen
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
| | - Bibek R Shome
- Department of Disease Investigation, ICAR-National Institute of Veterinary Epidemiology and Disease Informatics, Bengaluru, Karnataka, India
| | - Mark A Holmes
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
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15
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Bello Gonzalez TD, Kant A, Dijkstra Q, Marcato F, van Reenen K, Veldman KT, Brouwer MSM. Changes in Fecal Carriage of Extended-Spectrum β-Lactamase Producing Enterobacterales in Dutch Veal Calves by Clonal Spread of Klebsiella pneumoniae. Front Microbiol 2022; 13:866674. [PMID: 35814663 PMCID: PMC9260047 DOI: 10.3389/fmicb.2022.866674] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 05/31/2022] [Indexed: 01/14/2023] Open
Abstract
This study aimed to characterize the changes in fecal carriage of Extended-Spectrum β-Lactamase (ESBL) producing Enterobacterales (ESBL-PE) in a single Dutch veal calves. During the rearing period at the Dutch veal farm, a decrease in fecal carriage of cefotaxime-resistant Escherichia coli isolates was observed after 2 weeks at the veal farm, while an increase of cefotaxime-resistant Klebsiella pneumoniae isolates was demonstrated. E. coli and K. pneumoniae were isolated from rectal swabs collected from 110 veal calves in week 2, 6, 10, 18, and 24 after their arrival at the farm. ESBL-PE isolates were selectively cultured and identified by MALDI-TOF. ESBL genes were characterized by RT-PCR, PCRs, and amplicon sequencing. A total of 80 E. coli and 174 K. pneumoniae strains were isolated from 104 out of 110 veal calves. The prevalence of ESBL-E. coli decreased from week 2 (61%) to week 6 (7%), while an unexpected increase in ESBL-K. pneumoniae colonization was detected in week 6 (80%). The predominant ESBL genes detected in E. coli isolates were blaCTX-M-15 and the non-ESBL gene blaTEM-1a, while in K. pneumoniae blaCTX-M-14 gene was detected in all isolates. Four cefotaxime-resistant K. pneumoniae isolates were randomly selected and characterized in deep by transformation, PCR-based replicon typing, and whole-genome sequencing (WGS). The clonal relatedness of a subgroup of nine animals carrying K. pneumoniae ESBL genes was investigated by Multi Locus sequence typing (MLST). In four ESBL-K. pneumoniae isolates, blaCTX-M-14 was located on IncFIIK and IncFIINK plasmid replicons and the isolates were multi-drug resistant (MDR). MLST demonstrated a clonal spread of ESBL-K. pneumoniae ST107. To the best of our knowledge, this is the first study to report a change in fecal carriage of ESBL-PE over time in the same veal calf during the rearing period.
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Affiliation(s)
- Teresita d.J. Bello Gonzalez
- Department of Bacteriology, Host-Pathogen Interaction, and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, Netherlands
- *Correspondence: Teresita d.J. Bello Gonzalez,
| | - Arie Kant
- Department of Bacteriology, Host-Pathogen Interaction, and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Quillan Dijkstra
- Department of Bacteriology, Host-Pathogen Interaction, and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Francesca Marcato
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
| | - Kees van Reenen
- Wageningen Livestock Research, Wageningen University and Research, Wageningen, Netherlands
| | - Kees T. Veldman
- Department of Bacteriology, Host-Pathogen Interaction, and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, Netherlands
| | - Michael S. M. Brouwer
- Department of Bacteriology, Host-Pathogen Interaction, and Diagnostics Development, Wageningen Bioveterinary Research, Lelystad, Netherlands
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16
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Complete Genome Sequence of Klebsiella quasipneumoniae MMCC7, Isolated from an Eclectus Parrot (Eclectus roratus). Microbiol Resour Announc 2022; 11:e0017122. [PMID: 35467363 PMCID: PMC9119098 DOI: 10.1128/mra.00171-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Klebsiella quasipneumoniae MMCC7 is a multidrug- and heavy metal-resistant strain isolated from the feces of a pet shop eclectus parrot in Hong Kong. The complete genome, a single chromosome and circular plasmid (5,382,488 bp; G+C content, 57.79%), was determined by hybrid assembly.
