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Eliette AS, Elodie B, Arnaud M, Tiffany R, Aymé S, Pascal P. Idiosyncratic invasion trajectories of human bacterial pathogens facing temperature disturbances in soil microbial communities. Sci Rep 2024; 14:12375. [PMID: 38811807 PMCID: PMC11137084 DOI: 10.1038/s41598-024-63284-5] [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: 02/08/2024] [Accepted: 05/27/2024] [Indexed: 05/31/2024] Open
Abstract
Current knowledge about effects of disturbance on the fate of invaders in complex microbial ecosystems is still in its infancy. In order to investigate this issue, we compared the fate of Klebsiella pneumoniae (Kp) and Listeria monocytogenes (Lm) in soil microcosms. We then used environmental disturbances (freeze-thaw or heat cycles) to compare the fate of both invaders and manipulate soil microbial diversity. Population dynamics of the two pathogens was assessed over 50 days of invasion while microbial diversity was measured at times 0, 20 and 40 days. The outcome of invasion was strain-dependent and the response of the two invaders to disturbance differed. Resistance to Kp invasion was higher under the conditions where resident microbial diversity was the highest while a significant drop of diversity was linked to a higher persistence. In contrast, Lm faced stronger resistance to invasion in heat-treated microcosms where diversity was the lowest. Our results show that diversity is not a universal proxy of resistance to microbial invasion, indicating the need to properly assess other intrinsic properties of the invader, such as its metabolic repertoire, or the array of interactions between the invader and resident communities.
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Affiliation(s)
- Ascensio-Schultz Eliette
- Université de Bourgogne, University Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, 21000, Dijon, France
| | - Barbier Elodie
- Université de Bourgogne, University Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, 21000, Dijon, France
| | - Mounier Arnaud
- Université de Bourgogne, University Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, 21000, Dijon, France
| | - Raynaud Tiffany
- Université de Bourgogne, University Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, 21000, Dijon, France
| | - Spor Aymé
- Université de Bourgogne, University Bourgogne Franche-Comté, INRAE, Institut Agro, Agroécologie, 21000, Dijon, France
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2
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Bobis Camacho J, Nilsson J, Larsson DGJ, Flach CF. Evaluation of culture conditions for sewage-based surveillance of antibiotic resistance in Klebsiella pneumoniae. J Glob Antimicrob Resist 2024; 37:122-128. [PMID: 38552871 DOI: 10.1016/j.jgar.2024.03.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2023] [Revised: 01/24/2024] [Accepted: 03/09/2024] [Indexed: 04/28/2024] Open
Abstract
BACKGROUND Recent studies have shown promise in predicting clinical antibiotic resistance rates from sewage data. Few have focused on Klebsiella pneumoniae, despite its virulence and importance as carrier of antibiotic resistance. Several media have been suggested for the isolation of K. pneumoniae from complex samples. However, comprehensive evaluations of culture protocols for isolation of K. pneumoniae from sewage are lacking. METHODS Here, influent samples from a major Swedish sewage treatment plant were used to evaluate ten culture conditions in parallel: cultivation on Brilliant green containing Inositol-Nitrate-Deoxycholate agar (BIND), Bruce agar, Klebsiella ChromoSelect Selective agar®, MacConkey-Inositol-Carbenicillin, or Simmons Citrate Agar with Inositol (SCAI) incubated at either 37°C or 42°C for 44 h. The culture conditions were compared based on colony counts of presumed K. pneumoniae and identification precision assessed by matrix-assisted laser desorption/ionization time-of-flight mass spectrometry. RESULTS The sensitivity was lowest for BIND, whereas it was similar for the other media irrespective of incubation temperature. For four media, a better precision was observed after incubation at 42°C compared to 37°C, to a large extent explained by a lower frequency of captured Klebsiella oxytoca. SCAI incubated at 42°C showed the highest precision (84.4%). By combining this protocol with subsequent antibiotic resistance screening of collected isolates, low resistance rates in sewage K. pneumoniae were revealed, potentially reflecting the local resistance landscape. CONCLUSION When combined with downstream analyses, SCAI incubated at 42°C could be a valuable culture protocol for sewage-based studies on various aspects of K. pneumoniae epidemiology including antibiotic resistance prevalence.
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Affiliation(s)
- Julián Bobis Camacho
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Johanna Nilsson
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Dan Göran Joakim Larsson
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden
| | - Carl-Fredrik Flach
- Centre for Antibiotic Resistance Research in Gothenburg (CARe), University of Gothenburg, Gothenburg, Sweden; Department of Infectious Diseases, Institute of Biomedicine, University of Gothenburg, Gothenburg, Sweden.
