Variation among human, veterinary and environmental Mycobacterium chelonae-abscessus complex isolates observed using core genome phylogenomic analysis, targeted gene comparison, and anti-microbial susceptibility patterns

The genus Rhodococcus exhibits great potential for bioremediation applications due to its huge metabolic diversity, including biotransformation of aromatic and aliphatic compounds. Comparative genomic studies of this genus are limited to a small number of genomes, while the high number of sequenced strains to date could provide more information about the Rhodococcus diversity. Phylogenomic analysis of 327 Rhodococcus genomes and clustering of intergenomic distances identified 42 phylogenomic groups and 83 species-level clusters. Rarefaction models show that these numbers are likely to increase as new Rhodococcus strains are sequenced. The Rhodococcus genus possesses a small “hard” core genome consisting of 381 orthologous groups (OGs), while a “soft” core genome of 1253 OGs is reached with 99.16% of the genomes. Models of sequentially randomly added genomes show that a small number of genomes are enough to explain most of the shared diversity of the Rhodococcus strains, while the “open” pangenome and strain-specific genome evidence that the diversity of the genus will increase, as new genomes still add more OGs to the whole genomic set. Most rhodococci possess genes involved in the degradation of aliphatic and aromatic compounds, while short-chain alkane degradation is restricted to a certain number of groups, among which a specific particulate methane monooxygenase (pMMO) is only found in Rhodococcus sp. WAY2. The analysis of Rieske 2Fe-2S dioxygenases among rhodococci genomes revealed that most of these enzymes remain uncharacterized.

Download Full-text

A Mesophilic Aeromonas salmonicida Strain Isolated from an Unsuspected Host, the Migratory Bird Pied Avocet

Microorganisms ◽

10.3390/microorganisms7120592 ◽

2019 ◽

Vol 7 (12) ◽

pp. 592 ◽

Cited By ~ 2

Author(s):

Antony T. Vincent ◽

Alex Bernatchez ◽

Joachim Frey ◽

Steve J. Charette

Keyword(s):

Core Genome ◽

Growth Curves ◽

Migratory Bird ◽

Aeromonas Salmonicida ◽

The Body ◽

Phylogenomic Analysis ◽

Type Three Secretion System ◽

Genes Encoding ◽

Surrogate Host ◽

Type Three Secretion

Aeromonas salmonicida is a Gram-negative bacterium, known as a fish pathogen since its discovery. Although the species was initially considered psychrophilic, a mesophilic subspecies (pectinolytica) and many other mesophilic strains still not attributed to subspecies have been described in the last two decades. These mesophilic strains were sampled from various sources, including humans, and some of them are known to be pathogenic. In this study, we describe a strain, JF2480, which was isolated from the spleen, and also found the kidney and liver of a dead pied avocet (Recurvirostra avosetta), a type of migratory bird inhabiting aquatic environments. A core genome phylogenomic analysis suggests that JF2480 is taxonomically distant from other known A. salmonicida subspecies. The genome sequence confirms that the strain possesses key virulence genes that are present in the typical A. salmonicida psychrophilic subspecies, with the exception of the genes encoding the type three secretion system (T3SS). Bacterial virulence assays conducted on the surrogate host Dictyostelium discoideum amoeba confirmed that the strain is virulent despite the lack of T3SS. Bacterial growth curves showed that strain JF2480 grow well at 40 °C, the body temperature of the pied avocet, and even faster at 41 °C, compared to other mesophilic strains. Discovery of this strain further demonstrates the extent of the phylogenomic tree of this species. This study also suggests that A. salmonicida can infect a wider array of hosts than previously suspected and that we need to rethink the way we perceive A. salmonicida’s natural environment.

