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Leclercq A, Tourdjman M, Mattheus W, Friesema I, van Sorge NM, Halbedel S, Wilking H, Lecuit M. Outbreak of Listeriosis Associated with Consumption of Vegan Cheese. N Engl J Med 2024; 390:1439-1440. [PMID: 38631008 DOI: 10.1056/nejmc2400665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Affiliation(s)
| | | | | | - Ingrid Friesema
- Rijksinstituut voor Volksgezondheid en Milieu, Utrecht, the Netherlands
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Bogaerts B, Van den Bossche A, Verhaegen B, Delbrassinne L, Mattheus W, Nouws S, Godfroid M, Hoffman S, Roosens NHC, De Keersmaecker SCJ, Vanneste K. Closing the gap: Oxford Nanopore Technologies R10 sequencing allows comparable results to Illumina sequencing for SNP-based outbreak investigation of bacterial pathogens. J Clin Microbiol 2024:e0157623. [PMID: 38441926 DOI: 10.1128/jcm.01576-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2023] [Accepted: 02/09/2024] [Indexed: 03/08/2024] Open
Abstract
Whole-genome sequencing has become the method of choice for bacterial outbreak investigation, with most clinical and public health laboratories currently routinely using short-read Illumina sequencing. Recently, long-read Oxford Nanopore Technologies (ONT) sequencing has gained prominence and may offer advantages over short-read sequencing, particularly with the recent introduction of the R10 chemistry, which promises much lower error rates than the R9 chemistry. However, limited information is available on its performance for bacterial single-nucleotide polymorphism (SNP)-based outbreak investigation. We present an open-source workflow, Prokaryotic Awesome variant Calling Utility (PACU) (https://github.com/BioinformaticsPlatformWIV-ISP/PACU), for constructing SNP phylogenies using Illumina and/or ONT R9/R10 sequencing data. The workflow was evaluated using outbreak data sets of Shiga toxin-producing Escherichia coli and Listeria monocytogenes by comparing ONT R9 and R10 with Illumina data. The performance of each sequencing technology was evaluated not only separately but also by integrating samples sequenced by different technologies/chemistries into the same phylogenomic analysis. Additionally, the minimum sequencing time required to obtain accurate phylogenetic results using nanopore sequencing was evaluated. PACU allowed accurate identification of outbreak clusters for both species using all technologies/chemistries, but ONT R9 results deviated slightly more from the Illumina results. ONT R10 results showed trends very similar to Illumina, and we found that integrating data sets sequenced by either Illumina or ONT R10 for different isolates into the same analysis produced stable and highly accurate phylogenomic results. The resulting phylogenies for these two outbreaks stabilized after ~20 hours of sequencing for ONT R9 and ~8 hours for ONT R10. This study provides a proof of concept for using ONT R10, either in isolation or in combination with Illumina, for rapid and accurate bacterial SNP-based outbreak investigation.
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Affiliation(s)
- Bert Bogaerts
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | | | | | | | - Stéphanie Nouws
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Maxime Godfroid
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Stefan Hoffman
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Nancy H C Roosens
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | - Kevin Vanneste
- Transversal activities in Applied Genomics, Sciensano, Brussels, Belgium
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De Hert E, Baïli S, Vanden Driessche M, Jansens H, Vandamme S, Jacquemyn Y, Vodolazkaia A, Mukovnikova M, Mattheus W, Matheeussen V. Genital Infection Caused by Salmonella enterica Serovar Hvittingfoss: A Case Report. Pathogens 2023; 12:1316. [PMID: 38003781 PMCID: PMC10674701 DOI: 10.3390/pathogens12111316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2023] [Revised: 10/19/2023] [Accepted: 11/03/2023] [Indexed: 11/26/2023] Open
Abstract
BACKGROUND Nontyphoidal Salmonella serovars predominantly cause gastrointestinal infections. However, other clinical presentations, including urogenital infections, have been reported, although they are rather rare. CASE PRESENTATION This case is about a 33-year-old woman diagnosed with Salmonella enterica serovar Hvittingfoss (S. Hvittingfoss) bacteremia and endometritis six days post uterine aspiration in the context of a missed abortion. She had traveled to Indonesia two weeks prior to the positive blood and cervical culture. She never developed gastrointestinal symptoms but was found to carry S. Hvittingfoss in her stool sample. The patient was successfully treated with a seven-day course of iv ciprofloxacin. CONCLUSIONS S. Hvittingfoss is a rare serovar that has caused a few outbreaks of foodborne infections in Asia, the United States, and Australia. To the best of our knowledge, this is the first reported case of Salmonella urogenital infection caused by this serovar. Salmonella as a cause of urogenital infections is rare but not uncommon. Therefore, it should be considered in identifying members of the Enterobacterales among urogenital flora in cases of severe urogenital infections, especially when other cultures remain negative.
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Affiliation(s)
- Emilie De Hert
- Department of Microbiology, University Hospital Antwerp, 2650 Edegem, Belgium (V.M.)
| | - Sarah Baïli
- Department of Obstetrics and Gynecology, University Hospital Antwerp, 2650 Edegem, Belgium
| | | | - Hilde Jansens
- Department of Microbiology, University Hospital Antwerp, 2650 Edegem, Belgium (V.M.)
| | - Sarah Vandamme
- Department of Microbiology, University Hospital Antwerp, 2650 Edegem, Belgium (V.M.)
| | - Yves Jacquemyn
- Department of Obstetrics and Gynecology, University Hospital Antwerp, 2650 Edegem, Belgium
| | - Alexandra Vodolazkaia
- National Reference Centre for Salmonella and Shigella Species, Sciensano, 1050 Brussels, Belgium (W.M.)
| | - Marina Mukovnikova
- National Reference Centre for Salmonella and Shigella Species, Sciensano, 1050 Brussels, Belgium (W.M.)
| | - Wesley Mattheus
- National Reference Centre for Salmonella and Shigella Species, Sciensano, 1050 Brussels, Belgium (W.M.)
| | - Veerle Matheeussen
- Department of Microbiology, University Hospital Antwerp, 2650 Edegem, Belgium (V.M.)
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute (VAXINFECTIO), University of Antwerp, 2610 Wilrijk, Belgium
- Laboratory of Medical Biochemistry, University of Antwerp, 2610 Wilrijk, Belgium
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Van Puyvelde S, de Block T, Sridhar S, Bawn M, Kingsley RA, Ingelbeen B, Beale MA, Barbé B, Jeon HJ, Mbuyi-Kalonji L, Phoba MF, Falay D, Martiny D, Vandenberg O, Affolabi D, Rutanga JP, Ceyssens PJ, Mattheus W, Cuypers WL, van der Sande MAB, Park SE, Kariuki S, Otieno K, Lusingu JPA, Mbwana JR, Adjei S, Sarfo A, Agyei SO, Asante KP, Otieno W, Otieno L, Tahita MC, Lompo P, Hoffman IF, Mvalo T, Msefula C, Hassan-Hanga F, Obaro S, Mackenzie G, Deborggraeve S, Feasey N, Marks F, MacLennan CA, Thomson NR, Jacobs J, Dougan G, Kariuki S, Lunguya O. A genomic appraisal of invasive Salmonella Typhimurium and associated antibiotic resistance in sub-Saharan Africa. Nat Commun 2023; 14:6392. [PMID: 37872141 PMCID: PMC10593746 DOI: 10.1038/s41467-023-41152-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Accepted: 08/23/2023] [Indexed: 10/25/2023] Open
Abstract
Invasive non-typhoidal Salmonella (iNTS) disease manifesting as bloodstream infection with high mortality is responsible for a huge public health burden in sub-Saharan Africa. Salmonella enterica serovar Typhimurium (S. Typhimurium) is the main cause of iNTS disease in Africa. By analysing whole genome sequence data from 1303 S. Typhimurium isolates originating from 19 African countries and isolated between 1979 and 2017, here we show a thorough scaled appraisal of the population structure of iNTS disease caused by S. Typhimurium across many of Africa's most impacted countries. At least six invasive S. Typhimurium clades have already emerged, with ST313 lineage 2 or ST313-L2 driving the current pandemic. ST313-L2 likely emerged in the Democratic Republic of Congo around 1980 and further spread in the mid 1990s. We observed plasmid-borne as well as chromosomally encoded fluoroquinolone resistance underlying emergences of extensive-drug and pan-drug resistance. Our work provides an overview of the evolution of invasive S. Typhimurium disease, and can be exploited to target control measures.
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Affiliation(s)
- Sandra Van Puyvelde
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK.
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.
- Laboratory of Medical Microbiology, Vaccine & Infectious Disease Institute, University of Antwerp, Antwerp, Belgium.
| | | | - Sushmita Sridhar
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- Division of Infectious Disease, Massachusetts General Hospital, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Matt Bawn
- Quadram Institute Bioscience, Norwich, UK
- Earlham Institute, Norwich, UK
- Faculty of Biological Sciences, University of Leeds, Leeds, UK
| | - Robert A Kingsley
- Quadram Institute Bioscience, Norwich, UK
- School of Biological Science, University of East Anglia, Norwich, UK
| | - Brecht Ingelbeen
- Institute of Tropical Medicine, Antwerp, Belgium
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Mathew A Beale
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
| | | | - Hyon Jin Jeon
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK
- International Vaccine Institute, 1 Gwanak-ro, Seoul, 08826, Republic of Korea
- Madagascar Institute for Vaccine Research, University of Antananarivo, Antananarivo, Madagascar
| | - Lisette Mbuyi-Kalonji
- Department of Medical Biology, University Teaching Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo
- National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo
| | - Marie-France Phoba
- Department of Medical Biology, University Teaching Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo
- National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo
| | - Dadi Falay
- Department of Pediatrics, University Hospital of Kisangani, Kisangani, Democratic Republic of the Congo
| | - Delphine Martiny
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles-Universitair Laboratorium Brussel (LHUB-ULB), Université Libre de Bruxelles (ULB), 1000, Brussels, Belgium
- Faculty of Medicine and Pharmacy, University of Mons (UMONS), 7000, Mons, Belgium
| | - Olivier Vandenberg
- Department of Microbiology, Laboratoire Hospitalier Universitaire de Bruxelles-Universitair Laboratorium Brussel (LHUB-ULB), Université Libre de Bruxelles (ULB), 1000, Brussels, Belgium
- Division of Infection and Immunity, Faculty of Medical Sciences, University College London, London, UK
| | - Dissou Affolabi
- Centre National Hospitalier Universitaire Hubert Koutoukou Maga, Cotonou, Benin
| | - Jean Pierre Rutanga
- Institute of Tropical Medicine, Antwerp, Belgium
- College of Science and Technology, University of Rwanda, Kigali, Rwanda
| | - Pieter-Jan Ceyssens
- National Reference Center for Salmonella, Unit of Human Bacterial Diseases, Sciensano, J. Wytsmanstraat 14, B-1050, Brussels, Belgium
| | - Wesley Mattheus
- National Reference Center for Salmonella, Unit of Human Bacterial Diseases, Sciensano, J. Wytsmanstraat 14, B-1050, Brussels, Belgium
| | - Wim L Cuypers
- Institute of Tropical Medicine, Antwerp, Belgium
- Department of Computer Science, University of Antwerp, Antwerp, Belgium
| | - Marianne A B van der Sande
- Institute of Tropical Medicine, Antwerp, Belgium
- Julius Center for Health Sciences and Primary Care, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Se Eun Park
- International Vaccine Institute, 1 Gwanak-ro, Seoul, 08826, Republic of Korea
- Yonsei University Graduate School of Public Health, Seodaemun-gu, Seoul, 03722, Republic of Korea
| | - Simon Kariuki
- Kenya Medical Research Institute/Centre for Global Health Research, Kisumu, Kenya
| | - Kephas Otieno
- Kenya Medical Research Institute/Centre for Global Health Research, Kisumu, Kenya
| | - John P A Lusingu
- National Institute for Medical Research, Tanga, Tanzania
- Center for Medical Parasitology, Department of Immunology and Microbiology, University of Copenhagen, København, Denmark
| | - Joyce R Mbwana
- National Institute for Medical Research, Tanga, Tanzania
| | - Samuel Adjei
- University of Health & Allied Sciences, Ho, Volta Region, Ghana
| | - Anima Sarfo
- University of Health & Allied Sciences, Ho, Volta Region, Ghana
| | - Seth O Agyei
- University of Health & Allied Sciences, Ho, Volta Region, Ghana
| | - Kwaku P Asante
- Kintampo Health Research Centre, Research and Development Division, Ghana Health Service, Kintampo North Municipality, Ho, Volta Region, Ghana
| | | | | | - Marc C Tahita
- Institut de Recherche en Science de la Santé, Direction Régionale du Centre-Ouest/ClinicalResearch Unit of Nanoro, Nanoro, Burkina Faso
| | - Palpouguini Lompo
- Institut de Recherche en Science de la Santé, Direction Régionale du Centre-Ouest/ClinicalResearch Unit of Nanoro, Nanoro, Burkina Faso
| | | | - Tisungane Mvalo
- University of North Carolina Project, Lilongwe, Malawi
- Department of Pediatrics, School of Medicine, University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
| | - Chisomo Msefula
- Malawi Liverpool Wellcome Research Programme, Kamuzu University of Health Sciences, Blantyre, Malawi
| | - Fatimah Hassan-Hanga
- Department of Paediatrics, Bayero University, Kano, Nigeria
- Aminu Kano Teaching Hospital, Kano, Nigeria
| | - Stephen Obaro
- University of Nebraska Medical Center, Omaha, NE, USA
- International Foundation Against Infectious Diseases in Nigeria (IFAIN), Abuja, Nigeria
| | - Grant Mackenzie
- Medical Research Council Unit The Gambia at London School of Hygiene & Tropical Medicine, Fajara, The Gambia
- London School of Hygiene and Tropical Medicine, Keppel St, Bloomsbury, London, WC1E 7HT, UK
- Murdoch Children's Research Institute, Melbourne, VIC, Australia
| | | | - Nicholas Feasey
- University of North Carolina Project, Lilongwe, Malawi
- Department of Clinical Sciences, Liverpool School of Tropical Medicine, Liverpool, UK
| | - Florian Marks
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK
- International Vaccine Institute, 1 Gwanak-ro, Seoul, 08826, Republic of Korea
- Madagascar Institute for Vaccine Research, University of Antananarivo, Antananarivo, Madagascar
- Heidelberg Institute of Global Health, University of Heidelberg, Heidelberg, Germany
| | - Calman A MacLennan
- The Jenner Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
- Enteric and Diarrheal Diseases, Global Health, Bill & Melinda Gates Foundation, Seattle, WA, USA
| | - Nicholas R Thomson
- Parasites and Microbes Programme, Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK
- London School of Hygiene and Tropical Medicine, Keppel St, Bloomsbury, London, WC1E 7HT, UK
| | - Jan Jacobs
- Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Gordon Dougan
- Cambridge Institute of Therapeutic Immunology and Infectious Disease, University of Cambridge School of Clinical Medicine, Cambridge Biomedical Campus, Cambridge, CB2 0AW, UK
| | - Samuel Kariuki
- Centre for Microbiology Research, Kenya Medical Research Institute, Nairobi, Kenya
| | - Octavie Lunguya
- Department of Medical Biology, University Teaching Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo
- National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo
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Falay D, Hardy L, Bonebe E, Mattheus W, Ngbonda D, Lunguya O, Jacobs J. Intestinal carriage of invasive non-typhoidal Salmonella among household members of children with Salmonella bloodstream infection, Kisangani, DR Congo. Front Microbiol 2023; 14:1241961. [PMID: 37901802 PMCID: PMC10602682 DOI: 10.3389/fmicb.2023.1241961] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2023] [Accepted: 09/18/2023] [Indexed: 10/31/2023] Open
Abstract
Introduction Invasive non-typhoidal Salmonella (iNTS), mainly Salmonella Typhimurium and Salmonella Enteritidis, causes a severe burden in sub-Saharan Africa; however, its reservoir (animal or environmental) is unclear. The present study assessed healthy household members of index patients for intestinal carriage of Salmonella. Methods Index patients were admitted to the University Hospital of Kisangani (DR Congo), and Salmonella was grown from blood cultures. Household members were asked to provide three stool samples for culture for Salmonella. Salmonella Typhimurium and S. Enteritidis isolates from index patients, and household members were assessed for genetic relatedness using the multiple-locus variable number of tandem repeat analysis (MLVA), and the multilocus sequence type (ST) was determined by whole genome sequencing. Results Between May 2016 and January 2020, 22 households were visited. The index patient serotypes were Typhimurium, Enteritidis, Typhi, and Paratyphi C; II:42:r:-; and I:7:y:- (n = 8, 7, 5, and each 1, respectively). The median (range) delay between the index patient and household sampling was 25 days (2 days to 7.3 months); 203 household members provided at least one stool sample. In all, 15 (7.3%) Salmonella carriers were found in nine of 22 households. For one index patient, the household comprised S. Typhimurium in four household members, including the index patient, sampled 27 days after bloodstream infection; the MLVA types of these five isolates were similar. They belonged to ST313 lineage 2 and were closely related [0-1 allelic distance (AD) among the stool isolates and eight AD with the blood culture isolate]. In another household, the stool culture of the index patient (obtained 67 days after bloodstream infection) grew S. Enteritidis of the same MLVA type; both isolates belonged to the ST11 Central/Eastern African clade and were closely related (three AD). Discussion The present study provides evidence of household clustering of S. Typhimurium ST313 and intestinal carriage of iNTS several weeks after bloodstream infection.
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Affiliation(s)
- Dadi Falay
- Department of Pediatrics, University Hospital of Kisangani, Kisangani, Democratic Republic of Congo
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Liselotte Hardy
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Edmonde Bonebe
- Department of Microbiology, National Institute for Biomedical Research, Kinshasa, Democratic Republic of Congo
| | - Wesley Mattheus
- Division of Human Bacterial Diseases, Sciensano, Uccle, Belgium
| | - Dauly Ngbonda
- Department of Pediatrics, University Hospital of Kisangani, Kisangani, Democratic Republic of Congo
| | - Octavie Lunguya
- Department of Microbiology, National Institute for Biomedical Research, Kinshasa, Democratic Republic of Congo
- Department of Microbiology, University Teaching Hospital of Kinshasa, Kinshasa, Democratic Republic of Congo
| | - Jan Jacobs
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
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Shaw D, Abad R, Amin-Chowdhury Z, Bautista A, Bennett D, Broughton K, Cao B, Casanova C, Choi EH, Chu YW, Claus H, Coelho J, Corcoran M, Cottrell S, Cunney R, Cuypers L, Dalby T, Davies H, de Gouveia L, Deghmane AE, Demczuk W, Desmet S, Domenech M, Drew R, du Plessis M, Duarte C, Erlendsdóttir H, Fry NK, Fuursted K, Hale T, Henares D, Henriques-Normark B, Hilty M, Hoffmann S, Humphreys H, Ip M, Jacobsson S, Johnson C, Johnston J, Jolley KA, Kawabata A, Kozakova J, Kristinsson KG, Krizova P, Kuch A, Ladhani S, Lâm TT, León ME, Lindholm L, Litt D, Maiden MCJ, Martin I, Martiny D, Mattheus W, McCarthy ND, Meehan M, Meiring S, Mölling P, Morfeldt E, Morgan J, Mulhall R, Muñoz-Almagro C, Murdoch D, Murphy J, Musilek M, Mzabi A, Novakova L, Oftadeh S, Perez-Argüello A, Pérez-Vázquez M, Perrin M, Perry M, Prevost B, Roberts M, Rokney A, Ron M, Sanabria OM, Scott KJ, Sheppard C, Siira L, Sintchenko V, Skoczyńska A, Sloan M, Slotved HC, Smith AJ, Steens A, Taha MK, Toropainen M, Tzanakaki G, Vainio A, van der Linden MPG, van Sorge NM, Varon E, Vohrnova S, von Gottberg A, Yuste J, Zanella R, Zhou F, Brueggemann AB. Trends in invasive bacterial diseases during the first 2 years of the COVID-19 pandemic: analyses of prospective surveillance data from 30 countries and territories in the IRIS Consortium. Lancet Digit Health 2023; 5:e582-e593. [PMID: 37516557 PMCID: PMC10914672 DOI: 10.1016/s2589-7500(23)00108-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Revised: 03/22/2023] [Accepted: 05/25/2023] [Indexed: 07/31/2023]
Abstract
BACKGROUND The Invasive Respiratory Infection Surveillance (IRIS) Consortium was established to assess the impact of the COVID-19 pandemic on invasive diseases caused by Streptococcus pneumoniae, Haemophilus influenzae, Neisseria meningitidis, and Streptococcus agalactiae. We aimed to analyse the incidence and distribution of these diseases during the first 2 years of the COVID-19 pandemic compared to the 2 years preceding the pandemic. METHODS For this prospective analysis, laboratories in 30 countries and territories representing five continents submitted surveillance data from Jan 1, 2018, to Jan 2, 2022, to private projects within databases in PubMLST. The impact of COVID-19 containment measures on the overall number of cases was analysed, and changes in disease distributions by patient age and serotype or group were examined. Interrupted time-series analyses were done to quantify the impact of pandemic response measures and their relaxation on disease rates, and autoregressive integrated moving average models were used to estimate effect sizes and forecast counterfactual trends by hemisphere. FINDINGS Overall, 116 841 cases were analysed: 76 481 in 2018-19, before the pandemic, and 40 360 in 2020-21, during the pandemic. During the pandemic there was a significant reduction in the risk of disease caused by S pneumoniae (risk ratio 0·47; 95% CI 0·40-0·55), H influenzae (0·51; 0·40-0·66) and N meningitidis (0·26; 0·21-0·31), while no significant changes were observed for S agalactiae (1·02; 0·75-1·40), which is not transmitted via the respiratory route. No major changes in the distribution of cases were observed when stratified by patient age or serotype or group. An estimated 36 289 (95% prediction interval 17 145-55 434) cases of invasive bacterial disease were averted during the first 2 years of the pandemic among IRIS-participating countries and territories. INTERPRETATION COVID-19 containment measures were associated with a sustained decrease in the incidence of invasive disease caused by S pneumoniae, H influenzae, and N meningitidis during the first 2 years of the pandemic, but cases began to increase in some countries towards the end of 2021 as pandemic restrictions were lifted. These IRIS data provide a better understanding of microbial transmission, will inform vaccine development and implementation, and can contribute to health-care service planning and provision of policies. FUNDING Wellcome Trust, NIHR Oxford Biomedical Research Centre, Spanish Ministry of Science and Innovation, Korea Disease Control and Prevention Agency, Torsten Söderberg Foundation, Stockholm County Council, Swedish Research Council, German Federal Ministry of Health, Robert Koch Institute, Pfizer, Merck, and the Greek National Public Health Organization.