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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:S0264-410X(24)00248-2. [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] [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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Calland JK, Haukka K, Kpordze SW, Brusah A, Corbella M, Merla C, Samuelsen Ø, Feil EJ, Sassera D, Karikari AB, Saba CKS, Thorpe HA, Corander J. Population structure and antimicrobial resistance among Klebsiella isolates sampled from human, animal, and environmental sources in Ghana: a cross-sectional genomic One Health study. THE LANCET. MICROBE 2023; 4:e943-e952. [PMID: 37858320 DOI: 10.1016/s2666-5247(23)00208-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 06/22/2023] [Accepted: 06/26/2023] [Indexed: 10/21/2023]
Abstract
BACKGROUND One Health approaches to address the increasing threat of antimicrobial resistance (AMR) are gaining attention. However, data on the distribution and movement of bacteria and their AMR-associated genes between clinical and non-clinical sources are scarce, especially from low-income and middle-income countries. We aimed to analyse Klebsiella isolates from various sources in Ghana and compare the prevalence of AMR with datasets from two other countries. METHODS We conducted a cross-sectional genomic One Health study. Multiple clinical, environmental, and animal sources were sampled from 78 locations (eg, hospitals, residential areas, and farms) in and around Tamale, Ghana. Clinical samples were collected through routine screening and in cases of suspected infection between March 15 and Sept 15, 2019, and samples from the wider environment were collected during a dedicated sampling effort between the dates of Aug 19, 2018, and Sept 26, 2019. Sampling locations were approximately evenly distributed from the centre of the city and steadily outwards to capture both rural and urban locations. Samples with positive growth for Klebsiella were included. Isolates of Klebsiella were obtained from the samples using Simmons citrate agar medium and characterised by antimicrobial susceptibility testing and whole-genome sequencing. A comparative analysis with Klebsiella population surveys from Pavia, Italy, and Tromsø, Norway, was performed. AMR-associated and virulence genes were detected, and the population distribution of these genes was studied. FINDINGS Of 957 samples collected around Tamale, Ghana, 620 were positive for Klebsiella spp. 573 Klebsiella isolates were successfully sequenced, of which 370 were Klebsiella pneumoniae. Only two hospital isolates were carbapenem-resistant. Extended-spectrum β-lactamase (ESBL) genes were relatively common among the Ghanaian clinical isolates but rare in the environmental samples. Prevalence of ESBL genes in human-hospital disease samples was 64% (14 of 22 isolates) in Ghana and 44% (four of nine isolates) in Italy, and prevalence in human-hospital carriage samples was 7% (eight of 107) in Ghana and 13% (54 of 428) in Italy; the prevalence was higher in human-hospital disease samples than in human-hospital carriage samples in both countries, and prevalence across both samples in both countries was higher than in Norway. Ghanaian isolates showed evidence of high recombination rates (recombination events compared with point mutations [r/m] 9·455) and a considerable accessory gene overlap with isolates from Italy and Norway. INTERPRETATION Although several AMR-associated gene classes were observed relatively frequently in non-clinical sources, ESBL, carbapenemase, and virulence genes were predominantly present only in hospital samples. These results suggest that interventions should be focused on clinical settings to have the greatest effect on the prevalence and dissemination of AMR-associated genes. FUNDING European Research Council (742158), Academy of Finland EuroHPC grant, Trond Mohn Foundation (BATTALION grant), and Wellcome Trust.
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Affiliation(s)
- Jessica K Calland
- Oslo Centre for Biostatistics and Epidemiology, Oslo University Hospital, Oslo, Norway.
| | - Kaisa Haukka
- Department of Microbiology, University of Helsinki, Helsinki, Finland
| | - Stephen W Kpordze
- Department of Biotechnology, University for Development Studies, Tamale, Ghana
| | - Atanyiwoen Brusah
- Department of Biotechnology, University for Development Studies, Tamale, Ghana
| | - Marta Corbella
- Struttura Operativa Complessa di Microbiologia e Virologia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Cristina Merla
- Struttura Operativa Complessa di Microbiologia e Virologia, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Ørjan Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway; Department of Pharmacy, UiT The Arctic University of Norway, Tromsø, Norway
| | - Edward J Feil
- Milner Centre for Evolution, University of Bath, Bath, UK
| | - Davide Sassera
- Department of Biology and Biotechnology, University of Pavia, Pavia, Italy
| | - Akosua B Karikari
- Department of Clinical Microbiology, University for Development Studies, Tamale, Ghana
| | - Courage K S Saba
- Department of Microbiology, Faculty of Biosciences, University for Development Studies, Tamale, Ghana
| | - Harry A Thorpe
- Oslo Centre for Biostatistics and Epidemiology, University of Oslo, Oslo, Norway
| | - Jukka Corander
- Department of Mathematics and Statistics, University of Helsinki, Helsinki, Finland; Oslo Centre for Biostatistics and Epidemiology, University of Oslo, Oslo, Norway; Parasites and Microbes, Wellcome Sanger Institute, Cambridge, UK
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Cornacchia A, Janowicz A, Centorotola G, Saletti MA, Ranieri SC, Ancora M, Ripà P, Cammà C, Pomilio F, Chiaverini A. Multi-approach methods to predict cryptic carbapenem resistance mechanisms in Klebsiella pneumoniae detected in Central Italy. Front Microbiol 2023; 14:1242693. [PMID: 37700864 PMCID: PMC10493390 DOI: 10.3389/fmicb.2023.1242693] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 08/09/2023] [Indexed: 09/14/2023] Open
Abstract
The rapid emergence of carbapenem-resistant Klebsiella pneumoniae (Kp) strains in diverse environmental niches, even outside of the clinical setting, poses a challenge for the detection and the real-time monitoring of novel antimicrobial resistance trends using molecular and whole genome sequencing-based methods. The aim of our study was to understand cryptic resistance determinants responsible for the phenotypic carbapenem resistance observed in strains circulating in Italy by using a combined approach involving whole genome sequencing (WGS) and genome-wide association study (GWAS). In this study, we collected 303 Kp strains from inside and outside clinical settings between 2018-2022 in the Abruzzo region of Italy. The antimicrobial resistance profile of all isolates was assessed using both phenotypic and bioinformatic methods. We identified 11 strains resistant to carbapenems, which did not carry any known genetic determinants explaining their phenotype. The GWAS results showed that incongruent carbapenem-resistant phenotype was associated specifically with strains with two capsular types, KL13 and KL116 including genes involved in the capsule synthesis, encoding proteins involved in the assembly of the capsule biosynthesis apparatus, capsule-specific sugar synthesis, processing and export, polysaccharide pyruvyl transferase, and lipopolysaccharide biosynthesis protein. These preliminary results confirmed the potential of GWAS in identifying genetic variants present in KL13 and KL116 that could be associated with carbapenem resistance traits in Kp. The implementation of advanced methods, such as GWAS with increased antimicrobial resistance surveillance will potentially improve Kp infection treatment and patient outcomes.
