Updated functional annotation of the Mycobacterium bovis AF2122/97 reference genome

AbstractMycobacterium bovis AF2122/97 is the reference strain for the bovine tuberculosis bacillus. We here report an update to the M. bovis AF2122/97 genome annotation to reflect 616 new protein identifications which replace many of the old hypothetical coding sequences and proteins of unknown function in the genome. These changes integrate information from functional assignments of orthologous coding sequences in the Mycobacterium tuberculosis H37Rv genome. We have also added 69 additional new gene names.

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Updated Reference Genome Sequence and Annotation of Mycobacterium bovis AF2122/97

Genome Announcements ◽

10.1128/genomea.00157-17 ◽

2017 ◽

Vol 5 (14) ◽

Cited By ~ 22

Author(s):

Kerri M. Malone ◽

Damien Farrell ◽

Tod P. Stuber ◽

Olga T. Schubert ◽

Ruedi Aebersold ◽

...

Keyword(s):

Single Nucleotide Polymorphism ◽

Mycobacterium Bovis ◽

Genome Sequence ◽

Bovine Tuberculosis ◽

Reference Genome ◽

Nucleotide Polymorphism ◽

Single Nucleotide ◽

Coding Sequences ◽

Content Type ◽

Reference Genome Sequence

ABSTRACT We report here an update to the reference genome sequence of the bovine tuberculosis bacillus Mycobacterium bovis AF2122/97, generated using an integrative multiomics approach. The update includes 42 new coding sequences (CDSs), 14 modified annotations, 26 single-nucleotide polymorphism (SNP) corrections, and disclosure that the RD900 locus, previously described as absent from the genome, is in fact present.

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Genomic and temporal analyses of Mycobacterium bovis in southern Brazil

Microbial Genomics ◽

10.1099/mgen.0.000569 ◽

2021 ◽

Vol 7 (5) ◽

Author(s):

Rudielle de Arruda Rodrigues ◽

Flábio Ribeiro Araújo ◽

Alberto Martín Rivera Dávila ◽

Rodrigo Nestor Etges ◽

Julian Parkhill ◽

...

Keyword(s):

Population Structure ◽

Mycobacterium Bovis ◽

Type Species ◽

Southern Brazil ◽

Cattle Industry ◽

Content Type ◽

Cross Border ◽

Link Type ◽

High Level ◽

The 19Th Century

Mycobacterium bovis is a causal agent of bovine tuberculosis (bTB), one of the most important diseases currently facing the cattle industry worldwide. Tracing the source of M. bovis infections of livestock is an important tool for understanding the epidemiology of bTB and defining control/eradication strategies. In this study, whole genome sequencing (WGS) of 74 M . bovis isolates sourced from naturally infected cattle in the State of Rio Grande do Sul (RS), southern Brazil, was used to evaluate the population structure of M. bovis in the region, identify potential transmission events and date the introduction of clonal complex (CC) European 2 (Eu2). In silico spoligotyping identified 11 distinct patterns including four new profiles and two CCs, European 1 (Eu1) and Eu2. The analyses revealed a high level of genetic diversity in the majority of herds and identified putative transmission clusters that suggested that within- and between-herd transmission is occurring in RS. In addition, a comparison with other published M. bovis isolates from Argentina, Brazil, Paraguay and Uruguay demonstrated some evidence for a possible cross-border transmission of CC Eu1 into RS from Uruguay or Argentina. An estimated date for the introduction of CC Eu2 into RS in the middle of the 19th century correlated with the historical introduction of cattle into RS to improve existing local breeds. These findings contribute to the understanding of the population structure of M. bovis in southern Brazil and highlight the potential of WGS in surveillance and helping to identify bTB transmission.

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Isolates belonging to CDC group II-i belong predominantly to Sphingobacterium mizutaii Yabuuchi et al. 1983: emended descriptions of S. mizutaii and of the genus Sphingobacterium

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.037325-0 ◽

2012 ◽

Vol 62 (Pt_11) ◽

pp. 2598-2601 ◽

Cited By ~ 20

Author(s):

Georges Wauters ◽

Michèle Janssens ◽

Thierry De Baere ◽

Mario Vaneechoutte ◽

Pieter Deschaght

Keyword(s):

Type Species ◽

Gene Sequence ◽

Reference Strain ◽

Rrna Gene ◽

Content Type ◽

Link Type ◽

Group Ii ◽

Indole Production ◽

The 16S Rrna Gene

Two clinical strains, NF 296 and NF 931, present in our collection, were identified biochemically as members of CDC group II-i. Determination of the 16S rRNA gene sequence revealed highest similarity with strains of Sphingobacterium mizutaii . Because these strains produced indole, whereas S. mizutaii has been described as indole-negative, we also investigated the type strain and a reference strain of S. mizutaii , LMG 8340T ( = CCUG 15907T) and LMG 8341 ( = CCUG 15908), and found both strains also to be positive for indole production. These data warrant inclusion of some of the CDC group II-i strains into S. mizutaii and emended descriptions of Sphingobacterium mizutaii as indole-production-positive and of the genus Sphingobacterium as variable for indole production.