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Affiliation(s)
- David Shaw
- Nuffield Department of Population Health, Big Data Institute, University of Oxford, Oxford, UK
| | - Raquel Abad
- National Reference Laboratory for Meningococci, National Center of Microbiology, Instituto de Salud Carlos III, Madrid, Spain
| | - Zahin Amin-Chowdhury
- Immunisation and Countermeasures Division, UK Health Security Agency, London, UK
| | | | - Desiree Bennett
- Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland, Dublin, Ireland
| | - Karen Broughton
- Staphylococcus and Streptococcus Reference Section, AMRHAI, UK Health Security Agency, London, UK
| | - Bin Cao
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Carlo Casanova
- Swiss National Reference Center for Invasive Pneumococci, Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Eun Hwa Choi
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, South Korea
| | - Yiu-Wai Chu
- Department of Health, Microbiology Division, Public Health Laboratory Services Branch, Centre for Health Protection, Hong Kong Special Administrative Region, China
| | - Heike Claus
- University of Würzburg, Institute for Hygiene and Microbiology, National Reference Centre for Meningococci and Haemophilus influenzae, Würzburg, Germany
| | - Juliana Coelho
- Staphylococcus and Streptococcus Reference Section, AMRHAI, UK Health Security Agency, London, UK
| | - Mary Corcoran
- Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland, Dublin, Ireland; Department of Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | | | - Robert Cunney
- Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland, Dublin, Ireland; Department of Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland
| | - Lize Cuypers
- National Reference Centre for Streptococcus pneumoniae, University Hospitals Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Tine Dalby
- Statens Serum Institut, Department of Infectious Disease Epidemiology & Prevention, Copenhagen, Denmark
| | - Heather Davies
- Meningococcal Reference Laboratory, Institute of Environmental Science and Research, Porirua, New Zealand
| | - Linda de Gouveia
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Ala-Eddine Deghmane
- Institut Pasteur, Univeristé Paris Cité, Invasive Bacterial Infections Unit and National Reference Centre for Meningococci and Haemophilus influenzae, Paris, France
| | - Walter Demczuk
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Stefanie Desmet
- National Reference Centre for Streptococcus pneumoniae, University Hospitals Leuven, Leuven, Belgium; Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
| | - Mirian Domenech
- National Center for Microbiology and CIBER of Respiratory Research, Instituto de Salud Carlos III, Madrid, Spain
| | - Richard Drew
- Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland, Dublin, Ireland; Department of Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland; Clinical Innovation Unit, Rotunda, Dublin, Ireland
| | - Mignon du Plessis
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | | | - Helga Erlendsdóttir
- Department of Clinical Microbiology, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
| | - Norman K Fry
- Immunisation and Vaccine Preventable Diseases Division and Respiratory and Vaccine Preventable Bacteria Reference Unit, UK Health Security Agency, London, UK
| | - Kurt Fuursted
- Statens Serum Institut, Department of Bacteria, Parasites & Fungi, Copenhagen, Denmark
| | - Thomas Hale
- Blavatnik School of Government, University of Oxford, Oxford, UK
| | - Desiree Henares
- Microbiology Department, Institut Recerca Sant Joan de Déu, Hospital Sant Joan de Deu, Barcelona, Spain; CIBER of Epidemiology and Public Health, Madrid, Spain
| | - Birgitta Henriques-Normark
- Karolinska Institutet, Karolinska University Hospital, Public Health Agency of Sweden, Stockholm, Sweden
| | - Markus Hilty
- Swiss National Reference Center for Invasive Pneumococci, Institute for Infectious Diseases, University of Bern, Bern, Switzerland
| | - Steen Hoffmann
- Statens Serum Institut, Department of Bacteria, Parasites & Fungi, Copenhagen, Denmark
| | - Hilary Humphreys
- Department of Microbiology, Royal College of Surgeons in Ireland, Dublin, Ireland; Department of Clinical Microbiology, Beaumont Hospital, Dublin, Ireland
| | - Margaret Ip
- Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong Special Administrative Region, China
| | - Susanne Jacobsson
- National Reference Laboratory for Neisseria meningitidis, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | | | | | | | | | - Jana Kozakova
- National Reference Laboratory for Streptococcal Infections, Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - Karl G Kristinsson
- Department of Clinical Microbiology, Landspitali, The National University Hospital of Iceland, Reykjavik, Iceland
| | - Pavla Krizova
- National Reference Laboratory for Meningococcal Infections, Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - Alicja Kuch
- National Reference Centre for Bacterial Meningitis, Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | - Shamez Ladhani
- Immunisation and Countermeasures Division, UK Health Security Agency, London, UK
| | - Thiên-Trí Lâm
- University of Würzburg, Institute for Hygiene and Microbiology, National Reference Centre for Meningococci and Haemophilus influenzae, Würzburg, Germany
| | | | - Laura Lindholm
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - David Litt
- Respiratory and Vaccine Preventable Bacteria Reference Unit, UK Health Security Agency, London, UK
| | | | - Irene Martin
- National Microbiology Laboratory, Public Health Agency of Canada, Winnipeg, MB, Canada
| | - Delphine Martiny
- National Belgian Reference Centre for Haemophilus influenzae, Laboratoire des Hôpitaux Universitaires de Bruxelles-Universitair Laboratorium van Brussel, Brussels, Belgium; Faculty of Medicine and Pharmacy, University of Mons, Mons, Belgium
| | | | - Noel D McCarthy
- Population Health Medicine, Public Health and Primary Care, Trinity College Dublin, Dublin, Ireland
| | - Mary Meehan
- Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland, Dublin, Ireland
| | - Susan Meiring
- Division of Public Health Surveillance and Response, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Paula Mölling
- National Reference Laboratory for Neisseria meningitidis, Department of Laboratory Medicine, Clinical Microbiology, Faculty of Medicine and Health, Örebro University, Örebro, Sweden
| | | | - Julie Morgan
- Streptococcal Reference Laboratory, Institute of Environmental Science and Research Limited, Porirua, New Zealand
| | - Robert Mulhall
- Irish Meningitis and Sepsis Reference Laboratory, Children's Health Ireland, Dublin, Ireland
| | - Carmen Muñoz-Almagro
- Microbiology Department, Institut Recerca Sant Joan de Déu, Hospital Sant Joan de Deu, Barcelona, Spain; CIBER of Epidemiology and Public Health, Madrid, Spain; Medicine Department, Universitat Internacional de Catalunya, Barcelona, Spain
| | | | | | - Martin Musilek
- National Reference Laboratory for Meningococcal Infections, Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - Alexandre Mzabi
- Ministère de la Santé - Direction de la santé, Luxembourg, Luxembourg
| | - Ludmila Novakova
- National Reference Laboratory for Haemophilus Infections, Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - Shahin Oftadeh
- NSW Pneumococcal Reference Laboratory, Institute of Clinical Pathology and Medical Research - NSW Health Pathology, Sydney, NSW, Australia
| | - Amaresh Perez-Argüello
- Microbiology Department, Institut Recerca Sant Joan de Déu, Hospital Sant Joan de Deu, Barcelona, Spain
| | - Maria Pérez-Vázquez
- Laboratorio de Referencia e Investigación en Resistencia a Antibióticos e Infecciones Relacionadas con la Asistencia Sanitaria, Centro Nacional de Microbiología, Instituto de Salud Carlos III, Majadahonda, Madrid, Spain; CIBER de Enfermedades Infecciosas, Instituto de Salud Carlos III, Madrid, Spain
| | | | | | - Benoit Prevost
- National Belgian Reference Centre for Haemophilus influenzae, Laboratoire des Hôpitaux Universitaires de Bruxelles-Universitair Laboratorium van Brussel, Brussels, Belgium
| | | | - Assaf Rokney
- Public Health Laboratories-Jerusalem, Public Health Services, Ministry of Health, Jerusalem, Israel
| | - Merav Ron
- Public Health Laboratories-Jerusalem, Public Health Services, Ministry of Health, Jerusalem, Israel
| | | | - Kevin J Scott
- Bacterial Respiratory Infection Service, Scottish Microbiology Reference Laboratories, Glasgow Royal Infirmary, Glasgow, UK
| | - Carmen Sheppard
- Respiratory and Vaccine Preventable Bacteria Reference Unit, UK Health Security Agency, London, UK
| | - Lotta Siira
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Vitali Sintchenko
- NSW Pneumococcal Reference Laboratory, Institute of Clinical Pathology and Medical Research - NSW Health Pathology, Sydney, NSW, Australia; Sydney Institute for Infectious Diseases, University of Sydney, NSW, Australia
| | - Anna Skoczyńska
- National Reference Centre for Bacterial Meningitis, Department of Epidemiology and Clinical Microbiology, National Medicines Institute, Warsaw, Poland
| | | | | | - Andrew J Smith
- Bacterial Respiratory Infection Service, Scottish Microbiology Reference Laboratories, Glasgow Royal Infirmary, Glasgow, UK; College of Medical, Veterinary & Life Sciences, University of Glasgow, Glasgow, UK
| | - Anneke Steens
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment, Bilthoven, Netherlands
| | - Muhamed-Kheir Taha
- Institut Pasteur, Univeristé Paris Cité, Invasive Bacterial Infections Unit and National Reference Centre for Meningococci and Haemophilus influenzae, Paris, France
| | | | - Georgina Tzanakaki
- National Meningitis Reference Laboratory, Department of Public Health Policy, School of Public Health, University of West Attica, Athens, Greece
| | - Anni Vainio
- Finnish Institute for Health and Welfare, Helsinki, Finland
| | - Mark P G van der Linden
- Department of Medical Microbiology, German National Reference Centre for Streptococci, University Hospital RWTH Aachen, Aachen, Germany
| | - Nina M van Sorge
- Department of Medical Microbiology and Infection Prevention, and Netherlands Reference Laboratory for Bacterial Meningitis, Amsterdam University Medical Center, University of Amsterdam, Amsterdam, Netherlands
| | - Emmanuelle Varon
- Laboratory of Medical Biology and National Reference Centre for Pneumococci, Intercommunal Hospital of Créteil, Créteil, France
| | - Sandra Vohrnova
- National Reference Laboratory for Streptococcal Infections, Centre for Epidemiology and Microbiology, National Institute of Public Health, Prague, Czech Republic
| | - Anne von Gottberg
- Centre for Respiratory Diseases and Meningitis, National Institute for Communicable Diseases, Division of the National Health Laboratory Service, Johannesburg, South Africa
| | - Jose Yuste
- National Center for Microbiology and CIBER of Respiratory Research, Instituto de Salud Carlos III, Madrid, Spain
| | - Rosemeire Zanella
- National Laboratory for Meningitis and Pneumococcal Infections, Center of Bacteriology, Institute Adolfo Lutz, São Paulo, Brazil
| | - Fei Zhou
- Department of Pulmonary and Critical Care Medicine, Center of Respiratory Medicine, National Clinical Research Center for Respiratory Diseases, Institute of Respiratory Medicine, Chinese Academy of Medical Sciences, Peking Union Medical College, Beijing, China
| | - Angela B Brueggemann
- Nuffield Department of Population Health, Big Data Institute, University of Oxford, Oxford, UK.
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Diasi CN, Ceyssens PJ, Vodolazkaia A, Mukovnikova M, Dorval S, Bauraind O, Mattheus W. Salmonella Durban meningitis: case report and genomics study. BMC Infect Dis 2023; 23:338. [PMID: 37210495 DOI: 10.1186/s12879-023-08308-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2023] [Accepted: 05/05/2023] [Indexed: 05/22/2023] Open
Abstract
BACKGROUND Bacterial meningitis caused by non-typhoid Salmonella can be a fatal condition which is more common in low and middle-income countries. CASE PRESENTATION We report the case of a Salmonella meningitis in a Belgian six-month old male infant. The first clinical examination was reassuring, but after a few hours, his general state deteriorated. A blood test and a lumbar puncture were therefore performed. The cerebrospinal fluid analysis was compatible with a bacterial meningitis which was later identified by the NRC (National Reference Center) as Salmonella enterica serovar Durban. CONCLUSIONS In this paper, we present the clinical presentation, genomic typing, and probable sources of infection for an unusually rare serovar of Salmonella. Through an extended genomic analysis, we established its relationship to historical cases with links to Guinea.
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Affiliation(s)
- Christelle Nanga Diasi
- Department of Pediatrics, CHC, Clinique MontLégia, Liège, Belgium
- University of Liège (ULiège), 5Th Master in Pediatrics, Liège, Belgium
| | - Pieter-Jan Ceyssens
- Bacterial Diseases Division, Communicable and Infectious Diseases, National Reference Centre for Salmonella and Shigella, Scientific Institute of Public Health, Wytsmanstreet 14, B-1050, Brussels, Belgium
| | - Alexandra Vodolazkaia
- National Reference Centre for Salmonella and Shigella, Laboratory of Medical Microbiology, Communicable and Infectious Diseases, Scientific Institute of Public Health, Wytsmanstreet 14, B-1050, Brussels, Belgium
| | - Marina Mukovnikova
- National Reference Centre for Salmonella and Shigella, Laboratory of Medical Microbiology, Communicable and Infectious Diseases, Scientific Institute of Public Health, Wytsmanstreet 14, B-1050, Brussels, Belgium
| | - Sarah Dorval
- Department of Pediatrics, CHC, Clinique MontLégia, Liège, Belgium
- Pediatric Infectious Disease, Clinique MontLégia,, CHC, Liège, Belgium
| | - Olivia Bauraind
- Department of Pediatrics, CHC, Clinique MontLégia, Liège, Belgium
- Department of Pediatric Gastroenterology, Clinique MontLégia, CHC, Liège, Belgium
| | - Wesley Mattheus
- Bacterial Diseases Division, Communicable and Infectious Diseases, National Reference Centre for Salmonella and Shigella, Scientific Institute of Public Health, Wytsmanstreet 14, B-1050, Brussels, Belgium.
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8
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Cargnel M, Filippitzi ME, Van Cauteren D, Mattheus W, Botteldoorn N, Cambier L, Welby S. Assessing evidence of a potential Salmonella transmission across the poultry food chain. Zoonoses Public Health 2023; 70:22-45. [PMID: 36082435 DOI: 10.1111/zph.12998] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Revised: 06/23/2022] [Accepted: 08/17/2022] [Indexed: 01/07/2023]
Abstract
Enhanced Salmonella surveillance programmes in poultry were implemented in all European Member States, with minimum prevalence targets for a list of targeted serotypes to safeguard food and public health. Based on the Belgian Salmonella surveillance programme and focusing on poultry, the overarching aim of this study was to highlight possible Salmonella transmissions across the food chain (FC). For this purpose, firstly, the prevalence patterns of Salmonella (targeted and the most prevalent non-targeted) serotypes along the FC were described over time. Secondly, the effectiveness of the control measures against vertical transmission (breeders to 1-day-old broiler and layer chicks) was indirectly assessed by looking into the odds of targeted serotypes detection. Thirdly, it was appraised if Salmonella prevalence can significantly increase during broilers and layers production. In addition, it was tested if being tested negative at the end of production in broilers when tested positive at the entrance is serotype dependent (targeted vs. non-targeted serotypes). Results showed that, firstly, the prevalence patterns of the listed serotypes were inconstant over time and across the FC. Secondly, the odds of Salmonella targeted serotype detection in 1-day-old broiler and in 1-day-old layer flocks were lower than in breeder flocks while, thirdly, infection during broiler and layer production can lead to significant increase in positivity in subsequent samples. Finally, being infected by a targeted or by non-targeted serotype at the entrance of the flock poorly reflects the Salmonella status at the end of production. Note that this study did not make a distinction between the different sources of contamination and the effects of sampling methods and isolation methods should be subject to further investigation.
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Affiliation(s)
- Mickaël Cargnel
- Department of epidemiology and public health, Service of veterinary epidemiology, Sciensano, Brussels, Belgium
| | - Maria-Eleni Filippitzi
- Department of epidemiology and public health, Service of veterinary epidemiology, Sciensano, Brussels, Belgium
| | - Dieter Van Cauteren
- Department of epidemiology and public health, Service of epidemiology of infectious diseases, Sciensano, Brussels, Belgium
| | - Wesley Mattheus
- Department of human infectious diseases, Service of bacterial diseases, Sciensano, Brussels, Belgium
| | | | - Ludivine Cambier
- Federal Agency for the Safety of the Food Chain, Brussels, Belgium
| | - Sarah Welby
- Department of epidemiology and public health, Service of veterinary epidemiology, Sciensano, Brussels, Belgium.,UCB Brussels Belgium, Brussels, Belgium
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Falay D, Hardy L, Tanzito J, Lunguya O, Bonebe E, Peeters M, Mattheus W, Van Geet C, Verheyen E, Akaibe D, Katuala P, Ngbonda D, Weill FX, Pardos de la Gandara M, Jacobs J. Urban rats as carriers of invasive Salmonella Typhimurium sequence type 313, Kisangani, Democratic Republic of Congo. PLoS Negl Trop Dis 2022; 16:e0010740. [PMID: 36067238 PMCID: PMC9481155 DOI: 10.1371/journal.pntd.0010740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2022] [Revised: 09/16/2022] [Accepted: 08/13/2022] [Indexed: 11/18/2022] Open
Abstract
Background Invasive non-typhoidal Salmonella (iNTS–mainly serotypes Enteritidis and Typhimurium) are major causes of bloodstream infections in children in sub-Saharan Africa, but their reservoir remains unknown. We assessed iNTS carriage in rats in an urban setting endemic for iNTS carriage and compared genetic profiles of iNTS from rats with those isolated from humans. Methodology/Principal findings From April 2016 to December 2018, rats were trapped in five marketplaces and a slaughterhouse in Kisangani, Democratic Republic of the Congo. After euthanasia, blood, liver, spleen, and rectal content were cultured for Salmonella. Genetic relatedness between iNTS from rats and humans—obtained from blood cultures at Kisangani University Hospital—was assessed with multilocus variable-number tandem repeat (VNTR) analysis (MLVA), multilocus sequence typing (MLST) and core-genome MLST (cgMLST). 1650 live-capture traps yielded 566 (34.3%) rats (95.6% Rattus norvegicus, 4.4% Rattus rattus); 46 (8.1%) of them carried Salmonella, of which 13 had more than one serotype. The most common serotypes were II.42:r:- (n = 18 rats), Kapemba (n = 12), Weltevreden and Typhimurium (n = 10, each), and Dublin (n = 8). Salmonella Typhimurium belonged to MLST ST19 (n = 7 rats) and the invasive ST313 (n = 3, isolated from deep organs but not from rectal content). Sixteen human S. Typhimurium isolates (all ST313) were available for comparison: MLVA and cgMLST revealed two distinct rat-human clusters involving both six human isolates, respectively, i.e. in total 12/16 human ST313 isolates. All ST313 Typhimurium isolates from rats and humans clustered with the ST313 Lineage 2 isolates and most were multidrug resistant; the remaining isolates from rats including S. Typhimurium ST19 were pan-susceptible. Conclusion The present study provides evidence of urban rats as potential reservoirs of S. Typhimurium ST313 in an iNTS endemic area in sub-Saharan Africa. Dadi (°1974, DR Congo) is a Medical Doctor (Kisangani University 2005) with a master in pediatrics (Kisangani University 2015) with special interest in infectious diseases and tropical medicine. He has 11 years of field research experience. He was team member of scientific expedition “Boyekoli Ebale Congo” in 2010 as medical support for the researchers. He conducted work field in a multidisciplinary framework with biologists from faculty of sciences (university of Kisangani) exploring zoonotic diseases in several places in the Congo. Currently, he is doing his PhD research at KU Leuven and Institute of Tropical Medicine Antwerp (ITM), Belgium. Passionate about transmissible diseases, Dadi is exploring the potential reservoirs of non-typhoidal Salmonella in Kisangani, DR Congo.
