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Strakova N, Michova H, Shagieva E, Ovesna P, Karpiskova R, Demnerova K. Genotyping of Campylobacter jejuni and prediction tools of its antimicrobial resistance. Folia Microbiol (Praha) 2024; 69:207-219. [PMID: 37816942 PMCID: PMC10876727 DOI: 10.1007/s12223-023-01093-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 09/09/2023] [Indexed: 10/12/2023]
Abstract
Although Campylobacter jejuni is the pathogen responsible for the most common foodborne illness, tracing of the infection source remains challenging due to its highly variable genome. Therefore, one of the aim of the study was to compare three genotyping methods (MLST, PFGE, and mP-BIT) to determine the most effective genotyping tool. C. jejuni strains were divided into 4 clusters based on strain similarity in the cgMLST dendrogram. Subsequently, the dendrograms of the 3 tested methods were compared to determine the accuracy of each method compared to the reference cgMLST method. Moreover, a cost-benefit analysis has showed that MLST had the highest inverse discrimination index (97%) and required less workflow, time, fewer consumables, and low bacterial sample quantity. PFGE was shown to be obsolete both because of its low discriminatory power and the complexity of the procedure. Similarly, mP‑BIT showed low separation results, which was compensated by its high availability. Therefore, our data showed that MLST is the optimal tool for genotyping C. jejuni. Another aim was to compare the antimicrobial resistance to ciprofloxacin, erythromycin, and tetracycline in C. jejuni strains isolated from human, water, air, food, and animal samples by two gene sequence-based prediction methods and to compare them with the actual susceptibility of C. jejuni strains using the disc diffusion method. Both tools, ResFinder and RGI, synchronously predict the antimicrobial susceptibility of C. jejuni and either can be used.
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Affiliation(s)
- Nicol Strakova
- Veterinary Research Institute, Hudcova 296/70, Brno, Czech Republic.
| | - Hana Michova
- Laboratory of Food Microbiology, Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Ekaterina Shagieva
- Laboratory of Food Microbiology, Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
| | - Petra Ovesna
- Institute of Biostatistics and Analyses, Masaryk University, Brno, Czech Republic
| | - Renata Karpiskova
- Department of Public Health, Medical Faculty, Masaryk University, Brno, Czech Republic
| | - Katerina Demnerova
- Laboratory of Food Microbiology, Department of Biochemistry and Microbiology, University of Chemistry and Technology, Prague, Czech Republic
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Khatiebi S, Kiprotich K, Onyando Z, Wekesa C, Chi CN, Mulambalah C, Okoth P. Shotgun Metagenomic Analyses of Microbial Assemblages in the Aquatic Ecosystem of Winam Gulf of Lake Victoria, Kenya Reveals Multiclass Pollution. BIOMED RESEARCH INTERNATIONAL 2023; 2023:3724531. [PMID: 37521121 PMCID: PMC10382247 DOI: 10.1155/2023/3724531] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 06/19/2023] [Accepted: 06/22/2023] [Indexed: 08/01/2023]
Abstract
Lake Victoria, the second-largest freshwater lake in the world, provides an important source of food and income, particularly fish for both domestic consumption and for export market. In recent years, Lake Victoria has suffered massive pollution from both industrial and wastewater discharge. Microplastic biomes, pharmaceutical residues, drugs of abuse, heavy metals, agrochemicals, and personal care products are ubiquitous in the aquatic ecosystem of Winam Gulf. These pollutants are known to alter microbial assemblages in aquatic ecosystems with far-reaching ramification including a calamitous consequence to human health. Indeed, some of these pollutants have been associated with human cancers and antimicrobial resistance. There is a paucity of data on the microbial profiles of this important but heavily polluted aquatic ecosystem. The current study sought to investigate the metagenomic profiles of microbial assemblages in the Winam Gulf ecosystem. Water and sediment samples were collected from several locations within the study sites. Total genomic DNA pooled from all sampling sites was extracted and analyzed by whole-genome shotgun sequencing. Analyses revealed three major kingdoms: bacteria, archaea and eukaryotes belonging to 3 phyla, 13 classes, 14 families, 9 orders, 14 genera, and 10 species. Proteobacteria, Betaproteobacteria, Comamonadaceae, Burkholdariales, and Arcobacter were the dominated phyla, class, family, order, genera, and species, respectively. The Kyoto Encyclopedia of Genes and Genomes indicated the highest number of genes involved in metabolism. The presence of carbohydrate metabolism genes and enzymes was used to infer organic pollutions from sewage and agricultural runoffs. Similarly, the presence of xylene and nutrotoluene degradation genes and enzyme was used to infer industrial pollution into the lake. Drug metabolism genes lend credence to the possibility of pharmaceutical pollutants in water. Taken together, there is a clear indication of massive pollution. In addition, carbohydrate-active enzymes were the most abundant and included genes in glycoside hydrolases. Shotgun metagenomic analyses conveyed an understanding of the microbial communities of the massively polluted aquatic ecosystem of Winam Gulf, Lake Vicoria, Kenya. The current study documents the presence of multiclass pollutants in Lake Victoria and reveals information that might be useful for a potential bioremediation strategy using the native microbial communities.