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Busting biofilms: free-living amoebae disrupt preformed methicillin-resistant Staphylococcus aureus (MRSA) and Mycobacterium bovis biofilms

Microbiology ◽

10.1099/mic.0.000933 ◽

2020 ◽

Vol 166 (8) ◽

pp. 695-706 ◽

Cited By ~ 1

Author(s):

Kevin H. Martin ◽

Grace I. Borlee ◽

William H. Wheat ◽

Mary Jackson ◽

Bradley R. Borlee

Keyword(s):

Staphylococcus Aureus ◽

Mycobacterium Bovis ◽

Type Species ◽

Acanthamoeba Castellanii ◽

Methicillin Resistant ◽

Content Type ◽

Host Immune Responses ◽

Link Type ◽

Abiotic Surfaces ◽

Low Concentrations

Biofilm-associated infections are difficult to eradicate because of their ability to tolerate antibiotics and evade host immune responses. Amoebae and/or their secreted products may provide alternative strategies to inhibit and disperse biofilms on biotic and abiotic surfaces. We evaluated the potential of five predatory amoebae – Acanthamoeba castellanii, Acanthamoeba lenticulata, Acanthamoeba polyphaga, Vermamoeba vermiformis and Dictyostelium discoideum – and their cell-free secretions to disrupt biofilms formed by methicillin-resistant Staphylococcus aureus (MRSA) and Mycobacterium bovis . The biofilm biomass produced by MRSA and M. bovis was significantly reduced when co-incubated with A. castellanii, A. lenticulata and A. polyphaga, and their corresponding cell-free supernatants (CFS). Acanthamoeba spp. generally produced CFS that mediated biofilm dispersal rather than directly killing the bacteria; however, A. polyphaga CFS demonstrated active killing of MRSA planktonic cells when the bacteria were present at low concentrations. The active component(s) of the A. polyphaga CFS is resistant to freezing, but can be inactivated to differing degrees by mechanical disruption and exposure to heat. D. discoideum and its CFS also reduced preformed M. bovis biofilms, whereas V. vermiformis only decreased M. bovis biofilm biomass when amoebae were added. These results highlight the potential of using select amoebae species or their CFS to disrupt preformed bacterial biofilms.

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Population structure and transmission of Mycobacterium bovis in Ethiopia

Microbial Genomics ◽

10.1099/mgen.0.000539 ◽

2021 ◽

Vol 7 (5) ◽

Author(s):

Gizat Almaw ◽

Getnet Abie Mekonnen ◽

Adane Mihret ◽

Abraham Aseffa ◽

Hawult Taye ◽

...

Keyword(s):

Population Structure ◽

Mycobacterium Bovis ◽

Type Species ◽

Clonal Complex ◽

Variable Number Tandem Repeat ◽

Variable Number ◽

Good Representation ◽

Long Distance ◽

Content Type ◽

Link Type

Bovine tuberculosis (bTB) is endemic in cattle in Ethiopia, a country that hosts the largest national cattle herd in Africa. The intensive dairy sector, most of which is peri-urban, has the highest prevalence of disease. Previous studies in Ethiopia have demonstrated that the main cause is Mycobacterium bovis , which has been investigated using conventional molecular tools including deletion typing, spoligotyping and Mycobacterial interspersed repetitive unit-variable number tandem repeat (MIRU-VNTR). Here we use whole-genome sequencing to examine the population structure of M. bovis in Ethiopia. A total of 134 M . bovis isolates were sequenced including 128 genomes from 85 mainly dairy cattle and six genomes isolated from humans, originating from 12 study sites across Ethiopia. These genomes provided a good representation of the previously described population structure of M. bovis , based on spoligotyping and demonstrated that the population is dominated by the clonal complexes African 2 (Af2) and European 3 (Eu3). A range of within-host diversity was observed amongst the isolates and evidence was found for both short- and long-distance transmission. Detailed analysis of available genomes from the Eu3 clonal complex combined with previously published genomes revealed two distinct introductions of this clonal complex into Ethiopia between 1950 and 1987, likely from Europe. This work is important to help better understand bTB transmission in cattle in Ethiopia and can potentially inform national strategies for bTB control in Ethiopia and beyond.