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Affiliation(s)
- Dadi Falay
- Department of Pediatrics, University Hospital of Kisangani, Kisangani, the Democratic Republic of the Congo
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Liselotte Hardy
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- * E-mail:
| | - Jacques Tanzito
- Biodiversity Monitoring Center (Centre de Surveillance de la Biodiversité, CSB), Faculty of Science, University of Kisangani, Kisangani, the Democratic Republic of the Congo
| | - Octavie Lunguya
- Department of Medical Biology, National Institute for Biomedical Research, Kinshasa, the Democratic Republic of the Congo
- Department of Microbiology, University Teaching Hospital of Kinshasa, Kinshasa, Democratic Republic of the Congo
| | - Edmonde Bonebe
- Department of Medical Biology, National Institute for Biomedical Research, Kinshasa, the Democratic Republic of the Congo
| | - Marjan Peeters
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Wesley Mattheus
- Sciensano, Infectious Diseases in Humans, Bacterial Diseases, Brussels, Belgium
| | - Chris Van Geet
- Department of Cardiovascular Sciences and Pediatrics, KU Leuven and University Hospital Leuven, Leuven, Belgium
| | - Erik Verheyen
- OD Taxonomy & Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium
- Evolutionary Ecology, University of Antwerp, Antwerp, Belgium
| | - Dudu Akaibe
- Biodiversity Monitoring Center (Centre de Surveillance de la Biodiversité, CSB), Faculty of Science, University of Kisangani, Kisangani, the Democratic Republic of the Congo
| | - Pionus Katuala
- Biodiversity Monitoring Center (Centre de Surveillance de la Biodiversité, CSB), Faculty of Science, University of Kisangani, Kisangani, the Democratic Republic of the Congo
| | - Dauly Ngbonda
- Department of Pediatrics, University Hospital of Kisangani, Kisangani, the Democratic Republic of the Congo
| | - François-Xavier Weill
- Institut Pasteur, Université Paris Cité, Unité des bactéries pathogènes entériques, Paris, France
| | | | - Jan Jacobs
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
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Chanamé Pinedo L, Franz E, van den Beld M, Van Goethem N, Mattheus W, Veldman K, Bosch T, Mughini-Gras L, Pijnacker R. Changing epidemiology of Salmonella Enteritidis human infections in the Netherlands and Belgium, 2006 to 2019: a registry-based population study. Euro Surveill 2022; 27. [PMID: 36148675 PMCID: PMC9511682 DOI: 10.2807/1560-7917.es.2022.27.38.2101174] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BackgroundSalmonellosis remains the second most common zoonosis in the European Union despite a long-term decreasing trend. However, this trend has been reported to have stagnated in recent years, particularly for Salmonella enterica serotype Enteritidis (SE).AimTo describe temporal changes in the incidence of SE human infections, and in its associated factors between 2006 and 2019. In addition, we aim to determine which factors influenced the stagnated trend seen in recent years.MethodsData on culture-confirmed SE human infections from national surveillance registries in the Netherlands and Belgium between 2006 and 2019 were analysed using multivariable negative-binomial regression models with restricted cubic splines.ResultsSE incidence was significantly higher in summer and autumn than winter, in persons aged 0-4 years and 5-14 years than in persons ≥ 60 years, and increased with increasing proportions of travel-related and resistant SE infections. SE incidence decreased significantly in both countries until 2015, followed by an increasing trend, which was particularly pronounced in the Netherlands. Potential SE outbreaks in both countries and invasive infections in the Netherlands also increased after 2015.ConclusionThe increase in potential outbreaks and invasive infections since 2015 may partially explain the observed reversal of the decreasing trend. While these results provide insights into the possible causes of this trend reversal, attention should also be given to factors known to influence SE epidemiology at primary (animal) production and pathogen genomic levels.
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Affiliation(s)
- Linda Chanamé Pinedo
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Eelco Franz
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Maaike van den Beld
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | | | - Wesley Mattheus
- National Reference Centre for Salmonella and Shigella, Sciensano, Brussels, Belgium
| | - Kees Veldman
- Wageningen Bioveterinary Research (WBVR), Lelystad, the Netherlands
| | - Thijs Bosch
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Lapo Mughini-Gras
- Institute for Risk Assessment Sciences, Utrecht University, Utrecht, the Netherlands.,Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
| | - Roan Pijnacker
- Centre for Infectious Disease Control, National Institute for Public Health and the Environment (RIVM), Bilthoven, the Netherlands
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11
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Moerman G, Verleyen D, Rogiers P, Hoste J, Mattheus W, Floré K. Meningococcal pericarditis caused by the MenW:cc11 strain in an older adult. Acta Clin Belg 2022; 78:254-256. [PMID: 35904255 DOI: 10.1080/17843286.2022.2107315] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
Abstract
INTRODUCTION Invasive meningococcal disease (IMD) caused by Neisseria meningitidis is a disease with a high mortality and morbidity rate. Serogroup W meningococci (MenW) used to be associated with sporadic disease worldwide. In recent years, a surge in MenW incidence is being observed. REPORT An older adult presenting with acute onset shortness of breath, chest pain and fever, was diagnosed with pericarditis with meningococcemia due to MenW:ST11 strain. MenW infections are reported to have a higher case fatality rate and atypical clinical presentations: MenW has been identified in patients presenting with pneumonia, gastro-intestinal symptoms, arthritis, and pericarditis. DISCUSSION In Belgium, the National Reference Laboratory is also noticing an increase in serogroup Wmeningococcal disease. Recent epidemiological data for Belgium is reported in the article. MenW infections are reported to have a higher case fatality rate and atypical clinical presentations: MenW has been identified in patients presenting with pneumonia, gastro-intestinal symptoms, arthritis, and pericarditis. CONCLUSION When factors for poor prognosis are present in patients with pericarditi clinicians should be vigilant and search for the underlying aetiology .
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Affiliation(s)
| | - D Verleyen
- Cardiology, AZ Sint Lucas, Brugge, Belgium
| | - Ph Rogiers
- Pulmonology, AZ Sint Lucas, Brugge, Belgium
| | - J Hoste
- Internal Medicine, AZ Sint Lucas, Brugge, Belgium
| | - W Mattheus
- Sciensano, Meningococcal National Reference Centre, Ukkel, Belgium
| | - K Floré
- Laboratory Medicine, Medical Microbiology, AZ Sint Lucas Brugge, Belgium
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12
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Tack B, Phoba MF, Thong P, Lompo P, Hupko C, Desmet S, Martiny D, Mattheus W, De La Gandara MP, Mbuyi-Kalonji L, Kuijpers L, Prevost B, Barbé B, Vandenberg O, Lunguya O, Ruiz J, Jacobs J, Hardy L. Epidemiological cut-off value and antibiotic susceptibility test methods for azithromycin in a collection of multi-country invasive non-typhoidal Salmonella. Clin Microbiol Infect 2022; 28:1615-1623. [PMID: 35738320 DOI: 10.1016/j.cmi.2022.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 06/03/2022] [Accepted: 06/09/2022] [Indexed: 11/29/2022]
Abstract
OBJECTIVES Azithromycin is an alternative to treat invasive non-typhoidal Salmonella (iNTS) infections. We determined its epidemiological cut-off (ECOFF) and compared azithromycin susceptibility testing methods for iNTS. METHODS We used EUCAST ECOFFinder to determine the minimum inhibitory concentrations (MIC; obtained by broth microdilution) ECOFF and corresponding disk zone diameters of 515 iNTS from blood cultures in DR Congo, Burkina Faso, Rwanda, and Cambodia. Transferable resistance mechanisms were determined by polymerase chain reaction. We compared azithromycin susceptibility testing by semi-automated broth microdilution (customized Sensititre panel; reference), agar dilution, gradient tests (bioMérieux, Liofilchem, HiMedia; read at 80% (MIC80%) and 100% inhibition (MIC100%)) and disk diffusion (Rosco, Oxoid, BD, Liofilchem) for 161 wild and 198 non-wild type iNTS. RESULTS Azithromycin MIC ECOFF was 16 mg/l corresponding to a 12mm zone diameter; mphA was detected in 192/197 non-wild and 0/47 wild type iNTS. Categorical agreement was excellent (≥98%) for all methods. Essential agreement was very good for agar dilution (>90%), but moderate for gradient tests (MIC80%: 52 - 71% and MIC100%: 72 - 91%). Repeatability was good for all methods/brands. Interreader agreement was high for broth microdilution and agar dilution (all ≤1 twofold dilution difference) and disk diffusion (>96% ≤3mm difference), but lower for gradient tests (MIC80% & MIC100%: 83 - 94% ≤1 twofold dilution difference). CONCLUSIONS Azithromycin ECOFF of iNTS was 16 mg/l, i.e. equal to Salmonella Typhi. Disk diffusion is an accurate, precise, and user-friendly alternatives for agar dilution and broth microdilution. Reading gradient tests at 100% instead of 80% inhibition improved accuracy and precision.
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Affiliation(s)
- Bieke Tack
- Department of Clinical Sciences, Institute of Tropical Medicine - Antwerp Belgium; Department of Microbiology, Immunology and Transplantation, KU Leuven - Leuven Belgium.
| | - Marie-France Phoba
- Department of Microbiology, National Institute for Biomedical Research - Kinshasa Democratic Republic of the Congo; Department of Microbiology, University Teaching Hospital of Kinshasa - Kinshasa Democratic Republic of the Congo
| | - Phe Thong
- Sihanouk Hospital Center of Hope - Phnom Penh Cambodia
| | | | | | - Stefanie Desmet
- Department of Microbiology, Immunology and Transplantation, KU Leuven - Leuven Belgium; Clinical Department of Laboratory Medicine, University Hospitals Leuven - Leuven Belgium
| | - Delphine Martiny
- Department of Microbiology, Laboratoire des Hôpitaux Universitaires de Bruxelles - Universitaire Laboratorium Brussel (LHUB-ULB) - Bruxelles Belgium; Faculté de Médecine et Pharmacie, Université de Mons (UMONS), Mons, Belgium
| | - Wesley Mattheus
- Division of Human Bacterial Diseases, Sciensano - Uccle Belgium
| | - Maria Pardos De La Gandara
- Institut Pasteur, Université de Paris, Unité des Bactéries pathogènes entériques, Centre National de Référence des E. coli,Shigella et Salmonella - Paris France
| | - Lisette Mbuyi-Kalonji
- Department of Microbiology, National Institute for Biomedical Research - Kinshasa Democratic Republic of the Congo; Department of Microbiology, University Teaching Hospital of Kinshasa - Kinshasa Democratic Republic of the Congo
| | - Laura Kuijpers
- Department of Infectious Diseases, Leiden University Medical Center - Leiden The Netherlands
| | - Benoit Prevost
- Department of Microbiology, Laboratoire des Hôpitaux Universitaires de Bruxelles - Universitaire Laboratorium Brussel (LHUB-ULB) - Bruxelles Belgium
| | - Barbara Barbé
- Department of Clinical Sciences, Institute of Tropical Medicine - Antwerp Belgium
| | - Olivier Vandenberg
- Center for Environmental Health and Occupational Health, School of Public Health, Université Libre de Bruxelles - Brussels Belgium; Innovation and Business Development Unit, Laboratoire des Hôpitaux Universitaires de Bruxelles - Universitaire Laboratorium Brussel (LHUB-ULB) - Bruxelles Belgium; Division of Infection and Immunity, Faculty of Medical Sciences, University College London - London United Kingdom
| | - Octavie Lunguya
- Department of Microbiology, National Institute for Biomedical Research - Kinshasa Democratic Republic of the Congo; Department of Microbiology, University Teaching Hospital of Kinshasa - Kinshasa Democratic Republic of the Congo
| | - Joaquim Ruiz
- Grupo de Investigación en Dinámicas y Epidemiología de la Resistencia a Antimicrobianos - "One Health", Universidad Cientifica del Sur - Lima Peru
| | - Jan Jacobs
- Department of Clinical Sciences, Institute of Tropical Medicine - Antwerp Belgium; Department of Microbiology, Immunology and Transplantation, KU Leuven - Leuven Belgium
| | - Liselotte Hardy
- Department of Clinical Sciences, Institute of Tropical Medicine - Antwerp Belgium
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13
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Larkin L, Pardos de la Gandara M, Hoban A, Pulford C, Jourdan-Da Silva N, de Valk H, Browning L, Falkenhorst G, Simon S, Lachmann R, Dryselius R, Karamehmedovic N, Börjesson S, van Cauteren D, Laisnez V, Mattheus W, Pijnacker R, van den Beld M, Mossong J, Ragimbeau C, Vergison A, Thorstensen Brandal L, Lange H, Garvey P, Nielsen CS, Herrera León S, Varela C, Chattaway M, Weill FX, Brown D, McKeown P. Investigation of an international outbreak of multidrug-resistant monophasic Salmonella Typhimurium associated with chocolate products, EU/EEA and United Kingdom, February to April 2022. Euro Surveill 2022; 27. [PMID: 35426359 PMCID: PMC9012091 DOI: 10.2807/1560-7917.es.2022.27.15.2200314] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
An extensive multi-country outbreak of multidrug-resistant monophasic Salmonella Typhimurium infection in 10 countries with 150 reported cases, predominantly affecting young children, has been linked to chocolate products produced by a large multinational company. Extensive withdrawals and recalls of multiple product lines have been undertaken. With Easter approaching, widespread product distribution and the vulnerability of the affected population, early and effective real-time sharing of microbiological and epidemiological information has been of critical importance in effectively managing this serious food-borne incident.
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Affiliation(s)
- Lesley Larkin
- Gastrointestinal Infections and Food Safety (One Health Unit), UK Health Security Agency, London, United Kingdom
| | - Maria Pardos de la Gandara
- Institut Pasteur, Université Paris Cité, Centre National de Référence des E. coli, Shigella et Salmonella, Unité des Bactéries pathogènes entériques, Paris, France
| | - Ann Hoban
- Gastrointestinal Infections and Food Safety (One Health Unit), UK Health Security Agency, London, United Kingdom
| | - Caisey Pulford
- Gastrointestinal Infections and Food Safety (One Health Unit), UK Health Security Agency, London, United Kingdom
| | | | - Henriette de Valk
- Sante Publique France, Direction des Maladies Infectieuses Unité EAZ, Paris, France
| | - Lynda Browning
- Clinical and Protecting Health Directorate, Public Health Scotland, Glasgow, United Kingdom
| | - Gerhard Falkenhorst
- Robert Koch Institute, Department of Infectious Disease Epidemiology FG 35 - Gastrointestinal Infections, Zoonoses and Tropical Infections, Berlin, Germany
| | - Sandra Simon
- Robert Koch Institute, Department of Infectious Diseases, Unit for Enteropathogenic Bacteria and Legionella / National Reference Centre for Salmonella and other Bacterial Enterics, Wernigerode, Germany
| | - Raskit Lachmann
- Robert Koch Institute, Department of Infectious Disease Epidemiology FG 35 - Gastrointestinal Infections, Zoonoses and Tropical Infections, Berlin, Germany
| | - Rikard Dryselius
- Public Health Agency of Sweden, Unit for Zoonoses and Antibiotic Resistance, Stockholm, Sweden
| | - Nadja Karamehmedovic
- Public Health Agency of Sweden, Unit for laboratory surveillance of bacterial pathogens, Stockholm, Sweden
| | - Stefan Börjesson
- Public Health Agency of Sweden, Unit for Zoonoses and Antibiotic Resistance, Stockholm, Sweden
| | - Dieter van Cauteren
- Epidemiology of infectious diseases, Department of Epidemiology and Public Health, Sciensano, Brussels, Belgium
| | - Valeska Laisnez
- ECDC Fellowship Programme, Field Epidemiology path (EPIET), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
- Epidemiology of infectious diseases, Department of Epidemiology and Public Health, Sciensano, Brussels, Belgium
| | - Wesley Mattheus
- National Reference Centre for Salmonella and Shigella, Sciensano, Brussels, Belgium
| | - Roan Pijnacker
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, Bilthoven, Netherlands
| | - Maaike van den Beld
- National Institute for Public Health and the Environment (RIVM), Centre for Infectious Disease Control, Bilthoven, Netherlands
| | - Joël Mossong
- Health Inspection, Health Directorate, Luxembourg
| | - Catherine Ragimbeau
- Laboratoire National de Santé, Epidemiology and Microbial Genomics, Dudelange, Luxembourg
| | | | - Lin Thorstensen Brandal
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | - Heidi Lange
- Department of Infection Control and Preparedness, Norwegian Institute of Public Health, Oslo, Norway
| | | | - Charlotte Salgaard Nielsen
- ECDC Fellowship Programme, Field Epidemiology path (EPIET), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
- HSE -Health Protection Surveillance Centre, Dublin, Ireland
| | - Silvia Herrera León
- Instituto de Salud Carlos III. Centro Nacional de Microbiología, Madrid, Spain
| | - Carmen Varela
- Instituto de Salud Carlos III. CIBER epidemiología y salud pública. Madrid, Spain
| | - Marie Chattaway
- Specialist Scientific Reference Service (Salmonella), Gastrointestinal Bacteria Reference Unit, UK Health Security Agency, London, United Kingdom
| | - François-Xavier Weill
- Institut Pasteur, Université Paris Cité, Centre National de Référence des E. coli, Shigella et Salmonella, Unité des Bactéries pathogènes entériques, Paris, France
| | - Derek Brown
- Scottish Microbiology Reference Laboratories, Glasgow, United Kingdom
| | - Paul McKeown
- HSE -Health Protection Surveillance Centre, Dublin, Ireland
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14
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Jacquinet S, Mattheus W, Quoilin S, Wyndham-Thomas C, Martin C, Van der Linden D, Mulder A, Frère J, Schirvel C. Outbreak of invasive meningococcal disease caused by a meningococcus serogroup B in a nursery school, Wallonia, Belgium, 2018. Euro Surveill 2022; 27. [PMID: 35241214 PMCID: PMC8895469 DOI: 10.2807/1560-7917.es.2022.27.9.2100224] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Although most invasive meningococcal disease (IMD) cases are sporadic without identified transmission links, outbreaks can occur. We report three cases caused by meningococcus B (MenB) at a Belgian nursery school over 9 months. The first two cases of IMD occurred in spring and summer 2018 in healthy children (aged 3–5 years) attending the same classroom. Chemoprophylaxis was given to close contacts of both cases following regional guidelines. The third case, a healthy child of similar age in the same class as a sibling of one case, developed disease in late 2018. Microbiological analyses revealed MenB with identical finetype clonal complex 269 for Case 1 and 3 (unavailable for Case 2). Antimicrobial susceptibility testing revealed no antibiotic resistance. Following Case 3, after multidisciplinary discussion, chemoprophylaxis and 4CMenB (Bexsero) vaccination were offered to close contacts. In the 12-month follow-up of Case 3, no additional cases were reported by the school. IMD outbreaks are difficult to manage and generate public anxiety, particularly in the case of an ongoing cluster, despite contact tracing and management. This outbreak resulted in the addition of MenB vaccination to close contacts in Wallonian regional guidelines, highlighting the potential need and added value of vaccination in outbreak management.