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17
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Li SC, Huang JF, Hung YT, Wu HH, Wang JP, Lin JH, Chen ZW, Hsuan SL. In silico capsule locus typing for serovar prediction of Actinobacillus pleuropneumoniae. Microb Genom 2022; 8. [PMID: 35404221 PMCID: PMC9453067 DOI: 10.1099/mgen.0.000780] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
Abstract
Actinobacillus pleuropneumoniae is a causative agent of pleuropneumonia in pigs of all ages. A. pleuropneumoniae is divided into 19 serovars based on capsular polysaccharides (CPSs) and lipopolysaccharides. The serovars of isolates are commonly determined by serological tests and multiplex PCR. This study aimed to develop a genomic approach for in silico A. pleuropneumoniae typing by screening for the presence of the species-specific apxIV gene in whole-genome sequencing (WGS) reads and identifying capsule locus (KL) types in genome assemblies. A database of the A. pleuropneumoniae KL, including CPS synthesis and CPS export genes, was established and optimized for Kaptive. To test the developed genomic approach, WGS reads of 189 A. pleuropneumoniae isolates and those of 66 samples from 14 other bacterial species were analysed. ariba analysis showed that apxIV was detected in all 189 A. pleuropneumoniae samples. These apxIV-positive WGS reads were de novo assembled into genome assemblies and assessed. A total of 105 A. pleuropneumoniae genome assemblies that passed the quality assessment were analysed by Kaptive analysis against the A. pleuropneumoniae KL database. The results showed that 97 assemblies were classified and predicted as 13 serovars, which matched the serovar information obtained from the literature. The six genome assemblies from previously nontypable isolates were typed and predicted as serovars 17 and 18. Notably, one of the two “Actinobacillus porcitonsillarum” samples was apxIV positive, and its genome assembly was typed as KL03 with high identity and predicted as A. pleuropneumoniae serovar 3. Collectively, a genomic approach was established and could accurately determine the KL type of A. pleuropneumoniae isolates using WGS reads. This approach can be used with high-quality genome assemblies for predicting A. pleuropneumoniae serovars and for retrospective analysis.
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Affiliation(s)
- Siou-Cen Li
- Animal Technology Research Center, Agricultural Technology Research Institute, Miaoli, Taiwan, ROC
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan, ROC
| | - Jing-Fang Huang
- Animal Technology Research Center, Agricultural Technology Research Institute, Miaoli, Taiwan, ROC
| | - Yu-Ting Hung
- Animal Technology Research Center, Agricultural Technology Research Institute, Miaoli, Taiwan, ROC
| | - Hsiu-Hui Wu
- Animal Technology Research Center, Agricultural Technology Research Institute, Miaoli, Taiwan, ROC
| | - Jyh-Perng Wang
- Animal Technology Research Center, Agricultural Technology Research Institute, Miaoli, Taiwan, ROC
| | - Jiunn-Horng Lin
- Animal Technology Research Center, Agricultural Technology Research Institute, Miaoli, Taiwan, ROC
| | - Zeng-Weng Chen
- Animal Technology Research Center, Agricultural Technology Research Institute, Miaoli, Taiwan, ROC
| | - Shih-Ling Hsuan
- Graduate Institute of Veterinary Pathobiology, College of Veterinary Medicine, National Chung Hsing University, Taichung, Taiwan, ROC
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18
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Imade EE, Ajiboye TO, Fadiji AE, Onwudiwe DC, Babalola OO. Green synthesis of zinc oxide nanoparticles using plantain peel extracts and the evaluation of their antibacterial activity. SCIENTIFIC AFRICAN 2022. [DOI: 10.1016/j.sciaf.2022.e01152] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
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19
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Thorpe HA, Booton R, Kallonen T, Gibbon MJ, Couto N, Passet V, López-Fernández S, Rodrigues C, Matthews L, Mitchell S, Reeve R, David S, Merla C, Corbella M, Ferrari C, Comandatore F, Marone P, Brisse S, Sassera D, Corander J, Feil EJ. A large-scale genomic snapshot of Klebsiella spp. isolates in Northern Italy reveals limited transmission between clinical and non-clinical settings. Nat Microbiol 2022; 7:2054-2067. [PMID: 36411354 PMCID: PMC9712112 DOI: 10.1038/s41564-022-01263-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2021] [Accepted: 10/10/2022] [Indexed: 11/22/2022]