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Affiliation(s)
- Alessandra Cornacchia
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Via Campo Boario, Teramo, Italy
| | - Anna Janowicz
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Via Campo Boario, Teramo, Italy
| | - Gabriella Centorotola
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Via Campo Boario, Teramo, Italy
| | - Maria Antonietta Saletti
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Via Campo Boario, Teramo, Italy
| | - Sofia Chiatamone Ranieri
- Operative Unit of Clinical Pathology and Microbiology, Department of Services, ASL of Teramo, Teramo, Italy
| | - Massimo Ancora
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Via Campo Boario, Teramo, Italy
| | - Paola Ripà
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Via Campo Boario, Teramo, Italy
| | - Cesare Cammà
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Via Campo Boario, Teramo, Italy
| | - Francesco Pomilio
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Via Campo Boario, Teramo, Italy
| | - Alexandra Chiaverini
- Istituto Zooprofilattico Sperimentale dell’Abruzzo e del Molise “G. Caporale”, Via Campo Boario, Teramo, Italy
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Mourão J, Ribeiro-Almeida M, Novais C, Magalhães M, Rebelo A, Ribeiro S, Peixe L, Novais Â, Antunes P. From Farm to Fork: Persistence of Clinically Relevant Multidrug-Resistant and Copper-Tolerant Klebsiella pneumoniae Long after Colistin Withdrawal in Poultry Production. Microbiol Spectr 2023; 11:e0138623. [PMID: 37428073 PMCID: PMC10434174 DOI: 10.1128/spectrum.01386-23] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2023] [Accepted: 06/13/2023] [Indexed: 07/11/2023] Open
Abstract
Concerns about colistin-resistant bacteria in animal food-environmental-human ecosystems prompted the poultry sector to implement colistin restrictions and explore alternative trace metals/copper feed supplementation. The impact of these strategies on the selection and persistence of colistin-resistant Klebsiella pneumoniae in the whole poultry production chain needs clarification. We assessed colistin-resistant and copper-tolerant K. pneumoniae occurrence in chickens raised with inorganic and organic copper formulas from 1-day-old chicks to meat (7 farms from 2019 to 2020), after long-term colistin withdrawal (>2 years). Clonal diversity and K. pneumoniae adaptive features were characterized by cultural, molecular, and whole-genome-sequencing (WGS) approaches. Most chicken flocks (75%) carried K. pneumoniae at early and preslaughter stages, with a significant decrease (P < 0.05) in meat batches (17%) and sporadic water/feed contamination. High rates (>50%) of colistin-resistant/mcr-negative K. pneumoniae were observed among fecal samples, independently of feed. Most samples carried multidrug-resistant (90%) and copper-tolerant (81%; silA and pcoD positive and with a MICCuSO4 of ≥16 mM) isolates. WGS revealed accumulation of colistin resistance-associated mutations and F type multireplicon plasmids carrying antibiotic resistance and metal/copper tolerance genes. The K. pneumoniae population was polyclonal, with various lineages dispersed throughout poultry production. ST15-KL19, ST15-KL146, and ST392-KL27 and IncF plasmids were similar to those from global human clinical isolates, suggesting chicken production as a reservoir/source of clinically relevant K. pneumoniae lineages and genes with potential risk to humans through food and/or environmental exposure. Despite the limited mcr spread due to the long-term colistin ban, this action was ineffective in controlling colistin-resistant/mcr-negative K. pneumoniae, regardless of feed. This study provides crucial insights into the persistence of clinically relevant K. pneumoniae in the poultry production chain and highlights the need for continued surveillance and proactive food safety actions within a One Health perspective. IMPORTANCE The spread of bacteria resistant to last-resort antibiotics such as colistin throughout the food chain is a serious concern for public health. The poultry sector has responded by restricting colistin use and exploring alternative trace metals/copper feed supplements. However, it is unclear how and to which extent these changes impact the selection and persistence of clinically relevant Klebsiella pneumoniae throughout the poultry chain. We found a high occurrence of copper-tolerant and colistin-resistant/mcr-negative K. pneumoniae in chicken flocks, regardless of inorganic and organic copper formulas use and a long-term colistin ban. Despite the high K. pneumoniae isolate diversity, the occurrence of identical lineages and plasmids across samples and/or clinical isolates suggests poultry as a potential source of human K. pneumoniae exposure. This study highlights the need for continued surveillance and proactive farm-to-fork actions to mitigate the risks to public health, relevant for stakeholders involved in the food industry and policymakers tasked with regulating food safety.