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Affiliation(s)
- Stéphanie Jacquinet
- Epidemiology of infectious diseases, Department of Epidemiology and Public Health, Sciensano, Brussels, Belgium
| | - Wesley Mattheus
- National Reference Centre for Neisseria meningitidis, Sciensano, Brussels, Belgium
| | - Sophie Quoilin
- Epidemiology of infectious diseases, Department of Epidemiology and Public Health, Sciensano, Brussels, Belgium
| | - Chloé Wyndham-Thomas
- Epidemiology of infectious diseases, Department of Epidemiology and Public Health, Sciensano, Brussels, Belgium
| | - Charlotte Martin
- Infectious Diseases Department, CHU Saint-Pierre, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Dimitri Van der Linden
- Institut de Recherche Expérimentale et Clinique (IREC), UCLouvain, Brussels, Belgium.,Pediatric Infectious Diseases, General Pediatrics, Pediatric Department Cliniques universitaires Saint-Luc, Brussels, Belgium
| | - André Mulder
- Pediatric Intensive Care Unit, Centre Hospitalier Chrétien (CHC) Liège, Belgium
| | - Julie Frère
- University Department of Paediatrics, Centre Hospitalier Universitaire (CHU) Liège, Belgium
| | - Carole Schirvel
- Agence pour une vie de qualité, infection prevention and control, Wallonia, Belgium
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15
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Fischer N, Maex M, Mattheus W, Van den Bossche A, Van Cauteren D, Laisnez V, Hammami N, Ceyssens PJ. Genomic epidemiology of persistently circulating MDR Shigella sonnei strains associated with men who have sex with men (MSM) in Belgium (2013-19). J Antimicrob Chemother 2021; 77:89-97. [PMID: 34673959 PMCID: PMC8730680 DOI: 10.1093/jac/dkab377] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Accepted: 09/22/2021] [Indexed: 11/13/2022] Open
Abstract
Objectives Shigella sonnei resistant to first-line antibiotics azithromycin and ciprofloxacin are on the rise globally. The aim of this study was to describe the epidemiology of MDR S. sonnei in Belgium and to identify origins and circulating clusters through WGS. Methods We undertook demographic, temporal and geographical analysis of 930 S. sonnei isolates submitted to the Belgian National Reference Centre for Salmonella and Shigella between 2017 and 2019. Phylogenetic analysis of WGS data, genotyping and identification of genetic markers of antimicrobial resistance was performed on 372 Belgian isolates submitted between 2013 and 2019. Results S. sonnei was identified in 75% (930/1253) of Belgian Shigella isolates submitted between 2017 and 2019. Overall, 7% (69/930) of isolates were resistant to ciprofloxacin alone, 6% (57/930) showed reduced susceptibility to azithromycin alone, and 24% (223/930) exhibited both. Men were at higher risk of carrying a double resistant S. sonnei strain, compared with women (risk ratio = 8.6, 95% CI = 5.4–13.9). Phylogenetic analysis revealed four independent Belgian clusters of persistently circulating MDR strains, associated with men who have sex with men (MSM) and of the same genotypes as previously described international MSM-related clades. Belgian isolates carried various incompatibility (Inc)-type plasmids, the SpA plasmid and ESBL genes. Conclusions In Belgium, S. sonnei isolates from men are much more likely to be resistant to important first-line antibiotics than isolates from women. Multiple co-circulating MDR S. sonnei clusters of different genotypes were identified in the MSM community. Further studies on risk groups are needed for targeted prevention, improved clinical and public health management and antimicrobial stewardship in Belgium.
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Affiliation(s)
- Natalie Fischer
- European Programme for Public Health Microbiology (EUPHEM), European Centre for Disease Prevention and Control (ECDC), Gustav III:s Boulevard 40, 169 73 Solna, Sweden.,Division of Human Bacterial Diseases, Sciensano, Rue Engeland 642, 1180 Uccle, Belgium
| | - Margo Maex
- Division of Human Bacterial Diseases, Sciensano, Rue Engeland 642, 1180 Uccle, Belgium
| | - Wesley Mattheus
- Division of Human Bacterial Diseases, Sciensano, Rue Engeland 642, 1180 Uccle, Belgium
| | - An Van den Bossche
- Division of Human Bacterial Diseases, Sciensano, Rue Engeland 642, 1180 Uccle, Belgium
| | - Dieter Van Cauteren
- Service Epidemiology of Infectious Diseases, Sciensano, Rue Ernest Blerot 1, 1070 Anderlecht, Belgium
| | - Valeska Laisnez
- Service Epidemiology of Infectious Diseases, Sciensano, Rue Ernest Blerot 1, 1070 Anderlecht, Belgium.,Agentschap Zorg en Gezondheid, Koning Albert-II-laan 35 bus 33, 1030 Brussels, Belgium
| | - Naïma Hammami
- Agentschap Zorg en Gezondheid, Koning Albert-II-laan 35 bus 33, 1030 Brussels, Belgium
| | - Pieter-Jan Ceyssens
- Division of Human Bacterial Diseases, Sciensano, Rue Engeland 642, 1180 Uccle, Belgium
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16
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Van Goethem N, Van Den Bossche A, Ceyssens PJ, Lajot A, Coucke W, Vernelen K, Roosens NHC, De Keersmaecker SCJ, Van Cauteren D, Mattheus W. Coverage of the national surveillance system for human Salmonella infections, Belgium, 2016-2020. PLoS One 2021; 16:e0256820. [PMID: 34437638 PMCID: PMC8389443 DOI: 10.1371/journal.pone.0256820] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Accepted: 08/16/2021] [Indexed: 12/16/2022] Open
Abstract
Introduction The surveillance of human salmonellosis in Belgium is dependent on the referral of human Salmonella isolates to the National Reference Center (NRC). Knowledge of current diagnostic practices and the coverage of the national Salmonella surveillance system are important to correctly interpret surveillance data and trends over time, to estimate the true burden of salmonellosis in Belgium, and to evaluate the appropriateness of implementing whole-genome sequencing (WGS) at this central level. Methods The coverage of the NRC was defined as the proportion of all diagnosed human Salmonella cases in Belgium reported to the NRC and was assessed for 2019 via a survey among all licensed Belgian medical laboratories in 2019, and for 2016–2020 via a capture-recapture study using the Sentinel Network of Laboratories (SNL) as the external source. In addition, the survey was used to assess the impact of the implementation of culture-independent diagnostic tests (CIDTs) at the level of peripheral laboratory sites, as a potential threat to national public health surveillance programs. Results The coverage of the NRC surveillance system was estimated to be 83% and 85%, based on the results of the survey and on the two-source capture-recapture study, respectively. Further, the results of the survey indicated a limited use of CIDTs by peripheral laboratories in 2019. Conclusion Given the high coverage and the limited impact of CIDTs on the referral of isolates, we may conclude that the NRC can confidently monitor the epidemiological situation and identify outbreaks throughout the country. These findings may guide the decision to implement WGS at the level of the NRC and may improve estimates of the true burden of salmonellosis in Belgium.
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Affiliation(s)
- Nina Van Goethem
- Scientific Directorate of Epidemiology and Public Health, Sciensano, Brussels, Belgium
- Department of Epidemiology and Biostatistics, Institut de Recherche Expérimentale et Clinique, Faculty of Public Health, Université Catholique de Louvain, Woluwe-Saint-Lambert, Belgium
- * E-mail:
| | - An Van Den Bossche
- National Reference Centre for Salmonella and Shigella, Sciensano, Brussels, Belgium
| | - Pieter-Jan Ceyssens
- National Reference Centre for Salmonella and Shigella, Sciensano, Brussels, Belgium
| | - Adrien Lajot
- Scientific Directorate of Epidemiology and Public Health, Sciensano, Brussels, Belgium
| | - Wim Coucke
- Quality of laboratories, Sciensano, Brussels, Belgium
| | - Kris Vernelen
- Quality of laboratories, Sciensano, Brussels, Belgium
| | | | | | - Dieter Van Cauteren
- Scientific Directorate of Epidemiology and Public Health, Sciensano, Brussels, Belgium
| | - Wesley Mattheus
- National Reference Centre for Salmonella and Shigella, Sciensano, Brussels, Belgium
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17
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Gutema FD, Abdi RD, Agga GE, Firew S, Rasschaert G, Mattheus W, Crombe F, Duchateau L, Gabriël S, De Zutter L. Assessment of beef carcass contamination with Salmonella and E. coli O 157 in slaughterhouses in Bishoftu, Ethiopia. FoodContamination 2021. [DOI: 10.1186/s40550-021-00082-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
Abstract
Background
Salmonella and E. coli O157 are common causes of foodborne diseases. Evisceration and de-hiding steps can lead to carcass contamination during slaughter operation. In Ethiopia, information on the association between the presence of these pathogens in the rectal content and/or on the hide of cattle and their presence on the carcass is lacking.
Methods
The aim of this study was to assess the sources of beef carcass contamination with Salmonella and E. coli O157 during slaughter. Rectal contents and hide- and carcass-swabs (from three sites: foreleg, brisket and hind leg) were collected from 70 beef cattle at two small scale slaughterhouses. Isolates were genotyped by the Pulsed Field Gel Electrophoresis method and tested for resistance against 14 microbial drugs.
Results
Salmonella was detected at equal proportions (7.1%) in rectal content samples and hide swabs. E. coli O157 was detected in 8.6% of the rectal contents and 4.3% of the hide swabs. The proportion of contaminated carcasses was 8.6% for Salmonella and 7.1% for E. coli O157. Genetic linkage between the Salmonella and E. coli O157 isolates from the rectal contents and/or hides and carcasses were observed only in a few cases (2 and 1 carcasses, respectively) indicating the limited direct transfer of the pathogens from the feces and/or hide to the carcass during slaughter. Most carcasses became positive by cross contamination. All the S. Typhimurium isolates (n = 8) were multidrug resistant being resistant to ampicillin, chloramphenicol, sulfamethoxazole and tetracycline. The two S. Dublin isolates were resistant to colistin. All E. coli O157 isolates were susceptible to the antimicrobials tested.
Conclusion
The results indicated that cross contamination may be an important source for carcass contamination.
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18
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Buytaers FE, Saltykova A, Mattheus W, Verhaegen B, Roosens NHC, Vanneste K, Laisnez V, Hammami N, Pochet B, Cantaert V, Marchal K, Denayer S, De Keersmaecker SC. Application of a strain-level shotgun metagenomics approach on food samples: resolution of the source of a Salmonella food-borne outbreak. Microb Genom 2021; 7:000547. [PMID: 33826490 PMCID: PMC8208685 DOI: 10.1099/mgen.0.000547] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 02/23/2021] [Indexed: 02/04/2023] Open
Abstract
Food-borne outbreak investigation currently relies on the time-consuming and challenging bacterial isolation from food, to be able to link food-derived strains to more easily obtained isolates from infected people. When no food isolate can be obtained, the source of the outbreak cannot be unambiguously determined. Shotgun metagenomics approaches applied to the food samples could circumvent this need for isolation from the suspected source, but require downstream strain-level data analysis to be able to accurately link to the human isolate. Until now, this approach has not yet been applied outside research settings to analyse real food-borne outbreak samples. In September 2019, a Salmonella outbreak occurred in a hotel school in Bruges, Belgium, affecting over 200 students and teachers. Following standard procedures, the Belgian National Reference Center for human salmonellosis and the National Reference Laboratory for Salmonella in food and feed used conventional analysis based on isolation, serotyping and MLVA (multilocus variable number tandem repeat analysis) comparison, followed by whole-genome sequencing, to confirm the source of the contamination over 2 weeks after receipt of the sample, which was freshly prepared tartar sauce in a meal cooked at the school. Our team used this outbreak as a case study to deliver a proof of concept for a short-read strain-level shotgun metagenomics approach for source tracking. We received two suspect food samples: the full meal and some freshly made tartar sauce served with this meal, requiring the use of raw eggs. After analysis, we could prove, without isolation, that Salmonella was present in both samples, and we obtained an inferred genome of a Salmonella enterica subsp. enterica serovar Enteritidis that could be linked back to the human isolates of the outbreak in a phylogenetic tree. These metagenomics-derived outbreak strains were separated from sporadic cases as well as from another outbreak circulating in Europe at the same time period. This is, to our knowledge, the first Salmonella food-borne outbreak investigation uniquely linking the food source using a metagenomics approach and this in a fast time frame.
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Affiliation(s)
- Florence E. Buytaers
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Assia Saltykova
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
| | - Wesley Mattheus
- National Reference Center for Salmonella and Shigella spp., Sciensano, Brussels, Belgium
| | - Bavo Verhaegen
- National Reference Laboratory for Salmonella and Food-Borne Infections, Food-Borne Pathogens, Sciensano, Brussels, Belgium
| | | | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | | | - Brigitte Pochet
- Federal Agency for the Security of the Food Chain, Brussels, Belgium
| | - Vera Cantaert
- Federal Agency for the Security of the Food Chain, Brussels, Belgium
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium
- Department of Information Technology, IDlab, IMEC, Ghent University, Ghent, Belgium
- Department of Genetics, University of Pretoria, Pretoria, South Africa
| | - Sarah Denayer
- National Reference Laboratory for Salmonella and Food-Borne Infections, Food-Borne Pathogens, Sciensano, Brussels, Belgium
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19
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Ceyssens PJ, Van den Bossche A, Phan LK, Van Hoorde K, Mattheus W. A molecular assay for rapidly distinguishing the AviPro SALMONELLA VAC T vaccine strain from wild-type field isolates. J Microbiol Methods 2021; 184:106190. [PMID: 33766608 DOI: 10.1016/j.mimet.2021.106190] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Revised: 03/03/2021] [Accepted: 03/03/2021] [Indexed: 11/17/2022]
Abstract
Rapid differentiation of the AviPro Salmonella VAC T strain from wild-type Salmonella ser. Typhimurium isolates is essential for the monitoring of veterinary isolates and targeted control actions. The distinction between the two strain types is routinely made by phenotypic antimicrobial resistance testing, but this sometime leads to ambiguous results with major economic implications. In this study, we used whole-genome sequencing to identify conserved and specific mutations in resistance and virulence genes which enable to distinguish field and vaccine strains. Based on this information, we developed and validated (n = 199) a Luminex-based assay targeting seven specific single-nucleotide polymorphisms. This molecular test is able to distinguish both Salmonella ser. Typhimurium types with 100% sensitivity and specificity within one working day.
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Affiliation(s)
| | | | - Lac Kim Phan
- Unit of Human Bacterial Diseases, Sciensano, Belgium
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20
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Gutema FD, Rasschaert G, Agga GE, Merera O, Duguma AB, Abdi RD, Duchateau L, Mattheus W, Gabriël S, De Zutter L. Prevalence, Antimicrobial Resistance, and Molecular Characterization of Salmonella in Cattle, Beef, and Diarrheic Patients in Bishoftu, Ethiopia. Foodborne Pathog Dis 2021; 18:283-289. [PMID: 33567225 DOI: 10.1089/fpd.2020.2869] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Within Ethiopia, there is a lack of information on the genetic relatedness of Salmonella from cattle, beef, and diarrheic patients and its potential transmission from cattle to humans through consumption of contaminated beef. The objective of this study was to assess the prevalence and determine the serotypes, genetic relatedness, and antimicrobial resistance of Salmonella in cattle in two local slaughterhouses, in beef at retail shops, and in diarrheic patients in the only hospital in Bishoftu, Ethiopia. Salmonella was detected in 2.5% (6/240) of cattle samples, in 8.7% (11/127) of beef samples, and in 2.3% (5/216) of the diarrheic patients. Four Salmonella serotypes: Salmonella Typhimurium, Salmonella Eastbourne, Salmonella Saintpaul, and Salmonella Cotham were identified. Salmonella Typhimurium and Salmonella Eastbourne were isolated from cattle and beef, whereas Salmonella Saintpaul and Salmonella Cotham were isolated only from diarrheic patients. Except for serotype Salmonella Saintpaul, all isolates were grouped into five pulsotypes, of which two pulsotypes contained isolates from cattle and beef. Isolates from humans represented unique pulsotypes. Among the 22 Salmonella isolates tested, 95.5% were resistant to at least 1 of the 14 antimicrobials tested. Three Salmonella isolates originating from cattle were multidrug resistant. One human isolate was susceptible to all antimicrobials tested. More specifically, resistance to ampicillin, sulfamethoxazole, tetracycline, tigecycline, and trimethoprim were observed. The most frequently observed resistance was to sulfamethoxazole (90.9%, 20/22) followed by trimethoprim (22.7%, 5/22). The study revealed considerable Salmonella contamination of beef at retail shops, antimicrobial resistance to commonly used antimicrobials, and shared genetically similar Salmonella serotypes between cattle and beef; the link with humans could not be established. Still, the findings of Salmonella in cattle and beef, the propensity of transfer of Salmonella from cattle to beef coupled with the common consumption of raw/undercooked beef are likely to pose public health risk in Ethiopia.
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Affiliation(s)
- Fanta D Gutema
- Department of Microbiology, Immunology and Veterinary Public Health, College of Veterinary Medicine and Agriculture, Addis Ababa University, Bishoftu, Ethiopia.,Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Geertrui Rasschaert
- Technology and Food Science Unit, Flanders Research Institute for Agriculture, Fisheries and Food, Melle, Belgium
| | - Getahun E Agga
- Food Animal Environmental Systems Research Unit, U.S. Department of Agriculture, Agricultural Research Service, Bowling Green, Kentucky, USA
| | - Olana Merera
- College of Veterinary Medicine, Samara University, Samara, Ethiopia
| | - Addisu B Duguma
- Department of Internal Medicine, Bishoftu Hospital, Bishoftu, Ethiopia
| | - Reta D Abdi
- Department of Veterinary Biomedical Sciences, College of Veterinary Medicine, Long Island University, Greenvale, New York, USA
| | - Luc Duchateau
- Biometrics Research Center, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Wesley Mattheus
- Department of Human Bacterial Diseases, Sciensano, Brussels, Belgium
| | - Sarah Gabriël
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Lieven De Zutter
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
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Zeng H, Rasschaert G, De Zutter L, Mattheus W, De Reu K. Identification of the Source for Salmonella Contamination of Carcasses in a Large Pig Slaughterhouse. Pathogens 2021; 10:pathogens10010077. [PMID: 33477347 PMCID: PMC7831019 DOI: 10.3390/pathogens10010077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2020] [Revised: 01/11/2021] [Accepted: 01/14/2021] [Indexed: 11/16/2022] Open
Abstract
To identify the major source of Salmonella contamination in a pig slaughterhouse, samples were collected from the clean and unclean area and Salmonella isolates were further typed. Carcasses entering the clean area showed a Salmonella contamination rate of 96.7% in the oral cavity and 55.0% in the rectum content samples. Evisceration seemed not to be critical as the contamination rate of the carcasses was similar before (16.7%) and after (18.3%) this slaughter step. In the unclean area, a limited number of oral cavity samples were positive after bleeding, while a dramatic increase of positives was observed after dehairing. Salmonella was detected in up to 0.01 mL of the recycled water collected from the dehairing machine. Genotyping of Salmonella isolates showed that similar pulsotypes were present in the oral cavity and recycled water. Based on these observations it can be concluded that the recycled water used in the dehairing machine was the major source for the carcass contamination in this slaughterhouse.
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Affiliation(s)
- Hang Zeng
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Brusselsesteenweg 370, B-9090 Melle, Belgium; (H.Z.); (G.R.)
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium;
| | - Geertrui Rasschaert
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Brusselsesteenweg 370, B-9090 Melle, Belgium; (H.Z.); (G.R.)
| | - Lieven De Zutter
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium;
| | - Wesley Mattheus
- Infectious Diseases in Humans, Bacterial Diseases, Sciensano, B-1180 Brussels, Belgium;
| | - Koen De Reu
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Brusselsesteenweg 370, B-9090 Melle, Belgium; (H.Z.); (G.R.)
- Correspondence: ; Tel.: +32-9-272-3043
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22
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Zeng H, De Reu K, Gabriël S, Mattheus W, De Zutter L, Rasschaert G. Salmonella prevalence and persistence in industrialized poultry slaughterhouses. Poult Sci 2021; 100:100991. [PMID: 33610890 PMCID: PMC7905466 DOI: 10.1016/j.psj.2021.01.014] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Revised: 01/05/2021] [Accepted: 01/07/2021] [Indexed: 11/29/2022] Open
Abstract
Salmonella contamination sources and transmission routes were studied in 5 Belgian poultry slaughterhouses. Samples from the slaughter and cutting line after cleaning and disinfection were collected, as well as neck skin samples and thighs during slaughter of the first flock. In total, 680 swab and water samples were taken from the slaughter line before slaughter. In all slaughterhouses, Salmonella was notwithstanding cleaning and disinfection still isolated from the slaughter line before start of activities. The prevalence of Salmonella in the plucking area was 10.4% (38/365) (hanging area: 5.0%, scalding tank: 5.8%, plucking machine: 17.0%); in the evisceration room, 1.5% (2/138); and in the cutting area, 2.0% (3/149). No Salmonella (0/28) was found in samples from the chilling line. On neck skin samples taken from the various lines, Salmonella prevalence was 16.1% (48/299) after plucking, 16.0% (48/300) after evisceration, 23.3% (70/300) after chilling; on thighs, prevalence was 10.0% (24/240). Nine Salmonella serotypes were identified of which Salmonella Infantis was the most common serovar (53.8%), especially in slaughterhouse A. Two contamination causes were identified; first, although all flocks had an official Salmonella negative status, this was in one case incorrect and led to an enormous contamination of the neck skins of the flock and the slaughterline (i.e., cooling water). Second, molecular typing revealed cross-contamination from flocks slaughtered 1 d before sampling. Salmonella was apparently not always eliminated by the cleaning and disinfection process and able to contaminate the carcasses of the first slaughtered flock. In conclusion, the results of this study provided practical insights for poultry production to further improve their Salmonella control, for example, Salmonella status determination closer to the slaughter date, to adapt cleaning and disinfection protocols especially for critical machinery and better hygienic designed equipment.
