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Miller WG, Lopes BS, Ramjee M, Jay-Russell MT, Chapman MH, Williams TG, Wood DF, Gruntar I, Papić B, Forbes KJ. Campylobacter devanensis sp. nov., Campylobacter porcelli sp. nov., and Campylobacter vicugnae sp. nov., three novel Campylobacter lanienae-like species recovered from swine, small ruminants, and camelids. Int J Syst Evol Microbiol 2024; 74:006405. [PMID: 38842428 PMCID: PMC11261738 DOI: 10.1099/ijsem.0.006405] [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: 03/14/2024] [Accepted: 05/20/2024] [Indexed: 06/07/2024] Open
Abstract
In a previous study characterizing Campylobacter strains deficient in selenium metabolism, 50 strains were found to be similar to, but distinct from, the selenonegative species Campylobacter lanienae. Initial characterization based on multilocus sequence typing and the phylogeny of a set of 20 core genes determined that these strains form three putative taxa within the selenonegative cluster. A polyphasic study was undertaken here to further clarify their taxonomic position within the genus. The 50 selenonegative strains underwent phylogenetic analyses based on the sequences of the 16S rRNA gene and an expanded set of 330 core genes. Standard phenotypic testing was also performed. All strains were microaerobic and anaerobic, Gram-negative, spiral or curved cells with some displaying coccoid morphologies. Strains were motile, oxidase, catalase, and alkaline phosphatase positive, urease negative, and reduced nitrate. Strains within each clade had unique phenotypic profiles that distinguished them from other members of the genus. Core genome phylogeny clearly placed the 50 strains into three clades. Pairwise average nucleotide identity and digital DNA-DNA hybridization values were all below the recommended cut-offs for species delineation with respect to C. lanienae and other related Campylobacter species. The data presented here clearly show that these strains represent three novel species within the genus, for which the names Campylobacter devanensis sp. nov. (type strain RM3662T=LMG 33097T=NCTC 15074T), Campylobacter porcelli sp. nov. (type strain RM6137T=LMG 33098T=CCUG 77054T=NCTC 15075T) and Campylobacter vicugnae sp. nov. (type strain RM12175T=LMG 33099T=CCUG 77055T=NCTC 15076T) are proposed.
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Affiliation(s)
- William G. Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA, USA
| | - Bruno S. Lopes
- School of Health and Life Sciences, Teesside University, Middlesbrough, UK
- National Horizons Centre, Teesside University, Darlington, UK
| | - Meenakshi Ramjee
- Wolfson Wohl Cancer Research Centre, Glasgow. The University of Glasgow, Glasgow, UK
| | | | - Mary H. Chapman
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA, USA
| | - Tina G. Williams
- Bioproducts Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA, USA
| | - Delilah F. Wood
- Bioproducts Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA, USA
| | - Igor Gruntar
- University of Ljubljana, Veterinary Faculty, Institute of Microbiology and Parasitology, Ljubljana, Slovenia
| | - Bojan Papić
- University of Ljubljana, Veterinary Faculty, Institute of Microbiology and Parasitology, Ljubljana, Slovenia
| | - Ken J. Forbes
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, UK
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2
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Wu R, Payne M, Zhang L, Lan R. Uncovering the boundaries of Campylobacter species through large-scale phylogenetic and nucleotide identity analyses. mSystems 2024; 9:e0121823. [PMID: 38530055 PMCID: PMC11019964 DOI: 10.1128/msystems.01218-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2023] [Accepted: 02/21/2024] [Indexed: 03/27/2024] Open
Abstract
Campylobacter species are typically helical shaped, Gram-negative, and non-spore-forming bacteria. Species in this genus include established foodborne and animal pathogens as well as emerging pathogens. The accumulation of genomic data from the Campylobacter genus has increased exponentially in recent years, accompanied by the discovery of putative new species. At present, the lack of a standardized species boundary complicates distinguishing established and novel species. We defined the Campylobacter genus core genome (500 loci) using publicly available Campylobacter complete genomes (n = 498) and constructed a core genome phylogeny using 2,193 publicly available Campylobacter genomes to examine inter-species diversity and species boundaries. Utilizing 8,440 Campylobacter genomes representing 33 species and 8 subspecies, we found species delineation based on an average nucleotide identity (ANI) cutoff of 94.2% is consistent with the core genome phylogeny. We identified 60 ANI genomic species that delineated Campylobacter species in concordance with previous comparative genetic studies. All pairwise ANI genomic species pairs had in silico DNA-DNA hybridization scores of less than 70%, supporting their delineation as separate species. We provide the tool Campylobacter Genomic Species typer (CampyGStyper) that assigns ANI genomic species to query genomes based on ANI similarities to medoid genomes from each ANI genomic species with an accuracy of 99.96%. The ANI genomic species definitions proposed here allow consistent species definition in the Campylobacter genus and will facilitate the detection of novel species in the future.IMPORTANCEIn recent years, Campylobacter has gained recognition as the leading cause of bacterial gastroenteritis worldwide, leading to a substantial rise in the collection of genomic data of the Campylobacter genus in public databases. Currently, a standardized Campylobacter species boundary at the genomic level is absent, leading to challenges in detecting emerging pathogens and defining putative novel species within this genus. We used a comprehensive representation of genomes of the Campylobacter genus to construct a core genome phylogenetic tree. Furthermore, we found an average nucleotide identity (ANI) of 94.2% as the optimal cutoff to define the Campylobacter species. Using this cutoff, we identified 60 ANI genomic species which provided a standardized species definition and nomenclature. Importantly, we have developed Campylobacter Genomic Species typer (CampyGStyper), which can robustly and accurately assign these ANI genomic species to Campylobacter genomes, thereby aiding pathogen surveillance and facilitating evolutionary and epidemiological studies of existing and emerging pathogens in the genus Campylobacter.