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Affiliation(s)
- Sandra Khatiebi
- Department of Biological Sciences, School of Natural Science, Masinde Muliro University of Science and Technology, P.O. Box 190, 50100 Kakamega, Kenya
| | - Kelvin Kiprotich
- Department of Biological Sciences, School of Natural Science, Masinde Muliro University of Science and Technology, P.O. Box 190, 50100 Kakamega, Kenya
| | - Zedekiah Onyando
- Department of Biological Sciences, School of Natural Science, Masinde Muliro University of Science and Technology, P.O. Box 190, 50100 Kakamega, Kenya
| | - Clabe Wekesa
- Department of Biological Sciences, School of Natural Science, Masinde Muliro University of Science and Technology, P.O. Box 190, 50100 Kakamega, Kenya
| | - Celestine N. Chi
- Department of Medical Biochemistry and Microbiology, University of Uppsala, P.O. Box 582, 75123 Uppsala, Sweden
| | - Chrispinus Mulambalah
- Department of Medical Microbiology & Parasitology, School of Medicine, Moi University, P.O. Box 4606, 30100 Eldoret, Kenya
| | - Patrick Okoth
- Department of Biological Sciences, School of Natural Science, Masinde Muliro University of Science and Technology, P.O. Box 190, 50100 Kakamega, Kenya
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Dzianach PA, Pérez-Reche FJ, Strachan NJC, Forbes KJ, Dykes GA. The Use of Interdisciplinary Approaches to Understand the Biology of Campylobacter jejuni. Microorganisms 2022; 10:microorganisms10122498. [PMID: 36557751 PMCID: PMC9786101 DOI: 10.3390/microorganisms10122498] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Revised: 12/12/2022] [Accepted: 12/13/2022] [Indexed: 12/23/2022] Open
Abstract
Campylobacter jejuni is a bacterial pathogen recognised as a major cause of foodborne illness worldwide. While Campylobacter jejuni generally does not grow outside its host, it can survive outside of the host long enough to pose a health concern. This review presents an up-to-date description and evaluation of biological, mathematical, and statistical approaches used to understand the behaviour of this foodborne pathogen and suggests future avenues which can be explored. Specifically, the incorporation of mathematical modelling may aid the understanding of C. jejuni biofilm formation both outside and inside the host. Predictive studies may be improved by the introduction of more standardised protocols for assessments of disinfection methods and by assessment of novel physical disinfection strategies as well as assessment of the efficiency of plant extracts on C. jejuni eradication. A full description of the metabolic pathways of C. jejuni, which is needed for the successful application of metabolic models, is yet to be achieved. Finally, a shift from animal models (except for those that are a source of human campylobacteriosis) to human-specific data may be made possible due to recent technological advancements, and this may lead to more accurate predictions of human infections.
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Affiliation(s)
- Paulina A. Dzianach
- Geospatial Health and Development, Telethon Kids Institute, Perth 6009, Australia
| | - Francisco J. Pérez-Reche
- School of Natural and Computing Sciences, University of Aberdeen, Aberdeen AB24 3FX, UK
- Correspondence:
| | - Norval J. C. Strachan
- School of Natural and Computing Sciences, University of Aberdeen, Aberdeen AB24 3FX, UK
| | - Ken J. Forbes
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen AB24 3FX, UK
| | - Gary A. Dykes
- School of Agriculture and Food Sciences, University of Queensland, Brisbane 4072, Australia
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Nennig M, Clément A, Longueval E, Bernardi T, Ragimbeau C, Tresse O. Metaphenotypes associated with recurrent genomic lineages of Campylobacter jejuni responsible for human infections in Luxembourg. Front Microbiol 2022; 13:901192. [PMID: 36160185 PMCID: PMC9490421 DOI: 10.3389/fmicb.2022.901192] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2022] [Accepted: 08/01/2022] [Indexed: 11/13/2022] Open
Abstract
Campylobacter jejuni is a leading cause of foodborne illnesses worldwide. Although considered fragile, this microaerophilic bacterium is able to survive in various challenging environments, which subsequently constitutes multiple sources of transmission for human infection. To test the assumption of acquiring specific features for adaptation and survival, we established a workflow of phenotypic tests related to the survival and the persistence of recurrent and sporadic strains. A representative collection of 83 strains isolated over 13 years from human, mammal, poultry, and environmental sources in Luxembourg, representing different spreading patterns (endemic, epidemic, and sporadic), was screened for survival to oxidative stresses, for acclimating to aerobic conditions (AC), and for persistence on abiotic surfaces. Using the cgMLST Oxford typing scheme for WGS data, the collection was classified into genomic lineages corresponding to host-generalist strains (lineages A and D, CC ST-21), host-specific strains (lineage B, CC ST-257 and lineage C, CC ST-464) and sporadic strains. We established that when a strain survives concentrations beyond 0.25 mM superoxide stress, it is six times more likely to survive hyperoxide stress and that a highly adherent strain is 14 times more likely to develop a biofilm. Surprisingly, more than half of the strains could acclimate to AC but this capacity does not explain the difference between recurrent genomic lineages and sporadic strains and the survival to oxidative stresses, while recurrent strains have a significantly higher adhesion/biofilm formation capacity than sporadic ones. From this work, the genomic lineages with more stable genomes could be characterized by a specific combination of phenotypes, called metaphenotypes. From the functional genomic analyses, the presence of a potentially functional T6SS in the strains of lineage D might explain the propensity of these strains to be strong biofilm producers. Our findings support the hypothesis that phenotypical abilities contribute to the spatio-temporal adaptation and survival of stable genomic lineages. It suggests a selection of better-adapted and persistent strains in challenging stress environments, which could explain the prevalence of these lineages in human infections.