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Affiliation(s)
- H Zeng
- Flanders Research Institute For Agriculture, Fisheries and Food (ILVO), B-9090 Melle, Belgium; Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
| | - K De Reu
- Flanders Research Institute For Agriculture, Fisheries and Food (ILVO), B-9090 Melle, Belgium
| | - S Gabriël
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
| | - W Mattheus
- Sciensano, Infectious Diseases in Humans, Bacterial Diseases, B-1180 Brussels, Belgium
| | - L De Zutter
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, B-9820 Merelbeke, Belgium
| | - G Rasschaert
- Flanders Research Institute For Agriculture, Fisheries and Food (ILVO), B-9090 Melle, Belgium.
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23
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Jones G, Pardos de la Gandara M, Herrera-Leon L, Herrera-Leon S, Varela Martinez C, Hureaux-Roy R, Abdallah Y, Nisavanh A, Fabre L, Renaudat C, Mossong J, Mattheus W, Huard C, Le Borgne C, de Valk H, Weill FX, Jourdan-Da Silva N. Outbreak of Salmonella enterica serotype Poona in infants linked to persistent Salmonella contamination in an infant formula manufacturing facility, France, August 2018 to February 2019. ACTA ACUST UNITED AC 2020; 24. [PMID: 30940315 PMCID: PMC6446512 DOI: 10.2807/1560-7917.es.2019.24.13.1900161] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
We describe a Salmonella Poona outbreak involving 31 infant cases in France. Following outbreak detection on 18 January 2019, consumption of rice-based infant formula manufactured at a facility in Spain was identified as the probable cause, leading to a recall on 24 January. Whole genome sequencing analysis linked present outbreak isolates to a 2010–11 S. Poona outbreak in Spain associated with formula manufactured in the same facility, indicating a persistent source of contamination.
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Affiliation(s)
| | - Maria Pardos de la Gandara
- Centre National de Référence des Escherichia coli, Shigella et Salmonella, Institut Pasteur, Paris, France
| | - Laura Herrera-Leon
- National Centre for Microbiology, CIBER Epidemiologia y Salud Publica, Instituto de Salud Carlos III, Madrid, Spain
| | - Silvia Herrera-Leon
- National Centre for Microbiology, CIBER Epidemiologia y Salud Publica, Instituto de Salud Carlos III, Madrid, Spain
| | - Carmen Varela Martinez
- National Centre for Epidemiology, CIBER Epidemiologia y Salud Publica, Instituto de Salud Carlos III, Madrid, Spain
| | - Roselyne Hureaux-Roy
- Directorate of the Ministry of Economy in charge of consumers' affairs, Paris, France
| | - Yasmine Abdallah
- Directorate of the Ministry of Economy in charge of consumers' affairs, Paris, France
| | | | - Laetitia Fabre
- Centre National de Référence des Escherichia coli, Shigella et Salmonella, Institut Pasteur, Paris, France
| | - Charlotte Renaudat
- Centre National de Référence des Escherichia coli, Shigella et Salmonella, Institut Pasteur, Paris, France
| | - Joël Mossong
- Department of Microbiology, Laboratoire National de Santé, Dudelange, Luxembourg
| | - Wesley Mattheus
- National Reference Centre for Salmonella and Shigella, Sciensano, Brussels, Belgium
| | - Cécile Huard
- Direction Santé et Aide aux Personnes, Commission Communautaire Commune, Brussels, Belgium
| | | | | | - François-Xavier Weill
- Centre National de Référence des Escherichia coli, Shigella et Salmonella, Institut Pasteur, Paris, France
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24
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Phoba MF, Barbé B, Ley B, Van Puyvelde S, Post A, Mattheus W, Deborggraeve S, Lunguya O, Jacobs J. High genetic similarity between non-typhoidal Salmonella isolated from paired blood and stool samples of children in the Democratic Republic of the Congo. PLoS Negl Trop Dis 2020; 14:e0008377. [PMID: 32614856 PMCID: PMC7331982 DOI: 10.1371/journal.pntd.0008377] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 05/08/2020] [Indexed: 01/29/2023] Open
Abstract
BACKGROUND Non-typhoidal Salmonella (NTS) serotypes Typhimurium and Enteritidis are a major cause of bloodstream infections in children in sub-Saharan Africa but their reservoir is unknown. We compared pairs of NTS blood and stool isolates (with the same NTS serotype recovered in the same patient) for genetic similarity. METHODS Between November 2013 and April 2017, hospital-admitted children (29 days to 14 years) with culture-confirmed NTS bloodstream infections were enrolled in a cross-sectional study at Kisantu Hospital, DR Congo. Stool cultures for Salmonella were performed on a subset of enrolled children, as well as on a control group of non-febrile hospital-admitted children. Pairs of blood and stool NTS isolates were assessed for genetic similarity by multiple-locus variable-number of tandem repeats (MLVA) and genomics analysis. RESULTS A total of 299 children with NTS grown from blood cultures (Typhimurium 68.6%, Enteritidis 30.4%, other NTS 1.0%) had a stool sample processed; in 105 (35.1%) of them NTS was detected (Typhimurium 70.5%, Enteritidis 25.7%, other NTS 3.8%). A total of 87/105 (82.9%) pairs of blood and stool NTS isolates were observed (representing 29.1% of the 299 children). Among 1598 controls, the proportion of NTS stool excretion was 2.1% (p < 0.0001). MLVA types among paired isolates were identical in 82/87 (94.3%) pairs (27.4% of the 299 children; 61/66 (92.4%) in Typhimurium and 21/21 (100%) in Enteritidis pairs). Genomics analysis confirmed high genetic similarity within 41/43 (95.3%) pairs, showing a median SNP difference of 1 (range 0-77) and 1 (range 0-4) for Typhimurium and Enteritidis pairs respectively. Typhimurium and Enteritidis isolates belonged to sequence types ST313 lineage II and ST11 respectively. CONCLUSION Nearly 30% of children with NTS bloodstream infection showed stool excretion of an NTS isolate with high genetic similarity, adding to the evidence of humans as a potential reservoir for NTS.
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Affiliation(s)
- Marie-France Phoba
- Department of Microbiology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
- Department of Microbiology, University Hospital of Kinshasa, Democratic Republic of the Congo
| | - Barbara Barbé
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Benedikt Ley
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Sandra Van Puyvelde
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Annelies Post
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Wesley Mattheus
- Department of Human Bacterial Diseases, Sciensano, Brussels, Belgium
| | - Stijn Deborggraeve
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Octavie Lunguya
- Department of Microbiology, Institut National de Recherche Biomédicale, Kinshasa, Democratic Republic of the Congo
- Department of Microbiology, University Hospital of Kinshasa, Democratic Republic of the Congo
| | - Jan Jacobs
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology, Immunology and Transplantation, KU Leuven, Leuven, Belgium
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25
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Pletschette Z, De Groote E, Mattheus W, Waxweiler C, Creteur J, Grimaldi D. Meningococcaemia causing necrotizing cellulitis associated with acquired complement deficiency after gastric bypass surgery: a case report. BMC Infect Dis 2020; 20:361. [PMID: 32434466 PMCID: PMC7240913 DOI: 10.1186/s12879-020-05079-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Accepted: 05/11/2020] [Indexed: 12/02/2022] Open
Abstract
Background Neisseria meningitidis has rarely been described as an agent of necrotic soft tissue infection. Case presentation We report a case of a septic shock with necrotizing cellulitis due to Neisseria meningitidis serogroup W, treated by urgent extensive surgical debridement followed by skin grafts. The invasive meningococcal disease occurred together with a complement deficiency, possibly acquired after bypass surgery that took place 1 year before. Conclusions Necrotic tissue infections should be considered part of the invasive meningococcal diseases spectrum and should prompt clinicians to look for complement deficiencies. Gastric bypass surgery associated malnutrition may be implicated but further verification is needed.
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Affiliation(s)
- Zoe Pletschette
- Department of Intensive Care, Erasme Hospital, Université Libre de Bruxelles, 808 Route de Lennik, Brussels, Belgium.
| | - Elodie De Groote
- Department of Infectious Diseases, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Wesley Mattheus
- Meningococcal Reference Centre, Sciensano, Brussels, Belgium
| | - Charlotte Waxweiler
- Department of Plastic Surgery, Erasme Hospital, Université Libre de Bruxelles, Brussels, Belgium
| | - Jacques Creteur
- Department of Intensive Care, Erasme Hospital, Université Libre de Bruxelles, 808 Route de Lennik, Brussels, Belgium
| | - David Grimaldi
- Department of Intensive Care, Erasme Hospital, Université Libre de Bruxelles, 808 Route de Lennik, Brussels, Belgium
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26
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Mbuyi-Kalonji L, Barbé B, Nkoji G, Madinga J, Roucher C, Linsuke S, Hermy M, Heroes AS, Mattheus W, Polman K, Lutumba P, Phoba MF, Lunguya O, Jacobs J. Non-typhoidal Salmonella intestinal carriage in a Schistosoma mansoni endemic community in a rural area of the Democratic Republic of Congo. PLoS Negl Trop Dis 2020; 14:e0007875. [PMID: 32084128 PMCID: PMC7034803 DOI: 10.1371/journal.pntd.0007875] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2019] [Accepted: 10/25/2019] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Clinical observations and animal studies have suggested that Salmonella intestinal carriage is promoted by concurrent Schistosoma infection. The present study assessed association of Salmonella intestinal carriage and Schistosoma mansoni infection among individuals in a Schistosoma endemic area in sub-Saharan Africa. METHODS From November 2015 to March 2016, a cross-sectional community-wide study was conducted in Kifua II, a rural village in Kongo Central Province, Democratic Republic of Congo. Stool samples were collected and analyzed for Salmonella intestinal carriage (culture) and Schistosoma mansoni infection (Kato Katz microscopy with determination of egg load). Salmonella Typhimurium and Enteritidis isolates were assessed for genetic similarity with blood culture isolates obtained during the same period in a neighboring hospital using multi-locus variable-numbers tandem repeat analysis (MLVA). RESULTS A total of 1,108 participants were included (median age 15 years (IQR: 7-36), male-to-female ratio of 1:1.1). The overall prevalence of Schistosoma mansoni infection and non-typhoidal Salmonella carriage was 51.2% (95% CI: 48.2-54.1) and 3.4% (95% CI: 2.5-4.7) respectively, with 2.2% (95% CI: 1.5-3.2) of participants coinfected. The proportion of Salmonella carriage tended to be higher among Schistosoma mansoni infected participants compared to non-infected participants but this difference did not reach statistical significance (4.2% versus 2.6%, p = 0.132). However, the proportion of Salmonella carriage among participants with a heavy Schistosoma mansoni infection was significantly higher compared to those with a light and moderate infection (8.7% versus 3.2%, p = 0.012) and compared to Schistosoma mansoni negatives (8.7% versus 2.6%, p = 0.002). The 38 Salmonella isolates comprised five and four Enteritidis and Typhimurium serotypes respectively, the majority of them had MLVA types identical or similar to those observed among blood culture isolates. CONCLUSION Salmonella intestinal carriage was associated with a heavy intensity of Schistosoma mansoni infection. Further studies are needed to address causation.
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Affiliation(s)
- Lisette Mbuyi-Kalonji
- Department of Microbiology, National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo
- Department of Clinical Biology, Microbiology Unit, University Hospital of Kinshasa, Democratic Republic of the Congo
- * E-mail:
| | - Barbara Barbé
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Gaëlle Nkoji
- Department of Clinical Biology, Microbiology Unit, University Hospital of Kinshasa, Democratic Republic of the Congo
| | - Joule Madinga
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Institute of Health and Society, Université Catholique de Louvain, Brussels, Belgium
| | - Clémentine Roucher
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Sylvie Linsuke
- Department of Epidemiology, National Institute for Biomedical Research; Democratic Republic of the Congo
- Department of Tropical Medicine, University Hospital of Kinshasa, Democratic Republic of the Congo
| | - Marie Hermy
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Anne-Sophie Heroes
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
| | - Wesley Mattheus
- Department of Human Bacterial Diseases, Sciensano, Brussels, Belgium
| | - Katja Polman
- Department of Biomedical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Health Sciences, VU Amsterdam, Amsterdam, the Netherlands
| | - Pascal Lutumba
- Department of Epidemiology, National Institute for Biomedical Research; Democratic Republic of the Congo
- Department of Tropical Medicine, University Hospital of Kinshasa, Democratic Republic of the Congo
| | - Marie-France Phoba
- Department of Microbiology, National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo
- Department of Clinical Biology, Microbiology Unit, University Hospital of Kinshasa, Democratic Republic of the Congo
| | - Octavie Lunguya
- Department of Microbiology, National Institute for Biomedical Research, Kinshasa, Democratic Republic of the Congo
- Department of Clinical Biology, Microbiology Unit, University Hospital of Kinshasa, Democratic Republic of the Congo
| | - Jan Jacobs
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
- Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
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27
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Peeters L, Dewulf J, Boyen F, Brossé C, Vandersmissen T, Rasschaert G, Heyndrickx M, Cargnel M, Mattheus W, Pasmans F, Haesebrouck F, Maes D. Evaluation of group vaccination of sows and gilts against Salmonella Typhimurium with an attenuated vaccine in subclinically infected pig herds. Prev Vet Med 2020; 182:104884. [PMID: 32536448 DOI: 10.1016/j.prevetmed.2020.104884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Revised: 10/30/2019] [Accepted: 01/05/2020] [Indexed: 12/19/2022]
Abstract
Subclinical Salmonella Typhimurium infections occur frequently in pigs and constitute a major risk for human salmonellosis. With the currently available control measures, Salmonella Typhimurium infections in pigs remain difficult to control. Vaccination has been proposed to be an effective tool to control infections at farm level. In the current study, the effect of group vaccination of sows and gilts against Salmonella Typhimurium is evaluated on Salmonella prevalence in fecal and overshoe samples and ileocecal lymph nodes, and on serology in the sows and their offspring in three subclinically infected pig farms. In each farm, all sows and gilts were vaccinated twice, three weeks apart, with an attenuated histidine-adenine auxotrophic vaccine (Salmoporc®, IDT Biologika). From three months after the group vaccination onwards, all sows were given a booster dose three weeks before every farrowing. The farms were monitored bacteriologically and serologically from 12 months before until 15 months after the group vaccination. After group vaccination, no significant effect was detected in the prevalence of Salmonella Typhimurium in the fecal and overshoe samples collected in the sows (before: 2 %, after: 0 %) and their offspring at 18 weeks (before: 17 %, after: 11 %) and at 26 weeks of age (before: 15 %, after: 7 %), and when combining the results of the offspring at 18 and 26 weeks of age (before: 16 %, after: 9 %). Also, no significant effect was detected in the prevalence of Salmonella Typhimurium positive lymph nodes of sows (before and after: 0 %) and their offspring (before: 4 %, after: 7 %). Regarding serology, the mean S/P-ratios of the sows were significantly higher after the group vaccination, compared to before group vaccination (before: 1.50, after: 2.32, p < 0.001). The mean S/P-ratios of the offspring at slaughter age were significantly lower after the group vaccination, compared to before group vaccination (before: 1.71, after: 1.04, p = 0.001). In conclusion, group vaccination of sows and gilts resulted in a more beneficial serological status of the offspring, but did not significantly decrease Salmonella Typhimurium excretion and lymph node contamination.
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Affiliation(s)
- L Peeters
- Faculty of Veterinary Medicine, Department of Reproduction, Obstetrics and Herd Health, Ghent University, Merelbeke, Belgium.
| | - J Dewulf
- Faculty of Veterinary Medicine, Department of Reproduction, Obstetrics and Herd Health, Ghent University, Merelbeke, Belgium
| | - F Boyen
- Faculty of Veterinary Medicine, Department of Pathology, Bacteriology and Avian Diseases, Ghent University, Merelbeke, Belgium
| | - C Brossé
- Animal Health Care Flanders (DGZ), Lier, Belgium
| | | | - G Rasschaert
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - M Heyndrickx
- Faculty of Veterinary Medicine, Department of Pathology, Bacteriology and Avian Diseases, Ghent University, Merelbeke, Belgium; Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Melle, Belgium
| | - M Cargnel
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Sciensano, Brussels, Belgium
| | - W Mattheus
- Flanders Research Institute for Agriculture, Fisheries and Food (ILVO), Sciensano, Brussels, Belgium
| | - F Pasmans
- Faculty of Veterinary Medicine, Department of Pathology, Bacteriology and Avian Diseases, Ghent University, Merelbeke, Belgium
| | - F Haesebrouck
- Faculty of Veterinary Medicine, Department of Pathology, Bacteriology and Avian Diseases, Ghent University, Merelbeke, Belgium
| | - D Maes
- Faculty of Veterinary Medicine, Department of Reproduction, Obstetrics and Herd Health, Ghent University, Merelbeke, Belgium
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28
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Saltykova A, Mattheus W, Bertrand S, Roosens NHC, Marchal K, De Keersmaecker SCJ. Detailed Evaluation of Data Analysis Tools for Subtyping of Bacterial Isolates Based on Whole Genome Sequencing: Neisseria meningitidis as a Proof of Concept. Front Microbiol 2019; 10:2897. [PMID: 31921072 PMCID: PMC6930190 DOI: 10.3389/fmicb.2019.02897] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 12/02/2019] [Indexed: 12/19/2022] Open
Abstract
Whole genome sequencing is increasingly recognized as the most informative approach for characterization of bacterial isolates. Success of the routine use of this technology in public health laboratories depends on the availability of well-characterized and verified data analysis methods. However, multiple subtyping workflows are now often being used for a single organism, and differences between them are not always well described. Moreover, methodologies for comparison of subtyping workflows, and assessment of their performance are only beginning to emerge. Current work focuses on the detailed comparison of WGS-based subtyping workflows and evaluation of their suitability for the organism and the research context in question. We evaluated the performance of pipelines used for subtyping of Neisseria meningitidis, including the currently widely applied cgMLST approach and different SNP-based methods. In addition, the impact of the use of different tools for detection and filtering of recombinant regions and of different reference genomes were tested. Our benchmarking analysis included both assessment of technical performance of the pipelines and functional comparison of the generated genetic distance matrices and phylogenetic trees. It was carried out using replicate sequencing datasets of high- and low-coverage, consisting mainly of isolates belonging to the clonal complex 269. We demonstrated that cgMLST and some of the SNP-based subtyping workflows showed very good performance characteristics and highly similar genetic distance matrices and phylogenetic trees with isolates belonging to the same clonal complex. However, only two of the tested workflows demonstrated reproducible results for a group of more closely related isolates. Additionally, results of the SNP-based subtyping workflows were to some level dependent on the reference genome used. Interestingly, the use of recombination-filtering software generally reduced the similarity between the gene-by-gene and SNP-based methodologies for subtyping of N. meningitidis. Our study, where N. meningitidis was taken as an example, clearly highlights the need for more benchmarking comparative studies to eventually contribute to a justified use of a specific WGS data analysis workflow within an international public health laboratory context.
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Affiliation(s)
- Assia Saltykova
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
- IDLab, IMEC, Department of Information Technology, Ghent University, Ghent, Belgium
| | - Wesley Mattheus
- Belgian National Reference Centre for Neisseria, Human Bacterial Diseases, Sciensano, Brussels, Belgium
| | - Sophie Bertrand
- Belgian National Reference Centre for Neisseria, Human Bacterial Diseases, Sciensano, Brussels, Belgium
| | | | - Kathleen Marchal
- IDLab, IMEC, Department of Information Technology, Ghent University, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, VIB, Ghent University, Ghent, Belgium
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29
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Gand M, Mattheus W, Roosens NHC, Dierick K, Marchal K, De Keersmaecker SCJ, Bertrand S. A multiplex oligonucleotide ligation-PCR method for the genoserotyping of common Salmonella using a liquid bead suspension assay. Food Microbiol 2019; 87:103394. [PMID: 31948635 DOI: 10.1016/j.fm.2019.103394] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 08/21/2019] [Accepted: 11/20/2019] [Indexed: 01/14/2023]
Abstract
Salmonella is a major pathogen having a public health and economic impact in both humans and animals. Six serotypes of the Salmonella genus are mentioned in the Belgian and European regulation as to be rapidly excluded from the food chain (EU regulation N°2160/2003, Belgian royal decree 27/04/2017). The reference method for Salmonella serotyping, including slide-agglutination and biochemical tests, is time-consuming, expensive, not always objective, and therefore does not match the fast identification criteria required by the legislation. In this study, a molecular method, using genetic markers detected by Multiplex Oligonucleotide Ligation - PCR and Luminex technology, was developed for the identification of the 6 Salmonella serotypes and their variants subjected to an official control. The resulting method was validated with the analysis of 971 Salmonella isolated from different matrixes (human, animal, food or environment) and 33 non-Salmonella strains. The results were compared with the reference identifications, achieving an accuracy of 99.7%. The cost-effective high-throughput genoserotyping assay is performed in 1 day and generates objective results, thanks to the automatic interpretation of raw data using a barcode system. In conclusion, it is fully adapted to the implementation in first line laboratories and meets the requirements of the regulation.