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Affiliation(s)
- Ruochen Wu
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Michael Payne
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Li Zhang
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Ruiting Lan
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
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3
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Henaut-Jacobs S, Passarelli-Araujo H, Venancio TM. Comparative genomics and phylogenomics of Campylobacter unveil potential novel species and provide insights into niche segregation. Mol Phylogenet Evol 2023; 184:107786. [PMID: 37105244 DOI: 10.1016/j.ympev.2023.107786] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 03/17/2023] [Accepted: 04/13/2023] [Indexed: 04/29/2023]
Abstract
Campylobacter is a bacterial genus associated with community outbreaks and gastrointestinal symptoms. Studies on Campylobacter generally focus on specific pathogenic species such as C. coli and C. jejuni. Currently, there are thousands of publicly available Campylobacter genomes, allowing a more complete assessment of the genus diversity. In this work, we report a network-based analysis of all available Campylobacter genomes to explore the genus structure and diversity, revealing potentially new species and elucidating genus features. We also hypothesize that the previously established Clade III of C. coli is in fact a novel species (referred here as Campylobacter spp12). Finally, we found a negative correlation between pangenome fluidity and saturation coefficient, with potential implications to the lifestyles of distinct Campylobacter species. Since pangenome analysis depends on the number of available genomes, this correlation could help estimate pangenome metrics of Campylobacter species with less sequenced genomes, helping understand their lifestyle and niche adaptation. Together, our results indicate that the Campylobacter genus should be re-evaluated, with particular attention to the interplay between genome structure and niche segregation.
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Affiliation(s)
- Sarah Henaut-Jacobs
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil
| | - Hemanoel Passarelli-Araujo
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil; Departamento de Bioquímica e Imunologia, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil.
| | - Thiago M Venancio
- Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro, Campos dos Goytacazes, RJ, Brazil.
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4
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Soto-Beltrá N M, Lee BG, Amézquita-López BA, Quiñones B. Overview of methodologies for the culturing, recovery and detection of Campylobacter. INTERNATIONAL JOURNAL OF ENVIRONMENTAL HEALTH RESEARCH 2023; 33:307-323. [PMID: 35168460 DOI: 10.1080/09603123.2022.2029366] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Accepted: 01/11/2022] [Indexed: 06/14/2023]
Abstract
Campylobacter species are responsible for human gastroenteritis with diverse clinical spectra, ranging from acute watery or bloody diarrhea to life-threatening autoimmune disorders. Given the importance of Campylobacter in causing human illness, this article has reviewed the transmission and attribution sources as well as methodologies for the detection and virulence characterization of campylobacteria. The recovery and detection of Campylobacter from clinical, food and environmental samples has been achieved by the combinatorial use of selective enrichment and culturing methods. Biochemical, immunological, and nucleic acid-based methodologies have enabled the detection and differentiation of closely related Campylobacter isolates in foodborne outbreak investigations and have assessed the diversity and phylogenetic relationships of these bacterial pathogens. Analyses of motility, adherence, and invasiveness in host cells have assessed the pathogenic potential of campylobacteria. Further examination of determinants conferring antimicrobial resistance in Campylobacter have supported the growing need to closely monitor antimicrobials use in clinical and agricultural sectors.