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Affiliation(s)
- Joana Mourão
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Center for Innovative Biomedicine and Biotechnology (CIBB), University of Coimbra, Coimbra, Portugal
| | - Marisa Ribeiro-Almeida
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
| | - Carla Novais
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Mafalda Magalhães
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
| | - Andreia Rebelo
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- School of Medicine and Biomedical Sciences, University of Porto (ICBAS-UP), Porto, Portugal
- ESS, Polytechnic of Porto, Porto, Portugal
| | - Sofia Ribeiro
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Luísa Peixe
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Ângela Novais
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
| | - Patrícia Antunes
- UCIBIO—Applied Molecular Biosciences Unit, REQUIMTE, Laboratory of Microbiology, Department of Biological Sciences, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Associate Laboratory i4HB—Institute for Health and Bioeconomy, Faculty of Pharmacy, University of Porto, Porto, Portugal
- Faculty of Nutrition and Food Sciences, University of Porto, Porto, Portugal
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7
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Ndlovu T, Kgosietsile L, Motshwarakgole P, Ndlovu SI. Evaluation of Potential Factors Influencing the Dissemination of Multidrug-Resistant Klebsiella pneumoniae and Alternative Treatment Strategies. Trop Med Infect Dis 2023; 8:381. [PMID: 37624319 PMCID: PMC10459473 DOI: 10.3390/tropicalmed8080381] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2023] [Revised: 07/07/2023] [Accepted: 07/10/2023] [Indexed: 08/26/2023] Open
Abstract
The increasing reports of multidrug-resistant Klebsiella pneumoniae have emerged as a public health concern, raising questions about the potential routes for the evolution and dissemination of the pathogenic K. pneumoniae into environmental reservoirs. Potential drivers of the increased incidence of antimicrobial-resistant environmental K. pneumoniae include the eminent global climatic variations as a direct or indirect effect of human activities. The ability of microorganisms to adapt and grow at an exponential rate facilitates the distribution of environmental strains with acquired resistant mutations into water systems, vegetation, and soil which are major intersection points with animals and humans. The bacterial pathogen, K. pneumoniae, is one of the critical-priority pathogens listed by the World Health Organization, mostly associated with hospital-acquired infections. However, the increasing prevalence of pathogenic environmental strains with similar characteristics to clinical-antibiotic-resistant K. pneumoniae isolates is concerning. Considering the eminent impact of global climatic variations in the spread and dissemination of multidrug-resistant bacteria, in this review, we closely assess factors influencing the dissemination of this pathogen resulting in increased interaction with the environment, human beings, and animals. We also look at the recent developments in rapid detection techniques as part of the response measures to improve surveillance and preparedness for potential outbreaks. Furthermore, we discuss alternative treatment strategies that include secondary metabolites such as biosurfactants and plant extracts with high antimicrobial properties.
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Affiliation(s)
- Thando Ndlovu
- Department of Biological Sciences, Faculty of Science, University of Botswana, Private Bag UB, Gaborone 0022, Botswana; (L.K.); (P.M.)
| | - Lebang Kgosietsile
- Department of Biological Sciences, Faculty of Science, University of Botswana, Private Bag UB, Gaborone 0022, Botswana; (L.K.); (P.M.)
| | - Pako Motshwarakgole
- Department of Biological Sciences, Faculty of Science, University of Botswana, Private Bag UB, Gaborone 0022, Botswana; (L.K.); (P.M.)
| | - Sizwe I. Ndlovu
- Department of Biotechnology and Food Technology, Doornfontein Campus, University of Johannesburg, Johannesburg 2028, South Africa;
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8
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Santibañez-Bedolla KE, Orozco-Uriarte MJ, Alvarez-Canales JA, Macias AE, Amador-Medina LF. Oral colonization by gram-negative bacilli in patients with hematologic malignancies and solid tumors compared with healthy controls. BMC Oral Health 2023; 23:465. [PMID: 37422668 PMCID: PMC10329337 DOI: 10.1186/s12903-023-03172-y] [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: 03/22/2023] [Accepted: 06/24/2023] [Indexed: 07/10/2023] Open
Abstract
BACKGROUND Colonization of the oropharynx with gram-negative bacilli (GNB) is considered a negative prognostic factor in immunocompromised individuals. Hemato-oncologic patients represent a high-risk group due to their immunodeficiencies and associated treatments. This study aimed to determine the rates of oral colonization by GNB, associated factors, and clinical outcomes in patients with hematologic malignancies and solid tumors compared with healthy subjects. METHODS We conducted a comparative study of hemato-oncologic patients and healthy subjects from August to October 2022. Swabs were taken from the oral cavity; specimens with GNB were identified and tested for antimicrobial susceptibility. RESULTS We included 206 participants (103 hemato-oncologic patients and 103 healthy subjects). Hemato-oncologic patients had higher rates of oral colonization by GNB (34% vs. 17%, P = 0.007) and GNB resistant to third-generation cephalosporins (11.6% vs. 0%, P < 0.001) compared to healthy subjects. Klebsiella spp. was the predominant genus in both groups. The factor associated with oral colonization by GNB was a Charlson index ≥ 3, while ≥ 3 dental visits per year were a protective factor. Regarding colonization by resistant GNB in oncology patients, antibiotic therapy and a Charlson index ≥ 5 were identified as associated factors, while better physical functionality (ECOG ≤ 2) was associated with less colonization. Hemato-oncologic patients colonized with GNB had more 30-day infectious complications (30.5% vs. 2.9%, P = 0.0001) than non-colonized patients. CONCLUSION Oral colonization by GNB and resistant GNB are prevalent in cancer patients, especially those with higher scores on the severity scales. Infectious complications occurred more frequently in colonized patients. There is a knowledge gap about dental hygiene practices in hemato-oncologic patients colonized by GNB. Our results suggest that patients' hygienic-dietary habits, especially frequent dental visits, are a protective factor against colonization.
