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de Brito SG, Dias TS, Dos Santos Machado L, de Souza JB, da Cunha NC, de Almeida Pereira VL, Barreto ML, de Mello Figueiredo Cerqueira A, Neves FPG. Detection of Mycoplasma spp. in free-living seabirds. Braz J Microbiol 2024:10.1007/s42770-024-01409-8. [PMID: 38833117 DOI: 10.1007/s42770-024-01409-8] [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: 02/19/2024] [Accepted: 05/28/2024] [Indexed: 06/06/2024] Open
Abstract
This study aimed to investigate the presence of Mycoplasma spp. and identify the species of mycoplasma isolates obtained from seabirds found on Brazilian coastal beaches. Tracheal and cloacal swab samples were collected from 50 seabirds rescued by three conservation and marine animal rehabilitation centers located in Brazil. The tracheal and cloacal samples were subjected to mycoplasma culture and the isolates were identified through PCR. A "Mollicutes-specific" 16S rRNA PCR reaction was employed for triage. Four species-specific PCR reactions were used to detect Mycoplasma gallisepticum, Mycoplasma synoviae, Mycoplasma meleagridis, or M. gallinarum. The Mollicutes positive and species negative samples were submitted do 16S rRNA sequencing. Eighteen (36%) of 50 seabirds tested positive for mycoplasma by culture. In the PCR for the genus, 28 (56%) of 50 seabirds were positive for Mycoplasma spp., with 13 (26%) detected in the trachea, one (2%) in the cloaca, and 14 (28%) in both sites. In the species-specific PCR, M. gallisepticum was detected in 17.8%, and M. meleagridis in 17.8%. Both species were detected in 14.3%. Of the isolates not characterized at species level, we obtained ten sequences and they were divided into three clusters. The first cluster was closely related to M. meleagridis, the second to M. synoviae, and the third grouped M. tully, M. gallisepticum, and M. imitans. Four and five of nine species of seabirds studied had mycoplasma detected by culture or PCR, respectively. Mycoplasmas were found in the majority of the animals studied, with the highest prevalence proportionally found in Sula leucogaster, and the lowest in Fregata magnificens. The phylogenetic analysis identified Mycoplasma spp. adapted to aquatic birds.
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Affiliation(s)
- Samara Gomes de Brito
- Programa de Pós-Graduação Stricto Sensu Em Microbiologia E Parasitologia Aplicadas (PPGMPA), da Universidade Federal Fluminense, Niterói, RJ, Brazil.
| | - Thomas Salles Dias
- Departamento de Saúde Coletiva Veterinária E Saúde Pública, Faculdade de Veterinária, Universidade Federal Fluminense (UFF), Niterói, RJ, Brazil
| | - Leandro Dos Santos Machado
- Departamento de Saúde Coletiva Veterinária E Saúde Pública, Faculdade de Veterinária, Universidade Federal Fluminense (UFF), Niterói, RJ, Brazil
| | - Jenif Braga de Souza
- Instituto de Ciência E Tecnologia Em Biomodelos (ICTB), Fundação Oswaldo Cruz, Rio de Janeiro, RJ, Brazil
| | - Nathalie Costa da Cunha
- Departamento de Saúde Coletiva Veterinária E Saúde Pública, Faculdade de Veterinária, Universidade Federal Fluminense (UFF), Niterói, RJ, Brazil
| | - Virginia Léo de Almeida Pereira
- Departamento de Saúde Coletiva Veterinária E Saúde Pública, Faculdade de Veterinária, Universidade Federal Fluminense (UFF), Niterói, RJ, Brazil
| | - Maria Lúcia Barreto
- Departamento de Imunologia (GIM), Instituto de Biologia, Universidade Federal Fluminense (UFF), Niterói, RJ, Brazil
| | | | - Felipe Piedade Gonçalves Neves
- Programa de Pós-Graduação Stricto Sensu Em Microbiologia E Parasitologia Aplicadas (PPGMPA), da Universidade Federal Fluminense, Niterói, RJ, Brazil
- Departamento de Microbiologia E Parasitologia (MIP), Instituto Biomédico (CMB), Universidade Federal Fluminense (UFF), Niterói, RJ, Brazil
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Shaw CL, Bilich R, Duffy MA. A common multi-host parasite shows genetic structuring at the host species and population levels. Parasitology 2024:1-10. [PMID: 38616414 DOI: 10.1017/s0031182024000428] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/16/2024]
Abstract
Although individual parasite species commonly infect many populations across physical space as well as multiple host species, the extent to which parasites traverse physical and phylogenetic distances is unclear. Population genetic analyses of parasite populations can reveal how parasites move across space or between host species, including helping assess whether a parasite is more likely to infect a different host species in the same location or the same host species in a different location. Identifying these transmission barriers could be exploited for effective disease control. Here, we analysed population genetic structuring of the parasite Pasteuria ramosa in daphniid host species from different lakes. Outbreaks occurred most often in the common host species Daphnia dentifera and Daphnia retrocurva. The genetic distance between parasite samples tended to be smaller when samples were collected from the same lake, the same host species and closer in time. Within lakes, the parasite showed structure by host species and sampling date; within a host species, the parasite showed structure by lake and sampling date. However, despite this structuring, we found the same parasite genotype infecting closely related host species, and we sometimes found the same genotype in nearby lakes. Thus, P. ramosa experiences challenges infecting different host species and moving between populations, but doing so is possible. In addition, the structuring by sampling date indicates potential adaptation to or coevolution with host populations and supports prior findings that parasite population structure is dynamic during outbreaks.
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Affiliation(s)
- Clara L Shaw
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
- Department of Biology, University of Minnesota Duluth, Duluth, MN, USA
| | - Rebecca Bilich
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
| | - Meghan A Duffy
- Department of Ecology & Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA
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3
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Klose SM, Legione AR, Bushell RN, Browning GF, Vaz PK. Unveiling genome plasticity and a novel phage in Mycoplasma felis: Genomic investigations of four feline isolates. Microb Genom 2024; 10:001227. [PMID: 38546735 PMCID: PMC11004492 DOI: 10.1099/mgen.0.001227] [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: 01/09/2024] [Accepted: 03/18/2024] [Indexed: 04/12/2024] Open
Abstract
Mycoplasma felis has been isolated from diseased cats and horses, but to date only a single fully assembled genome of this species, of an isolate from a horse, has been characterized. This study aimed to characterize and compare the completely assembled genomes of four clinical isolates of M. felis from three domestic cats, assembled with the aid of short- and long-read sequencing methods. The completed genomes encoded a median of 759 ORFs (range 743-777) and had a median average nucleotide identity of 98.2 % with the genome of the available equid origin reference strain. Comparative genomic analysis revealed the occurrence of multiple horizontal gene transfer events and significant genome reassortment. This had resulted in the acquisition or loss of numerous genes within the Australian felid isolate genomes, encoding putative proteins involved in DNA transfer, metabolism, DNA replication, host cell interaction and restriction modification systems. Additionally, a novel mycoplasma phage was detected in one Australian felid M. felis isolate by genomic analysis and visualized using cryo-transmission electron microscopy. This study has highlighted the complex genomic dynamics in different host environments. Furthermore, the sequences obtained in this work will enable the development of new diagnostic tools, and identification of future infection control and treatment options for the respiratory disease complex in cats.
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Affiliation(s)
- Sara M. Klose
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, VIC, Australia
- Institute of Molecular Medicine and Experimental Immunology, Faculty of Medicine, University of Bonn, NRW, Germany
| | - Alistair R. Legione
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, VIC, Australia
| | - Rhys N. Bushell
- Department of Veterinary Clinical Sciences, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, VIC, Australia
| | - Glenn F. Browning
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, VIC, Australia
| | - Paola K. Vaz
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, Faculty of Science, The University of Melbourne, VIC, Australia
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Klose SM, Legione AR, Monotti I, Bushell RN, Sugiyama T, Browning GF, Vaz PK. Genomic characterization of Mycoplasma edwardii isolated from a dog bite induced cat wound reveals multiple horizontal gene transfer events and loss of the CRISPR/Cas system. J Med Microbiol 2024; 73. [PMID: 38167305 DOI: 10.1099/jmm.0.001788] [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] [Indexed: 01/05/2024] Open
Abstract
A domestic short hair cat (Felis catus) suffering from a purulent wound infection resulting from a dog bite was sampled for bacterial culture and isolation as the wound had been unresponsive to prolonged antimicrobial treatment. A mycoplasma was isolated from the wound. Whole genome sequencing of the isolate was performed using short-read Illumina and long-read Oxford Nanopore chemistry, and the organism was identified as Mycoplasma edwardii. Comparison of the genome sequence of the isolate to a reference M. edwardii genome sequence (canid isolate) identified the loss of several key bacterial factors involved in genome editing, as well the insertion of several novel ORFs most closely related to those found in other canine mycoplasmas, specifically Mycoplasma canis, M. cynos, M. molare and M. maculosa. This is only the second known report of disease caused by M. edwardii in a non-canid species, and the first report of it infecting and causing clinical disease in a cat.
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Affiliation(s)
- Sara M Klose
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, University of Melbourne, VIC, Australia
- Institute of Molecular Medicine and Experimental Immunology, Faculty of Medicine, University of Bonn, NRW, Germany
| | - Alistair R Legione
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, University of Melbourne, VIC, Australia
| | - Isobel Monotti
- U-Vet, Department of Veterinary Clinical Sciences, Melbourne Veterinary School, University of Melbourne, VIC, Australia
| | - Rhys N Bushell
- U-Vet, Department of Veterinary Clinical Sciences, Melbourne Veterinary School, University of Melbourne, VIC, Australia
| | - Takanori Sugiyama
- U-Vet, Department of Veterinary Clinical Sciences, Melbourne Veterinary School, University of Melbourne, VIC, Australia
- Present address: Animalius Vet, WA, Australia
| | - Glenn F Browning
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, University of Melbourne, VIC, Australia
| | - Paola K Vaz
- Asia-Pacific Centre for Animal Health, Melbourne Veterinary School, University of Melbourne, VIC, Australia
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Guesdon G, Gourgues G, Rideau F, Ipoutcha T, Manso-Silván L, Jules M, Sirand-Pugnet P, Blanchard A, Lartigue C. Combining Fusion of Cells with CRISPR-Cas9 Editing for the Cloning of Large DNA Fragments or Complete Bacterial Genomes in Yeast. ACS Synth Biol 2023; 12:3252-3266. [PMID: 37843014 PMCID: PMC10662353 DOI: 10.1021/acssynbio.3c00248] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Indexed: 10/17/2023]
Abstract
The genetic engineering of genome fragments larger than 100 kbp is challenging and requires both specific methods and cloning hosts. The yeast Saccharomyces cerevisiae is considered as a host of choice for cloning and engineering whole or partial genomes from viruses, bacteria, and algae. Several methods are now available to perform these manipulations, each with its own limitations. In order to extend the range of yeast cloning strategies, a new approach combining two already described methods, Fusion cloning and CReasPy-Cloning, was developed. The CReasPy-Fusion method allows the simultaneous cloning and engineering of megabase-sized genomes in yeast by the fusion of bacterial cells with yeast spheroplasts carrying the CRISPR-Cas9 system. With this new approach, we demonstrate the feasibility of cloning and editing whole genomes from several Mycoplasma species belonging to different phylogenetic groups. We also show that CReasPy-Fusion allows the capture of large genome fragments with high efficacy, resulting in the successful cloning of selected loci in yeast. We finally identify bacterial nuclease encoding genes as barriers for CReasPy-Fusion by showing that their removal from the donor genome improves the cloning efficacy.
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Affiliation(s)
- Gabrielle Guesdon
- Univ.
Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave
d’Ornon, France
| | - Géraldine Gourgues
- Univ.
Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave
d’Ornon, France
| | - Fabien Rideau
- Univ.
Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave
d’Ornon, France
| | - Thomas Ipoutcha
- Univ.
Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave
d’Ornon, France
| | - Lucía Manso-Silván
- CIRAD,
UMR ASTRE, F-34398 Montpellier, France
- ASTRE,
Univ. Montpellier, CIRAD, INRAE, F-34398 Montpellier, France
| | - Matthieu Jules
- Université
Paris-Saclay, INRAE, AgroParisTech, Micalis Institute, F-78350 Jouy-en-Josas, France
| | - Pascal Sirand-Pugnet
- Univ.
Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave
d’Ornon, France
| | - Alain Blanchard
- Univ.
Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave
d’Ornon, France
| | - Carole Lartigue
- Univ.
Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave
d’Ornon, France
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Thézé J, Ambroset C, Barry S, Masseglia S, Colin A, Tricot A, Tardy F, Bailly X. Genome-wide phylodynamic approach reveals the epidemic dynamics of the main Mycoplasma bovis subtype circulating in France. Microb Genom 2023; 9:mgen001067. [PMID: 37486749 PMCID: PMC10438803 DOI: 10.1099/mgen.0.001067] [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: 12/08/2022] [Accepted: 06/19/2023] [Indexed: 07/25/2023] Open
Abstract
Mycoplasma bovis is a major aetiological agent of bovine respiratory disease worldwide. Genome-based analyses are increasingly being used to monitor the genetic diversity and global distribution of M. bovis, complementing existing subtyping schemes based on locus sequencing. However, these analyses have so far provided limited information on the spatiotemporal and population dynamics of circulating subtypes. Here we applied a genome-wide phylodynamic approach to explore the epidemic dynamics of 88 French M. bovis strains collected between 2000 and 2019 in France and belonging to the currently dominant polC subtype 2 (st2). A strong molecular clock signal detected in the genomic data enabled robust phylodynamic inferences, which estimated that the M. bovis st2 population in France is composed of two lineages that successively emerged from independent introductions of international strains. The first lineage appeared around 2000 and supplanted the previously established antimicrobial-susceptible polC subtype 1. The second lineage, which is likely more transmissible, progressively replaced the first M. bovis st2 lineage population from 2005 onward and became predominant after 2010. Analyses also showed a brief decline in this second M. bovis st2 lineage population in around 2011, possibly due to the challenge from the concurrent emergence of M. bovis polC subtype 3 in France. Finally, we identified non-synonymous mutations in genes associated with lineages, which raises prospects for identifying new surveillance molecular markers. A genome-wide phylodynamic approach provides valuable resources for monitoring the evolution and epidemic dynamics of circulating M. bovis subtypes, and may prove critical for developing more effective surveillance systems and disease control strategies.