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Affiliation(s)
- Marcela Soto-Beltrá N
- Facultad de Ciencias Químico Biológicas, Universidad Autónoma de Sinaloa, Culiacán, México
| | - Bertram G Lee
- Produce Safety and Microbiology Research Unit, United States Department of Agriculture/Agricultural Research Service,Western Regional Research Center, Albany, CA, USA
| | | | - Beatriz Quiñones
- Produce Safety and Microbiology Research Unit, United States Department of Agriculture/Agricultural Research Service,Western Regional Research Center, Albany, CA, USA
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Selenium Metabolism and Selenoproteins in Prokaryotes: A Bioinformatics Perspective. Biomolecules 2022; 12:biom12070917. [PMID: 35883471 PMCID: PMC9312934 DOI: 10.3390/biom12070917] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 01/25/2023] Open
Abstract
Selenium (Se) is an important trace element that mainly occurs in the form of selenocysteine in selected proteins. In prokaryotes, Se is also required for the synthesis of selenouridine and Se-containing cofactor. A large number of selenoprotein families have been identified in diverse prokaryotic organisms, most of which are thought to be involved in various redox reactions. In the last decade or two, computational prediction of selenoprotein genes and comparative genomics of Se metabolic pathways and selenoproteomes have arisen, providing new insights into the metabolism and function of Se and their evolutionary trends in bacteria and archaea. This review aims to offer an overview of recent advances in bioinformatics analysis of Se utilization in prokaryotes. We describe current computational strategies for the identification of selenoprotein genes and generate the most comprehensive list of prokaryotic selenoproteins reported to date. Furthermore, we highlight the latest research progress in comparative genomics and metagenomics of Se utilization in prokaryotes, which demonstrates the divergent and dynamic evolutionary patterns of different Se metabolic pathways, selenoprotein families, and selenoproteomes in sequenced organisms and environmental samples. Overall, bioinformatics analyses of Se utilization, function, and evolution may contribute to a systematic understanding of how this micronutrient is used in nature.
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6
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Parisi A, Chiara M, Caffara M, Mion D, Miller WG, Caruso M, Manzari C, Florio D, Capozzi L, D'Erchia AM, Manzulli V, Zanoni RG. Campylobacter vulpis sp. nov. isolated from wild red foxes. Syst Appl Microbiol 2021; 44:126204. [PMID: 33895623 DOI: 10.1016/j.syapm.2021.126204] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2020] [Revised: 03/21/2021] [Accepted: 03/28/2021] [Indexed: 12/27/2022]
Abstract
During a sampling of wild red foxes (Vulpes vulpes) for the detection of Epsilonproteobacteria, 14 strains were isolated from the caecal contents of 14 epidemiologically-unrelated animals. A genus-specific PCR indicated that the isolates belonged to the genus Campylobacter. Based on the results of a species-specific PCR, the isolates were initially identified as C. upsaliensis. However, multi-locus sequence typing (MLST) revealed that the isolates were significantly different from the C. upsaliensis present in the MLST database. A polyphasic study, including conventional biochemical and tolerance characteristics, morphology by transmission electron microscopy (TEM), MALDI-TOF analysis, and genetic comparisons based on partial 16S rDNA and atpA gene sequences, was undertaken. Finally, the complete genome sequence of the type strain 251/13T and the draft genome sequences of the other isolates were determined. Average nucleotide identity, average amino acid identity and in silico DNA-DNA hybridization analyses confirmed that the isolates represent a novel taxon for which the name Campylobacter vulpis sp. nov. is proposed, with isolate 251/13T (=CCUG 70587T = LMG 30110T) as the type strain. In order to allow a rapid discrimination of C. vulpis from the closely-related C. upsaliensis, a specific PCR test was designed, based on atpA gene sequences.
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Affiliation(s)
- Antonio Parisi
- Experimental Zooprophylactic Institute of Apulia and Basilicata, Via Manfredonia 20, 71121 Foggia, Italy.