Download Full-text

Finegoldia magna Isolated from Orthopedic Joint Implant-Associated Infections

Journal of Clinical Microbiology ◽

10.1128/jcm.00866-17 ◽

2017 ◽

Vol 55 (11) ◽

pp. 3283-3291 ◽

Cited By ~ 5

Author(s):

Bo Söderquist ◽

Sanna Björklund ◽

Bengt Hellmark ◽

Anders Jensen ◽

Holger Brüggemann

Keyword(s):

Surgical Treatment ◽

Core Genome ◽

Phylogenomic Analysis ◽

Orthopedic Implant ◽

Nucleotide Polymorphisms ◽

Gram Positive ◽

Content Type ◽

Flight Mass Spectrometry ◽

Joint Implant

ABSTRACTThe anaerobic Gram-positive coccusFinegoldia magnais a rare cause of infections of bone and joints. The aim of this study was to describe the microbiological and clinical characteristics of orthopedic implant-associated infections caused byF. magna. We retrospectively analyzed samples consisting of anaerobic Gram-positive cocci and samples already identified asF. magnafrom patients with orthopedic infections. The isolates found were determined to the species level using matrix-assisted laser desorption ionization–time of flight mass spectrometry (MALDI-TOF MS). The antibiotic susceptibility pattern was determined by Etest. Whole-genome sequencing (WGS) was performed. Clinical data were extracted from each patient's journal. In nine patients, orthopedic joint implant-associated infections were identified as being caused byF. magna. The isolates were susceptible to most of the antibiotics tested, with the exception of rifampin and moxifloxacin in a few cases. Five of the nine infections were monomicrobial. The most common antibiotic used to treat the infection was penicillin V, but five of the nine patients received a combination of antibiotics. Eight patients underwent surgical treatment, with extraction of the implant performed in seven cases and reimplantation in only two cases. The WGS showed a relatively small core genome, with 126,647 single nucleotide polymorphisms identified within the core genome. A phylogenomic analysis revealed that the isolates clustered into two distinct clades. Orthopedic implant-associated infections caused byF. magnaare rare, but the bacteria are generally susceptible to antibiotics. Despite this, surgical treatment combined with long-term antibiotics is often necessary. The WGS analysis revealed a high heterogeneity and suggested the existence of at least two differentFinegoldiaspecies.

Download Full-text

Clinical significance, biochemical features, and susceptibility patterns of sporadic isolates of the Mycobacterium chelonae-like organism.

Journal of Clinical Microbiology ◽

10.1128/jcm.31.12.3231-3239.1993 ◽

1993 ◽

Vol 31 (12) ◽

pp. 3231-3239 ◽

Cited By ~ 63

Author(s):

R J Wallace ◽

V A Silcox ◽

M Tsukamura ◽

B A Brown ◽

J O Kilburn ◽

...

Keyword(s):

Clinical Significance ◽

Mycobacterium Chelonae ◽

Susceptibility Patterns ◽

Biochemical Features

Download Full-text

Phylogenomic analysis shows that ‘Bacillus vanillea’ is a later heterotypic synonym of Bacillus siamensis

INTERNATIONAL JOURNAL OF SYSTEMATIC AND EVOLUTIONARY MICROBIOLOGY ◽

10.1099/ijsem.0.000444 ◽

2015 ◽

Vol 65 (Pt_10) ◽

pp. 3507-3510 ◽

Cited By ~ 16

Author(s):

Christopher A. Dunlap

Keyword(s):