Abstract
The Klebsiella group, found in humans, livestock, plants, soil, water and wild animals, is genetically and ecologically diverse. Many species are opportunistic pathogens and can harbour diverse classes of antimicrobial resistance genes. Healthcare-associated Klebsiella pneumoniae clones that are non-susceptible to carbapenems can spread rapidly, representing a high public health burden. Here we report an analysis of 3,482 genome sequences representing 15 Klebsiella species sampled over a 17-month period from a wide range of clinical, community, animal and environmental settings in and around the Italian city of Pavia. Northern Italy is a hotspot for hospital-acquired carbapenem non-susceptible Klebsiella and thus a pertinent setting to examine the overlap between isolates in clinical and non-clinical settings. We found no genotypic or phenotypic evidence for non-susceptibility to carbapenems outside the clinical environment. Although we noted occasional transmission between clinical and non-clinical settings, our data point to a limited role of animal and environmental reservoirs in the human acquisition of Klebsiella spp. We also provide a detailed genus-wide view of genomic diversity and population structure, including the identification of new groups.
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Affiliation(s)
- Harry A. Thorpe
- grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Oslo, Norway
| | - Ross Booton
- grid.5337.20000 0004 1936 7603Bristol Veterinary School, University of Bristol, Bristol, UK
| | - Teemu Kallonen
- grid.410552.70000 0004 0628 215XDepartment of Clinical Microbiology, Turku University Hospital, Turku, Finland
| | - Marjorie J. Gibbon
- grid.7340.00000 0001 2162 1699The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK
| | - Natacha Couto
- grid.7340.00000 0001 2162 1699The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK
| | - Virginie Passet
- grid.508487.60000 0004 7885 7602Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Sebastián López-Fernández
- grid.508487.60000 0004 7885 7602Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Carla Rodrigues
- grid.508487.60000 0004 7885 7602Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Louise Matthews
- grid.8756.c0000 0001 2193 314XBoyd Orr Centre for Population and Ecosystem Health, School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Sonia Mitchell
- grid.8756.c0000 0001 2193 314XBoyd Orr Centre for Population and Ecosystem Health, School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Richard Reeve
- grid.8756.c0000 0001 2193 314XBoyd Orr Centre for Population and Ecosystem Health, School of Biodiversity, One Health and Veterinary Medicine, College of Medical, Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Sophia David
- grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
| | - Cristina Merla
- grid.419425.f0000 0004 1760 3027Microbiology and Virology Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Marta Corbella
- grid.419425.f0000 0004 1760 3027Microbiology and Virology Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Carolina Ferrari
- grid.419425.f0000 0004 1760 3027Microbiology and Virology Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Francesco Comandatore
- grid.4708.b0000 0004 1757 2822Romeo ed Enrica Invernizzi Pediatric Research Center, Department of Biomedical and Clinical Sciences Luigi Sacco, Università di Milano, Milan, Italy
| | - Piero Marone
- grid.419425.f0000 0004 1760 3027Microbiology and Virology Unit, Fondazione Istituto di Ricovero e Cura a Carattere Scientifico Policlinico San Matteo, Pavia, Italy
| | - Sylvain Brisse
- grid.508487.60000 0004 7885 7602Institut Pasteur, Université Paris Cité, Biodiversity and Epidemiology of Bacterial Pathogens, Paris, France
| | - Davide Sassera
- grid.8982.b0000 0004 1762 5736Department of Biology and Biotechnology, Università di Pavia, Pavia, Italy
| | - Jukka Corander
- grid.5510.10000 0004 1936 8921Department of Biostatistics, University of Oslo, Oslo, Norway ,grid.10306.340000 0004 0606 5382Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK ,grid.7737.40000 0004 0410 2071Department of Mathematics and Statistics, Helsinki Institute of Information Technology, University of Helsinki, Helsinki, Finland
| | - Edward J. Feil
- grid.7340.00000 0001 2162 1699The Milner Centre for Evolution, Department of Life Sciences, University of Bath, Bath, UK
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