| | - Matteo Chiara
- Department of Biosciences, University of Milan, Via Celoria 26, 20133 Milano, Italy
| | - Monica Caffara
- Department of Veterinary Medical Sciences, Alma Mater Studiorum Università di Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia, Bologna, Italy
| | - Domenico Mion
- Department of Veterinary Medical Sciences, Alma Mater Studiorum Università di Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia, Bologna, Italy
| | - William G Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, CA, USA
| | - Marta Caruso
- Experimental Zooprophylactic Institute of Apulia and Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
| | - Caterina Manzari
- Institute of Biomembranes and Bioenergetics, Italian National Research Council, Via Amendola 165A, 70126 Bari, Italy
| | - Daniela Florio
- Department of Veterinary Medical Sciences, Alma Mater Studiorum Università di Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia, Bologna, Italy
| | - Loredana Capozzi
- Experimental Zooprophylactic Institute of Apulia and Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
| | - Anna Maria D'Erchia
- Institute of Biomembranes and Bioenergetics, Italian National Research Council, Via Amendola 165A, 70126 Bari, Italy; Department of Biosciences, Biotechnology and Biopharmaceutics, University of Bari "A. Moro", Via Orabona, 4, 70126 Bari, Italy
| | - Viviana Manzulli
- Experimental Zooprophylactic Institute of Apulia and Basilicata, Via Manfredonia 20, 71121 Foggia, Italy
| | - Renato Giulio Zanoni
- Department of Veterinary Medical Sciences, Alma Mater Studiorum Università di Bologna, Via Tolara di Sopra 50, 40064 Ozzano Emilia, Bologna, Italy
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7
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Parker CT, Cooper KK, Schiaffino F, Miller WG, Huynh S, Gray HK, Olortegui MP, Bardales PG, Trigoso DR, Penataro-Yori P, Kosek MN. Genomic Characterization of Campylobacter jejuni Adapted to the Guinea Pig ( Cavia porcellus) Host. Front Cell Infect Microbiol 2021; 11:607747. [PMID: 33816330 PMCID: PMC8012767 DOI: 10.3389/fcimb.2021.607747] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 02/22/2021] [Indexed: 11/13/2022] Open
Abstract
Campylobacter jejuni is the leading bacterial cause of gastroenteritis worldwide with excessive incidence in low-and middle-income countries (LMIC). During a survey for C. jejuni from putative animal hosts in a town in the Peruvian Amazon, we were able to isolate and whole genome sequence two C. jejuni strains from domesticated guinea pigs (Cavia porcellus). The C. jejuni isolated from guinea pigs had a novel multilocus sequence type that shared some alleles with other C. jejuni collected from guinea pigs. Average nucleotide identity and phylogenetic analysis with a collection of C. jejuni subsp. jejuni and C. jejuni subsp. doylei suggest that the guinea pig isolates are distinct. Genomic comparisons demonstrated gene gain and loss that could be associated with guinea pig host specialization related to guinea pig diet, anatomy, and physiology including the deletion of genes involved with selenium metabolism, including genes encoding the selenocysteine insertion machinery and selenocysteine-containing proteins.
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Affiliation(s)
- Craig T Parker
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, US Department of Agriculture, Albany, CA, United States
| | - Kerry K Cooper
- School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, AZ, United States
| | - Francesca Schiaffino
- Faculty of Veterinary Medicine, Universidad Peruana Cayetano Heredia, Lima, Peru.,The Division of Infectious Diseases and International Health and Public Health Sciences, University of Virginia, Charlottesville, VA, United States
| | - William G Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, US Department of Agriculture, Albany, CA, United States
| | - Steven Huynh
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, US Department of Agriculture, Albany, CA, United States
| | - Hannah K Gray
- Whiting School of Engineering, Johns Hopkins University, Baltimore, MD, United States
| | | | | | | | - Pablo Penataro-Yori
- The Division of Infectious Diseases and International Health and Public Health Sciences, University of Virginia, Charlottesville, VA, United States.,Biomedical Research, Asociación Benéfica PRISMA, Iquitos, Peru
| | - Margaret N Kosek
- The Division of Infectious Diseases and International Health and Public Health Sciences, University of Virginia, Charlottesville, VA, United States.,Biomedical Research, Asociación Benéfica PRISMA, Iquitos, Peru
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8
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Biogeographic and Evolutionary Patterns of Trace Element Utilization in Marine Microbial World. GENOMICS PROTEOMICS & BIOINFORMATICS 2021; 19:958-972. [PMID: 33631428 PMCID: PMC9402790 DOI: 10.1016/j.gpb.2021.02.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2018] [Revised: 01/23/2019] [Accepted: 06/06/2019] [Indexed: 12/01/2022]
Abstract
Trace elements are required by all organisms, which are key components of many enzymes catalyzing important biological reactions. Many trace element-dependent proteins have been characterized; however, little is known about their occurrence in microbial communities in diverse environments, especially the global marine ecosystem. Moreover, the relationships between trace element utilization and different types of environmental stressors are unclear. In this study, we used metagenomic data from the Global Ocean Sampling expedition project to identify the biogeographic distribution of genes encoding trace element-dependent proteins (for copper, molybdenum, cobalt, nickel, and selenium) in a variety of marine and non-marine aquatic samples. More than 56,000 metalloprotein and selenoprotein genes corresponding to nearly 100 families were predicted, becoming the largest dataset of marine metalloprotein and selenoprotein genes reported to date. In addition, samples with enriched or depleted metalloprotein/selenoprotein genes were identified, suggesting an active or inactive usage of these micronutrients in various sites. Further analysis of interactions among the elements showed significant correlations between some of them, especially those between nickel and selenium/copper. Finally, investigation of the relationships between environmental conditions and metalloprotein/selenoprotein families revealed that many environmental factors might contribute to the evolution of different metalloprotein and/or selenoprotein genes in the marine microbial world. Our data provide new insights into the utilization and biological roles of these trace elements in extant marine microbes, and might also be helpful for the understanding of how these organisms have adapted to their local environments.