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Affiliation(s)
- Julien Thézé
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint-Genès-Champanelle, France
| | - Chloé Ambroset
- Université de Lyon, ANSES, VetAgro Sup, UMR Mycoplasmoses animales, Lyon, France
| | - Séverine Barry
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint-Genès-Champanelle, France
| | - Sébastien Masseglia
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint-Genès-Champanelle, France
| | - Adélie Colin
- Université de Lyon, ANSES, VetAgro Sup, UMR Mycoplasmoses animales, Lyon, France
| | - Agnès Tricot
- Université de Lyon, ANSES, VetAgro Sup, UMR Mycoplasmoses animales, Lyon, France
| | - Florence Tardy
- Université de Lyon, ANSES, VetAgro Sup, UMR Mycoplasmoses animales, Lyon, France
| | - Xavier Bailly
- Université Clermont Auvergne, INRAE, VetAgro Sup, UMR EPIA, Saint-Genès-Champanelle, France
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Reinoso-Pérez MT, Dhondt KV, Levitskiy AA, Dupont G, Tulman ER, Geary SJ, Dhondt AA. Are Purple Finches (Haemorhous purpureus) the Next Host for a Mycoplasmal Conjunctivitis Epidemic? Avian Dis 2023; 67:42-48. [PMID: 37140110 DOI: 10.1637/aviandiseases-d-22-00047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 01/04/2023] [Indexed: 03/17/2023]
Abstract
Ever since 1994, when the bacterial pathogen Mycoplasma gallisepticum jumped from poultry to wild birds, it has been assumed that the primary host species of this pathogen in wild North American birds was the house finch (Haemorhous mexicanus), in which disease prevalence was higher than in any other bird species. Here we tested two hypotheses to explain a recent increase in disease prevalence in purple finches (Haemorhous purpureus) around Ithaca, New York. Hypothesis 1 is that, as M. gallisepticum evolved and became more virulent, it has also become better adapted to other finches. If this is correct, early isolates of M. gallisepticum should cause less-severe eye lesions in purple finches than in house finches, while more-recent isolates should cause eye lesions of similar severity in the two species. Hypothesis 2 is that, as house finch abundance declined following the M. gallisepticum epidemic, purple finches around Ithaca increased in abundance relative to house finches and purple finches are thus more frequently exposed to M. gallisepticum-infected house finches. This would then lead to an increase in M. gallisepticum prevalence in purple finches. Following an experimental infection with an early and a more-recent M. gallisepticum isolate, eye lesions in purple finches were more severe than in house finches. This did not a support Hypothesis 1; similarly, an analysis of Project Feeder Watch data collected around Ithaca did not show differences in changes in purple and house finches' abundance since 2006, a result which does not support Hypothesis 2. We conclude that purple finch populations will, unlike those of house finches, not suffer a severe decline because of a M. gallisepticum epidemic.
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Affiliation(s)
| | - Keila V. Dhondt
- Department of Microbiology and Immunology, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853
| | | | - Gates Dupont
- Department of Ecology and Evolution, Princeton University Princeton NJ 08544
| | - Edan R. Tulman
- Center of Excellence for Vaccine Research, Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, CN 06269
| | - Steven J. Geary
- Center of Excellence for Vaccine Research, Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, CN 06269
| | - André A. Dhondt
- Laboratory of Ornithology, Cornell University, Ithaca, NY 14850
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Ruden RM, Adelman JS. Modulating disease phenotype in a songbird: A role for inflammation in disease tolerance? JOURNAL OF EXPERIMENTAL ZOOLOGY. PART A, ECOLOGICAL AND INTEGRATIVE PHYSIOLOGY 2023; 339:83-91. [PMID: 36127806 DOI: 10.1002/jez.2655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 08/02/2022] [Accepted: 08/26/2022] [Indexed: 12/15/2022]
Abstract
Individual animals vary greatly in their responses to infection, either killing off the invading pathogen (resistance) or minimizing the per-pathogen costs of infection on host fitness (tolerance). Though we understand little about the physiological drivers of tolerance in wild animals, phenotypically, it manifests as milder clinical signs of disease. Here, we use a well-described disease system, finch mycoplasmosis, to evaluate the role of inflammation in disease tolerance. House finches (Haemorhous mexicanus) infected with the bacterial pathogen Mycoplasma gallisepticum (MG) develop conjunctival pathology that satisfies the cardinal signs of inflammation. We report on a captive trial performed in 2016 and replicated in 2018 that tested whether chemotherapeutics, specifically nonsteroidal anti-inflammatory drugs (NSAIDs), can reduce lesion severity, thus pushing individuals toward more tolerant phenotypes. Though birds treated with NSAIDs in the first trial developed milder pathology per unit pathogen load, we found no effect of treatment in the second trial, perhaps due to natural variation in baseline tolerance within the source population across years. Second-trial control birds developed markedly milder pathology than first-year controls, suggesting that the effect of trial swamped the effect of treatment in this study. Moving forward, using birds from a population in which the disease is absent or only recently emerged-and so tolerance has not yet been selected for-may better elucidate the role of pro-inflammatory mediators in disease tolerance.
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Affiliation(s)
- Rachel M Ruden
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, Iowa, USA.,Iowa Department of Natural Resources, Ames, Iowa, USA
| | - James S Adelman
- Department of Natural Resource Ecology and Management, Iowa State University, Ames, Iowa, USA.,Department of Biological Sciences, University of Memphis, Memphis, Tennessee, USA
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9
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García-Santibañez T, Rosenblueth M, Bolaños LM, Martínez-Romero J, Martínez-Romero E. The divergent genome of Scorpion Group 1 (SG1) intracellular bacterium from the venom glands of Vaejovis smithi (Scorpiones: Vaejovidae). Syst Appl Microbiol 2022; 45:126358. [PMID: 36174465 DOI: 10.1016/j.syapm.2022.126358] [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: 05/13/2022] [Revised: 08/12/2022] [Accepted: 09/07/2022] [Indexed: 10/31/2022]
Abstract
Scorpions were among the first animals on land around 430 million years ago. Like many arachnids, scorpions have evolved complex venoms used to paralyze their prey and for self-defense. Here we sequenced and analyzed the metagenomic DNA from venom glands from Vaejovis smithi scorpions. A metagenome-assembled genome (MAG) of 624,025 bp was obtained corresponding to the previously reported Scorpion Group 1 (SG1). The SG1 genome from venom glands had a low GC content (25.8%) characteristic of reduced genomes, many hypothetical genes and genes from the reported minimal set of bacterial genes. Phylogenomic reconstructions placed the uncultured SG1 distant from other reported bacteria constituting a taxonomic novelty. By PCR we detected SG1 in all tested venom glands from 30 independent individuals. Microscopically, we observed SG1 inside epithelial cells from the venom glands using FISH and its presence in scorpion embryos suggested that SG1 is transferred from mother to offspring.
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Affiliation(s)
| | - Mónica Rosenblueth
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
| | - Luis M Bolaños
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico; School of Biosciences, University of Exeter, Exeter, UK
| | - Julio Martínez-Romero
- Centro de Ciencias Genómicas, Universidad Nacional Autónoma de México, Cuernavaca, Mexico
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10
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Ambroset C, Peticca A, Tricot A, Tardy F. Genomic features of Mycoplasma bovis subtypes currently circulating in France. BMC Genomics 2022; 23:603. [PMID: 35986252 PMCID: PMC9392320 DOI: 10.1186/s12864-022-08818-9] [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: 06/07/2022] [Accepted: 08/04/2022] [Indexed: 12/04/2022] Open
Abstract
Background Mycoplasma (M.) bovis is a major etiological agent of bovine respiratory disease, which is the most economically costly disease of cattle worldwide. Cattle disease surveillance on M. bovis is increasingly using gene-based techniques, such as multilocus sequence typing (MLST), or genome-based techniques such as core genome MLST that both require only partial genomic data. However, accurate up-to-date surveillance also demands complete, circular genomes that can be used as reference to track the evolution of the different lineages. Yet, in France, two of the main subtypes currently circulating still have no representing genome in public databases. Here, to address this gap, we provide and compare three new complete M. bovis genomes obtained from recent clinical isolates that represent major subtypes circulating in France and Europe. Results Genomes were obtained using a hybrid assembly strategy (Illumina and Nanopore) with fine-tuning of settings and inputs used in the Unicycler assembly pipeline, such as size selection of reads and quality trimming of the FASTQ files. The main characteristics and synteny of the genomes were compared. The three genomes mainly differed by their content in terms of mobile genetic elements, i.e. integrative conjugative elements (ICE) and insertion sequences (IS), a feature that impacts their structure. For instance, strain L15527, representing subtype3 (st3), harbours an exceptionally high number of ICEs, which results in a bigger-sized genome than all those previously described and could be associated with the propensity of st3 to gain and fix mutations through chromosomal transfer mechanisms. In contrast, strain F9160, of st1, is very close to the PG45 type strain isolated in 1961 in the USA, and harbours a huge number of IS. These features may be associated with an evolution towards a host-restricted state or in a “closed” host or environment reservoir until a recent re-emergence. Conclusions Whole-genome comparison of the three French M. bovis subtypes provides valuable resources for future studies combining epidemiology, phylogenetic data, and phylodynamic methods. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08818-9.
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11
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Zaayman M, Wheatley RM. Fitness costs of CRISPR-Cas systems in bacteria. MICROBIOLOGY (READING, ENGLAND) 2022; 168. [PMID: 35849532 DOI: 10.1099/mic.0.001209] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
CRISPR-Cas systems provide bacteria with both specificity and adaptability in defence against invading genetic elements. From a theoretical perspective, CRISPR-Cas systems confer many benefits. However, they are observed at an unexpectedly low prevalence across the bacterial domain. While these defence systems can be gained horizontally, fitness costs may lead to selection against their carriage. Understanding the source of CRISPR-related fitness costs will help us to understand the evolutionary dynamics of CRISPR-Cas systems and their role in shaping bacterial genome evolution. Here, we review our current understanding of the potential fitness costs associated with CRISPR-Cas systems. In addition to potentially restricting the acquisition of genetic material that could confer fitness benefits, we explore five alternative biological factors that from a theoretical perspective may influence the fitness costs associated with CRISPR-Cas system carriage: (1) the repertoire of defence mechanisms a bacterium has available to it, (2) the potential for a metabolic burden, (3) larger-scale population and environmental factors, (4) the phenomenon of self-targeting spacers, and (5) alternative non-defence roles for CRISPR-Cas.
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12
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Targeted sequencing analysis of Mycoplasma gallisepticum isolates in chicken layer and breeder flocks in Thailand. Sci Rep 2022; 12:9900. [PMID: 35701517 PMCID: PMC9198072 DOI: 10.1038/s41598-022-14066-4] [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: 01/28/2022] [Accepted: 05/31/2022] [Indexed: 12/03/2022] Open
Abstract
Mycoplasma gallisepticum (MG) is one of the most economically important pathogens worldwide. MG affects the respiratory system and impairs growth performance in poultry. In developing countries, the most widely used technique to identify MG is the conventional PCR assay. In this study, 24 MG isolates collected from Thailand farms with unvaccinated chickens during 2002–2020 were characterized by gene-targeted sequencing (GTS), followed by phylogenetic analysis using unweighted pair group method with arithmetic mean. These 24 Thai MG isolates differed from vaccine strains, including the F, ts-11 and 6/85 strains. One isolate showed 99.5–100% genetic similarity to the F strain with 4 partial gene analyses. This result may have been due to contamination from vaccinated flocks because the F strain is the most commonly used vaccine strain in Thailand. However, the GTS analysis using the partial MG genes in this study showed that the isolates could be grouped into different patterns based on individual gene sequences. The phylogenetic analysis of partial mgc2, gapA, pvpA and lp gene sequences classified the Thai MG isolates into 7, 11, 7 and 2 groups, respectively. In conclusion, at least 2 partial MG genes, especially partial gapA and mgc2 genes, are needed to differentiate MG isolates.