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Affiliation(s)
- Mathieu Gand
- Sciensano, Infectious Diseases in Humans, Bacterial Diseases, B-1180 Brussels, Belgium; Department of Information Technology, IDLab, Imec, Ghent University, B-9052 Ghent, Belgium
| | - Wesley Mattheus
- Sciensano, Infectious Diseases in Humans, Bacterial Diseases, B-1180 Brussels, Belgium.
| | - Nancy H C Roosens
- Sciensano, Transversal Activities in Applied Genomics, B-1050 Brussels, Belgium
| | - Katelijne Dierick
- Sciensano, Infectious Diseases in Humans, Food Pathogen, B-1050 Brussels, Belgium
| | - Kathleen Marchal
- Department of Information Technology, IDLab, Imec, Ghent University, B-9052 Ghent, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, B-9052 Ghent, Belgium
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Post AS, Diallo SN, Guiraud I, Lompo P, Tahita MC, Maltha J, Van Puyvelde S, Mattheus W, Ley B, Thriemer K, Rouamba E, Derra K, Deborggraeve S, Tinto H, Jacobs J. Supporting evidence for a human reservoir of invasive non-Typhoidal Salmonella from household samples in Burkina Faso. PLoS Negl Trop Dis 2019; 13:e0007782. [PMID: 31609964 PMCID: PMC6812844 DOI: 10.1371/journal.pntd.0007782] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2019] [Revised: 10/24/2019] [Accepted: 09/14/2019] [Indexed: 11/18/2022] Open
Abstract
Background Salmonella Typhimurium and Enteritidis are major causes of bloodstream infection in children in sub-Saharan Africa. This study assessed evidence for their zoonotic versus human reservoir. Methods Index patients were children with blood culture confirmed Salmonella infection recruited during a microbiological surveillance study in Nanoro, rural Burkina between May 2013 and August 2014. After consent, their households were visited. Stool from household members and livestock (pooled samples per species) as well as drinking water were cultured for Salmonella. Isolates with identical serotype obtained from index patient and any household sample were defined as “paired isolates” and assessed for genetic relatedness by multilocus variable number tandem-repeat analysis (MLVA) and whole-genome sequencing (WGS). Results Twenty-nine households were visited for 32/42 (76.2%) eligible index patients: two households comprised two index patients each, and in a third household the index patient had a recurrent infection. Among the 32 index patients, serotypes were Salmonella Typhimurium (n = 26), Salmonella Enteritidis (n = 5) and Salmonella Freetown (n = 1). All Typhimurium isolates were sequence type (ST)313. Median delay between blood culture sampling and household visits was 13 days (range 6–26). Salmonella was obtained from 16/186 (8.6%) livestock samples (13 serotypes) and 18/290 (6.2%) household members (9 serotypes). None of the water samples yielded Salmonella. Paired Salmonella Typhimurium isolates were obtained from three households representing four index patients. MLVA types were identical in two pairs and similar in the third (consisting of two index patients and one household member). WGS showed a strong genetic relatedness with 0 to 2 core genome SNPs difference between pairs on a household level. Livestock samples did not yield any Salmonella Typhimurium or Salmonella Enteritidis, and the latter was exclusively obtained from blood culture. Other serotypes shared by human and/or livestock carriers in the same household were Salmonella Derby, Drac, Tennessee and Muenster. Conclusions/Significance The current study provides further evidence of a human reservoir for invasive non-Typhoidal Salmonella (iNTS) in sub-Saharan Africa. Non-Typhoidal Salmonella—particularly Salmonella Typhimurium sequence type (ST) 313—are among the most common causes of bloodstream infection in children in sub-Saharan Africa. To assess transmission and reservoir of this invasive serotype we performed a blood culture surveillance study among children < 15 years (index patients) in Nanoro, rural Burkina Faso. In case of blood culture confirmed invasive Non-Typhoidal Salmonella (iNTS) infection among index patients a household survey was performed, during which stool samples from household members, stool samples from livestock and water samples were obtained and cultured for Salmonella. Salmonella isolates obtained from blood culture of index patients were compared for genetic relatedness with Salmonella isolates obtained from samples taken from their corresponding household. In three households we found Salmonella Typhimurium ST 313 among both index patient and the stool sample of a household member, we found a strong genetic relatedness within each pair. There were no matching serotypes between index patients and livestock samples or water samples within households. Clusters from other serotypes were restricted to stool samples from household members and different species of livestock. Our results support the theory that iNTS has a human reservoir.
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Affiliation(s)
- Annelies S. Post
- Department of Clinical Sciences, Institute of Tropical Medicine (ITM), Antwerp, Belgium
- Nijmegen Institute of International Health, Radboud university medical centre, Nijmegen, the Netherlands
- * E-mail: (ASP); (SND)
| | - Seydou Nakanabo Diallo
- IRSS/Clinical Research Unit of Nanoro (CRUN), Nanoro, Burkina Faso
- Centre Muraz, Bobo-Dioulasso, Burkina Faso
- * E-mail: (ASP); (SND)
| | - Issa Guiraud
- IRSS/Clinical Research Unit of Nanoro (CRUN), Nanoro, Burkina Faso
- Center for Molecular and Vascular Biology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Palpouguini Lompo
- IRSS/Clinical Research Unit of Nanoro (CRUN), Nanoro, Burkina Faso
- Center for Molecular and Vascular Biology, University of Leuven (KU Leuven), Leuven, Belgium
| | | | - Jessica Maltha
- Department of Clinical Sciences, Institute of Tropical Medicine (ITM), Antwerp, Belgium
- Center for Molecular and Vascular Biology, University of Leuven (KU Leuven), Leuven, Belgium
| | - Sandra Van Puyvelde
- Department of Biomedical Sciences, Institute of Tropical Medicine (ITM), Antwerp, Belgium
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, United Kingdom
| | - Wesley Mattheus
- Belgian National Centre for Salmonella, Sciensano, Brussels, Belgium
| | - Benedikt Ley
- Department of Clinical Sciences, Institute of Tropical Medicine (ITM), Antwerp, Belgium
- Department for Global Health, Menzies School of Health Research, Darwin, Australia
| | - Kamala Thriemer
- Department of Clinical Sciences, Institute of Tropical Medicine (ITM), Antwerp, Belgium
- Department for Global Health, Menzies School of Health Research, Darwin, Australia
| | - Eli Rouamba
- IRSS/Clinical Research Unit of Nanoro (CRUN), Nanoro, Burkina Faso
| | - Karim Derra
- IRSS/Clinical Research Unit of Nanoro (CRUN), Nanoro, Burkina Faso
| | - Stijn Deborggraeve
- Department of Biomedical Sciences, Institute of Tropical Medicine (ITM), Antwerp, Belgium
| | - Halidou Tinto
- IRSS/Clinical Research Unit of Nanoro (CRUN), Nanoro, Burkina Faso
- Centre Muraz, Bobo-Dioulasso, Burkina Faso
- Université supérieur des sciences de la santé, Université polytechnique de Bobo-Dioulasso, Burkina Faso
| | - Jan Jacobs
- Department of Clinical Sciences, Institute of Tropical Medicine (ITM), Antwerp, Belgium
- Department of Microbiology and Immunology, University of Leuven (KU Leuven), Leuven, Belgium
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Gand M, Mattheus W, Saltykova A, Roosens N, Dierick K, Marchal K, De Keersmaecker SCJ, Bertrand S. Development of a real-time PCR method for the genoserotyping of Salmonella Paratyphi B variant Java. Appl Microbiol Biotechnol 2019; 103:4987-4996. [PMID: 31062054 PMCID: PMC6536469 DOI: 10.1007/s00253-019-09854-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2019] [Revised: 04/09/2019] [Accepted: 04/14/2019] [Indexed: 11/30/2022]
Abstract
Discriminating between D-tartrate fermenting and non-fermenting strains of Salmonella enterica subsp. enterica serotype Paratyphi B is of major importance as these two variants have different pathogenic profiles. While D-tartrate non-fermenting S. Paratyphi B isolates are the causative agent of typhoid-like fever, D-tartrate fermenting isolates (also called variant Java) of the same serotype trigger the less dangerous gastroenteritis. The determination of S. Paratyphi B variants requires a time-consuming process and complex biochemical tests. Therefore, a quadruplex real-time PCR method, based on the allelic discrimination of molecular markers selected from the scientific literature and from whole genome sequencing data produced in-house, was developed in this study, to be applied to Salmonella isolates. This method was validated with the analysis of 178 S. Paratyphi B (D-tartrate fermenting and non-fermenting) and other serotypes reaching an accuracy, compared with the classical methods, of 98% for serotyping by slide agglutination and 100% for replacement of the biochemical test. The developed real-time PCR permits to save time and to obtain an accurate identification of a S. Paratyphi B serotype and its D-tartrate fermenting profile, which is needed in routine laboratories for fast and efficient diagnostics.
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Affiliation(s)
- Mathieu Gand
- Sciensano, Infectious Diseases in Humans, Bacterial Diseases, Rue Engeland 642, 1180, Brussels, Belgium
- Department of Information Technology, IDLab, imec, Ghent University, 9052, Ghent, Belgium
| | - Wesley Mattheus
- Sciensano, Infectious Diseases in Humans, Bacterial Diseases, Rue Engeland 642, 1180, Brussels, Belgium.
| | - Assia Saltykova
- Department of Information Technology, IDLab, imec, Ghent University, 9052, Ghent, Belgium
- Sciensano, Transversal Activities in Applied Genomics, 1050, Brussels, Belgium
| | - Nancy Roosens
- Sciensano, Transversal Activities in Applied Genomics, 1050, Brussels, Belgium
| | - Katelijne Dierick
- Sciensano, Infectious Diseases in Humans, Food Pathogen, 1050, Brussels, Belgium
| | - Kathleen Marchal
- Department of Information Technology, IDLab, imec, Ghent University, 9052, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052, Ghent, Belgium
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Ventola E, Bogaerts B, De Keersmaecker SCJ, Vanneste K, Roosens NHC, Mattheus W, Ceyssens PJ. Shifting national surveillance of Shigella infections toward geno-serotyping by the development of a tailored Luminex assay and NGS workflow. Microbiologyopen 2019; 8:e00807. [PMID: 30924299 PMCID: PMC6692546 DOI: 10.1002/mbo3.807] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 01/09/2019] [Accepted: 01/10/2019] [Indexed: 02/01/2023] Open
Abstract
The phylogenetically closely related Shigella species and enteroinvasive Escherichia coli (EIEC) are responsible for millions of episodes of bacterial dysenteriae worldwide. Given its distinct epidemiology and public health relevance, only Shigellae are subject to mandatory reporting and follow‐up by public health authorities. However, many clinical laboratories struggle to differentiate non‐EIEC, EIEC, and Shigella in their current workflows, leading to inaccuracies in surveillance and rising numbers of misidentified E. coli samples at the National Reference Centre (NRC). In this paper, we describe two novel tools to enhance Shigella surveillance. First, we developed a low‐cost Luminex‐based multiplex assay combining five genetic markers for species identification with 11 markers for serotype prediction for S. sonnei and S. flexneri isolates. Using a test panel of 254 clinical samples, this assay has a sensitivity of 100% in differentiation of EIEC/Shigella pathotype from non‐EIEC strains, and 68.7% success rate in distinction of Shigella and EIEC. A novel, and particularly successful marker was a Shigella‐specific deletion in the spermidine acetyltransferase gene speG, reflecting its metabolic decay. For Shigella serotype prediction, the multiplex assay scored a sensitivity and specificity of 96.6% and 98.4%, respectively. All discrepancies were analyzed with whole‐genome sequencing and shown to be related to causative mutations (stop codons, indels, and promoter mutations) in glycosyltransferase genes. This observation spurred the development of an in silico workflow which extracts the Shigella serotype from Next‐Generation Sequencing (NGS) data, taking into account gene functionality. Both tools will be implemented in the workflow of the NRC, and will play a major role in the shift from phenotypic to genotyping‐based surveillance of shigellosis in Belgium.
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Affiliation(s)
- Eleonora Ventola
- National Reference Centre of Salmonella and Shigella, Brussels, Belgium.,Department of Biology and Biotechnology "C. Darwin", "Sapienza" Università di Roma, Rome, Italy
| | - Bert Bogaerts
- Transversal activities in Applied Genomics, Brussels, Belgium
| | | | - Kevin Vanneste
- Transversal activities in Applied Genomics, Brussels, Belgium
| | | | - Wesley Mattheus
- National Reference Centre of Salmonella and Shigella, Brussels, Belgium
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Bogaerts B, Winand R, Fu Q, Van Braekel J, Ceyssens PJ, Mattheus W, Bertrand S, De Keersmaecker SCJ, Roosens NHC, Vanneste K. Validation of a Bioinformatics Workflow for Routine Analysis of Whole-Genome Sequencing Data and Related Challenges for Pathogen Typing in a European National Reference Center: Neisseria meningitidis as a Proof-of-Concept. Front Microbiol 2019; 10:362. [PMID: 30894839 PMCID: PMC6414443 DOI: 10.3389/fmicb.2019.00362] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2018] [Accepted: 02/12/2019] [Indexed: 12/22/2022] Open
Abstract
Despite being a well-established research method, the use of whole-genome sequencing (WGS) for routine molecular typing and pathogen characterization remains a substantial challenge due to the required bioinformatics resources and/or expertise. Moreover, many national reference laboratories and centers, as well as other laboratories working under a quality system, require extensive validation to demonstrate that employed methods are "fit-for-purpose" and provide high-quality results. A harmonized framework with guidelines for the validation of WGS workflows does currently, however, not exist yet, despite several recent case studies highlighting the urgent need thereof. We present a validation strategy focusing specifically on the exhaustive characterization of the bioinformatics analysis of a WGS workflow designed to replace conventionally employed molecular typing methods for microbial isolates in a representative small-scale laboratory, using the pathogen Neisseria meningitidis as a proof-of-concept. We adapted several classically employed performance metrics specifically toward three different bioinformatics assays: resistance gene characterization (based on the ARG-ANNOT, ResFinder, CARD, and NDARO databases), several commonly employed typing schemas (including, among others, core genome multilocus sequence typing), and serogroup determination. We analyzed a core validation dataset of 67 well-characterized samples typed by means of classical genotypic and/or phenotypic methods that were sequenced in-house, allowing to evaluate repeatability, reproducibility, accuracy, precision, sensitivity, and specificity of the different bioinformatics assays. We also analyzed an extended validation dataset composed of publicly available WGS data for 64 samples by comparing results of the different bioinformatics assays against results obtained from commonly used bioinformatics tools. We demonstrate high performance, with values for all performance metrics >87%, >97%, and >90% for the resistance gene characterization, sequence typing, and serogroup determination assays, respectively, for both validation datasets. Our WGS workflow has been made publicly available as a "push-button" pipeline for Illumina data at https://galaxy.sciensano.be to showcase its implementation for non-profit and/or academic usage. Our validation strategy can be adapted to other WGS workflows for other pathogens of interest and demonstrates the added value and feasibility of employing WGS with the aim of being integrated into routine use in an applied public health setting.
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Affiliation(s)
- Bert Bogaerts
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Raf Winand
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Qiang Fu
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Julien Van Braekel
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | | | | | | | | | - Nancy H C Roosens
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
| | - Kevin Vanneste
- Transversal Activities in Applied Genomics, Sciensano, Brussels, Belgium
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Bertrand S, De Lamine de Bex G, Wildemauwe C, Lunguya O, Phoba MF, Ley B, Jacobs J, Vanhoof R, Mattheus W. Correction: Multi Locus Variable-Number Tandem Repeat (MLVA) Typing Tools Improved the Surveillance of Salmonella Enteritidis: A 6 Years Retrospective Study. PLoS One 2018; 13:e0198527. [PMID: 29847577 PMCID: PMC5976203 DOI: 10.1371/journal.pone.0198527] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022] Open
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Van Damme I, Mattheus W, Bertrand S, De Zutter L. Quantification of hygiene indicators and Salmonella in the tonsils, oral cavity and rectal content samples of pigs during slaughter. Food Microbiol 2018; 71:120-128. [DOI: 10.1016/j.fm.2017.03.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2016] [Revised: 02/01/2017] [Accepted: 03/12/2017] [Indexed: 11/25/2022]
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Saltykova A, Wuyts V, Mattheus W, Bertrand S, Roosens NHC, Marchal K, De Keersmaecker SCJ. Comparison of SNP-based subtyping workflows for bacterial isolates using WGS data, applied to Salmonella enterica serotype Typhimurium and serotype 1,4,[5],12:i:. PLoS One 2018; 13:e0192504. [PMID: 29408896 PMCID: PMC5800660 DOI: 10.1371/journal.pone.0192504] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Accepted: 01/24/2018] [Indexed: 12/05/2022] Open
Abstract
Whole genome sequencing represents a promising new technology for subtyping of bacterial pathogens. Besides the technological advances which have pushed the approach forward, the last years have been marked by considerable evolution of the whole genome sequencing data analysis methods. Prior to application of the technology as a routine epidemiological typing tool, however, reliable and efficient data analysis strategies need to be identified among the wide variety of the emerged methodologies. In this work, we have compared three existing SNP-based subtyping workflows using a benchmark dataset of 32 Salmonella enterica subsp. enterica serovar Typhimurium and serovar 1,4,[5],12:i:- isolates including five isolates from a confirmed outbreak and three isolates obtained from the same patient at different time points. The analysis was carried out using the original (high-coverage) and a down-sampled (low-coverage) datasets and two different reference genomes. All three tested workflows, namely CSI Phylogeny-based workflow, CFSAN-based workflow and PHEnix-based workflow, were able to correctly group the confirmed outbreak isolates and isolates from the same patient with all combinations of reference genomes and datasets. However, the workflows differed strongly with respect to the SNP distances between isolates and sensitivity towards sequencing coverage, which could be linked to the specific data analysis strategies used therein. To demonstrate the effect of particular data analysis steps, several modifications of the existing workflows were also tested. This allowed us to propose data analysis schemes most suitable for routine SNP-based subtyping applied to S. Typhimurium and S. 1,4,[5],12:i:-. Results presented in this study illustrate the importance of using correct data analysis strategies and to define benchmark and fine-tune parameters applied within routine data analysis pipelines to obtain optimal results.
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Affiliation(s)
- Assia Saltykova
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health, Brussels, Belgium
- Department of Information Technology, IDLab, Ghent University, IMEC, Ghent, Belgium
| | - Véronique Wuyts
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health, Brussels, Belgium
| | - Wesley Mattheus
- Bacterial Diseases Division, Communicable and Infectious Diseases, Scientific Institute of Public Health, Brussels, Belgium
| | - Sophie Bertrand
- Bacterial Diseases Division, Communicable and Infectious Diseases, Scientific Institute of Public Health, Brussels, Belgium
| | - Nancy H. C. Roosens
- Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health, Brussels, Belgium
| | - Kathleen Marchal
- Department of Information Technology, IDLab, Ghent University, IMEC, Ghent, Belgium
- Department of Plant Biotechnology and Bioinformatics, Ghent University, VIB, Ghent, Belgium
- University of Pretoria, Pretoria, South Africa
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Boonyarittichaikij R, Verbrugghe E, Dekeukeleire D, De Beelde R, Rouffaer LO, Haesendonck R, Strubbe D, Mattheus W, Bertrand S, Pasmans F, Bonte D, Verheyen K, Lens L, Martel A. Salmonella Typhimurium DT193 and DT99 are present in great and blue tits in Flanders, Belgium. PLoS One 2017; 12:e0187640. [PMID: 29112955 PMCID: PMC5675436 DOI: 10.1371/journal.pone.0187640] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 10/23/2017] [Indexed: 11/29/2022] Open
Abstract
Endemic infections with the common avian pathogen Salmonella enterica subspecies enterica serovar Typhimurium (Salmonella Typhimurium) may incur a significant cost on the host population. In this study, we determined the potential of endemic Salmonella infections to reduce the reproductive success of blue (Cyanistes caeruleus) and great (Parus major) tits by correlating eggshell infection with reproductive parameters. The fifth egg of each clutch was collected from nest boxes in 19 deciduous forest fragments. Out of the 101 sampled eggs, 7 Salmonella Typhimurium isolates were recovered. The low bacterial prevalence was reflected by a similarly low serological prevalence in the fledglings. In this study with a relatively small sample size, presence of Salmonella did not affect reproductive parameters (egg volume, clutch size, number of nestlings and number of fledglings), nor the health status of the fledglings. However, in order to clarify the impact on health and reproduction a larger number of samples have to be analyzed. Phage typing showed that the isolates belonged to the definitive phage types (DT) 193 and 99, and multi-locus variable number tandem repeat analysis (MLVA) demonstrated a high similarity among the tit isolates, but distinction to human isolates. These findings suggest the presence of passerine-adapted Salmonella strains in free-ranging tit populations with host pathogen co-existence.