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9
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Chen D, McKune SL, Singh N, Yousuf Hassen J, Gebreyes W, Manary MJ, Bardosh K, Yang Y, Diaz N, Mohammed A, Terefe Y, Roba KT, Ketema M, Ameha N, Assefa N, Rajashekara G, Deblais L, Ghanem M, Yimer G, Havelaar AH. Campylobacter Colonization, Environmental Enteric Dysfunction, Stunting, and Associated Risk Factors Among Young Children in Rural Ethiopia: A Cross-Sectional Study From the Campylobacter Genomics and Environmental Enteric Dysfunction (CAGED) Project. Front Public Health 2021; 8:615793. [PMID: 33553097 PMCID: PMC7862945 DOI: 10.3389/fpubh.2020.615793] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Accepted: 12/17/2020] [Indexed: 11/19/2022] Open
Abstract
Livestock farming provides a possible mechanism by which smallholder farmers can meet their household need for animal source foods (ASF), which may reduce the risk of stunting. However, direct/indirect contacts with domestic animals may increase colonization by Campylobacter spp., which has been associated with Environmental Enteric Dysfunction (EED) and stunting. A cross-sectional study involving 102 randomly selected children between 12 and 16 months of age was conducted in rural eastern Ethiopia to establish prevalence rates of Campylobacter colonization, EED, and stunting, and evaluate potential risk factors. Data were collected between September and December 2018. The prevalence of EED and stunting was 50% (95% CI: 40-60%) and 41% (95% CI: 32-51%), respectively. Among enrolled children, 56% had consumed some ASF in the previous 24 h; 47% had diarrhea and 50% had fever in the past 15 days. 54, 63, 71 or 43% of households owned at least one chicken, cow/bull, goat, or sheep; 54 (53%) households kept chickens indoors overnight and only half of these confined the animals. Sanitation was poor, with high levels of unimproved latrines and open defecation. Most households had access to an improved source of drinking water. The prevalence of Campylobacter colonization was 50% (95% CI: 41-60%) by PCR. In addition to the thermotolerant species Campylobacter jejuni, Campylobacter coli and Campylobacter upsaliensis, non-thermotolerant species related to Campylobacter hyointestinalis and Campylobacter fetus were frequently detected by Meta-total RNA sequencing (MeTRS). Current breastfeeding and ASF consumption increased the odds of Campylobacter detection by PCR, while improved drinking water supply decreased the odds of EED. No risk factors were significantly associated with stunting. Further studies are necessary to better understand reservoirs and transmission pathways of Campylobacter spp. and their potential impact on child health.
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Affiliation(s)
- Dehao Chen
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL, United States
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
| | - Sarah L. McKune
- Department of Environmental and Global Health, College of Public Health and Health Professions, University of Florida, Gainesville, FL, United States
- Center for African Studies, University of Florida, Gainesville, FL, United States
| | - Nitya Singh
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
- Department of Animal Sciences, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
| | - Jemal Yousuf Hassen
- Department of Rural Development and Agricultural Extension, Haramaya University, Dire Dawa, Ethiopia
| | - Wondwossen Gebreyes
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, United States
| | - Mark J. Manary
- Department of Pediatrics, Washington University in St. Louis, St. Louis, MO, United States
| | - Kevin Bardosh
- Department of Anthropology, University of Florida, Gainesville, FL, United States
| | - Yang Yang
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
- Department of Biostatistics, College of Public Health and Health Professions & College of Medicine, University of Florida, Gainesville, FL, United States
| | - Nicholas Diaz
- Center for African Studies, University of Florida, Gainesville, FL, United States
| | | | - Yitagele Terefe
- College of Veterinary Medicine, Haramaya University, Dire Dawa, Ethiopia
| | - Kedir Teji Roba
- College of Health and Medical Sciences, Haramaya University, Dire Dawa, Ethiopia
| | - Mengistu Ketema
- School of Agricultural Economics and Agribusiness, Haramaya University, Dire Dawa, Ethiopia
| | - Negassi Ameha
- School of Animal and Range Science, Haramaya University, Dire Dawa, Ethiopia
| | - Nega Assefa
- College of Health and Medical Sciences, Haramaya University, Dire Dawa, Ethiopia
| | - Gireesh Rajashekara
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, United States
| | - Loïc Deblais
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, United States
| | - Mostafa Ghanem