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Dawood A, Algharib SA, Zhao G, Zhu T, Qi M, Delai K, Hao Z, Marawan MA, Shirani I, Guo A. Mycoplasmas as Host Pantropic and Specific Pathogens: Clinical Implications, Gene Transfer, Virulence Factors, and Future Perspectives. Front Cell Infect Microbiol 2022; 12:855731. [PMID: 35646746 PMCID: PMC9137434 DOI: 10.3389/fcimb.2022.855731] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2022] [Accepted: 04/04/2022] [Indexed: 12/28/2022] Open
Abstract
Mycoplasmas as economically important and pantropic pathogens can cause similar clinical diseases in different hosts by eluding host defense and establishing their niches despite their limited metabolic capacities. Besides, enormous undiscovered virulence has a fundamental role in the pathogenesis of pathogenic mycoplasmas. On the other hand, they are host-specific pathogens with some highly pathogenic members that can colonize a vast number of habitats. Reshuffling mycoplasmas genetic information and evolving rapidly is a way to avoid their host's immune system. However, currently, only a few control measures exist against some mycoplasmosis which are far from satisfaction. This review aimed to provide an updated insight into the state of mycoplasmas as pathogens by summarizing and analyzing the comprehensive progress, current challenge, and future perspectives of mycoplasmas. It covers clinical implications of mycoplasmas in humans and domestic and wild animals, virulence-related factors, the process of gene transfer and its crucial prospects, the current application and future perspectives of nanotechnology for diagnosing and curing mycoplasmosis, Mycoplasma vaccination, and protective immunity. Several questions remain unanswered and are recommended to pay close attention to. The findings would be helpful to develop new strategies for basic and applied research on mycoplasmas and facilitate the control of mycoplasmosis for humans and various species of animals.
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Affiliation(s)
- Ali Dawood
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Department of Medicine and Infectious Diseases, Faculty of Veterinary Medicine, University of Sadat City, Sadat City, Egypt
- Hubei Hongshan Laboratory, Wuhan, China
| | - Samah Attia Algharib
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- National Reference Laboratory of Veterinary Drug Residues (HZAU) and MAO Key Laboratory for Detection of Veterinary Drug Residues, HZAU, Wuhan, China
- Department of Clinical Pathology, Faculty of Veterinary Medicine, Benha University, Toukh, Egypt
| | - Gang Zhao
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan, China
| | - Tingting Zhu
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan, China
| | - Mingpu Qi
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan, China
| | - Kong Delai
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
| | - Zhiyu Hao
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan, China
| | - Marawan A. Marawan
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, China
- Infectious Diseases, Faculty of Veterinary Medicine, Benha University, Toukh, Egypt
| | - Ihsanullah Shirani
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, China
- Para-Clinic Department, Faculty of Veterinary Medicine, Jalalabad, Afghanistan
| | - Aizhen Guo
- The State Key Laboratory of Agricultural Microbiology, (HZAU), Wuhan, China
- College of Veterinary Medicine, Huazhong Agricultural University, Wuhan, China
- Hubei Hongshan Laboratory, Wuhan, China
- Hubei International Scientific and Technological Cooperation Base of Veterinary Epidemiology, Huazhong Agricultural University, Wuhan, China
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14
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Ipoutcha T, Gourgues G, Lartigue C, Blanchard A, Sirand-Pugnet P. Genome Engineering in Mycoplasma gallisepticum Using Exogenous Recombination Systems. ACS Synth Biol 2022; 11:1060-1067. [PMID: 35167277 DOI: 10.1021/acssynbio.1c00541] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Mycoplasma gallisepticum (Mgal) is a common pathogen of poultry worldwide that has recently spread to North American house finches after a single host shift in 1994. The molecular determinants of Mgal virulence and host specificity are still largely unknown, mostly due to the absence of efficient methods for functional genomics. After evaluating two exogenous recombination systems derived from phages found in the phylogenetically related Spiroplasma phoeniceum and the more distant Bacillus subtilis, the RecET-like system from B. subtilis was successfully used for gene inactivation and targeted replacement in Mgal. In a second step, the Cre-lox recombination system was used for the removal of the antibiotic resistance marker in recombinant mutants. This study therefore describes the first genetic tool for targeted genome engineering of Mgal and demonstrates the efficiency of heterologous recombination systems in minimal bacteria.
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Affiliation(s)
- Thomas Ipoutcha
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France
| | - Géraldine Gourgues
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France
| | - Carole Lartigue
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France
| | - Alain Blanchard
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France
| | - Pascal Sirand-Pugnet
- Univ. Bordeaux, INRAE, Biologie du Fruit et Pathologie, UMR 1332, F-33140 Villenave d’Ornon, France
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15
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Fischer L, Liebing J, Völker I, Baudler L, Gethöffer F, Voigt U, Heffels-Redmann U, Wohlsein P, Siebert U, Lierz M. Occurrence and relevance of Mycoplasma spp. in free-ranging pheasants from northwestern Germany. EUR J WILDLIFE RES 2022. [DOI: 10.1007/s10344-021-01557-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
AbstractSince 2008/2009, the population of free-ranging ring-necked pheasants was recorded to decrease all over Germany. Various Mycoplasma (M.) spp. are causing severe respiratory signs in captive game bird species. Furthermore, M. gallisepticum is responsible for massive die-offs in consequence to severe conjunctivitis in house finches in the USA. Therefore, the prevalence of mycoplasmas in free-ranging pheasants was investigated and a potential impact on the population decline of pheasants discussed. Within this study, 150 free-ranging pheasants were sampled via tracheal swabs and tissue samples of the trachea and the periorbital skin, as the latter displayed inflammatory alterations in previous studies. In total, 177 samples were investigated for the presence of mycoplasmas using cultural and molecular biological methods. In 76 birds, necropsy was performed additionally. In total, 73.7% (51/76) of the examined pheasants had periorbital skin alterations. Furthermore, 64.4% (114/177) of the samples tested positive for mycoplasmas via PCR. Overall, 102/177 samples (57.6%, 78/105 tracheal swabs, 19/51 skin tissue, 5/21 trachea tissue) tested positive for mycoplasmas via culture. Mycoplasma gallinaceum (n = 50), M. pullorum (n = 45), M. glycophilum (n = 43), M. iners (n = 11), and M. gallinarum (n = 5) were frequently isolated. In 45 cases (45.9%), multiple Mycoplasma spp. were isolated from one sample. All examined samples tested negative for M. gallisepticum. Of 51 skin samples investigated for mycoplasmas, 24 (47.1%) showed inflammatory skin alterations in histology, and 58.3% (14/24) of these samples tested positive for Mycoplasma spp. additionally. Overall, there was a significant correlation between inflammatory altered skin samples and the detection of mycoplasmas in periorbital skin samples. Based on the present results, the isolated Mycoplasma spp. may play a role as facultative agents for the observed inflammatory skin alterations. However, additional investigation is needed to confirm this presumption.
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16
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Muhammad J, Rabbani M, Sheikh AA, Rabaan AA, Khan A, Haq IU, Ghori MT, Khan SA, Akbar A. Molecular detection of Mycoplasma gallisepticum in different poultry breeds of Abbottabad and Rawalpindi, Pakistan. BRAZ J BIOL 2021; 83:e246514. [PMID: 34378682 DOI: 10.1590/1519-6984.246514] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2020] [Accepted: 01/27/2021] [Indexed: 11/22/2022] Open
Abstract
The poultry sector in Pakistan is contributing mainly in bridging gap between demand and supply for protein. Mycoplasma gallisepticum is an emerging bacterium causing serious problems in poultry industry of Pakistan. A cross-sectional study was conducted to evaluate the M. gallisepticum load in poultry populated regions of Pakistan. Total 600 serum and 600 swab samples were collected, 200 from each broiler, layers and breeders poultry in Rawalpindi and Abbottabad districts. Serum samples were analyzed through ELISA for seroprevalence. Swabs were cultured on Frey's medium followed by PCR and partial mgc2 gene sequencing. Results of seroprevalence of M. gallisepticum showed that layers (75%, n=150) are more positive as compared to breeders (70%, n=140) and broilers (50%, n=100). Typical colonies of the M. gallisepticum were observed in breeder (26.5%), followed by layer (21%) and broilers (9%). A total of 37.1% (n=42) samples were identified positive through PCR out of total 113 cultured based positive samples. A total of six M. gallisepticum isolates of current study showed 98-99 percent similarity with previously reported isolates on the basis of mgc2 gene partial sequencing. The M. gallisepticum was found highly prevalent in different poultry breads. Results of this study would add into basic data and provide a direction for livestock sector to strengthen a control strategy for mycoplasmosis in poultry farms.
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Affiliation(s)
- J Muhammad
- The University of Haripur, Department of Microbiology, Haripur, Pakistan.,University of Veterinary and Animal Sciences, University Diagnostic Lab, Lahore, Pakistan
| | - M Rabbani
- University of Veterinary and Animal Sciences, Department of Microbiology, Lahore, Pakistan
| | - A A Sheikh
- University of Veterinary and Animal Sciences, University Diagnostic Lab, Lahore, Pakistan
| | - A A Rabaan
- Johns Hopkins Aramco Healthcare, Molecular Diagnostic Laboratory, Dhahran, Saudi Arabia
| | - A Khan
- The University of Haripur, Department of Public Health & Nutrition, Haripur, Pakistan
| | - I Ul Haq
- The University of Haripur, Department of Public Health & Nutrition, Haripur, Pakistan
| | - M T Ghori
- The Islamia University of Bahawalpur, Department of Clinical Medicine and Surgery, Punjab, Pakistan
| | - S A Khan
- University of Balochistan, Department of Microbiology, Quetta, Balochistan, Pakistan
| | - A Akbar
- University of Balochistan, Department of Microbiology, Quetta, Balochistan, Pakistan
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17
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Profile of Scott Edwards. Proc Natl Acad Sci U S A 2021; 118:2106799118. [PMID: 34001594 DOI: 10.1073/pnas.2106799118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
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18
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Gates DE, Staley M, Tardy L, Giraudeau M, Hill GE, McGraw KJ, Bonneaud C. Levels of pathogen virulence and host resistance both shape the antibody response to an emerging bacterial disease. Sci Rep 2021; 11:8209. [PMID: 33859241 PMCID: PMC8050079 DOI: 10.1038/s41598-021-87464-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 03/24/2021] [Indexed: 11/09/2022] Open
Abstract
Quantifying variation in the ability to fight infection among free-living hosts is challenging and often constrained to one or a few measures of immune activity. While such measures are typically taken to reflect host resistance, they can also be shaped by pathogen effects, for example, if more virulent strains trigger more robust immune responses. Here, we test the extent to which pathogen-specific antibody levels, a commonly used measure of immunocompetence, reflect variation in host resistance versus pathogen virulence, and whether these antibodies effectively clear infection. House finches (Haemorhous mexicanus) from resistant and susceptible populations were inoculated with > 50 isolates of their novel Mycoplasma gallisepticum pathogen collected over a 20-year period during which virulence increased. Serum antibody levels were higher in finches from resistant populations and increased with year of pathogen sampling. Higher antibody levels, however, did not subsequently give rise to greater reductions in pathogen load. Our results show that antibody responses can be shaped by levels of host resistance and pathogen virulence, and do not necessarily signal immune clearance ability. While the generality of this novel finding remains unclear, particularly outside of mycoplasmas, it cautions against using antibody levels as implicit proxies for immunocompetence and/or host resistance.
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Affiliation(s)
- Daisy E Gates
- Centre for Ecology and Conservation, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
| | - Molly Staley
- Department Biological Science, Auburn University, Auburn, Alabama, 36849-5414, USA.,Biology Department, Loyola University Chicago, Chicago, IL, 60660-1537, USA
| | - Luc Tardy
- Centre for Ecology and Conservation, University of Exeter, Penryn, Cornwall, TR10 9FE, UK
| | - Mathieu Giraudeau
- Centre for Ecology and Conservation, University of Exeter, Penryn, Cornwall, TR10 9FE, UK.,School of Life Sciences, Arizona State University, Tempe, AZ, 85287-4501, USA.,Centre for Ecological and Evolutionary Research On Cancer, UMR CNRS/IRD/UM 5290 MIVEGEC, 34394, Montpellier, France
| | - Geoffrey E Hill
- Department Biological Science, Auburn University, Auburn, Alabama, 36849-5414, USA
| | - Kevin J McGraw
- School of Life Sciences, Arizona State University, Tempe, AZ, 85287-4501, USA
| | - Camille Bonneaud
- Centre for Ecology and Conservation, University of Exeter, Penryn, Cornwall, TR10 9FE, UK.
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Luzuriaga-Neira A, Sandmeier FC, Weitzman CL, Tracy CR, Bauschlicher SN, Tillett RL, Alvarez-Ponce D. Mycoplasma agassizii, an opportunistic pathogen of tortoises, shows very little genetic variation across the Mojave and Sonoran Deserts. PLoS One 2021; 16:e0245895. [PMID: 33534823 PMCID: PMC7857612 DOI: 10.1371/journal.pone.0245895] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Accepted: 01/10/2021] [Indexed: 12/01/2022] Open
Abstract
Mycoplasma agassizii is a common cause of upper respiratory tract disease in Mojave desert tortoises (Gopherus agassizii). So far, only two strains of this bacterium have been sequenced, and very little is known about its patterns of genetic diversity. Understanding genetic variability of this pathogen is essential to implement conservation programs for their threatened, long-lived hosts. We used next generation sequencing to explore the genomic diversity of 86 cultured samples of M. agassizii collected from mostly healthy Mojave and Sonoran desert tortoises in 2011 and 2012. All samples with enough sequencing coverage exhibited a higher similarity to M. agassizii strain PS6T (collected in Las Vegas Valley, Nevada) than to strain 723 (collected in Sanibel Island, Florida). All eight genomes with a sequencing coverage over 2x were subjected to multiple analyses to detect single-nucleotide polymorphisms (SNPs). Strikingly, even though we detected 1373 SNPs between strains PS6T and 723, we did not detect any SNP between PS6T and our eight samples. Our whole genome analyses reveal that M. agassizii strain PS6T may be present across a wide geographic extent in healthy Mojave and Sonoran desert tortoises.