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Domestication of Campylobacter jejuni NCTC 11168

Microbial Genomics ◽

10.1099/mgen.0.000279 ◽

2019 ◽

Vol 5 (7) ◽

Author(s):

Ben Pascoe ◽

Lisa K. Williams ◽

Jessica K. Calland ◽

Guillaume Meric ◽

Matthew D. Hitchings ◽

...

Keyword(s):

Genetic Variation ◽

Campylobacter Jejuni ◽

Type Species ◽

Reference Strain ◽

Careful Consideration ◽

Trait Variation ◽

Content Type ◽

Link Type ◽

The Uk ◽

Reference Strains

Reference and type strains of well-known bacteria have been a cornerstone of microbiology research for decades. The sharing of well-characterized isolates among laboratories has run in parallel with research efforts and enhanced the reproducibility of experiments, leading to a wealth of knowledge about trait variation in different species and the underlying genetics. Campylobacter jejuni strain NCTC 11168, deposited at the National Collection of Type Cultures in 1977, has been adopted widely as a reference strain by researchers worldwide and was the first Campylobacter for which the complete genome was published (in 2000). In this study, we collected 23 C . jejuni NCTC 11168 reference isolates from laboratories across the UK and compared variation in simple laboratory phenotypes with genetic variation in sequenced genomes. Putatively identical isolates, identified previously to have aberrant phenotypes, varied by up to 281 SNPs (in 15 genes) compared to the most recent reference strain. Isolates also display considerable phenotype variation in motility, morphology, growth at 37 °C, invasion of chicken and human cell lines, and susceptibility to ampicillin. This study provides evidence of ongoing evolutionary change among C. jejuni isolates as they are cultured in different laboratories and highlights the need for careful consideration of genetic variation within laboratory reference strains. This article contains data hosted by Microreact.

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Arsenicicoccus dermatophilus sp. nov., a hypha-forming bacterium isolated from the skin of greater flamingos (Phoenicopterus roseus) with pododermatitis

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijs.0.048546-0 ◽

2013 ◽

Vol 63 (Pt_11) ◽

pp. 4046-4051 ◽

Cited By ~ 10

Author(s):

Stefanie Gobeli ◽

Andreas Thomann ◽

Fabia Wyss ◽

Kathrin Kuehni-Boghenbor ◽

Isabelle Brodard ◽

...

Keyword(s):

Type Strain ◽

Type Species ◽

Reference Strain ◽

Polymyxin B ◽

Wall Structure ◽

Rrna Gene ◽

Phenotypic Characteristics ◽

Content Type ◽

Link Type ◽

Greater Flamingos

Dermatophilus -like bacteria were observed in histological examinations of samples of diseased foot skin from greater flamingos (Phoenicopterus roseus) living in zoological gardens in Switzerland. When grown on TSA-SB containing polymyxin B, the bacteria isolated from these skin samples formed hyphae, as is typical for Dermatophilus congolensis , but these bacteria were non-haemolytic. The closest relatives based on 16S rRNA gene sequences were the two members of the genus Arsenicicoccus , Arsenicicoccus bolidensis and Arsenicicoccus piscis . A representative of the isolated strains shared 34.3 % DNA–DNA relatedness with the type strain of A. bolidensis , 32.3 % with the type strain of A. piscis and 34.5 % with the type strain of D. congolensis , demonstrating that these strains do not belong to any of these species. The phenotypic characteristics differed from those of members of the genus Arsenicicoccus as well as from those of D. congolensis . The G+C content of strain KM 894/11T was 71.6 mol%. The most abundant fatty acids were iso-C15 : 0, summed feature 3 (including C16 : 1ω7c and/or iso-C15 : 0 2-OH) and C18 : 1ω9c. MK-8(H4) was the predominant menaquinone. Cell-wall structure analysis revealed that the peptidoglycan type was A3γ ll-Dpm–Gly (type A41.1). Based on genotypic and chemotaxonomic characteristics, the isolated strains represent a novel species within the genus Arsenicicoccus , for which the name Arsenicicoccus dermatophilus sp. nov. is proposed. The type strain is KM 894/11T ( = DSM 25571T = CCUG 62181T = CCOS 690T), and strain KM 1/12 ( = DSM 25572 = CCUG 62182 = CCOS 691) is a reference strain.