- Department of Veterinary Preventive Medicine, The Ohio State University, Columbus, OH, United States
| | - Getnet Yimer
- Global One Health initiative, Office of International Affairs, The Ohio State University, Eastern Africa Regional Office, Addis Ababa, Ethiopia
| | - Arie H. Havelaar
- Emerging Pathogens Institute, University of Florida, Gainesville, FL, United States
- Department of Animal Sciences, Institute of Food and Agricultural Sciences, University of Florida, Gainesville, FL, United States
- Institute for Sustainable Food Systems, University of Florida, Gainesville, FL, United States
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10
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Zhang Y, Zheng J. Bioinformatics of Metalloproteins and Metalloproteomes. Molecules 2020; 25:molecules25153366. [PMID: 32722260 PMCID: PMC7435645 DOI: 10.3390/molecules25153366] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Revised: 07/17/2020] [Accepted: 07/22/2020] [Indexed: 12/14/2022] Open
Abstract
Trace metals are inorganic elements that are required for all organisms in very low quantities. They serve as cofactors and activators of metalloproteins involved in a variety of key cellular processes. While substantial effort has been made in experimental characterization of metalloproteins and their functions, the application of bioinformatics in the research of metalloproteins and metalloproteomes is still limited. In the last few years, computational prediction and comparative genomics of metalloprotein genes have arisen, which provide significant insights into their distribution, function, and evolution in nature. This review aims to offer an overview of recent advances in bioinformatic analysis of metalloproteins, mainly focusing on metalloprotein prediction and the use of different metals across the tree of life. We describe current computational approaches for the identification of metalloprotein genes and metal-binding sites/patterns in proteins, and then introduce a set of related databases. Furthermore, we discuss the latest research progress in comparative genomics of several important metals in both prokaryotes and eukaryotes, which demonstrates divergent and dynamic evolutionary patterns of different metalloprotein families and metalloproteomes. Overall, bioinformatic studies of metalloproteins provide a foundation for systematic understanding of trace metal utilization in all three domains of life.
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Affiliation(s)
- Yan Zhang
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China;
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518055, China
- Correspondence: ; Tel.: +86-755-2692-2024
| | - Junge Zheng
- Shenzhen Key Laboratory of Marine Bioresources and Ecology, College of Life Sciences and Oceanography, Shenzhen University, Shenzhen 518055, China;
- Shenzhen-Hong Kong Institute of Brain Science-Shenzhen Fundamental Research Institutions, Shenzhen 518055, China
- Shenzhen Bay Laboratory, Shenzhen 518055, China
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11
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On SLW, Miller WG, Biggs PJ, Cornelius AJ, Vandamme P. A critical rebuttal of the proposed division of the genus Arcobacter into six genera using comparative genomic, phylogenetic, and phenotypic criteria. Syst Appl Microbiol 2020; 43:126108. [PMID: 32847783 DOI: 10.1016/j.syapm.2020.126108] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2020] [Revised: 06/06/2020] [Accepted: 06/22/2020] [Indexed: 12/22/2022]
Abstract
The proposal to restructure the genus Arcobacter into six distinct genera was critically examined using: comparative analyses of up to 80 Epsilonproteobacterial genome sequences (including 26 arcobacters); phylogenetic analyses of three housekeeping genes and also 342 core genes; and phenotypic criteria. Genome sequences were analysed with tools to calculate Percentage of Conserved Proteins, Average Amino-acid Identity, BLAST-based Average Nucleotide Identity, in silico DNA-DNA hybridisation values, genome-wide Average Nucleotide Identity, Alignment Fractions and G+C percentages. Genome analyses revealed the genus Arcobacter sensu lato to be relatively homogenous, and phylogenetic analyses clearly distinguished the group from other Epsilonproteobacteria. Genomic distinction of the genera proposed by Pérez-Cataluña et al. [2018] was not supported by any of the measures used and a subsequent risk of strain misidentification clearly identified. Similarly, phenotypic analyses supported the delineation of Arcobacter sensu lato but did not justify the position of the proposed novel genera. The present polyphasic taxonomic study strongly supports the continuance of the classification of "aerotolerant campylobacters" as Arcobacter and refutes the proposed genus-level subdivision of Pérez-Cataluña et al. [2018].