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Affiliation(s)
- Agusto Luzuriaga-Neira
- Department of Biology, University of Nevada Reno, Reno, Nevada, United States of America
| | - Franziska C. Sandmeier
- Biology Department, Colorado State University, Pueblo, Colorado, United States of America
- * E-mail: (FCS); (DAP)
| | - Chava L. Weitzman
- Department of Biological Sciences, Virginia Polytechnic Institute, Blacksburg, Virginia, United States of America
| | - C. Richard Tracy
- Department of Biology, University of Nevada Reno, Reno, Nevada, United States of America
| | - Shalyn N. Bauschlicher
- Biology Department, Colorado State University, Pueblo, Colorado, United States of America
| | - Richard L. Tillett
- Nevada Center for Bioinformatics, University of Nevada, Reno, Nevada, United States of America
| | - David Alvarez-Ponce
- Department of Biology, University of Nevada Reno, Reno, Nevada, United States of America
- * E-mail: (FCS); (DAP)
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20
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Gerth M, Martinez-Montoya H, Ramirez P, Masson F, Griffin JS, Aramayo R, Siozios S, Lemaitre B, Mateos M, Hurst GDD. Rapid molecular evolution of Spiroplasma symbionts of Drosophila. Microb Genom 2021; 7:000503. [PMID: 33591248 PMCID: PMC8208695 DOI: 10.1099/mgen.0.000503] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 01/22/2021] [Indexed: 12/21/2022] Open
Abstract
Spiroplasma is a genus of Mollicutes whose members include plant pathogens, insect pathogens and endosymbionts of animals. Spiroplasma phenotypes have been repeatedly observed to be spontaneously lost in Drosophila cultures, and several studies have documented a high genomic turnover in Spiroplasma symbionts and plant pathogens. These observations suggest that Spiroplasma evolves quickly in comparison to other insect symbionts. Here, we systematically assess evolutionary rates and patterns of Spiroplasma poulsonii, a natural symbiont of Drosophila. We analysed genomic evolution of sHy within flies, and sMel within in vitro culture over several years. We observed that S. poulsonii substitution rates are among the highest reported for any bacteria, and around two orders of magnitude higher compared with other inherited arthropod endosymbionts. The absence of mismatch repair loci mutS and mutL is conserved across Spiroplasma, and likely contributes to elevated substitution rates. Further, the closely related strains sMel and sHy (>99.5 % sequence identity in shared loci) show extensive structural genomic differences, which potentially indicates a higher degree of host adaptation in sHy, a protective symbiont of Drosophila hydei. Finally, comparison across diverse Spiroplasma lineages confirms previous reports of dynamic evolution of toxins, and identifies loci similar to the male-killing toxin Spaid in several Spiroplasma lineages and other endosymbionts. Overall, our results highlight the peculiar nature of Spiroplasma genome evolution, which may explain unusual features of its evolutionary ecology.
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Affiliation(s)
- Michael Gerth
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
- Present address: Department of Biological and Medical Sciences, Oxford Brookes University, Oxford, UK
| | - Humberto Martinez-Montoya
- Laboratorio de Genética y Genómica Comparativa, Unidad Académica Multidisciplinaria Reynosa Aztlán, Universidad Autónoma de Tamaulipas, Reynosa, Mexico
| | - Paulino Ramirez
- Department of Cell Systems and Anatomy, University of Texas Health San Antonio, San Antonio, TX, USA
| | - Florent Masson
- Global Health Institute, School of Life Sciences, Swiss Federal Institute of Technology Lausanne (École Polytechnique Fédérale de Lausanne), Lausanne, Switzerland
| | - Joanne S. Griffin
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Rodolfo Aramayo
- Department of Biology, Texas A&M University, College Station, TX, USA
| | - Stefanos Siozios
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
| | - Bruno Lemaitre
- Global Health Institute, School of Life Sciences, Swiss Federal Institute of Technology Lausanne (École Polytechnique Fédérale de Lausanne), Lausanne, Switzerland
| | - Mariana Mateos
- Department of Ecology and Conservation Biology, Texas A&M University, College Station, TX, USA
| | - Gregory D. D. Hurst
- Institute of Infection, Veterinary and Ecological Sciences, University of Liverpool, Liverpool, UK
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21
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Molecular Differentiation of Mycoplasma gallisepticum Outbreaks: A Last Decade Study on Italian Farms Using GTS and MLST. Vaccines (Basel) 2020; 8:vaccines8040665. [PMID: 33182244 PMCID: PMC7712042 DOI: 10.3390/vaccines8040665] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2020] [Revised: 11/05/2020] [Accepted: 11/05/2020] [Indexed: 11/17/2022] Open
Abstract
Mycoplasma gallisepticum (MG) infects many avian species and leads to significant economic losses in the poultry industry. Transmission of this pathogen occurs both horizontally and vertically, and strategies to avoid the spread of MG rely on vaccination and the application of biosecurity measures to maintain breeder groups as pathogen-free. Two live attenuated MG vaccine strains are licensed in Italy: 6/85 and ts-11. After their introduction, the implementation of adequate genotyping tools became necessary to distinguish between field and vaccine strains and to guarantee proper infection monitoring activity. In this study, 40 Italian MG isolates collected between 2010–2019 from both vaccinated and unvaccinated farms were genotyped using gene-targeted sequencing (GTS) of the cythadesin gene mgc2 and multilocus sequence typing (MLST) based on six housekeeping genes. The discriminatory power of GTS typing ensures 6/85-like strain identification, but the technique does not allow the identification ts-11 strains; conversely, MLST differentiates both vaccine strains, describing more detailed interrelation structures. Our study describes MG genetic scenario within a mixed farming context. In conclusion, the use of adequate typing methods is essential to understand the evolutionary dynamics of MG strains in a particular area and to conduct epidemiological investigations in the avian population.
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22
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Loire E, Ibrahim AI, Manso-Silván L, Lignereux L, Thiaucourt F. A whole-genome worldwide molecular epidemiology approach for contagious caprine pleuropneumonia. Heliyon 2020; 6:e05146. [PMID: 33083610 PMCID: PMC7550919 DOI: 10.1016/j.heliyon.2020.e05146] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 08/16/2020] [Accepted: 09/29/2020] [Indexed: 12/03/2022] Open
Abstract
Contagious caprine pleuropneumonia is an infectious and contagious disease affecting goats and wildlife ruminants, mostly in Africa and Asia. It is caused by a mycoplasma, Mycoplasma capricolum susbp. capripneumoniae, which is very fastidious. This may be the reason why there are few reports of its isolation and characterization. This study describes the development of a whole genome typing strategy based on sequencing reads assemblies on a reference genome (Abomsa, GenBank accession LM995445) and extraction of informative single nucleotide polymorphism. FASTA sequences inferred from the variant calling files were used to establish a comprehensive phylogenetic tree based on 2880 SNPs. This tree included a total of 34 strains originating from all the regions where CCPP has been detected, as well as strains isolated from wildlife. A recent isolate from West-Niger was positioned closely to another 1995 East-Niger isolate, an indication that CCPP may be extending westward in Africa. Six 2013 Tanzanian isolates had identical sequences in spite of diverse geographical origins. This could be explained by the clonal expansion of a virulent strain at that time in East Africa. Although all strains isolated from wildlife in the Middle East were in the same phylogenetic group, this may not sign an adaptation to new hosts. The most probable explanation for wildlife contamination remains the contact with goats. This strategy will easily accommodate new data in the near future and should become a gold-standard high-resolution typing procedure for the surveillance of contagious caprine pleuropneumonia.
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Affiliation(s)
- Etienne Loire
- CIRAD-ASTRE, Montpellier, France.,OIE/FAO World Reference Laboratory for CCPP, France.,INRA, UMR1309 ASTRE, Montpellier, France
| | | | - Lucía Manso-Silván
- CIRAD-ASTRE, Montpellier, France.,OIE/FAO World Reference Laboratory for CCPP, France.,INRA, UMR1309 ASTRE, Montpellier, France
| | - Louis Lignereux
- Research Unit for Epidemiology and Risk Analysis Applied to Veterinary Sciences (UREAR-ULiège), Centre of Fundamental and Applied Research for Animals and Health (FARAH), Faculty of Veterinary Medicine, University of Liège, Liège, Belgium.,School of Animal and Veterinary Sciences, University of Adelaide, Roseworthy, 5371, South Australia, Australia
| | - François Thiaucourt
- CIRAD-ASTRE, Montpellier, France.,OIE/FAO World Reference Laboratory for CCPP, France.,INRA, UMR1309 ASTRE, Montpellier, France
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23
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Ayala AJ, Yabsley MJ, Hernandez SM. A Review of Pathogen Transmission at the Backyard Chicken-Wild Bird Interface. Front Vet Sci 2020; 7:539925. [PMID: 33195512 PMCID: PMC7541960 DOI: 10.3389/fvets.2020.539925] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 08/13/2020] [Indexed: 01/31/2023] Open
Abstract
Habitat conversion and the expansion of domesticated, invasive species into native habitats are increasingly recognized as drivers of pathogen emergence at the agricultural-wildlife interface. Poultry agriculture is one of the largest subsets of this interface, and pathogen spillover events between backyard chickens and wild birds are becoming more commonly reported. Native wild bird species are under numerous anthropogenic pressures, but the risks of pathogen spillover from domestic chickens have been historically underappreciated as a threat to wild birds. Now that the backyard chicken industry is one of the fastest growing industries in the world, it is imperative that the principles of biosecurity, specifically bioexclusion and biocontainment, are legislated and implemented. We reviewed the literature on spillover events of pathogens historically associated with poultry into wild birds. We also reviewed the reasons for biosecurity failures in backyard flocks that lead to those spillover events and provide recommendations for current and future backyard flock owners.
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Affiliation(s)
- Andrea J. Ayala
- Department of Population Health, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Michael J. Yabsley
- Daniel B. Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, United States
- Southeastern Cooperative Wildlife Disease Study, Athens, GA, United States
| | - Sonia M. Hernandez
- Daniel B. Warnell School of Forestry and Natural Resources, University of Georgia, Athens, GA, United States
- Southeastern Cooperative Wildlife Disease Study, Athens, GA, United States
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Wang G, Song G, Xu Y. Association of CRISPR/Cas System with the Drug Resistance in Klebsiella pneumoniae. Infect Drug Resist 2020; 13:1929-1935. [PMID: 32606841 PMCID: PMC7320894 DOI: 10.2147/idr.s253380] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 06/09/2020] [Indexed: 12/24/2022] Open
Abstract
Background Klebsiella pneumoniae is a common opportunistic pathogen and its production of extended-spectrum β-lactamases (ESBL) and carbapenemases leads to drug resistance. Clustered regularly interspaced short palindromic repeats (CRISPRs) and their associated genes (Cas) are widespread in the genome of many bacteria and are a defense mechanism against foreign invaders such as plasmids and viruses. Purpose To investigate the prevalence of the CRISPR/Cas system in wild type strains of K. pneumoniae in the hospital and its association with drug resistance. Materials and Methods A total of 136 strains were collected and characterized their susceptibility to antimicrobial agents. The prevalence of CRISPR/Cas system was detected by PCR and DNA sequencing was analyzed by CRISPRFinder. The statistical analysis of the results was performed by SPSS. Results We found that 50/136 (37%) isolates produced ESBL and 30/136 (22%) isolates were resistant to carbapenems. These isolates were liable to be multidrug resistant against β-lactams, quinolones, and aminoglycosides. Among the carbapenem-resistant isolates, blaKPC was the main drug resistance-associated gene and different types of ESBL and AmpC genes were present. Resistance to β-lactams, quinolones, aminoglycosides, tetracyclines, and β-lactams/enzyme inhibitor were higher in absence of the CRISPR/Cas system. Eighteen spacers within the CRISPR arrays matched with the genomes of plasmids or phages, some of which carried drug resistance genes. Conclusion ESBL-producing and carbapenem-resistant K. pneumoniae are more likely to develop multidrug resistance and show an inverse correlation between drug resistance and CRISPR/Cas system. Absence of CRISPR/Cas modules allow for the acquisition of external drug resistance genes.
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Affiliation(s)
- Gang Wang
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, People's Republic of China
| | - Guobin Song
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, People's Republic of China
| | - Yuanhong Xu
- Department of Clinical Laboratory, The First Affiliated Hospital of Anhui Medical University, Hefei, Anhui Province, People's Republic of China
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25
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Kovács ÁB, Kreizinger Z, Forró B, Grózner D, Mitter A, Marton S, Bali K, Sawicka A, Tomczyk G, Bányai K, Gyuranecz M. The core genome multi-locus sequence typing of Mycoplasma anserisalpingitidis. BMC Genomics 2020; 21:403. [PMID: 32539834 PMCID: PMC7296915 DOI: 10.1186/s12864-020-06817-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Accepted: 06/09/2020] [Indexed: 01/17/2023] Open
Abstract
BACKGROUND Mycoplasma anserisalpingitidis is a waterfowl pathogen that mainly infects geese, can cause significant economic losses and is present worldwide. With the advance of whole genome sequencing technologies, new methods are available for the researchers; one emerging methodology is the core genome Multi-Locus Sequence Typing (cgMLST). The core genome contains a high percentage of the coding DNA sequence (CDS) set of the studied strains. The cgMLST schemas are powerful genotyping tools allowing for the investigation of potential epidemics, and precise and reliable classification of the strains. Although whole genome sequences of M. anserisalpingitidis strains are available, to date, no cgMLST schema has been published for this species. RESULTS In this study, Illumina short reads of 81 M. anserisalpingitidis strains were used, including samples from Hungary, Poland, Sweden, and China. Draft genomes were assembled with the SPAdes software and analysed with the online available chewBBACA program. User made modifications in the program enabled analysis of mycoplasmas and provided similar results as the conventional SeqSphere+ software. The threshold of the presence of CDS in the strains was set to 93% due to the quality of the draft genomes, resulting in the most accurate and robust schema. Three hundred thirty-one CDSs constituted our cgMLST schema (representing 42,77% of the whole CDS set of M. anserisalpingitidis ATCC BAA-2147), and a Neighbor joining tree was created using the allelic profiles. The correlation was observed between the strains' cgMLST profile and geographical origin; however, strains from the same integration but different locations also showed close relationship. Strains isolated from different tissue samples of the same animal revealed highly similar cgMLST profiles. CONCLUSIONS The Neighbor joining tree from the cgMLST schema closely resembled the real-life spatial and temporal relationships of the strains. The incongruences between background data and the cgMLST profile in the strains from the same integration can be because of the higher probability of contacts between the flocks. This schema can help with the epidemiological investigation and can be used as a basis for further studies.