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Affiliation(s)
- Karla E. Santibañez-Bedolla
- Bajio Regional High Specialty Hospital, San Carlos La Roncha C.P. 37544, Leon Guanajuato, Mexico
- Department of Medicine, University of Guanajuato, San Carlos La Roncha C.P. 37660, Leon Guanajuato, Mexico
| | - Maria J. Orozco-Uriarte
- Department of Medicine, University of Guanajuato, San Carlos La Roncha C.P. 37660, Leon Guanajuato, Mexico
| | - Jose A. Alvarez-Canales
- Bajio Regional High Specialty Hospital, San Carlos La Roncha C.P. 37544, Leon Guanajuato, Mexico
- Department of Medicine, University of Guanajuato, San Carlos La Roncha C.P. 37660, Leon Guanajuato, Mexico
| | - Alejandro E. Macias
- Department of Medicine, University of Guanajuato, San Carlos La Roncha C.P. 37660, Leon Guanajuato, Mexico
| | - Lauro F. Amador-Medina
- Bajio Regional High Specialty Hospital, San Carlos La Roncha C.P. 37544, Leon Guanajuato, Mexico
- Department of Medicine, University of Guanajuato, San Carlos La Roncha C.P. 37660, Leon Guanajuato, Mexico
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9
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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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10
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Janecko N, Zamudio R, Palau R, Bloomfield SJ, Mather AE. Repeated cross-sectional study identifies differing risk factors associated with microbial contamination in common food products in the United Kingdom. Food Microbiol 2023; 111:104196. [PMID: 36681400 DOI: 10.1016/j.fm.2022.104196] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 11/01/2022] [Accepted: 11/26/2022] [Indexed: 11/30/2022]
Abstract
All foods carry microbes, many of which are harmless, but foods can also carry pathogens and/or microbial indicators of contamination. Limited information exists on the co-occurrence of microbes of food safety concern and the factors associated with their presence. Here, a population-based repeated cross-sectional design was used to determine the prevalence and co-occurrence of Escherichia coli, Klebsiella spp., Salmonella spp. and Vibrio spp. in key food commodities - chicken, pork, prawns, salmon and leafy greens. Prevalence in 1,369 food samples for these four target bacterial genera/species varied, while 25.6% of all samples had at least two of the target bacteria and eight different combinations of bacteria were observed as co-occurrence profiles in raw prawns. Imported frozen chicken was 6.4 times more likely to contain Salmonella than domestic chicken, and imported salmon was 5.5 times more likely to be contaminated with E. coli. Seasonality was significantly associated with E. coli and Klebsiella spp. contamination in leafy greens, with higher detection in summer and autumn. Moreover, the odds of Klebsiella spp. contamination were higher in summer in chicken and pork samples. These results provide insight on the bacterial species present on foods at retail, and identify factors associated with the presence of individual bacteria, which are highly relevant for food safety risk assessments and the design of surveillance programmes.
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Affiliation(s)
- Nicol Janecko
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, United Kingdom
| | - Roxana Zamudio
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, United Kingdom
| | - Raphaëlle Palau
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, United Kingdom
| | - Samuel J Bloomfield
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, United Kingdom
| | - Alison E Mather
- Quadram Institute Bioscience, Norwich Research Park, Norwich NR4 7UQ, United Kingdom; University of East Anglia, Norwich NR4 7TJ, United Kingdom.