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Affiliation(s)
- Stephen L W On
- Department of Wine, Food and Molecular Biosciences, Lincoln University, Springs Road, Lincoln 7467, New Zealand.
| | - William G Miller
- US Department of Agriculture, Produce Safety and Microbiology Research Unit, Albany, CA, USA
| | - Patrick J Biggs
- Bioinformatics and Statistics Group, School of Fundamental Sciences, Massey University, Palmerston North, New Zealand; mEpiLab, School of Veterinary Science, Massey University, Palmerston North, New Zealand
| | - Angela J Cornelius
- Institute of Environmental Science and Research, Christchurch, New Zealand
| | - Peter Vandamme
- Laboratory of Microbiology, Faculty of Sciences, Ghent University, K.L. Ledeganckstraat 35, B-9000 Ghent, Belgium
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Abstract
Campylobacter is among the four main causes of gastroenteritis worldwide and has increased in both developed and developing countries over the last 10 years. The vast majority of reported Campylobacter infections are caused by Campylobacter jejuni and, to a lesser extent, C. coli; however, the increasing recognition of other emerging Campylobacter pathogens is urgently demanding a better understanding of how these underestimated species cause disease, transmit, and evolve. In parallel to the enhanced clinical awareness of campylobacteriosis due to improved diagnostic protocols, the application of high-throughput sequencing has increased the number of whole-genome sequences available to dozens of strains of many emerging campylobacters. This has allowed for comprehensive comparative pathogenomic analyses for several species, such as C. fetus and C. concisus These studies have started to reveal the evolutionary forces shaping their genomes and have brought to light many genomic features related to pathogenicity in these neglected species, promoting the development of new tools and approaches relevant for clinical microbiology. Despite the need for additional characterization of genomic diversity in emerging campylobacters, the increasing body of literature describing pathogenomic studies on these species deserves to be discussed from an integrative perspective. This review compiles the current knowledge and highlights future work toward deepening our understanding about genome dynamics and the mechanisms governing the evolution of pathogenicity in emerging Campylobacter species, which is urgently needed to develop strategies to prevent or control the spread of these pathogens.
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Affiliation(s)
- Daniela Costa
- Microbial Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Sección Genética Evolutiva, Facultad de Ciencias, Universidad de la República, Montevideo, Uruguay
| | - Gregorio Iraola
- Microbial Genomics Laboratory, Institut Pasteur de Montevideo, Montevideo, Uruguay
- Center for Integrative Biology, Universidad Mayor, Santiago de Chile, Chile
- Wellcome Sanger Institute, Hinxton, United Kingdom
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13
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Complete Genome Sequence of the Arcobacter bivalviorum Type Strain LMG 26154. Microbiol Resour Announc 2018; 7:MRA01076-18. [PMID: 30533664 PMCID: PMC6256687 DOI: 10.1128/mra.01076-18] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/04/2018] [Indexed: 11/20/2022] Open
Abstract
Arcobacters are routinely recovered from marine environments, and multiple Arcobacter species have been isolated from shellfish. Arcobacter bivalviorum was recovered from mussels collected in the Ebro Delta in northeastern Spain. This report describes the complete whole-genome sequence of the A. bivalviorum type strain LMG 26154 (= F4T = CECT 7835T).
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Complete Genome Sequence of the Arcobacter trophiarum Type Strain LMG 25534. Microbiol Resour Announc 2018; 7:MRA01110-18. [PMID: 30533698 PMCID: PMC6256567 DOI: 10.1128/mra.01110-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 09/07/2018] [Indexed: 02/06/2023] Open
Abstract
Arcobacter species have been recovered from food and/or food animals, and several of these species are potential human pathogens. Arcobacter trophiarum was recovered from fecal samples taken from pigs on two Belgian farms. Arcobacter species have been recovered from food and/or food animals, and several of these species are potential human pathogens. Arcobacter trophiarum was recovered from fecal samples taken from pigs on two Belgian farms. This study describes the whole-genome sequence of the A. trophiarum type strain LMG 25534 (=64T =CCUG 59229T).
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Complete Genome Sequence of the Arcobacter halophilus Type Strain CCUG 53805. Microbiol Resour Announc 2018; 7:MRA01077-18. [PMID: 30533711 PMCID: PMC6256642 DOI: 10.1128/mra.01077-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 09/12/2018] [Indexed: 11/20/2022] Open
Abstract
Many Arcobacter spp. are free living and are routinely recovered from marine environments. Many Arcobacter spp. are free living and are routinely recovered from marine environments. Arcobacter halophilus was isolated from hypersaline lagoon water in the Hawaiian islands, and it was demonstrated to be an obligate halophile. This study describes the complete whole-genome sequence of the A. halophilus type strain, CCUG 53805 (= LA31BT = ATCC BAA-1022T).