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Affiliation(s)
- Áron B Kovács
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt 21, Budapest, H-1143, Hungary
| | - Zsuzsa Kreizinger
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt 21, Budapest, H-1143, Hungary
| | - Barbara Forró
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt 21, Budapest, H-1143, Hungary
| | - Dénes Grózner
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt 21, Budapest, H-1143, Hungary
| | - Alexa Mitter
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt 21, Budapest, H-1143, Hungary
| | - Szilvia Marton
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt 21, Budapest, H-1143, Hungary
| | - Krisztina Bali
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt 21, Budapest, H-1143, Hungary
| | - Anna Sawicka
- Department of Poultry Diseases, National Veterinary Research Institute, Aleja Partyzantow 57, 24-100, Pulawy, Poland
| | - Grzegorz Tomczyk
- Department of Poultry Diseases, National Veterinary Research Institute, Aleja Partyzantow 57, 24-100, Pulawy, Poland
| | - Krisztián Bányai
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt 21, Budapest, H-1143, Hungary
| | - Miklós Gyuranecz
- Institute for Veterinary Medical Research, Centre for Agricultural Research, Hungária krt 21, Budapest, H-1143, Hungary. .,Department of Microbiology and Infectious Diseases, University of Veterinary Medicine, H-1078 István utca 2, Budapest, Hungary.
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26
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Ghanem M, El-Gazzar M. Development of a Multilocus Sequence Typing Assay for Mycoplasma gallisepticum. Avian Dis 2020; 63:693-702. [PMID: 31865685 DOI: 10.1637/aviandiseases-d-19-00072] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 08/29/2019] [Indexed: 11/05/2022]
Abstract
Mycoplasma gallisepticum (MG) is the most pathogenic avian mycoplasma species. It affects commercial and noncommercial poultry and wild birds. Current MG sequence typing methods rely on the partial sequence of one or more surface antigen genes. Multilocus sequence typing (MLST), a widely used typing method for many human and animal pathogens, relies on conserved housekeeping genes. Recently, MLST assays have been developed for Mycoplasma synoviae (MS) and Mycoplasma iowae. Additionally, a whole genome-based core genome MLST (cgMLST) assay has been developed for MG and MS. However, cgMLST can be implemented only on pure isolates and cannot be applied to clinical samples. Here, we have developed a seven-locus-based MLST scheme for MG that can be applied directly on clinical samples without the need for isolation. The seven loci were selected from 425 genes recently used for the cgMLST assay. A total of 101 diverse MG samples, including isolates and clinical samples, were typed with the newly developed seven-locus MLST. The phylogeny and discriminatory power of the seven-locus MLST were evaluated and compared with the cgMLST and gene-targeted sequencing methods currently used for MG sequence typing. The seven-locus MLST provided optimum discriminatory power and congruent phylogeny to cgMLST. Additionally, a database for MG MLST was created and is currently available for public use online. This assay will increase accessibility to MG sequence typing and provide a stable and expandable nomenclature compatible with cgMLST. The seven-locus MLST assay represents an important tool for epidemiologic investigation of MG that can contribute to better control and eradication efforts.
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Affiliation(s)
- Mostafa Ghanem
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210,
| | - Mohamed El-Gazzar
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, OH 43210
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27
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Dowling AJ, Hill GE, Bonneaud C. Multiple differences in pathogen-host cell interactions following a bacterial host shift. Sci Rep 2020; 10:6779. [PMID: 32322086 PMCID: PMC7176683 DOI: 10.1038/s41598-020-63714-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2019] [Accepted: 04/01/2020] [Indexed: 12/15/2022] Open
Abstract
Novel disease emergence is often associated with changes in pathogen traits that enable pathogen colonisation, persistence and transmission in the novel host environment. While understanding the mechanisms underlying disease emergence is likely to have critical implications for preventing infectious outbreaks, such knowledge is often based on studies of viral pathogens, despite the fact that bacterial pathogens may exhibit very different life histories. Here, we investigate the ability of epizootic outbreak strains of the bacterial pathogen, Mycoplasma gallisepticum, which jumped from poultry into North American house finches (Haemorhous mexicanus), to interact with model avian cells. We found that house finch epizootic outbreak strains of M. gallisepticum displayed a greater ability to adhere to, invade, persist within and exit from cultured chicken embryonic fibroblasts, than the reference virulent (R_low) and attenuated (R_high) poultry strains. Furthermore, unlike the poultry strains, the house finch epizootic outbreak strain HF_1994 displayed a striking lack of cytotoxicity, even exerting a cytoprotective effect on avian cells. Our results suggest that, at epizootic outbreak in house finches, M. gallisepticum was particularly adept at using the intra-cellular environment, which may have facilitated colonisation, dissemination and immune evasion within the novel finch host. Whether this high-invasion phenotype is similarly displayed in interactions with house finch cells, and whether it contributed to the success of the host shift, remains to be determined.
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Affiliation(s)
- Andrea J Dowling
- Biosciences, College of Life and Environmental Science, Penryn Campus, University of Exeter, Cornwall, TR10 9FE, UK.
| | - Geoffrey E Hill
- Department of Biological Sciences, Auburn University, Auburn, AL36849-5414, USA
| | - Camille Bonneaud
- Biosciences, College of Life and Environmental Science, Penryn Campus, University of Exeter, Cornwall, TR10 9FE, UK.
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28
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Occurrence of Mycoplasma gallisepticum in wild birds: A systematic review and meta-analysis. PLoS One 2020; 15:e0231545. [PMID: 32298318 PMCID: PMC7162529 DOI: 10.1371/journal.pone.0231545] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2020] [Accepted: 03/25/2020] [Indexed: 12/30/2022] Open
Abstract
Mycoplasma gallisepticum is one of the most important poultry pathogens that can also infect wild birds, but knowledge of potential non-poultry hosts that could be reservoirs of M. gallisepticum is limited. For the paper presented here, we screened three databases (PubMed, Scopus, and the Web of Knowledge) to find articles on the occurrence of M. gallisepticum in different wild bird species that were published between 1951 and 2018. Among 314 studies found, we selected and included 50 original articles that met the pre-established criteria. From those publications we extracted the following information: name of the first author, year of publication, year of sample isolation, country, region, number of birds sampled, number of birds tested by each method, number of positive samples, diagnostic criteria, and if birds were wild or captive. Because different detection techniques were used to confirm the presence of M. gallisepticum in one animal, we decided to perform the meta analyses separately for each method. The estimated prevalence of M. gallisepticum in wild birds was different by each method of detection. Our summary revealed that M. gallisepticum was present in 56 species of bird belonging to 11 different orders, of which 21 species were reported suffering both past and current infection. Our work provides information on wild bird species that could be considered potential reservoirs or carriers of M. gallisepticum and could be helpful to set the direction for future research on the spread and phylogeny of M. gallisepticum in different hosts.
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29
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Henschen AE, Adelman JS. What Does Tolerance Mean for Animal Disease Dynamics When Pathology Enhances Transmission? Integr Comp Biol 2020; 59:1220-1230. [PMID: 31141137 DOI: 10.1093/icb/icz065] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Host competence, or how well an individual transmits pathogens, varies substantially within and among animal populations. As this variation can alter the course of epidemics and epizootics, revealing its underlying causes will help predict and control the spread of disease. One host trait that could drive heterogeneity in competence is host tolerance, which minimizes fitness losses during infection without decreasing pathogen load. In many cases, tolerance should increase competence by extending infectious periods and enabling behaviors that facilitate contact among hosts. However, we argue that the links between tolerance and competence are more varied. Specifically, the different physiological and behavioral mechanisms by which hosts achieve tolerance should have a range of effects on competence, enhancing the ability to transmit pathogens in some circumstances and impeding it in others. Because tissue-based pathology (damage) that reduces host fitness is often critical for pathogen transmission, we focus on two mechanisms that can underlie tolerance at the tissue level: damage-avoidance and damage-repair. As damage-avoidance reduces transmission-enhancing pathology, this mechanism is likely to decrease host competence and pathogen transmission. In contrast, damage-repair does not prevent transmission-relevant pathology from occurring. Rather, damage-repair provides new, healthy tissues that pathogens can exploit, likely extending the infectious period and increasing host competence. We explore these concepts through graphical models and present three disease systems in which damage-avoidance and damage-repair alter host competence in the predicted directions. Finally, we suggest that by incorporating these links, future theoretical studies could provide new insights into infectious disease dynamics and host-pathogen coevolution.
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Affiliation(s)
- Amberleigh E Henschen
- Department of Natural Resource Ecology and Management, Iowa State University, 339 Science Hall II, 2310 Pammel Drive, Ames, IA 50011, USA
| | - James S Adelman
- Department of Natural Resource Ecology and Management, Iowa State University, 339 Science Hall II, 2310 Pammel Drive, Ames, IA 50011, USA
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30
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Bensch S. Scott V. Edwards—Recipient of the 2019 Molecular Ecology Prize. Mol Ecol 2020; 29:20-22. [DOI: 10.1111/mec.15348] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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31
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Jaÿ M, Tardy F. Contagious Agalactia In Sheep And Goats: Current Perspectives. VETERINARY MEDICINE (AUCKLAND, N.Z.) 2019; 10:229-247. [PMID: 31921613 PMCID: PMC6938181 DOI: 10.2147/vmrr.s201847] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/15/2019] [Accepted: 11/07/2019] [Indexed: 12/15/2022]
Abstract
Contagious agalactia (CA) is a disease caused equally by four Mycoplasma species, in single or mixed infections. Clinical signs are multiple, including mastitis, arthritis, keratoconjunctivitis, pneumonia, and septicemia, non-specific, and expressed differently depending whether sheep or goats are affected, on causative mycoplasmas as well as type of husbandry. CA has been reported worldwide and its geographic distribution maps to that of small ruminant breeding areas. However, as current diagnostic tests are expensive and difficult to implement, it is certainly underdiagnosed and prevalence data are only available for a few countries. CA control relies on vaccines, chemotherapy and good herd management practices. It requires long-term commitment but is often unsuccessful, with frequent clinical relapses. The persistence of the etiological agents, despite their overall susceptibility to antimicrobials, comes from their genetic plasticity and capacity to escape the host immune response. The existence of asymptomatic carriers and the numerous sources of infections contribute to rapid spread of the disease and complicate the control and prevention efforts. Here we review all these aspects in order to highlight recent progress made and identify gaps in knowledge or tools needed for better disease management. Discussion also underlines the detrimental effect of contagious agalactia on small ruminant welfare.
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Affiliation(s)
- Maryne Jaÿ
- Université de Lyon, ANSES, Laboratoire de Lyon, VetAgro Sup, UMR Mycoplasmoses des Ruminants, Lyon69364, France
| | - Florence Tardy
- Université de Lyon, ANSES, Laboratoire de Lyon, VetAgro Sup, UMR Mycoplasmoses des Ruminants, Lyon69364, France
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32
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Sheffer MM, Uhl G, Prost S, Lueders T, Urich T, Bengtsson MM. Tissue- and Population-Level Microbiome Analysis of the Wasp Spider Argiope bruennichi Identified a Novel Dominant Bacterial Symbiont. Microorganisms 2019; 8:E8. [PMID: 31861544 PMCID: PMC7023434 DOI: 10.3390/microorganisms8010008] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 12/16/2019] [Accepted: 12/17/2019] [Indexed: 02/07/2023] Open
Abstract
Many ecological and evolutionary processes in animals depend upon microbial symbioses. In spiders, the role of the microbiome in these processes remains mostly unknown. We compared the microbiome between populations, individuals, and tissue types of a range-expanding spider, using 16S rRNA gene sequencing. Our study is one of the first to go beyond targeting known endosymbionts in spiders and characterizes the total microbiome across different body compartments (leg, prosoma, hemolymph, book lungs, ovaries, silk glands, midgut, and fecal pellets). Overall, the microbiome differed significantly between populations and individuals, but not between tissue types. The microbiome of the wasp spider Argiope bruennichi features a novel dominant bacterial symbiont, which is abundant in every tissue type in spiders from geographically distinct populations and that is also present in offspring. The novel symbiont is affiliated with the Tenericutes, but has low sequence identity (<85%) to all previously named taxa, suggesting that the novel symbiont represents a new bacterial clade. Its presence in offspring implies that it is vertically transmitted. Our results shed light on the processes that shape microbiome differentiation in this species and raise several questions about the implications of the novel dominant bacterial symbiont on the biology and evolution of its host.