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Affiliation(s)
- Morgane Nennig
- Epidemiology and Microbial Genomics, Laboratoire National de Santé, Dudelange, Luxembourg
- UMR-1280 PhAN, INRAE, Nantes, France
| | - Arnaud Clément
- BioFilm Control, Biopôle Clermont-Limagne, Saint-Beauzire, France
| | - Emmanuelle Longueval
- Epidemiology and Microbial Genomics, Laboratoire National de Santé, Dudelange, Luxembourg
| | - Thierry Bernardi
- BioFilm Control, Biopôle Clermont-Limagne, Saint-Beauzire, France
| | - Catherine Ragimbeau
- Epidemiology and Microbial Genomics, Laboratoire National de Santé, Dudelange, Luxembourg
- *Correspondence: Catherine Ragimbeau,
| | - Odile Tresse
- UMR-1280 PhAN, INRAE, Nantes, France
- Odile Tresse,
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Anis N, Bonifait L, Quesne S, Baugé L, Yassine W, Guyard-Nicodème M, Chemaly M. Survival of Campylobacter jejuni Co-Cultured with Salmonella spp. in Aerobic Conditions. Pathogens 2022; 11:pathogens11070812. [PMID: 35890056 PMCID: PMC9323934 DOI: 10.3390/pathogens11070812] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2022] [Revised: 07/11/2022] [Accepted: 07/14/2022] [Indexed: 11/28/2022] Open
Abstract
Campylobacter and Salmonella are responsible for the two major foodborne zoonotic diseases in Europe; poultry is the main infection source. Campylobacter cannot grow under aerobic conditions, but can show aerobic survival when co-cultured with other microorganisms; however, its interaction with Salmonella has not been studied yet. In this study, these two bacteria were co-cultured under controlled aerobic conditions. Different concentrations and strains of C. jejuni were incubated with or without different Salmonella serotypes (10 CFU) at 37 °C for 16 h. C. jejuni did not grow after incubation with or without Salmonella. The survival of C. jejuni was observed only for the highest initial concentration of 6 log CFU/mL with or without Salmonella. However, its survival was significantly higher when co-cultured with Salmonella. No survival was observed at lower concentrations. C. jejuni survival was positively affected by the presence of Salmonella but depended on the Salmonella serotype, the C. jejuni strain and the initial concentration. On the other hand, the Salmonella enumerations were not affected by C. jejuni. Our results suggest potential interactions between Salmonella and C. jejuni that require further investigations for a clearer understanding of their behavior in natural habitats.
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Affiliation(s)
- Nagham Anis
- Unit for Hygiene and Quality of Poultry and Pork Products, Laboratory of Ploufragan-Plouzané-Niort, ANSES, 22440 Ploufragan, France; (N.A.); (L.B.); (S.Q.); (L.B.); (M.C.)
| | - Laetitia Bonifait
- Unit for Hygiene and Quality of Poultry and Pork Products, Laboratory of Ploufragan-Plouzané-Niort, ANSES, 22440 Ploufragan, France; (N.A.); (L.B.); (S.Q.); (L.B.); (M.C.)
| | - Ségolène Quesne
- Unit for Hygiene and Quality of Poultry and Pork Products, Laboratory of Ploufragan-Plouzané-Niort, ANSES, 22440 Ploufragan, France; (N.A.); (L.B.); (S.Q.); (L.B.); (M.C.)
| | - Louise Baugé
- Unit for Hygiene and Quality of Poultry and Pork Products, Laboratory of Ploufragan-Plouzané-Niort, ANSES, 22440 Ploufragan, France; (N.A.); (L.B.); (S.Q.); (L.B.); (M.C.)
| | - Wissam Yassine
- Faculty of Sciences, Lebanese University, Beirut 10999, Lebanon;
| | - Muriel Guyard-Nicodème
- Unit for Hygiene and Quality of Poultry and Pork Products, Laboratory of Ploufragan-Plouzané-Niort, ANSES, 22440 Ploufragan, France; (N.A.); (L.B.); (S.Q.); (L.B.); (M.C.)
- Correspondence: ; Tel.: +33-296-016-211
| | - Marianne Chemaly
- Unit for Hygiene and Quality of Poultry and Pork Products, Laboratory of Ploufragan-Plouzané-Niort, ANSES, 22440 Ploufragan, France; (N.A.); (L.B.); (S.Q.); (L.B.); (M.C.)
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