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Affiliation(s)
- R. Boonyarittichaikij
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, Merelbeke, Belgium
- Department of Clinical Sciences and Public Health, Faculty of Veterinary Science, Mahidol University, Phuttamonthon, Nakhon Pathom, Thailand
| | - E. Verbrugghe
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, Merelbeke, Belgium
| | - D. Dekeukeleire
- Terrestrial Ecology Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, Gent, Belgium
| | - R. De Beelde
- Terrestrial Ecology Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, Gent, Belgium
- Forest & Nature Laboratory, Department Forest and Water Management, Ghent University, Gontrode, Belgium
| | - L. O. Rouffaer
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, Merelbeke, Belgium
| | - R. Haesendonck
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, Merelbeke, Belgium
| | - D. Strubbe
- Terrestrial Ecology Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, Gent, Belgium
- Center for Macroecology, Evolution and Climate, Natural History Museum of Denmark, University of Copenhagen, Universitetsparken 15, Copenhagen, Denmark
| | - W. Mattheus
- NRC Salmonella and Shigella Bacterial Diseases Division, Scientific Institute of Public Health, Juliette Wytsmanstraat 14, Brussels, Belgium
| | - S. Bertrand
- NRC Salmonella and Shigella Bacterial Diseases Division, Scientific Institute of Public Health, Juliette Wytsmanstraat 14, Brussels, Belgium
| | - F. Pasmans
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, Merelbeke, Belgium
| | - D. Bonte
- Terrestrial Ecology Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, Gent, Belgium
| | - K. Verheyen
- Forest & Nature Laboratory, Department Forest and Water Management, Ghent University, Gontrode, Belgium
| | - L. Lens
- Terrestrial Ecology Unit, Department of Biology, Ghent University, K.L. Ledeganckstraat 35, Gent, Belgium
| | - A. Martel
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, Merelbeke, Belgium
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Biasino W, De Zutter L, Mattheus W, Bertrand S, Uyttendaele M, Van Damme I. Correlation between slaughter practices and the distribution of Salmonella and hygiene indicator bacteria on pig carcasses during slaughter. Food Microbiol 2017; 70:192-199. [PMID: 29173627 DOI: 10.1016/j.fm.2017.10.003] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Revised: 10/04/2017] [Accepted: 10/09/2017] [Indexed: 01/12/2023]
Abstract
This study investigated the distribution of hygiene indicator bacteria and Salmonella on pig carcasses. Moreover, the relation between hygiene indicator counts and Salmonella presence as well as associations between specific slaughter practices and carcass contamination were determined for each carcass area. Seven Belgian pig slaughterhouses were visited three times to swab five randomly selected carcasses at nine different areas, after evisceration and trimming. Information about slaughter practices was collected using a questionaire. In all samples, the E. coli and Salmonella presence was analyzed and Enterobacteriaceae and total aerobic bacteria were quantified. Average total aerobic counts ranged from 3.1 (loin, pelvic duct, ham) to 4.4 log10 CFU/cm2 (foreleg). Median Enterobacteriaceae numbers varied between 0.4 (ham) an 1.8 log10 CFU/cm2 (foreleg). E. coli and Salmonella presence ranged from 15% (elbow) to 89% (foreleg) and 5% (elbow) to 38% (foreleg), respectively. Positive relations were found between hygiene indicator counts and Salmonella presence at the head, sternum, loin and throat. Several slaughter practices, such as splitting the head and incising tonsils, were associated with higher levels of hygiene indicator bacteria and Salmonella. These findings can be used to educate slaughterhouse personnel and estimate the public health risk involved in consumption of different pork cuts.
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Affiliation(s)
- W Biasino
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium.
| | - L De Zutter
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium
| | - W Mattheus
- Section of Bacterial Diseases, NRC Salmonella, Scientific Institute of Public Health, J. Wytsmanstreet 14, B-1050 Brussels, Belgium
| | - S Bertrand
- Section of Bacterial Diseases, NRC Salmonella, Scientific Institute of Public Health, J. Wytsmanstreet 14, B-1050 Brussels, Belgium
| | - M Uyttendaele
- Laboratory of Food Microbiology and Food Preservation (LFMFP), Department of Food Safety and Food Quality, Faculty of Bio-Science Engineering, Ghent University, Coupure Links 653, B-9000 Ghent, Belgium
| | - I Van Damme
- Department of Veterinary Public Health and Food Safety, Faculty of Veterinary Medicine, Ghent University, Salisburylaan 133, B-9820 Merelbeke, Belgium
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39
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Peters T, Bertrand S, Björkman JT, Brandal LT, Brown DJ, Erdõsi T, Heck M, Ibrahem S, Johansson K, Kornschober C, Kotila SM, Le Hello S, Lienemann T, Mattheus W, Nielsen EM, Ragimbeau C, Rumore J, Sabol A, Torpdahl M, Trees E, Tuohy A, de Pinna E. Multi-laboratory validation study of multilocus variable-number tandem repeat analysis (MLVA) for Salmonella enterica serovar Enteritidis, 2015. ACTA ACUST UNITED AC 2017; 22:30477. [PMID: 28277220 PMCID: PMC5356433 DOI: 10.2807/1560-7917.es.2017.22.9.30477] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2016] [Accepted: 05/10/2016] [Indexed: 11/20/2022]
Abstract
Multilocus variable-number tandem repeat analysis (MLVA) is a rapid and reproducible typing method that is an important tool for investigation, as well as detection, of national and multinational outbreaks of a range of food-borne pathogens. Salmonella enterica serovar Enteritidis is the most common Salmonella serovar associated with human salmonellosis in the European Union/European Economic Area and North America. Fourteen laboratories from 13 countries in Europe and North America participated in a validation study for MLVA of S. Enteritidis targeting five loci. Following normalisation of fragment sizes using a set of reference strains, a blinded set of 24 strains with known allele sizes was analysed by each participant. The S. Enteritidis 5-loci MLVA protocol was shown to produce internationally comparable results as more than 90% of the participants reported less than 5% discrepant MLVA profiles. All 14 participating laboratories performed well, even those where experience with this typing method was limited. The raw fragment length data were consistent throughout, and the inter-laboratory validation helped to standardise the conversion of raw data to repeat numbers with at least two countries updating their internal procedures. However, differences in assigned MLVA profiles remain between well-established protocols and should be taken into account when exchanging data.
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Affiliation(s)
| | | | | | | | - Derek J Brown
- Scottish Microbiology Reference Laboratories, Glasgow, United Kingdom
| | - Tímea Erdõsi
- National Center for Epidemiology, Budapest, Hungary
| | - Max Heck
- National Institute for Public Health and the Environment, Bilthoven, The Netherlands
| | - Salha Ibrahem
- National Institute for Health and Welfare, Helsinki, Finland
| | - Karin Johansson
- European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | | | - Saara M Kotila
- European Centre for Disease Prevention and Control (ECDC), Solna, Sweden
| | | | - Taru Lienemann
- National Institute for Health and Welfare, Helsinki, Finland
| | | | | | | | | | - Ashley Sabol
- Centers for Disease Control and Prevention, Atlanta, USA
| | | | - Eija Trees
- Centers for Disease Control and Prevention, Atlanta, USA
| | - Alma Tuohy
- University Hospital Galway, Galway, Ireland
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40
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Fonteneau L, Jourdan Da Silva N, Fabre L, Ashton P, Torpdahl M, Müller L, Bouchrif B, El Boulani A, Valkanou E, Mattheus W, Friesema I, Herrera Leon S, Varela Martínez C, Mossong J, Severi E, Grant K, Weill FX, Gossner CM, Bertrand S, Dallman T, Le Hello S. Multinational outbreak of travel-related Salmonella Chester infections in Europe, summers 2014 and 2015. ACTA ACUST UNITED AC 2017; 22. [PMID: 28230522 PMCID: PMC5322187 DOI: 10.2807/1560-7917.es.2017.22.7.30463] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 02/06/2017] [Indexed: 02/04/2023]
Abstract
Between 2014 and 2015, the European Centre for Disease Prevention and Control was informed of an increase in numbers of Salmonella enterica serotype Chester cases with travel to Morocco occurring in six European countries. Epidemiological and microbiological investigations were conducted. In addition to gathering information on the characteristics of cases from the different countries in 2014, the epidemiological investigation comprised a matched case-case study involving French patients with salmonellosis who travelled to Morocco that year. A univariate conditional logistic regression was performed to quantify associations. The microbiological study included a whole genome sequencing (WGS) analysis of clinical and non-human isolates of S. Chester of varied place and year of isolation. A total of 162 cases, mostly from France, followed by Belgium, the Netherlands, Spain, Denmark and Sweden were reported, including 86 (53%) women. The median age per country ranged from 3 to 38 years. Cases of S. Chester were more likely to have eaten in a restaurant and visited the coast of Morocco. The results of WGS showed five multilocus sequence types (ST), with 96 of 153 isolates analysed clustering into a tight group that corresponded to a novel ST, ST1954. Of these 96 isolates, 46 (48%) were derived from food or patients returning from Morocco and carried two types of plasmids containing either qnrS1 or qnrB19 genes. This European-wide outbreak associated with travel to Morocco was likely a multi-source outbreak with several food vehicles contaminated by multidrug-resistant S. Chester strains.
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Affiliation(s)
- Laure Fonteneau
- Santé publique France, the French national public health agency, Saint-Maurice, France.,European Programme for Intervention Epidemiology Training (EPIET), European Centre for Disease Prevention and Control (ECDC), Stockholm, Sweden
| | | | - Laetitia Fabre
- Institut Pasteur, French National Reference Center for E. coli, Shigella and Salmonella, Paris, France
| | - Philip Ashton
- Public Health England, Gastrointestinal Bacterial Reference Unit, London, England
| | | | | | - Brahim Bouchrif
- Institut Pasteur du Maroc, Sécurité alimentaire et environnement, Casablanca, Morocco
| | | | - Eleni Valkanou
- NRL Salmonella & AMR, Veterinary Laboratory of Chalkida, Greece
| | | | - Ingrid Friesema
- Netherlands National Institute for Public Health and the Environment (RIVM), the Netherlands
| | | | | | | | - Ettore Severi
- European Centre for Disease Prevention and Control, Stockholm, Sweden
| | - Kathie Grant
- Public Health England, Gastrointestinal Bacterial Reference Unit, London, England
| | - François-Xavier Weill
- Institut Pasteur, French National Reference Center for E. coli, Shigella and Salmonella, Paris, France
| | - Céline M Gossner
- European Centre for Disease Prevention and Control, Stockholm, Sweden.,School of Public Health and Primary Care (CAPHRI), Maastricht University Medical Center (MUMC+), Maastricht, the Netherlands
| | | | - Tim Dallman
- Public Health England, Gastrointestinal Bacterial Reference Unit, London, England
| | - Simon Le Hello
- Institut Pasteur, French National Reference Center for E. coli, Shigella and Salmonella, Paris, France
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41
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Whittaker R, Dias JG, Ramliden M, Ködmön C, Economopoulou A, Beer N, Pastore Celentano L, Kanitz E, Richter L, Mattheus W, Bleyenheuft C, Georgieva T, Simeonovski I, Vučina VV, Filipović SK, Koliou M, Bagatzouni DP, Krizova P, Sebestova H, Hoffmann S, Valentiner-Branth P, Kerbo N, Peetso R, Kuusi M, Toropainen M, Parent I, Taha MK, Vogel U, Hellenbrand W, Georgakopoulou T, Tzanakaki G, Krisztalovics K, Tirczka T, Gudnason T, Hardardottir H, O'Lorcain P, Bennett D, D'Ancona F, Stefanelli P, Savrasova L, Vasilevska D, Kuprevičienė N, Liausedienė R, Demuth I, Scheiden G, Melillo JM, Caruana P, van der Ende A, Mollema L, Caugant D, Blystad H, Skoczyńska A, Zota L, Pana M, Grgič Vitek M, Paragi M, Cano R, Abad R, Lepp T, Campbell H. The epidemiology of invasive meningococcal disease in EU/EEA countries, 2004–2014. Vaccine 2017; 35:2034-2041. [DOI: 10.1016/j.vaccine.2017.03.007] [Citation(s) in RCA: 130] [Impact Index Per Article: 18.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Revised: 02/24/2017] [Accepted: 03/03/2017] [Indexed: 12/28/2022]
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Bertrand S, Ceyssens PJ, Yde M, Dierick K, Boyen F, Vanderpas J, Vanhoof R, Mattheus W. Diversity of Listeria monocytogenes Strains of Clinical and Food Chain Origins in Belgium between 1985 and 2014. PLoS One 2016; 11:e0164283. [PMID: 27723768 PMCID: PMC5056710 DOI: 10.1371/journal.pone.0164283] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2016] [Accepted: 09/22/2016] [Indexed: 11/18/2022] Open
Abstract
Listeriosis is a rare but severe disease, mainly caused by Listeria monocytogenes. This study shows the results of the laboratory-based surveillance of Listeriosis in Belgium over the period 1985-2014. Besides the incidence and some demographic data we present also more detailed microbiological and molecular characteristics of human strains isolated since 2000. The strains from the latter period were compared to food and animal strains from the same period. Our study shows that different food matrices were commonly contaminated with L. monocytogenes presenting the same PFGE profile as in patient's isolates. Since 1985, we observed a significant decrease in incidence of the Materno-Neonatal cases (from 0.15 to 0.04 cases /100,000 inhabitants-year), which is probably to be attributed to active prevention campaigns targeting pregnant women. Despite the strengthening of different control measures by the food industry, the incidence of non-Materno-Neonatal listeriosis increased in Belgium (from 0.3 to 0.7 cases /100,000 inhabitants-year), probably due to the rise of highly susceptible patients in an aging population. This significant increase found in non-Materno-Neonatal cases (slope coefficient 7.42%/year, P<0.0001) can be attributed to significant increase in incidence of isolates belonging to serovars 1/2a (n = 393, slope coefficient 6.62%/year, P<0.0001). Although resistance to antimicrobials is rare among L. monocytogenes isolates, a trend to increasing MIC values is evident with chloramphenicol, amoxicillin, tetracycline and ciprofloxacin. We show that fluoroquinolone resistance is not linked to chromosomal mutations, but caused by a variety of efflux pumps. Our study also shows that huge majority of known underlying pathologies (426 out of 785 cases) were cancers (185/426, 43.1%) and haematological malignancies (75/185, 40.5%). Moreover the risk population is susceptible to low levels of contamination in food stressing the need of prevention campaigns specifically targeting these persons.
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Affiliation(s)
- S. Bertrand
- Section of Bacterial Diseases, NRC Listeria, Scientific Institute of Public Health, Brussels, Belgium
| | - P. J. Ceyssens
- Section of Bacterial Diseases, NRC Listeria, Scientific Institute of Public Health, Brussels, Belgium
| | - M. Yde
- Section of Bacterial Diseases, NRC Listeria, Scientific Institute of Public Health, Brussels, Belgium
| | - K. Dierick
- Section of Foodborne Pathogens, NRL Listeria monocytogenes, Scientific Institute of Public Health, Brussels, Belgium
| | - F. Boyen
- Department of Pathology, Bacteriology and Avian Diseases, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - J. Vanderpas
- Medical Microbiology Laboratory, Scientific Institute of Public Health, Brussels, Belgium
| | - R. Vanhoof
- Section of Bacterial Diseases, NRC Listeria, Scientific Institute of Public Health, Brussels, Belgium
| | - W. Mattheus
- Section of Bacterial Diseases, NRC Listeria, Scientific Institute of Public Health, Brussels, Belgium
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43
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Kalonji LM, Post A, Phoba MF, Falay D, Ngbonda D, Muyembe JJ, Bertrand S, Ceyssens PJ, Mattheus W, Verhaegen J, Barbé B, Kuijpers L, Van Geet C, Lunguya O, Jacobs J. Invasive Salmonella Infections at Multiple Surveillance Sites in the Democratic Republic of the Congo, 2011-2014. Clin Infect Dis 2016; 61 Suppl 4:S346-53. [PMID: 26449951 DOI: 10.1093/cid/civ713] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND This study reports the microbiological landscape of Salmonella Typhi and invasive nontyphoidal Salmonella (iNTS) in the Democratic Republic of the Congo (DRC). METHODS Blood cultures obtained from hospital-admitted patients suspected of bloodstream infection (BSI) in 4 of 11 provinces in DRC (Kinshasa, Bas-Congo, Equateur, and Orientale) were processed. Sampling had started in 2007; the results for the period 2011-2014 are reported. RESULTS Salmonella Typhi and iNTS were cultured from 194 (1.4%) and 840 (5.9%), respectively, of 14,110 BSI episodes and ranked first among BSI pathogens in adults (65/300 [21.7%]) and children (783/1901 [41.2%]), respectively. A total of 948 of 1034 (91.7%) isolates were available for analysis (164 Salmonella Typhi and 784 iNTS). Salmonella Typhimurium and Salmonella Enteritidis represented 386 (49.2%) and 391 (49.9%), respectively, of iNTS isolates, fluctuating over time and geography and increasing during the rainy season. Adults accounted for <5% of iNTS BSI episodes. Children <5 years accounted for 20.3% of Salmonella Typhi BSI episodes. Among Salmonella Typhi, rates of multidrug resistance and decreased ciprofloxacin susceptibility (DCS) were 37.8% and 37.2%, respectively, and 18.3% displayed combined multidrug resistance and DCS; rates of azithromycin and ceftriaxone resistance were 0.6% and absent, respectively. Among NTS isolates, ≥80% (79.7% of Salmonella Enteritidis and 90.2% of Salmonella Typhimurium isolates) showed multidrug resistance, and <2.5% showed DCS. Combined extended-spectrum β-lactamase production (blaTEM-1 gene) and azithromycin resistance was noted in 12.7% of Salmonella Typhimurium isolates, appearing in Bas-Congo from 2013 onward. CONCLUSIONS Salmonella Typhi and NTS are major causes of BSI in DRC; their antimicrobial resistance is increasing.