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Affiliation(s)
- Monica M. Sheffer
- Zoological Institute and Museum, University of Greifswald, 17489 Greifswald, Germany;
| | - Gabriele Uhl
- Zoological Institute and Museum, University of Greifswald, 17489 Greifswald, Germany;
| | - Stefan Prost
- LOEWE-Center for Translational Biodiversity Genomics, Senckenberg Museum, 60325 Frankfurt, Germany;
- South African National Biodiversity Institute, National Zoological Gardens of South Africa, Pretoria 0001, South Africa
| | - Tillmann Lueders
- Bayreuth Center of Ecology and Environmental Research, University of Bayreuth, 95448 Bayreuth, Germany;
| | - Tim Urich
- Institute of Microbiology, University of Greifswald, 174897 Greifswald, Germany;
| | - Mia M. Bengtsson
- Institute of Microbiology, University of Greifswald, 174897 Greifswald, Germany;
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Ipoutcha T, Tsarmpopoulos I, Talenton V, Gaspin C, Moisan A, Walker CA, Brownlie J, Blanchard A, Thebault P, Sirand-Pugnet P. Multiple Origins and Specific Evolution of CRISPR/Cas9 Systems in Minimal Bacteria ( Mollicutes). Front Microbiol 2019; 10:2701. [PMID: 31824468 PMCID: PMC6882279 DOI: 10.3389/fmicb.2019.02701] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2019] [Accepted: 11/07/2019] [Indexed: 12/13/2022] Open
Abstract
CRISPR/Cas systems provide adaptive defense mechanisms against invading nucleic acids in prokaryotes. Because of its interest as a genetic tool, the Type II CRISPR/Cas9 system from Streptococcus pyogenes has been extensively studied. It includes the Cas9 endonuclease that is dependent on a dual-guide RNA made of a tracrRNA and a crRNA. Target recognition relies on crRNA annealing and the presence of a protospacer adjacent motif (PAM). Mollicutes are currently the bacteria with the smallest genome in which CRISPR/Cas systems have been reported. Many of them are pathogenic to humans and animals (mycoplasmas and ureaplasmas) or plants (phytoplasmas and some spiroplasmas). A global survey was conducted to identify and compare CRISPR/Cas systems found in the genome of these minimal bacteria. Complete or degraded systems classified as Type II-A and less frequently as Type II-C were found in the genome of 21 out of 52 representative mollicutes species. Phylogenetic reconstructions predicted a common origin of all CRISPR/Cas systems of mycoplasmas and at least two origins were suggested for spiroplasmas systems. Cas9 in mollicutes were structurally related to the S. aureus Cas9 except the PI domain involved in the interaction with the PAM, suggesting various PAM might be recognized by Cas9 of different mollicutes. Structure of the predicted crRNA/tracrRNA hybrids was conserved and showed typical stem-loop structures pairing the Direct Repeat part of crRNAs with the 5' region of tracrRNAs. Most mollicutes crRNA/tracrRNAs showed G + C% significantly higher than the genome, suggesting a selective pressure for maintaining stability of these secondary structures. Examples of CRISPR spacers matching with mollicutes phages were found, including the textbook case of Mycoplasma cynos strain C142 having no prophage sequence but a CRISPR/Cas system with spacers targeting prophage sequences that were found in the genome of another M. cynos strain that is devoid of a CRISPR system. Despite their small genome size, mollicutes have maintained protective means against invading DNAs, including restriction/modification and CRISPR/Cas systems. The apparent lack of CRISPR/Cas systems in several groups of species including main pathogens of humans, ruminants, and plants suggests different evolutionary routes or a lower risk of phage infection in specific ecological niches.
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Affiliation(s)
- Thomas Ipoutcha
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France.,Université de Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France
| | - Iason Tsarmpopoulos
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France.,Université de Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France
| | - Vincent Talenton
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France.,Université de Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France
| | - Christine Gaspin
- INRA, Mathématiques et Informatique Appliquées de Toulouse, Université de Toulouse, Toulouse, France
| | - Annick Moisan
- INRA, Mathématiques et Informatique Appliquées de Toulouse, Université de Toulouse, Toulouse, France
| | - Caray A Walker
- School of Life Sciences, Anglia Ruskin University, Cambridge, United Kingdom
| | - Joe Brownlie
- Department of Pathobiology and Population Sciences, Royal Veterinary College, University of London, London, United Kingdom
| | - Alain Blanchard
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France.,Université de Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France
| | | | - Pascal Sirand-Pugnet
- INRA, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France.,Université de Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, Villenave d'Ornon, France
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Perez K, Mullen N, Canter JA, Ley DH, May M. Phenotypic diversity in an emerging mycoplasmal disease. Microb Pathog 2019; 138:103798. [PMID: 31639466 DOI: 10.1016/j.micpath.2019.103798] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 10/08/2019] [Accepted: 10/11/2019] [Indexed: 11/27/2022]
Abstract
The avian pathogen Mycoplasma gallisepticum (MG) is a known pathogen of poultry, and newly emerged pathogen of house finches wherein it is associated with lethal conjunctivitis. Factors present in MG that are known to mediate virulence include cytadherence, sialidase activity, peroxide production, and biofilm formation. We have quantitatively assessed these factors for MG isolates from house finches from a temporal and geographic distribution across the continental United States that show differing capacity for virulence in vivo. Statistically significant (P < 0.05) differences were observed across strains for sialidase activity, cytadherence, and hydrogen peroxide production. Sialidase activity increased over time in geographically static populations, but did not correlate with time overall. All strains were able to bind α-2,6-linked sialic acid. No strains were found to bind α-2,3-linked sialic acid. All strains produced biofilms in vitro; however, no significant differences were observed in the density of biofilms across strains. Quantitative variance in virulence-associated traits is consistent with within-host evolutionary adaptation in response to a change in ecological niche by a parasitic pathogen.
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Affiliation(s)
- Kailey Perez
- Department of Biomedical Sciences, University of New England, Biddeford, ME, USA
| | - Nathan Mullen
- Department of Biomedical Sciences, University of New England, Biddeford, ME, USA
| | - Jessica A Canter
- Department of Pathobiology and Veterinary Science, University of Connecticut, Storrs, CT, USA
| | - David H Ley
- Department of Population Health and Pathobiology, North Carolina State University, Raleigh, NC, USA
| | - Meghan May
- Department of Biomedical Sciences, University of New England, Biddeford, ME, USA.
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Staley M, Bonneaud C, McGraw KJ, Vleck CM, Hill GE. Detection of Mycoplasma gallisepticum in House Finches ( Haemorhous mexicanus) from Arizona. Avian Dis 2019; 62:14-17. [PMID: 29620468 DOI: 10.1637/11610-021317-reg.1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
In 1994, an endemic poultry pathogen, Mycoplasma gallisepticum (MG), was identified as the causative agent of a novel disease in house finches ( Haemorhous mexicanus). After an initial outbreak in Maryland, MG spread rapidly throughout eastern North American populations of house finches. Subsequently, MG spread slowly through the northern interior of North America and then into the Pacific Northwest, finally reaching California in 2006. Until 2009, there were no reports of MG in the southwestern United States east of California. In August 2011, after reports of house finches displaying conjunctivitis characteristic of MG infection in Arizona, we trapped house finches at bird feeders in central Arizona (Tempe) and southern Arizona (Tucson and Green Valley) to assay for MG infection. Upon capture, we noted whether birds exhibited conjunctivitis, and we collected choanal swabs to test for the presence of MG DNA using PCR. We detected MG in finches captured from Green Valley (in ∼12% of birds captured), but not in finches from Tucson or Tempe. Based on resampling of house finches at these sites in July 2014, we suggest that central Arizona finches likely remain unexposed to MG. We also suggest that low urban connectivity between arid habitats of southern and central Arizona or a reduction in the prevalence of MG after its initial arrival in Arizona may be limiting the spread of MG from south to north in Arizona. In addition, the observed conjunctivitis-like signs in house finches that were negative for MG by PCR may be caused primarily by avian pox virus.
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Affiliation(s)
- Molly Staley
- A Department of Biological Sciences, Auburn University, Auburn, AL 36849.,B Chicago Zoological Society, Brookfield, IL 60513
| | - Camille Bonneaud
- D Centre for Ecology and Conservation, University of Exeter, Penryn, Cornwall TR10 9EF, United Kingdom
| | - Kevin J McGraw
- E School of Life Sciences, Arizona State University, Tempe, AZ 85287
| | - Carol M Vleck
- F Department of Ecology, Evolution, and Organismal Biology, Iowa State University, Ames, IA 50011
| | - Geoffrey E Hill
- A Department of Biological Sciences, Auburn University, Auburn, AL 36849
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Bonneaud C, Weinert LA, Kuijper B. Understanding the emergence of bacterial pathogens in novel hosts. Philos Trans R Soc Lond B Biol Sci 2019; 374:20180328. [PMID: 31401968 PMCID: PMC6711297 DOI: 10.1098/rstb.2018.0328] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Our understanding of the ecological and evolutionary context of novel infections is largely based on viral diseases, even though bacterial pathogens may display key differences in the processes underlying their emergence. For instance, host-shift speciation, in which the jump of a pathogen into a novel host species is followed by the specialization on that host and the loss of infectivity of previous host(s), is commonly observed in viruses, but less often in bacteria. Here, we suggest that the extent to which pathogens evolve host generalism or specialism following a jump into a novel host will depend on their level of adaptation to dealing with different environments, their rates of molecular evolution and their ability to recombine. We then explore these hypotheses using a formal model and show that the high levels of phenotypic plasticity, low rates of evolution and the ability to recombine typical of bacterial pathogens should reduce their propensity to specialize on novel hosts. Novel bacterial infections may therefore be more likely to result in transient spillovers or increased host ranges than in host shifts. Finally, consistent with our predictions, we show that, in two unusual cases of contemporary bacterial host shifts, the bacterial pathogens both have small genomes and rapid rates of substitution. Further tests are required across a greater number of emerging pathogens to assess the validity of our hypotheses. This article is part of the theme issue ‘Dynamic and integrative approaches to understanding pathogen spillover’.
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Affiliation(s)
- Camille Bonneaud
- Centre for Ecology and Conservation, University of Exeter, Penryn TR10 9FE, UK
| | - Lucy A Weinert
- Department of Veterinary Medicine, University of Cambridge, Cambridge CB3 0ES, UK
| | - Bram Kuijper
- Centre for Ecology and Conservation, University of Exeter, Penryn TR10 9FE, UK
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Contrasting evolution of virulence and replication rate in an emerging bacterial pathogen. Proc Natl Acad Sci U S A 2019; 116:16927-16932. [PMID: 31371501 PMCID: PMC6708350 DOI: 10.1073/pnas.1901556116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
With increasing antibiotic resistance, there is a pressing need to understand how host resistance naturally influences bacterial virulence and replication rates. We test this in an infection experiment using 55 isolates of a bacterium, which were collected over the course of the epidemic following its natural emergence in a North American songbird. We demonstrate virulence has increased linearly from outbreak to the present day, encompassing >150,000 bacterial generations. Despite this, bacterial replication rate only increased during the initial spread of host resistance but not thereafter. Thus, contrary to common assumptions, virulence and replication rates can evolve independently, particularly after the initial spread of host resistance. Host resistance through immune clearance is predicted to favor pathogens that are able to transmit faster and are hence more virulent. Increasing pathogen virulence is, in turn, typically assumed to be mediated by increasing replication rates. However, experiments designed to test how pathogen virulence and replication rates evolve in response to increasing host resistance, as well as the relationship between the two, are rare and lacking for naturally evolving host–pathogen interactions. We inoculated 55 isolates of Mycoplasma gallisepticum, collected over 20 y from outbreak, into house finches (Haemorhous mexicanus) from disease-unexposed populations, which have not evolved protective immunity to M. gallisepticum. We show using 3 different metrics of virulence (body mass loss, symptom severity, and putative mortality rate) that virulence has increased linearly over >150,000 bacterial generations since outbreak (1994 to 2015). By contrast, while replication rates increased from outbreak to the initial spread of resistance (1994 to 2004), no further increases have occurred subsequently (2007 to 2015). Finally, as a consequence, we found that any potential mediating effect of replication rate on virulence evolution was restricted to the period when host resistance was initially increasing in the population. Taken together, our results show that pathogen virulence and replication rates can evolve independently, particularly after the initial spread of host resistance. We hypothesize that the evolution of pathogen virulence can be driven primarily by processes such as immune manipulation after resistance spreads in host populations.
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Shabbir MAB, Shabbir MZ, Wu Q, Mahmood S, Sajid A, Maan MK, Ahmed S, Naveed U, Hao H, Yuan Z. CRISPR-cas system: biological function in microbes and its use to treat antimicrobial resistant pathogens. Ann Clin Microbiol Antimicrob 2019; 18:21. [PMID: 31277669 PMCID: PMC6611046 DOI: 10.1186/s12941-019-0317-x] [Citation(s) in RCA: 53] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2019] [Accepted: 06/06/2019] [Indexed: 12/13/2022] Open
Abstract
The development of antibiotic resistance in bacteria is a major public health threat. Infection rates of resistant pathogens continue to rise against nearly all antimicrobials, which has led to development of different strategies to combat the antimicrobial resistance. In this review, we discuss how the newly popular CRISPR-cas system has been applied to combat antibiotic resistance in both extracellular and intracellular pathogens. We also review a recently developed method in which nano-size CRISPR complex was used without any phage to target the mecA gene. However, there is still challenge to practice these methods in field against emerging antimicrobial resistant pathogens.