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11
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Saddam S, Khan M, Jamal M, Rehman SU, Slama P, Horky P. Multidrug resistant Klebsiella Pneumoniae reservoir and their capsular resistance genes in cow farms of district Peshawar, Pakistan. PLoS One 2023; 18:e0282245. [PMID: 36848367 PMCID: PMC9970052 DOI: 10.1371/journal.pone.0282245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2022] [Accepted: 02/10/2023] [Indexed: 03/01/2023] Open
Abstract
Klebsiella pneumoniae is a major zoonotic pathogen that causes a variety of severe illnesses as well as mastitis. The distribution of mastitis-causing K. Pneumoniae and its virulence factors vary by country and geographical location. The present study aimed to find out the occurrence of Multidrug-resistant (MDR) K. Pneumoniae and their capsular resistance genes which were undocumented previously in cow farms of district Peshawar, Pakistan. A total of 700 milk samples from symptomatic mastitic cows were screened for MDR K. Pneumoniae. Furthermore, the characterization of capsular resistance genes was done by molecular techniques. Among these samples, K. pneumoniae was found 180/700 (25.7%), while MDR K. pneumoniae was found 80/180 (44.4%). The antibiogram analysis revealed high resistance to Vancomycin (95%) while highly sensitive to Ceftazidime (80%). The distribution of capsular genes shows the most common serotype K2 gene 39/80 (48.7%), followed by serotype K1 gene 34/80 (42.5%), serotype K5 17/80 (21.2%), and serotype K54 13/80 (16.2), respectively. Moreover, the co-occurrence of serotypes K1+K2 was found at 11.25%, KI+K5 was 05%, K1+K54 was 3.75%, and K2+K5 was 7.5%, respectively. A statistically significant association (p ≤ 0.05) was found between predicted and discovered K. pneumoniae values. In conclusion, the presence of MDR K. pneumoniae in combination with capsular genes may be a possible threat to dairy farm animals and humans in Peshawar, Pakistan. It may give us special attention to follow up on hygienic practices in livestock management.
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Affiliation(s)
- Saddam Saddam
- Department of Microbiology, Abdul Wali Khan University Mardan, Mardan, Pakistan
| | - Muddasir Khan
- Centre of Biotechnology and Microbiology, University of Peshawar, Peshawar, Pakistan
| | - Muhsin Jamal
- Department of Microbiology, Abdul Wali Khan University Mardan, Mardan, Pakistan
- * E-mail:
| | - Sadeeq Ur Rehman
- College of Veterinary Sciences and Animal Husbandry, Abdul Wali Khan University, Mardan, Pakistan
| | - Petr Slama
- Department of Animal Morphology, Physiology and Genetics, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
| | - Pavel Horky
- Department of Animal Nutrition and Forage Production, Faculty of AgriSciences, Mendel University in Brno, Brno, Czech Republic
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12
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Emamjomeh M, Mohd Hashim A, Abdul-Mutalib NA, Khairil Mokhtar NF, Mustapha NA, Maeda T, Amin-Nordin S. Profiling bacterial communities and foodborne pathogens on food-associated surface following contact with raw beef, chicken and pork using 16S amplicon metagenomics. Food Control 2023. [DOI: 10.1016/j.foodcont.2023.109698] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/23/2023]
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13
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Draft Genomic Sequence for Klebsiella pneumoniae 060517CS3-g, a Bacterium Harboring Multidrug Resistance Genes, Isolated from Retail Ground Chicken Meat. Microbiol Resour Announc 2023; 12:e0094922. [PMID: 36475878 PMCID: PMC9872595 DOI: 10.1128/mra.00949-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Klebsiella pneumoniae is an important foodborne pathogen that can cause human infections. Here, we report the draft genomic sequence for K. pneumoniae 060517CS3-g, isolated from retail ground chicken meat, which has several antibiotic resistance genes, multiple plasmids, and genes that may result in its hypervirulence based on the sequence data.
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14
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Zhang F, Meng Y, Xu L, Tian Y, Lu H, Xie J, Ma R, Li M, Li B. KbvR mutant of Klebsiella pneumoniae affects the synthesis of type 1 fimbriae and provides protection to mice as a live attenuated vaccine. Vet Res 2022; 53:97. [DOI: 10.1186/s13567-022-01116-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 08/30/2022] [Indexed: 11/28/2022] Open
Abstract
AbstractKlebsiella pneumoniae is a leading cause of severe infections in humans and animals, and the emergence of multidrug-resistant strains highlights the need to develop effective vaccines for preventing such infections. Live attenuated vaccines are attractive vaccine candidates available in the veterinary field. We recently characterized that the K. pneumoniae kbvR (Klebsiella biofilm and virulence regulator) mutant was a highly attenuated strain in the mice model. In the present study, the characterization, safety, and protective efficacy of ΔkbvR strain as a live attenuated vaccine were evaluated. The synthesis and activity of type 1 fimbriae were increased in the ΔkbvR strain. All mice inoculated by the subcutaneous route with 105, 106, and 107 colony-forming units (CFU) doses of the ΔkbvR strain survived. Subcutaneous immunization with two doses of 105 or 107 CFU ΔkbvR elicited a robust humoral immune response, and provided protection against the following K. pneumoniae intraperitoneal infection. The antisera of mice immunized with 105 CFU dose improved the opsonophagocytic ability and complement-mediated lysis not only to the same serotype strain but also to the different serotype strain. The passive transfer of antisera from 105 CFU dose-immunized mice provided protection against K. pneumoniae infection. Overall, our results suggest the great potential of the ΔkbvR strain as a novel vaccine candidate against K. pneumoniae infections in herds or humans.