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Complete Genome Sequence of the Arcobacter mytili Type Strain LMG 24559. Microbiol Resour Announc 2018; 7:MRA01078-18. [PMID: 30533637 PMCID: PMC6256660 DOI: 10.1128/mra.01078-18] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 08/20/2018] [Indexed: 01/28/2023] Open
Abstract
Multiple Arcobacter species have been recovered from fresh and contaminated waters, marine environments, and shellfish. Arcobacter mytili was recovered in 2006 from mussels collected from the Ebro River delta in Catalonia, Spain. Multiple Arcobacter species have been recovered from fresh and contaminated waters, marine environments, and shellfish. Arcobacter mytili was recovered in 2006 from mussels collected from the Ebro River delta in Catalonia, Spain. This study describes the complete whole-genome sequence of the A. mytili type strain LMG 24559 (=F2075T =CECT 7386T).
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Miller WG, Yee E. Complete Genome Sequence of the Arcobacter skirrowii Type Strain LMG 6621. Microbiol Resour Announc 2018; 7:e01308-18. [PMID: 30533756 PMCID: PMC6256491 DOI: 10.1128/mra.01308-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 10/11/2018] [Indexed: 11/20/2022] Open
Abstract
Arcobacter skirrowii is a species of veterinary importance, originally recovered from the feces, aborted fetuses, and preputial fluids of livestock. We present here the whole-genome sequence of the A. skirrowii type strain LMG 6621 (= 449/80T = CCUG 10374T), isolated in the United Kingdom from a lamb diarrheal fecal sample.
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Affiliation(s)
- William G. Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA
| | - Emma Yee
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA
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Miller WG, Yee E, Bono JL. Complete Genome Sequence of the Arcobacter suis Type Strain LMG 26152. Microbiol Resour Announc 2018; 7:e01307-18. [PMID: 30533764 PMCID: PMC6256499 DOI: 10.1128/mra.01307-18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2018] [Accepted: 10/10/2018] [Indexed: 11/25/2022] Open
Abstract
Arcobacter species are prevalent in pigs, and strains have been isolated from pig feces and pork meat; some Arcobacter strains may be porcine abortifacients. Arcobacter suis was recovered from pork meat in Spain. This study describes the whole-genome sequence of the A. suis type strain LMG 26152 (=F41T =CECT 7833T).
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Affiliation(s)
- William G. Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA
| | - Emma Yee
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA
| | - James L. Bono
- Meat Safety and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Clay Center, Nebraska, USA
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Miller WG, Yee E, Bono JL. Complete Genome Sequence of the Arcobacter ellisii Type Strain LMG 26155. Microbiol Resour Announc 2018; 7:e01268-18. [PMID: 30533751 PMCID: PMC6256587 DOI: 10.1128/mra.01268-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 09/30/2018] [Indexed: 01/05/2023] Open
Abstract
Arcobacter spp. are highly prevalent in contaminated environmental waters and have been recovered from both freshwater and seawater, with several species isolated from shellfish. Arcobacter ellisii was recovered from mussels collected in Catalonia, Spain. This study describes the whole-genome sequence of the A. ellisii type strain LMG 26155 (=F79-6T =CECT 7837T).
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Affiliation(s)
- William G. Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA
| | - Emma Yee
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA
| | - James L. Bono
- Meat Safety and Quality Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Clay Center, Nebraska, USA
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Miller WG, Yee E, Huynh S, Parker CT. Complete Genome Sequence of the Arcobacter marinus Type Strain JCM 15502. Microbiol Resour Announc 2018; 7:e01269-18. [PMID: 30533748 PMCID: PMC6256584 DOI: 10.1128/mra.01269-18] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 10/03/2018] [Indexed: 02/02/2023] Open
Abstract
Arcobacter species are often recovered from marine environments and are isolated from both seawater and shellfish. Arcobacter marinus was recovered from the homogenate of a sample containing surface seawater, seaweed, and a starfish. This study describes the whole-genome sequence of the A. marinus type strain JCM 15502 (= CL-S1T = KCCM 90072T).
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Affiliation(s)
- William G. Miller
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA
| | - Emma Yee
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA
| | - Steven Huynh
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA
| | - Craig T. Parker
- Produce Safety and Microbiology Research Unit, Agricultural Research Service, U.S. Department of Agriculture, Albany, California, USA
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Complete Genome Sequence of the Hippuricase-Positive Campylobacter avium Type Strain LMG 24591. GENOME ANNOUNCEMENTS 2017; 5:5/43/e01221-17. [PMID: 29074672 PMCID: PMC5658510 DOI: 10.1128/genomea.01221-17] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Campylobacter avium is a thermotolerant Campylobacter species that has been isolated from poultry. C. avium was also the second hippuricase-positive species to be identified within Campylobacter. Here, we present the genome sequence of the C. avium type strain LMG 24591 (=CCUG 56292T), isolated in 2006 from a broiler chicken in Italy.
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