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Affiliation(s)
- Muhammad Abu Bakr Shabbir
- China MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Muhammad Zubair Shabbir
- Quality Operation Laboratory at University of Veterinary and Animal Sciences, Lahore, 54600, Pakistan
| | - Qin Wu
- National Reference Laboratory of Veterinary Drug Residues and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Sammina Mahmood
- Department of Botany, University of Education, Bank Road Campus, Lahore, Pakistan
| | - Abdul Sajid
- China MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.,College of Veterinary Sciences and Animal Husbandry, Abdul Wali Khan University, Mardan, 23200, Pakistan
| | - Muhammad Kashif Maan
- China MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Saeed Ahmed
- China MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China
| | - Umer Naveed
- The Roslin Institute, University of Edinburgh, Edinburgh, Scotland, UK
| | - Haihong Hao
- China MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
| | - Zonghui Yuan
- China MOA Laboratory for Risk Assessment of Quality and Safety of Livestock and Poultry Products, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China. .,National Reference Laboratory of Veterinary Drug Residues and MOA Key Laboratory for the Detection of Veterinary Drug Residues in Foods, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.
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39
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Tang H, Hood ME, Ren Z, Li H, Zhao Y, Wolfe LM, Li D, Wang H. Specificity and seasonal prevalence of anther smut disease
Microbotryum
on sympatric Himalayan
Silene
species. J Evol Biol 2019; 32:451-462. [DOI: 10.1111/jeb.13427] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 02/03/2019] [Accepted: 02/05/2019] [Indexed: 11/26/2022]
Affiliation(s)
- Hui Tang
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of Sciences Kunming Yunnan China
- Kunming College of Life ScienceUniversity of Chinese Academy of Sciences Kunming Yunnan China
| | | | - Zong‐Xin Ren
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of Sciences Kunming Yunnan China
| | - Hai‐Dong Li
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of Sciences Kunming Yunnan China
| | - Yan‐Hui Zhao
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of Sciences Kunming Yunnan China
| | - Lorne M. Wolfe
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of Sciences Kunming Yunnan China
| | - De‐Zhu Li
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of Sciences Kunming Yunnan China
- Kunming College of Life ScienceUniversity of Chinese Academy of Sciences Kunming Yunnan China
- Germplasm Bank of Wild SpeciesKunming Institute of BotanyChinese Academy of Sciences Kunming Yunnan China
| | - Hong Wang
- Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyChinese Academy of Sciences Kunming Yunnan China
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40
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García-Zea JA, de la Herrán R, Robles Rodríguez F, Navajas-Pérez R, Ruiz Rejón C. Detection and variability analyses of CRISPR-like loci in the H. pylori genome. PeerJ 2019; 7:e6221. [PMID: 30648020 PMCID: PMC6330956 DOI: 10.7717/peerj.6221] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Accepted: 12/05/2018] [Indexed: 12/16/2022] Open
Abstract
Helicobacter pylori is a human pathogenic bacterium with a high genomic plasticity. Although the functional CRISPR-Cas system has not been found in its genome, CRISPR-like loci have been recently identified. In this work, 53 genomes from different geographical areas are analyzed for the search and analysis of variability of this type of structure. We confirm the presence of a locus that was previously described in the VlpC gene in al lgenomes, and we characterize new CRISPR-like loci in other genomic locations. By studying the variability and gene location of these loci, the evolution and the possible roles of these sequences are discussed. Additionally, the usefulness of this type of sequences as a phylogenetic marker has been demonstrated, associating the different strains by geographical area.
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Affiliation(s)
| | - Roberto de la Herrán
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | | | - Rafael Navajas-Pérez
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
| | - Carmelo Ruiz Rejón
- Departamento de Genética, Facultad de Ciencias, Universidad de Granada, Granada, Spain
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Ekundayo TC, Okoh AI. Pathogenomics of Virulence Traits of Plesiomonas shigelloides That Were Deemed Inconclusive by Traditional Experimental Approaches. Front Microbiol 2018; 9:3077. [PMID: 30627119 PMCID: PMC6309461 DOI: 10.3389/fmicb.2018.03077] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 11/29/2018] [Indexed: 12/31/2022] Open
Abstract
One of the major challenges of modern medicine includes the failure of conventional protocols to characterize the pathogenicity of emerging pathogens. This is particularly apparent in the case of Plesiomonas shigelloides. Although a number of infections have been linked to this microorganism, experimental evidence of its virulence factors (VFs), obtained by traditional approaches, is somewhat inconclusive. Hence, it remains unclear whether P. shigelloides is a true or opportunistic one. In the current study, four publicly available whole-genome sequences of P. shigelloides (GN7, NCTC10360, 302-73, and LS1) were profiled using bioinformatics platforms to determine the putative candidate VFs to characterize the bacterial pathogenicity. Overall, 134 unique open reading frames (ORFs) were identified that were homologous or orthologous to virulence genes identified in other pathogens. Of these, 52.24% (70/134) were jointly shared by the strains. The numbers of strain-specific virulence traits were 4 in LS1; 7 in NCTC10360; 10 in 302-73; and 15 in GN7. The pathogenicity islands (PAIs) common to all the strains accounted for 24.07% ORFs. The numbers of PAIs exclusive to each strain were 8 in 302-73; 11 in NCTC10360; 14 in GN7; and 18 in LS1. A PAI encoding Vibrio cholerae ToxR-activated gene d protein was specific to 302-73, GN7, and NCTC10360 strains. Out of 33 antibiotic multi-resistance genes identified, 16 (48.48%) genes were intrinsic to all strains. Further, 17 (22.08%) of 77 antibiotic resistance islands were found in all the strains. Out of 23 identified distinct insertion sequences, 13 were only harbored by strain LS1. The number of intact prophages identified in the strains was 1 in GN7; 2 in 302-73; and 2 in NCTC10360. Further, 1 CRISPR element was identified in LS1; 2 in NCTC10360; and 8 in 302-73. Fifteen (78.95%) of 19 secretion systems and secretion effector variants were identified in all the strains. In conclusion, certain P. shigelloides strains might possess VFs associated with gastroenteritis and extraintestinal infections. However, the role of host factors in the onset of infections should not be undermined.
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Affiliation(s)
- Temitope C. Ekundayo
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa
- Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
- Department of Biological Sciences, University of Medical Sciences, Ondo City, Nigeria
| | - Anthony I. Okoh
- SAMRC Microbial Water Quality Monitoring Centre, University of Fort Hare, Alice, South Africa
- Applied and Environmental Microbiology Research Group, Department of Biochemistry and Microbiology, University of Fort Hare, Alice, South Africa
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42
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Sapountzis P, Zhukova M, Shik JZ, Schiott M, Boomsma JJ. Reconstructing the functions of endosymbiotic Mollicutes in fungus-growing ants. eLife 2018; 7:e39209. [PMID: 30454555 PMCID: PMC6245734 DOI: 10.7554/elife.39209] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Accepted: 10/16/2018] [Indexed: 12/25/2022] Open
Abstract
Mollicutes, a widespread class of bacteria associated with animals and plants, were recently identified as abundant abdominal endosymbionts in healthy workers of attine fungus-farming leaf-cutting ants. We obtained draft genomes of the two most common strains harbored by Panamanian fungus-growing ants. Reconstructions of their functional significance showed that they are independently acquired symbionts, most likely to decompose excess arginine consistent with the farmed fungal cultivars providing this nitrogen-rich amino-acid in variable quantities. Across the attine lineages, the relative abundances of the two Mollicutes strains are associated with the substrate types that foraging workers offer to fungus gardens. One of the symbionts is specific to the leaf-cutting ants and has special genomic machinery to catabolize citrate/glucose into acetate, which appears to deliver direct metabolic energy to the ant workers. Unlike other Mollicutes associated with insect hosts, both attine ant strains have complete phage-defense systems, underlining that they are actively maintained as mutualistic symbionts.
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Affiliation(s)
- Panagiotis Sapountzis
- Centre for Social Evolution, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Mariya Zhukova
- Centre for Social Evolution, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Jonathan Z Shik
- Centre for Social Evolution, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Morten Schiott
- Centre for Social Evolution, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
| | - Jacobus J Boomsma
- Centre for Social Evolution, Department of BiologyUniversity of CopenhagenCopenhagenDenmark
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43
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Moronato ML, Cecchinato M, Facchetti G, Mainenti M, Gobbo F, Catania S. Application of different laboratory techniques to monitor the behaviour of a Mycoplasma synoviae vaccine (MS-H) in broiler breeders. BMC Vet Res 2018; 14:357. [PMID: 30458824 PMCID: PMC6245925 DOI: 10.1186/s12917-018-1669-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 10/24/2018] [Indexed: 11/11/2022] Open
Abstract
Background Mycoplasma synoviae (MS) is a major poultry pathogen which causes severe economic losses in all the productive sectors. The prevalence of MS in European countries has increased in the last few years, leading to greater attention to the available methods to prevent its spread. The main strategy currently applied for its containment is the development and maintenance of MS-free breeder flocks. A live MS vaccine (MS-H) obtained by mutagenizing an Australian field strain has recently been introduced in Italy. The aim of the present study was to evaluate the vaccine behaviour in broiler breeder groups at different production stages and the effectiveness of the available laboratory tests in discriminating the MS-H from a field strain. Results The vaccine diffused extensively through the population, shown by the wide serological response (over 80% of positive samples in RSA and 85% in ELISA), the high serological titres, the positivity of all the tracheal samples collected during the production phase by MS PCR and the positivity by cultivation from tracheal swabs at the end-point (55 weeks after vaccination). In contrast, only one swab from a sternal bursa was positive in MS PCR, while all the joint and oviduct samples were negative. There was no evidence of vertical transmission. Different genotyping techniques were used to achieve a clear classification of the MS positive samples. The vlhA and the obg gene analysis showed that most of the strains were homologous with the vaccine, but some ambiguous samples were further investigated with the multi locus sequence typing (MLST) scheme which confirmed the homology. Conclusions The development of a multi-technique approach to monitor vaccinated avian flocks, based both on serological and biomolecular methods, is advised as well as the use of effective genotyping techniques to analyse the MS strains circulating in high densely populated poultry areas. Electronic supplementary material The online version of this article (10.1186/s12917-018-1669-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- M L Moronato
- Department of Animal Medicine Production and Health - MAPS, Università degli Studi di Padova, Viale dell'Università 16, 35020. Legnaro, Padova, Italy. .,Avian Medicine Laboratory Mycoplasma Unit - SCT1, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020. Legnaro, Padova, Italy.
| | - M Cecchinato
- Department of Animal Medicine Production and Health - MAPS, Università degli Studi di Padova, Viale dell'Università 16, 35020. Legnaro, Padova, Italy
| | - G Facchetti
- Veterinary practitioner. Avicola Alimentare Monteverde SRL. Via San Donato, 107, 25038. Rovato, Brescia, Italy
| | - M Mainenti
- Istituto Zooprofilattico Sperimentale di Verona, SCT1, Via S. Giacomo 5, 37135, Verona, Italy
| | - F Gobbo
- Avian Medicine Laboratory Mycoplasma Unit - SCT1, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020. Legnaro, Padova, Italy
| | - S Catania
- Avian Medicine Laboratory Mycoplasma Unit - SCT1, Istituto Zooprofilattico Sperimentale delle Venezie, Viale dell'Università 10, 35020. Legnaro, Padova, Italy
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Van den Bergh B, Swings T, Fauvart M, Michiels J. Experimental Design, Population Dynamics, and Diversity in Microbial Experimental Evolution. Microbiol Mol Biol Rev 2018; 82:e00008-18. [PMID: 30045954 PMCID: PMC6094045 DOI: 10.1128/mmbr.00008-18] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
In experimental evolution, laboratory-controlled conditions select for the adaptation of species, which can be monitored in real time. Despite the current popularity of such experiments, nature's most pervasive biological force was long believed to be observable only on time scales that transcend a researcher's life-span, and studying evolution by natural selection was therefore carried out solely by comparative means. Eventually, microorganisms' propensity for fast evolutionary changes proved us wrong, displaying strong evolutionary adaptations over a limited time, nowadays massively exploited in laboratory evolution experiments. Here, we formulate a guide to experimental evolution with microorganisms, explaining experimental design and discussing evolutionary dynamics and outcomes and how it is used to assess ecoevolutionary theories, improve industrially important traits, and untangle complex phenotypes. Specifically, we give a comprehensive overview of the setups used in experimental evolution. Additionally, we address population dynamics and genetic or phenotypic diversity during evolution experiments and expand upon contributing factors, such as epistasis and the consequences of (a)sexual reproduction. Dynamics and outcomes of evolution are most profoundly affected by the spatiotemporal nature of the selective environment, where changing environments might lead to generalists and structured environments could foster diversity, aided by, for example, clonal interference and negative frequency-dependent selection. We conclude with future perspectives, with an emphasis on possibilities offered by fast-paced technological progress. This work is meant to serve as an introduction to those new to the field of experimental evolution, as a guide to the budding experimentalist, and as a reference work to the seasoned expert.