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15
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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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16
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Sydow K, Eger E, Schwabe M, Heiden SE, Bohnert JA, Franzenburg S, Jurischka C, Schierack P, Schaufler K. Geno- and Phenotypic Characteristics of a Klebsiella pneumoniae ST20 Isolate with Unusual Colony Morphology. Microorganisms 2022; 10:microorganisms10102063. [PMID: 36296341 PMCID: PMC9606995 DOI: 10.3390/microorganisms10102063] [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: 09/15/2022] [Revised: 10/10/2022] [Accepted: 10/16/2022] [Indexed: 11/16/2022] Open
Abstract
Klebsiella pneumoniae is a common member of the intestinal flora of vertebrates. In addition to opportunistic representatives, hypervirulent (hvKp) and antibiotic-resistant K. pneumoniae (ABR-Kp) occur. While ABR-Kp isolates often cause difficult-to-treat diseases due to limited therapeutic options, hvKp is a pathotype that can infect healthy individuals often leading to recurrent infection. Here, we investigated the clinical K. pneumoniae isolate PBIO3459 obtained from a blood sample, which showed an unusual colony morphology. By combining whole-genome and RNA sequencing with multiple in vitro and in vivo virulence-associated assays, we aimed to define the respective Klebsiella subtype and explore the unusual phenotypic appearance. We demonstrate that PBIO3459 belongs to sequence type (ST)20 and carries no acquired resistance genes, consistent with phenotypic susceptibility tests. In addition, the isolate showed low-level virulence, both at genetic and phenotypic levels. We thus suggest that PBIO3459 is an opportunistic (commensal) K. pneumoniae isolate. Genomic comparison of PBIO3459 with closely related ABR-Kp ST20 isolates revealed that they differed only in resistance genes. Finally, the unusual colony morphology was mainly associated with carbohydrate and amino acid transport and metabolism. In conclusion, our study reveals the characteristics of a Klebsiella sepsis isolate and suggests that opportunistic representatives likely acquire and accumulate antibiotic resistances that subsequently enable their emergence as ABR-Kp pathogens.
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Affiliation(s)
- Katharina Sydow
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany
| | - Elias Eger
- Institute of Infection Medicine, Christian-Albrecht University Kiel and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Michael Schwabe
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany
| | - Stefan E. Heiden
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany
| | - Jürgen A. Bohnert
- Friedrich Loeffler-Institute of Medical Microbiology, University Medicine Greifswald, 17475 Greifswald, Germany
| | - Sören Franzenburg
- Institute of Clinical Molecular Biology, Christian-Albrecht University Kiel and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
| | - Christoph Jurischka
- Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, 01968 Senftenberg, Germany
| | - Peter Schierack
- Faculty of Environment and Natural Sciences, Brandenburg University of Technology Cottbus-Senftenberg, 01968 Senftenberg, Germany
| | - Katharina Schaufler
- Pharmaceutical Microbiology, Institute of Pharmacy, University of Greifswald, 17489 Greifswald, Germany
- Institute of Infection Medicine, Christian-Albrecht University Kiel and University Medical Center Schleswig-Holstein, 24105 Kiel, Germany
- Correspondence: ; Tel.: +49-3834-420-4869
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17
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Brunn AA, Roustit M, Kadri-Alabi Z, Guardabassi L, Waage J. A Meta-Analysis to Estimate Prevalence of Resistance to Tetracyclines and Third Generation Cephalosporins in Enterobacteriaceae Isolated from Food Crops. Antibiotics (Basel) 2022; 11:antibiotics11101424. [PMID: 36290083 PMCID: PMC9598472 DOI: 10.3390/antibiotics11101424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 09/29/2022] [Accepted: 10/10/2022] [Indexed: 11/16/2022] Open
Abstract
Application of human and animal waste to fields and water sources and on-farm antimicrobial usage are documented contributors to the occurrence of antimicrobial resistance (AMR) in agricultural domains. This meta-analysis aimed to determine the prevalence of resistance to tetracycline (TET) and third generation cephalosporins (3GC) in Enterobacteriaceae isolated from food crops. TET was selected in view of its wide use in agriculture, whereas 3GC were selected because of the public health concerns of reported resistance to these critically important antibiotics in the environment. Forty-two studies from all six world regions published between 2010 and 2022 met the eligibility criteria. A random effects model estimated that 4.63% (95% CI: 2.57%, 7.18%; p-value: <0.0001) and 3.75% (95%CI: 2.13%, 5.74%; p-value: <0.0001) of surveyed food crops harboured Enterobacteriaceae resistant to TET and 3GC, respectively. No significant differences were observed between pre- and post-harvest stages of the value chain. 3GC resistance prevalence estimates in food crops were highest for the African region (6.59%; 95% CI: 2.41%, 12.40%; p-value: <0.0001) and lowest for Europe (1.84%; 95% CI: 0.00%, 6.02%; p-value: <0.0001). Considering the rare use of 3GC in agriculture, these results support its inclusion for AMR surveillance in food crops. Integrating food crops into One Health AMR surveillance using harmonized sampling methods could confirm trends highlighted here.