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The open pan-genome architecture and virulence landscape of Mycobacterium bovis

Microbial Genomics ◽

10.1099/mgen.0.000664 ◽

2021 ◽

Vol 7 (10) ◽

Author(s):

Ana C. Reis ◽

Mónica V. Cunha

Keyword(s):

Mycobacterium Bovis ◽

Type Species ◽

Genome Structure ◽

Genome Architecture ◽

Evolutionary Potential ◽

Content Type ◽

Accessory Genome ◽

Pan Genome ◽

Link Type ◽

Clusters Of Orthologous Groups

Animal tuberculosis (TB) is an emergent disease caused by Mycobacterium bovis , one of the animal-adapted ecotypes of the Mycobacterium tuberculosis complex (MTC). In this work, whole-genome comparative analyses of 70 M . bovis were performed to gain insights into the pan-genome architecture. The comparison across M. bovis predicted genome composition enabled clustering into the core- and accessory-genome components, with 2736 CDS for the former, while the accessory moiety included 3897 CDS, of which 2656 are restricted to one/two genomes only. These analyses predicted an open pan-genome architecture, with an average of 32 CDS added by each genome and show the diversification of discrete M. bovis subpopulations supported by both core- and accessory-genome components. The functional annotation of the pan-genome classified each CDS into one or several COG (Clusters of Orthologous Groups) categories, revealing ‘transcription’ (total average CDSs, n=258), ‘lipid metabolism and transport’ (n=242), ‘energy production and conversion’ (n=214) and ‘unknown function’ (n=876) as the most represented. The closer analysis of polymorphisms in virulence-related genes in a restrict group of M. bovis from a multi-host system enabled the identification of clade-monomorphic non-synonymous SNPs, illustrating clade-specific virulence landscapes and correlating with disease severity. This first comparative pan-genome study of a diverse collection of M. bovis encompassing all clonal complexes indicates a high percentage of accessory genes and denotes an open, dynamic non-conservative pan-genome structure, with high evolutionary potential, defying the canons of MTC biology. Furthermore, it shows that M. bovis can shape its virulence repertoire, either by acquisition and loss of genes or by SNP-based diversification, likely towards host immune evasion, adaptation and persistence.

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Mannheimia pernigra sp. nov., isolated from bovine respiratory tract

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.004643 ◽

2021 ◽

Author(s):

Peter Kuhnert ◽

Isabelle Brodard ◽

Lutz Schönecker ◽

Hatice Akarsu ◽

Henrik Christensen ◽

...

Keyword(s):

Type Species ◽

Reference Strain ◽

New Taxon ◽

Species Status ◽

Content Type ◽

Identification Schemes ◽

Link Type ◽

Distinct Cluster ◽

Veal Calf ◽

Phenotypic Methods

Over a period of 1 year, 270 isolates identified as Taxon 39 of Bisgaard were obtained from the nasopharynx of veal calves at 11 epidemiologically independent Swiss fattening farms. Two isolates from each farm and the Australian Taxon 39 reference strain BNO311 were further characterized by genetic and phenotypic methods. Phylogenetic analysis of 16S rRNA and recN gene sequences placed the isolates in a single, distinct cluster within the genus Mannheimia . As to the rpoB gene, most isolates clustered together, but four strains formed a separate cluster close to Mannheimia varigena . Genome sequence analysis of isolates from both rpoB clusters confirmed their species status, with an average nucleotide identity (ANI) >98.9 % between isolates and <84 % to the closest species, M. varigena . Based upon whole genome sequences, the G+C content was determined as 39.1 mol%. Similarly, analysis of MALDI-TOF MS reference spectra clustered the isolates clearly separated from the other Mannheimia species, making this the method of choice for identification. In addition, numerous biochemical markers based on classical as well as commercial identification schemes were determined, allowing separation from other Mannheimia species and identification of the new taxon. Major fatty acids for strain 17CN0883T are C14 : 0, C16 : 0, C16 : 1 ω7c and C18 : 1 ω7c. Major respiratory quinones are ubiquinone-7 and ubiquinone-8. We propose the name Mannheimia pernigra sp. nov. for former Taxon 39 of Bisgaard. The type strain is 17CN0883T (=CCUG 74657T=DSM 111153T) isolated from a veal calf in Switzerland.

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