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Affiliation(s)
- Bram Van den Bergh
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
- Douglas Lab, Department of Entomology, Cornell University, Ithaca, New York, USA
| | - Toon Swings
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
| | - Maarten Fauvart
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
- imec, Leuven, Belgium
| | - Jan Michiels
- Laboratory of Symbiotic and Pathogenic Interactions, Centre of Microbial and Plant Genetics, KU Leuven-University of Leuven, Leuven, Belgium
- Michiels Lab, Center for Microbiology, VIB, Leuven, Belgium
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45
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Rocha EPC. Neutral Theory, Microbial Practice: Challenges in Bacterial Population Genetics. Mol Biol Evol 2018; 35:1338-1347. [DOI: 10.1093/molbev/msy078] [Citation(s) in RCA: 51] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Affiliation(s)
- Eduardo P C Rocha
- Microbial Evolutionary Genomics, Institut Pasteur, Paris, France
- CNRS, UMR3525, Paris, France
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46
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Li P, Xu J, Rao HM, Li X, Zhang YK, Jiang F, Wu WX. Mechanism of Apoptosis Induction by Mycoplasmal Nuclease MGA_0676 in Chicken Embryo Fibroblasts. Front Cell Infect Microbiol 2018; 8:105. [PMID: 29670864 PMCID: PMC5893762 DOI: 10.3389/fcimb.2018.00105] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Accepted: 03/19/2018] [Indexed: 12/22/2022] Open
Abstract
MGA_0676 has been characterized as a Mycoplasma gallisepticum nuclease that can induce apoptosis of chicken cells. However, the mechanism by which MGA_0676 induces apoptosis has remained unclear. In this study, we evaluated MGA_0676-induced apoptosis and internalization in immortalized chicken embryo fibroblasts (DF-1) and cancer cell lines. The internalization of MGA_0676 was proven through caveolin-mediated endocytosis by blocking the endocytosis with specific inhibitors or with siRNA. We identified the Thif domain of NEDD8-activating enzyme E1 regulatory subunit (NAE) in DF-1 as the target region interacting with the SNC domain of MGA_0676. The interaction between the Thif and SNC domains was observed co-located in the perinuclear and nuclear of DF-1. We found that the interaction between NAE and MGA_0676 increased the ability of apoptosis and accelerated the process of cullin neddylation in DF-1 cells, in turn activating NF-κB. This resulted in the observed aggregation of NF-κB in the nuclei of DF-1 cells. Moreover, the apoptosis induced by MGA_0676 decreased significantly when NF-κB was inhibited by siRNA or BAY 11-7082 or when NAE was silenced by siRNA. Overall, our results demonstrate that MGA_0676 is internalized through caveolin-mediated endocytosis, interacts with SNC-dependent Thif to accelerate the process of cullin neddylation and activates NF-κB in DF-1 cells, ultimately playing a key role in apoptosis in chicken cells. Our results indicate MGA_0676 constitutes a critical etiological virulence factor of the respiratory disease caused by M. gallisepticum. This study also opens a venue to investigate MGA_0676 as a potential candidate as pro-apoptotic drug in cancer studies.
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Affiliation(s)
- Peng Li
- Key Laboratory of Animal Epidemiology and Zoonosis, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Jian Xu
- Institute of Animal Husbandry and Veterinary Medicine, Beijing Academy of Agricultural and Forestry Sciences, Beijing, China
| | - Hong-Mei Rao
- Key Laboratory of Animal Epidemiology and Zoonosis, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Xia Li
- Key Laboratory of Animal Epidemiology and Zoonosis, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Yun-Ke Zhang
- Key Laboratory of Animal Epidemiology and Zoonosis, College of Veterinary Medicine, China Agricultural University, Beijing, China
| | - Fei Jiang
- Veterinary Diagnostic Laboratory, China Animal Disease Control Center, Beijing, China
| | - Wen-Xue Wu
- Key Laboratory of Animal Epidemiology and Zoonosis, College of Veterinary Medicine, China Agricultural University, Beijing, China
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47
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Bacterial Pathogen Emergence Requires More than Direct Contact with a Novel Passerine Host. Infect Immun 2018; 86:IAI.00863-17. [PMID: 29311238 PMCID: PMC5820954 DOI: 10.1128/iai.00863-17] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Accepted: 12/22/2017] [Indexed: 12/31/2022] Open
Abstract
While direct contact may sometimes be sufficient to allow a pathogen to jump into a new host species, in other cases, fortuitously adaptive mutations that arise in the original donor host are also necessary. Viruses have been the focus of most host shift studies, so less is known about the importance of ecological versus evolutionary processes to successful bacterial host shifts. Here we tested whether direct contact with the novel host was sufficient to enable the mid-1990s jump of the bacterium Mycoplasma gallisepticum from domestic poultry to house finches (Haemorhous mexicanus). We experimentally inoculated house finches with two genetically distinct M. gallisepticum strains obtained either from poultry (Rlow) or from house finches (HF1995) during an epizootic outbreak. All 15 house finches inoculated with HF1995 became infected, whereas Rlow successfully infected 12 of 15 (80%) inoculated house finches. Comparisons among infected birds showed that, relative to HF1995, Rlow achieved substantially lower bacterial loads in the host respiratory mucosa and was cleared faster. Furthermore, Rlow-infected finches were less likely to develop clinical symptoms than HF1995-infected birds and, when they did, displayed milder conjunctivitis. The lower infection success of Rlow relative to HF1995 was not, however, due to a heightened host antibody response to Rlow. Taken together, our results indicate that contact between infected poultry and house finches was not, by itself, sufficient to explain the jump of M. gallisepticum to house finches. Instead, mutations arising in the original poultry host would have been necessary for successful pathogen emergence in the novel finch host.
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48
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Vinkler M, Leon AE, Kirkpatrick L, Dalloul RA, Hawley DM. Differing House Finch Cytokine Expression Responses to Original and Evolved Isolates of Mycoplasma gallisepticum. Front Immunol 2018. [PMID: 29403495 DOI: 10.3389/fimmu.2018.00013/full] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
The recent emergence of the poultry bacterial pathogen Mycoplasma gallisepticum (MG) in free-living house finches (Haemorhous mexicanus), which causes mycoplasmal conjunctivitis in this passerine bird species, resulted in a rapid coevolutionary arms-race between MG and its novel avian host. Despite extensive research on the ecological and evolutionary dynamics of this host-pathogen system over the past two decades, the immunological responses of house finches to MG infection remain poorly understood. We developed seven new probe-based one-step quantitative reverse transcription polymerase chain reaction assays to investigate mRNA expression of house finch cytokine genes (IL1B, IL6, IL10, IL18, TGFB2, TNFSF15, and CXCLi2, syn. IL8L). These assays were then used to describe cytokine transcription profiles in a panel of 15 house finch tissues collected at three distinct time points during MG infection. Based on initial screening that indicated strong pro-inflammatory cytokine expression during MG infection at the periorbital sites in particular, we selected two key house finch tissues for further characterization: the nictitating membrane, i.e., the internal eyelid in direct contact with MG, and the Harderian gland, the secondary lymphoid tissue responsible for regulation of periorbital immunity. We characterized cytokine responses in these two tissues for 60 house finches experimentally inoculated either with media alone (sham) or one of two MG isolates: the earliest known pathogen isolate from house finches (VA1994) or an evolutionarily more derived isolate collected in 2006 (NC2006), which is known to be more virulent. We show that the more derived and virulent isolate NC2006, relative to VA1994, triggers stronger local inflammatory cytokine signaling, with peak cytokine expression generally occurring 3-6 days following MG inoculation. We also found that the extent of pro-inflammatory interleukin 1 beta signaling was correlated with conjunctival MG loads and the extent of clinical signs of conjunctivitis, the main pathological effect of MG in house finches. These results suggest that the pathogenicity caused by MG infection in house finches is largely mediated by host pro-inflammatory immune responses, with important implications for the dynamics of host-pathogen coevolution.
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Affiliation(s)
- Michal Vinkler
- Faculty of Science, Department of Zoology, Charles University, Prague, Czechia
| | - Ariel E Leon
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Laila Kirkpatrick
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Rami A Dalloul
- Avian Immunobiology Laboratory, Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Dana M Hawley
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
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Vinkler M, Leon AE, Kirkpatrick L, Dalloul RA, Hawley DM. Differing House Finch Cytokine Expression Responses to Original and Evolved Isolates of Mycoplasma gallisepticum. Front Immunol 2018; 9:13. [PMID: 29403495 PMCID: PMC5786573 DOI: 10.3389/fimmu.2018.00013] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2017] [Accepted: 01/04/2018] [Indexed: 01/25/2023] Open
Abstract
The recent emergence of the poultry bacterial pathogen Mycoplasma gallisepticum (MG) in free-living house finches (Haemorhous mexicanus), which causes mycoplasmal conjunctivitis in this passerine bird species, resulted in a rapid coevolutionary arms-race between MG and its novel avian host. Despite extensive research on the ecological and evolutionary dynamics of this host-pathogen system over the past two decades, the immunological responses of house finches to MG infection remain poorly understood. We developed seven new probe-based one-step quantitative reverse transcription polymerase chain reaction assays to investigate mRNA expression of house finch cytokine genes (IL1B, IL6, IL10, IL18, TGFB2, TNFSF15, and CXCLi2, syn. IL8L). These assays were then used to describe cytokine transcription profiles in a panel of 15 house finch tissues collected at three distinct time points during MG infection. Based on initial screening that indicated strong pro-inflammatory cytokine expression during MG infection at the periorbital sites in particular, we selected two key house finch tissues for further characterization: the nictitating membrane, i.e., the internal eyelid in direct contact with MG, and the Harderian gland, the secondary lymphoid tissue responsible for regulation of periorbital immunity. We characterized cytokine responses in these two tissues for 60 house finches experimentally inoculated either with media alone (sham) or one of two MG isolates: the earliest known pathogen isolate from house finches (VA1994) or an evolutionarily more derived isolate collected in 2006 (NC2006), which is known to be more virulent. We show that the more derived and virulent isolate NC2006, relative to VA1994, triggers stronger local inflammatory cytokine signaling, with peak cytokine expression generally occurring 3-6 days following MG inoculation. We also found that the extent of pro-inflammatory interleukin 1 beta signaling was correlated with conjunctival MG loads and the extent of clinical signs of conjunctivitis, the main pathological effect of MG in house finches. These results suggest that the pathogenicity caused by MG infection in house finches is largely mediated by host pro-inflammatory immune responses, with important implications for the dynamics of host-pathogen coevolution.
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Affiliation(s)
- Michal Vinkler
- Faculty of Science, Department of Zoology, Charles University, Prague, Czechia
| | - Ariel E. Leon
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Laila Kirkpatrick
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Rami A. Dalloul
- Avian Immunobiology Laboratory, Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg, VA, United States
| | - Dana M. Hawley
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, United States
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Ghanem M, Wang L, Zhang Y, Edwards S, Lu A, Ley D, El-Gazzar M. Core Genome Multilocus Sequence Typing: a Standardized Approach for Molecular Typing of Mycoplasma gallisepticum. J Clin Microbiol 2018; 56:JCM.01145-17. [PMID: 29070657 PMCID: PMC5744223 DOI: 10.1128/jcm.01145-17] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2017] [Accepted: 10/14/2017] [Indexed: 02/07/2023] Open
Abstract
Mycoplasma gallisepticum is the most virulent and economically important Mycoplasma species for poultry worldwide. Currently, M. gallisepticum strain differentiation based on sequence analysis of 5 loci remains insufficient for accurate outbreak investigation. Recently, whole-genome sequences (WGS) of many human and animal pathogens have been successfully used for microbial outbreak investigations. However, the massive sequence data and the diverse properties of different genes within bacterial genomes results in a lack of standard reproducible methods for comparisons among M. gallisepticum whole genomes. Here, we proposed the development of a core genome multilocus sequence typing (cgMLST) scheme for M. gallisepticum strains and field isolates. For development of this scheme, a diverse collection of 37 M. gallisepticum genomes was used to identify cgMLST targets. A total of 425 M. gallisepticum conserved genes (49.85% of M. gallisepticum genome) were selected as core genome targets. A total of 81 M. gallisepticum genomes from 5 countries on 4 continents were typed using M. gallisepticum cgMLST. Analyses of phylogenetic trees generated by cgMLST displayed a high degree of agreement with geographical and temporal information. Moreover, the high discriminatory power of cgMLST allowed differentiation between M. gallisepticum strains of the same outbreak. M. gallisepticum cgMLST represents a standardized, accurate, highly discriminatory, and reproducible method for differentiation among M. gallisepticum isolates. cgMLST provides stable and expandable nomenclature, allowing for comparison and sharing of typing results among laboratories worldwide. cgMLST offers an opportunity to harness the tremendous power of next-generation sequencing technology in applied avian mycoplasma epidemiology at both local and global levels.
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Affiliation(s)
- Mostafa Ghanem
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, USA
- Faculty of Veterinary Medicine, Alexandria University, Rasheed El-Mahmoudeya, Markaz Rasheed, El Beheira Governorate, Egypt
| | - Leyi Wang
- Animal Disease Diagnostic Laboratory, Ohio Department of Agriculture, Reynoldsburg, Ohio, USA
| | - Yan Zhang
- Animal Disease Diagnostic Laboratory, Ohio Department of Agriculture, Reynoldsburg, Ohio, USA
| | - Scott Edwards
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - Amanda Lu
- Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, Massachusetts, USA
| | - David Ley
- Department of Population Health and Pathobiology, College of Veterinary Medicine, North Carolina State University, Raleigh, North Carolina, USA
| | - Mohamed El-Gazzar
- Department of Veterinary Preventive Medicine, College of Veterinary Medicine, The Ohio State University, Columbus, Ohio, USA
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