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Affiliation(s)
- Ariel A. Brunn
- Department of Public Health, Environment and Society, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
- Correspondence:
| | - Manon Roustit
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London NW1 0TU, UK
| | - Zaharat Kadri-Alabi
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London NW1 0TU, UK
| | - Luca Guardabassi
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London NW1 0TU, UK
- Department of Veterinary and Animal Sciences, University of Copenhagen, 1165 Copenhagen, Denmark
| | - Jeff Waage
- Department of Disease Control, London School of Hygiene and Tropical Medicine, London WC1E 7HT, UK
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Lindstedt K, Buczek D, Pedersen T, Hjerde E, Raffelsberger N, Suzuki Y, Brisse S, Holt K, Samuelsen Ø, Sundsfjord A. Detection of Klebsiella pneumoniae human gut carriage: a comparison of culture, qPCR, and whole metagenomic sequencing methods. Gut Microbes 2022; 14:2118500. [PMID: 36045603 PMCID: PMC9450895 DOI: 10.1080/19490976.2022.2118500] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Klebsiella pneumoniae is an important opportunistic healthcare-associated pathogen and major contributor to the global spread of antimicrobial resistance. Gastrointestinal colonization with K. pneumoniae is a major predisposing risk factor for infection and forms an important hub for the dispersal of resistance. Current culture-based detection methods are time consuming, give limited intra-sample abundance and strain diversity information, and have uncertain sensitivity. Here we investigated the presence and abundance of K. pneumoniae at the species and strain level within fecal samples from 103 community-based adults by qPCR and whole metagenomic sequencing (WMS) compared to culture-based detection. qPCR demonstrated the highest sensitivity, detecting K. pneumoniae in 61.2% and 75.8% of direct-fecal and culture-enriched sweep samples, respectively, including 52/52 culture-positive samples. WMS displayed lower sensitivity, detecting K. pneumoniae in 71.2% of culture-positive fecal samples at a 0.01% abundance cutoff, and was inclined to false positives in proportion to the relative abundance of other Enterobacterales present. qPCR accurately quantified K. pneumoniae to 16 genome copies/reaction while WMS could estimate relative abundance to at least 0.01%. Quantification by both methods correlated strongly with each other (Spearman's rho = 0.91). WMS also supported accurate intra-sample K. pneumoniae sequence type (ST)-level diversity detection from fecal microbiomes to 0.1% relative abundance, agreeing with the culture-based detected ST in 16/19 samples. Our results show that qPCR and WMS are sensitive and reliable tools for detection, quantification, and strain analysis of K. pneumoniae from fecal samples with potential to support infection control and enhance insights in K. pneumoniae gastrointestinal ecology.
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Affiliation(s)
- Kenneth Lindstedt
- Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway,CONTACT Kenneth Lindstedt
| | - Dorota Buczek
- Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Torunn Pedersen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Erik Hjerde
- Department of Chemistry, UiT the Arctic University of Norway, Tromsø, Norway
| | - Niclas Raffelsberger
- Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway,Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway
| | - Yutaka Suzuki
- Department of Computational Biology and Medical Sciences, The University of Tokyo, Tokyo, Japan
| | - Sylvain Brisse
- Biodiversity and Epidemiology of Bacterial Pathogens Unit, Institut Pasteur, Université Paris Cité, Paris, France
| | - Kathryn Holt
- Department of Infectious Diseases, Central Clinical School, Monash University, Melbourne, Australia,Department of Infection Biology, London School of Hygiene and Tropical Medicine, London, UK
| | - Ørjan Samuelsen
- Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway,Department of Pharmacy, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway
| | - Arnfinn Sundsfjord
- Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, Norway,Norwegian National Advisory Unit on Detection of Antimicrobial Resistance, Department of Microbiology and Infection Control, University Hospital of North Norway, Tromsø, Norway,Arnfinn Sundsfjord Department of Medical Biology, Faculty of Health Sciences, UiT the Arctic University of Norway, Tromsø, 9038, Norway
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19
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Phenotypic and Genetic Characterization of Klebsiella pneumoniae Isolates from Wild Animals in Central Italy. Animals (Basel) 2022; 12:ani12111347. [PMID: 35681810 PMCID: PMC9179660 DOI: 10.3390/ani12111347] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 05/23/2022] [Accepted: 05/24/2022] [Indexed: 11/16/2022] Open
Abstract
Despite Klebsiella pneumoniae being widely recognized as a nosocomial pathogen, there is a critical lack in defining its reservoirs and sources of infections. Most studies on risk factors have focused on multidrug-resistant (MDR) isolates and clinically-oriented questions. Over a two-year period, we sampled 131 wild animals including mammal and bird species from three regions of Central Italy. All typical colonies isolated from the analytical portions were confirmed by real-time PCR and identified by MALDI-TOF mass spectrometry (MALDI-TOF MS). All confirmed K. pneumoniae isolates were tested for antimicrobial susceptibility to 29 antimicrobials and subjected to whole genome sequencing. Typical colonies were detected in 17 samples (13%), which were identified as K. pneumoniae (n = 16) and as K. quasipneumoniae (n = 1) by MALDI-TOF MS. The antimicrobial susceptibility profile showed that all the isolates were resistant to β-lactams (ceftobiprole, cloxacillin, cefazolin) and tetracycline; resistance to ertapenem and trimethoprim was observed and nine out of 16 K. pneumoniae isolates (56.2%) were classified as MDR. Genomic characterization allowed the detection of fluoroquinolone resistance-associated efflux pumps, fosfomycin and β-lactamase resistance genes, and virulence genes in the overall dataset. The cluster analysis of two isolates detected from wild boar with available clinical genomes showed the closest similarity. This study highlights the link between humans, domestic animals, and wildlife, showing that the current knowledge on this ecological context is lacking and that the potential health risks are underestimated.
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