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Affiliation(s)
- Lisette Mbuyi Kalonji
- Department of Clinical Microbiology, National Institute for Biomedical Research Department of Microbiology, University Hospital of Kinshasa, Democratic Republic of the Congo
| | - Annelies Post
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Marie-France Phoba
- Department of Clinical Microbiology, National Institute for Biomedical Research Department of Microbiology, University Hospital of Kinshasa, Democratic Republic of the Congo
| | - Dadi Falay
- Department of Pediatrics, University Hospital of Kisangani, Democratic Republic of the Congo
| | - Dauly Ngbonda
- Department of Pediatrics, University Hospital of Kisangani, Democratic Republic of the Congo
| | - Jean-Jacques Muyembe
- Department of Clinical Microbiology, National Institute for Biomedical Research Department of Microbiology, University Hospital of Kinshasa, Democratic Republic of the Congo
| | - Sophie Bertrand
- Belgian National Centre for Salmonella, Scientific Institute of Public Health, Brussels
| | - Pieter-Jan Ceyssens
- Belgian National Centre for Salmonella, Scientific Institute of Public Health, Brussels
| | - Wesley Mattheus
- Belgian National Centre for Salmonella, Scientific Institute of Public Health, Brussels
| | | | - Barbara Barbé
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Laura Kuijpers
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Chris Van Geet
- Department of Pediatrics Department of Cardiovascular Sciences, KU Leuven, Belgium
| | - Octavie Lunguya
- Department of Clinical Microbiology, National Institute for Biomedical Research Department of Microbiology, University Hospital of Kinshasa, Democratic Republic of the Congo
| | - Jan Jacobs
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium Department of Microbiology and Immunology
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44
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Falay D, Kuijpers LMF, Phoba MF, De Boeck H, Lunguya O, Vakaniaki E, Bertrand S, Mattheus W, Ceyssens PJ, Vanhoof R, Devlieger H, Van Geet C, Verheyen E, Ngbonda D, Jacobs J. Microbiological, clinical and molecular findings of non-typhoidal Salmonella bloodstream infections associated with malaria, Oriental Province, Democratic Republic of the Congo. BMC Infect Dis 2016; 16:271. [PMID: 27286886 PMCID: PMC4902913 DOI: 10.1186/s12879-016-1604-1] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2015] [Accepted: 06/01/2016] [Indexed: 02/05/2023] Open
Abstract
Background In sub-Saharan Africa, non-typhoidal Salmonella (NTS) can cause bloodstream infections, referred to as invasive non-typhoidal Salmonella disease (iNTS disease); it can occur in outbreaks and is often preceded by malaria. Data from Central Africa is limited. Methods Clinical, microbiological and molecular findings of NTS recovered in a blood culture surveillance project (2009–2014) were analyzed. Results In March-July 2012 there was an epidemic increase in malaria infections in the Oriental Province of the Democratic Republic of the Congo (DRC). In one referral hospital, overall hospital admissions in June 2012 were 2.6 times higher as compared to the same period in the years before and after (336 versus an average of 128 respectively); numbers of malaria cases and blood transfusions were nearly three- and five-fold higher respectively (317 versus 112 and 250 versus 55). Case fatality rates (in-hospital deaths versus all admissions) peaked at 14.6 %. Salmonella Typhimurium and Salmonella Enteritidis together accounted for 88.9 % of pathogens isolated from blood cultures collected during an outreach visit to the affected districts in June 2012. Children infected with Salmonella Enteritidis (33 patient files available) tended to be co-infected with Plasmodium falciparum more often than children infected with Salmonella Typhimurium (40 patients files available) (81.8 % versus 62.5 %). Through the microbiological surveillance project (May 2009–May 2014) 113 unique NTS isolates were collected (28.5 % (113/396) of pathogens); most (95.3 %) were recovered from children < 15 years. Salmonella Typhimurium (n = 54) and Salmonella Enteritidis (n = 56) accounted for 47.8 % and of 49.6 % NTS isolates respectively. Multilocus variable-number tandem-repeat analysis (MLVA) revealed more heterogeneity for Salmonella Typhimurium than for Salmonella Enteritidis. Most (82/96, 85.4 %) NTS isolates that were available for antibiotic susceptibility testing were multidrug resistant. All isolates were susceptible to ceftriaxone and azithromycin. Conclusion During the peak of an epidemic increase in malaria in the DRC in 2012, a high proportion of multidrug resistant Salmonella Typhimurium and Salmonella Enteritidis were isolated from blood cultures. Overall, the two serovars showed subtle differences in clinical presentation and genetic diversity. Electronic supplementary material The online version of this article (doi:10.1186/s12879-016-1604-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Dadi Falay
- Department of Pediatrics, University Hospital of Kisangani, Kisangani, the Democratic Republic of the Congo
| | - Laura Maria Francisca Kuijpers
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium. .,Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium.
| | - Marie-France Phoba
- Department of Clinical Microbiology, National Institute for Biomedical Research, Kinshasa, the Democratic Republic of the Congo
| | - Hilde De Boeck
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium
| | - Octavie Lunguya
- Department of Clinical Microbiology, National Institute for Biomedical Research, Kinshasa, the Democratic Republic of the Congo
| | - Emmanuel Vakaniaki
- General Referral Hospital of Kabondo, Kisangani, the Democratic Republic of the Congo
| | - Sophie Bertrand
- Belgian National Centre for Salmonella, Scientific Institute of Public Health, Brussels, Belgium
| | - Wesley Mattheus
- Belgian National Centre for Salmonella, Scientific Institute of Public Health, Brussels, Belgium
| | - Pieter-Jan Ceyssens
- Belgian National Centre for Salmonella, Scientific Institute of Public Health, Brussels, Belgium
| | - Raymond Vanhoof
- Belgian National Centre for Salmonella, Scientific Institute of Public Health, Brussels, Belgium
| | - Hugo Devlieger
- Department of Pediatrics, University Hospital of Leuven, KU Leuven, Leuven, Belgium
| | - Chris Van Geet
- Department of Pediatrics, University Hospital of Leuven, KU Leuven, Leuven, Belgium
| | - Erik Verheyen
- OD Taxonomy & Phylogeny, Royal Belgian Institute of Natural Sciences, Brussels, Belgium.,Evolutionary Ecology, University of Antwerp, Antwerp, Belgium
| | - Dauly Ngbonda
- Department of Pediatrics, University Hospital of Kisangani, Kisangani, the Democratic Republic of the Congo
| | - Jan Jacobs
- Department of Clinical Sciences, Institute of Tropical Medicine, Antwerp, Belgium.,Department of Microbiology and Immunology, KU Leuven, Leuven, Belgium
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Ceyssens PJ, Garcia-Graells C, Fux F, Botteldoorn N, Mattheus W, Wuyts V, De Keersmaecker S, Dierick K, Bertrand S. Development of a Luminex xTAG®assay for cost-effective multiplex detection of β-lactamases in Gram-negative bacteria. J Antimicrob Chemother 2016; 71:2479-83. [DOI: 10.1093/jac/dkw201] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 04/29/2016] [Indexed: 01/23/2023] Open
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Ceyssens PJ, Van Bambeke F, Mattheus W, Bertrand S, Fux F, Van Bossuyt E, Damée S, Nyssen HJ, De Craeye S, Verhaegen J, Tulkens PM, Vanhoof R. Molecular Analysis of Rising Fluoroquinolone Resistance in Belgian Non-Invasive Streptococcus pneumoniae Isolates (1995-2014). PLoS One 2016; 11:e0154816. [PMID: 27227336 PMCID: PMC4881901 DOI: 10.1371/journal.pone.0154816] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2015] [Accepted: 04/19/2016] [Indexed: 11/25/2022] Open
Abstract
We present the results of a longitudinal surveillance study (1995–2014) on fluoroquinolone resistance (FQ-R) among Belgian non-invasive Streptococcus pneumoniae isolates (n = 5,602). For many years, the switch to respiratory fluoroquinolones for the treatment of (a)typical pneumonia had no impact on FQ-R levels. However, since 2011 we observed a significant decrease in susceptibility towards ciprofloxacin, ofloxacin and levofloxacin with peaks of 9.0%, 6.6% and 3.1% resistant isolates, respectively. Resistance to moxifloxacin arised sporadically, and remained <1% throughout the entire study period. We observed classical topoisomerase mutations in gyrA (n = 25), parC (n = 46) and parE (n = 3) in varying combinations, arguing against clonal expansion of FQ-R. The impact of recombination with co-habiting commensal streptococci on FQ-R remains marginal (10.4%). Notably, we observed that a rare combination of DNA Gyrase mutations (GyrA_S81L/GyrB_P454S) suffices for high-level moxifloxacin resistance, contrasting current model. Interestingly, 85/422 pneumococcal strains display MICCIP values which were lowered by at least four dilutions by reserpine, pointing at involvement of efflux pumps in FQ-R. In contrast to susceptible strains, isolates resistant to ciprofloxacin significantly overexpressed the ABC pump PatAB in comparison to reference strain S. pneumoniae ATCC 49619, but this could only be linked to disruptive terminator mutations in a fraction of these. Conversely, no difference in expression of the Major Facilitator PmrA, unaffected by reserpine, was noted between susceptible and resistant S. pneumoniae strains. Finally, we observed that four isolates displayed intermediate to high-level ciprofloxacin resistance without any known molecular resistance mechanism. Focusing future molecular studies on these isolates, which are also commonly found in other studies, might greatly assist in the battle against rising pneumococcal drug resistance.
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Affiliation(s)
- Pieter-Jan Ceyssens
- Unit of Bacterial Diseases, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
| | - Françoise Van Bambeke
- Pharmacologie cellulaire et moléculaire, Louvain Drug Research Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Wesley Mattheus
- Unit of Bacterial Diseases, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
| | - Sophie Bertrand
- Unit of Bacterial Diseases, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
| | - Frédéric Fux
- Unit of Bacterial Diseases, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
| | - Eddie Van Bossuyt
- Unit of Bacterial Diseases, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
| | - Sabrina Damée
- Unit of Bacterial Diseases, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
| | - Henry-Jean Nyssen
- Unit of Foodborne Pathogens, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
| | - Stéphane De Craeye
- Unit of Foodborne Pathogens, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
| | - Jan Verhaegen
- Laboratory of Clinical Bacteriology and Mycology, KULeuven, 3000 Leuven, Belgium
| | | | - Paul M. Tulkens
- Pharmacologie cellulaire et moléculaire, Louvain Drug Research Institute, Université Catholique de Louvain, 1200 Brussels, Belgium
| | - Raymond Vanhoof
- Unit of Bacterial Diseases, Scientific Institute of Public Health (WIV-ISP), 1050 Brussels, Belgium
- * E-mail:
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Mattheus W, Hanquet G, Collard JM, Vanhoof R, Bertrand S. Changes in Meningococcal Strains in the Era of a Serogroup C Vaccination Campaign: Trends and Evolution in Belgium during the Period 1997-2012. PLoS One 2015; 10:e0139615. [PMID: 26425857 PMCID: PMC4591272 DOI: 10.1371/journal.pone.0139615] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2015] [Accepted: 09/14/2015] [Indexed: 11/28/2022] Open
Abstract
BACKGROUND Invasive meningococcal disease (IMD) is a major cause of bacterial meningitides and septicaemia. This study shows the results of the laboratory-based surveillance of IMD in Belgium over the period 1997-2012. METHODS The results are based on microbiological and molecular laboratory surveillance of 2997 clinical isolates of N. meningitides received by the Belgian Meningococcal Reference Centre (BMRC) over the period 1997-2012. RESULTS Serogroup B has always been a major cause of meningococcal disease in Belgium, with P3.4 as most frequent serotype till 2008, while an increase in non-serotypable strains has been observed in the last few years. Clonal complexes cc-41/44 and cc-269 are most frequently observed in serogroup B strains. In the late nineties, the incidence of serogroup C disease increased considerably and peaked in 2001, mainly associated with phenotypes C:2a:P1.5,2, C:2a:P1.5 and C:2a:P1.2 (ST-11/ET-37 clonal complex). The introduction of the meningococcal C conjugate vaccine has been followed by an 88% significant decrease in serogroup C disease from 2001 to 2004 nationally, yet sharper in Flanders (92%) compared to Wallonia (77%). Since 2008 a difference in incidence of serogroup C was observed in Flanders (0-0.1/100,000) versus Wallonia (0.1-0.3/100,000). CONCLUSION This study showed the change in epidemiology and strain population over a 16 years period spanning an exhaustive vaccination campaign and highlights the influence of regional vaccination policies with different cohorts sizes on short and long-term IMD incidences.
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Affiliation(s)
- Wesley Mattheus
- Sections of Bacterial Diseases, Scientific Institute of Public Health, Brussels, Belgium
| | - Germaine Hanquet
- Medical Epidemiologist, Health Care Knowledge Centre, Brussels, Belgium
| | - Jean-Marc Collard
- Sections of Bacterial Diseases, Scientific Institute of Public Health, Brussels, Belgium
| | - Raymond Vanhoof
- Sections of Bacterial Diseases, Scientific Institute of Public Health, Brussels, Belgium
| | - Sophie Bertrand
- Sections of Bacterial Diseases, Scientific Institute of Public Health, Brussels, Belgium
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Wuyts V, Denayer S, Roosens NHC, Mattheus W, Bertrand S, Marchal K, Dierick K, De Keersmaecker SCJ. Whole Genome Sequence Analysis of Salmonella Enteritidis PT4 Outbreaks from a National Reference Laboratory's Viewpoint. PLoS Curr 2015; 7:ecurrents.outbreaks.aa5372d90826e6cb0136ff66bb7a62fc. [PMID: 26468422 PMCID: PMC4593640 DOI: 10.1371/currents.outbreaks.aa5372d90826e6cb0136ff66bb7a62fc] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
INTRODUCTION In April and May 2014, two suspected egg-related outbreaks of Salmonella enterica subsp. enterica serovar Enteritidis (S. Enteritidis) were investigated by the Belgian National Reference Laboratory of Foodborne Outbreaks. Both the suspected food and human isolates being available, and this for both outbreaks, made these the ideal case study for a retrospective whole genome sequencing (WGS) analysis with the goal to investigate the feasibility of this technology for outbreak investigation by a National Reference Laboratory or National Reference Centre without thorough bioinformatics expertise. METHODS The two outbreaks were originally investigated epidemiologically with a standard questionnaire and with serotyping, phage typing, multiple-locus variable-number of tandem repeats analysis (MLVA) and antimicrobial susceptibility testing as classical microbiological methods. Retrospectively, WGS of six outbreak isolates was done on an Illumina HiSeq. Analysis of the WGS data was performed with currently available, user-friendly software and tools, namely CLC Genomics Workbench, the tools available on the server of the Center for Genomic Epidemiology and BLAST Ring Image Generator (BRIG). RESULTS To all collected human and food outbreak isolates, classical microbiological investigation assigned phage type PT4 (variant phage type PT4a for one human isolate) and MLVA profile 3-10-5-4-1, both of which are common for human isolates in Belgium. The WGS analysis confirmed the link between food and human isolates for each of the outbreaks and clearly discriminated between the two outbreaks occurring in a same time period, thereby suggesting a non-common source of contamination. Also, an additional plasmid carrying an antibiotic resistance gene was discovered in the human isolate with the variant phage type PT4a. DISCUSSION For the two investigated outbreaks occurring at geographically separated locations, the gold standard classical microbiological subtyping methods were not sufficiently discriminative to distinguish between or assign a common origin of contamination for the two outbreaks, while WGS analysis could do so. This case study demonstrated the added value of WGS for outbreak investigations by confirming and/or discriminating food and human isolates between and within outbreaks. It also proved the feasibility of WGS as complementary or even future replacing (sub)typing method for the average routine laboratory.
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Affiliation(s)
- Véronique Wuyts
- Department of Microbial and Molecular Systems, Centre of Microbial and Plant Genetics, KU Leuven, Leuven, Belgium; Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; Platform Biotechnology and Molecular Biology, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium
| | - Sarah Denayer
- Scientific Institute of Public Health (WIV-ISP), Scientific Service of Foodborne Pathogens, NRL Foodborne Outbreaks, Brussels, Belgium
| | - Nancy H C Roosens
- Scientific Institute of Public Health (WIV-ISP), Platform Biotechnology and Molecular Biology, Brussels, Belgium
| | - Wesley Mattheus
- National Reference Centre for Salmonella and Shigella, Bacterial Diseases Division, Communicable and infectious Diseases, Scientific Institute of Public Health, Brussels, Belgium
| | - Sophie Bertrand
- National Reference Centre for Salmonella and Shigella, Bacterial Diseases Division, Communicable and Infectious Diseases, Scientific Institute of Public Health (WIV-ISP), Brussels, Belgium
| | - Kathleen Marchal
- Department of Plant Biotechnology and Bioinformatics, Ghent University, Ghent, Belgium; Department of Information Technology, Ghent University, IMinds, Ghent, Belgium
| | - Katelijne Dierick
- Scientific Institute of Public Health (WIV-ISP), Scientific Service of Foodborne Pathogens, NRL Foodborne Outbreaks, Brussels, Belgium
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Wuyts V, Mattheus W, Roosens NHC, Marchal K, Bertrand S, De Keersmaecker SCJ. A multiplex oligonucleotide ligation-PCR as a complementary tool for subtyping of Salmonella Typhimurium. Appl Microbiol Biotechnol 2015. [PMID: 26205523 PMCID: PMC4561068 DOI: 10.1007/s00253-015-6831-7] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Subtyping below the serovar level is essential for surveillance and outbreak detection and investigation of Salmonella enterica subsp. enterica serovar Typhimurium (S. Typhimurium) and its monophasic variant 1,4,[5],12:i:- (S. 1,4,[5],12:i:-), frequent causes of foodborne infections. In an attempt to overcome the intrinsic shortcomings of currently used subtyping techniques, a multiplex oligonucleotide ligation-PCR (MOL-PCR) assay was developed which combines different types of molecular markers in a high-throughput microsphere suspension array. The 52 molecular markers include prophage genes, amplified fragment length polymorphism (AFLP) elements, Salmonella genomic island 1 (SGI1), allantoinase gene allB, MLVA locus STTR10, antibiotic resistance genes, single nucleotide polymorphisms (SNPs) and phase 2 flagellar gene fljB. The in vitro stability of these markers was confirmed in a serial passage experiment. The validation of the MOL-PCR assay for subtyping of S. Typhimurium and S. 1,4,[5],12:i:- on 519 isolates shows that the method is rapid, reproducible, flexible, accessible, easy to use and relatively inexpensive. Additionally, a 100 % typeability and a discriminatory power equivalent to that of phage typing were observed, and epidemiological concordance was assessed on isolates of 2 different outbreaks. Furthermore, a data analysis method is provided so that the MOL-PCR assay allows for objective, computerised data analysis and data interpretation of which the results can be easily exchanged between different laboratories in an international surveillance network.
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Affiliation(s)
- Véronique Wuyts
- Department of Microbial and Molecular Systems, KU Leuven, Kasteelpark Arenberg 20 bus 2460, 3001, Leuven, Belgium
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Bertrand S, De Lamine de Bex G, Wildemauwe C, Lunguya O, Phoba MF, Ley B, Jacobs J, Vanhoof R, Mattheus W. Multi locus variable-number tandem repeat (MLVA) typing tools improved the surveillance of Salmonella enteritidis: a 6 years retrospective study. PLoS One 2015; 10:e0117950. [PMID: 25693200 PMCID: PMC4334661 DOI: 10.1371/journal.pone.0117950] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Accepted: 01/05/2015] [Indexed: 11/18/2022] Open
Abstract
Surveillance of Salmonella enterica subsp. enterica serovar Enteritidis is generally considered to benefit from molecular techniques like multiple-locus variable-number of tandem repeats analysis (MLVA), which allow early detection and confinement of outbreaks. Here, a surveillance study, including phage typing, antimicrobial susceptibility testing and MLVA on 1,535 S. Enteritidis isolates collected between 2007 and 2012, was used to evaluate the added value of MLVA for public health surveillance in Belgium. Phage types PT4, PT8, PT21, PT1, PT6, PT14b, PT28 and PT13 dominate the Belgian S. Enteritidis population. The isolates of S. Enteritidis were most frequently susceptible to all antibiotics tested. 172 different MLVA profiles were detected, of which 9 frequent profiles included 67.2% of the S. Enteritidis population. During a serial passage experiment on selected isolates to investigate the in vitro stability of the 5 MLVA loci, no variations over time were observed indicating that the MLVA profiles were stable. The MLVA profile of isolates originating from different outbreaks in the Democratic Republic of the Congo (DRC) between 2010 and 2011 were distinct from any of the MLVA profiles found in Belgian isolates throughout the six year observational period and demonstrates that MLVA improves public health surveillance of S. Enteritidis. However, MLVA should be complemented with other subtyping methods when investigating outbreaks is caused by the most common MLVA profile.
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Affiliation(s)
- Sophie Bertrand
- National Reference Centre for Salmonellas, Bacterial Diseases Division, Communicable and Infectious Diseases, Scientific Institute of Public Health, Brussels, Belgium
- * E-mail:
| | - Guillaume De Lamine de Bex
- National Reference Centre for Salmonellas, Bacterial Diseases Division, Communicable and Infectious Diseases, Scientific Institute of Public Health, Brussels, Belgium
| | - Christa Wildemauwe
- National Reference Centre for Salmonellas, Bacterial Diseases Division, Communicable and Infectious Diseases, Scientific Institute of Public Health, Brussels, Belgium
| | - Octavie Lunguya
- Department of Clinical Microbiology, National Institute for Biomedical Research, Kinshasa, The Democratic Republic of Congo
| | - Marie France Phoba
- Department of Clinical Microbiology, National Institute for Biomedical Research, Kinshasa, The Democratic Republic of Congo
| | - Benedikt Ley
- Institute of Tropical Medicine Antwerp, Antwerp, Belgium
| | - Jan Jacobs
- Institute of Tropical Medicine Antwerp, Antwerp, Belgium
- Department of Microbiology and Immunology, Faculty of Medicine, University of Leuven, Belgium
| | - Raymond Vanhoof
- National Reference Centre for Salmonellas, Bacterial Diseases Division, Communicable and Infectious Diseases, Scientific Institute of Public Health, Brussels, Belgium
| | - Wesley Mattheus
- National Reference Centre for Salmonellas, Bacterial Diseases Division, Communicable and Infectious Diseases, Scientific Institute of Public Health, Brussels, Belgium
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