Dna Hybridization ◽

Core Genome ◽

Phylogenetic Analyses ◽

Draft Genome ◽

Genomic Analysis ◽

Comparative Genomic ◽

Phylogenomic Analysis ◽

Sequencing Analysis ◽

Emended Description ◽

Type Strains

‘Bacillus vanillea’ XY18 ( = CGMCC 8629 = NCCB 100507) was isolated from cured vanilla beans and involved in the formation of vanilla aroma compounds. A draft genome of this strain was assembled and yielded a length of 3.71 Mbp with a DNA G+C content of 46.3 mol%. Comparative genomic analysis with its nearest relatives showed only minor differences between this strain and the genome of the Bacillus siamensis KCTC 13613T ( = BCC 22614T = KACC 16244T), with a calculated DNA–DNA hybridization (DDH) value of 91.2 % and an average nucleotide identity (ANI) of 98.9 %. This DDH value is well above the recommended 70 % threshold for species delineation, as well as the ANI threshold of 95 %. In addition, the results of morphological, physiological, chemotaxonomic and phylogenetic analyses indicate that the type strains of these two taxa are highly similar with phenotype coherence. A core genome multi-locus sequencing analysis was conducted for the strains and the results show that ‘Bacillus vanillea’ XY18 clusters closely to the type strain of Bacillus siamensis. Therefore, it is proposed that the species ‘Bacillus vanillea’ XY18 ( = CGMCC 8629 = NCCB 100507) should be reclassified as a later heterotypic synonym of Bacillus siamensis KCTC 13613T ( = BCC 22614T = KACC 16244T). An emended description of Bacillus siamensis is provided.

Download Full-text

Phylogenomic Investigation of IncI1-Iγ Plasmids Harboring blaCMY-2 and blaSHV-12 in Salmonella enterica and Escherichia coli in Multiple Countries

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.02546-18 ◽

2019 ◽

Vol 63 (7) ◽

Cited By ~ 4

Author(s):

Luis Ricardo Castellanos ◽

Linda van der Graaf-van Bloois ◽

Pilar Donado-Godoy ◽

Dik J. Mevius ◽

Jaap A. Wagenaar ◽

...

Keyword(s):

Escherichia Coli ◽

Salmonella Enterica ◽

Core Genome ◽

Common Ancestor ◽

Phylogenomic Analysis ◽

Evolutionary Relatedness ◽

Sequence Types

ABSTRACT The objective of this study was to elucidate the genetic and evolutionary relatedness of blaCMY-2- and blaSHV-12-carrying IncI1-Iγ plasmids. Phylogenomic analysis based on core genome alignments and gene presence/absence was performed for different IncI1-Iγ sequence types (STs). Most IncI1-Iγ/ST12 and IncI1-Iγ/ST231 plasmids had near-identical core genomes. The data suggest that widely occurring blaCMY-2-carrying IncI1-Iγ/ST12 plasmids originate from a common ancestor. In contrast, blaSHV-12 was inserted independently into different IncI1-Iγ/ST231-related plasmids.

Download Full-text

Phylogenomic analysis for Campylobacter fetus ocurring in Argentina

Veterinary World ◽

10.14202/vetworld.2021.1165-1179 ◽

2021 ◽

pp. 1165-1179

Author(s):

Pablo Daniel Farace ◽

José Matías Irazoqui ◽

Claudia Graciela Morsella ◽

Juan Agustín García ◽

María Alejandra Méndez ◽

...

Keyword(s):

Phylogenetic Analysis ◽

Core Genome ◽

Global Analysis ◽

Local Maximum ◽

Economic Losses ◽

Phylogenomic Analysis ◽

Local Strains ◽

Campylobacter Fetus ◽

New Variant ◽

Pampas Region

Background and Aim: Campylobacter fetus is one of the most important pathogens that severely affects livestock industry worldwide. C. fetus mediated bovine genital campylobacteriosis infection in cattle has been associated with significant economic losses in livestock production in the Pampas region, the most productive area of Argentina. The present study aimed to establish the genomic relationships between C. fetus strains, isolated from the Pampas region, at local and global levels. The study also explored the utility of multi-locus sequence typing (MLST) as a typing technique for C. fetus. Materials and Methods: For pangenome and phylogenetic analysis, whole genome sequences for 34 C. fetus strains, isolated from cattle in Argentina were downloaded from GenBank. A local maximum likelihood (ML) tree was constructed and linked to a Microreact project. In silico analysis based on MLST was used to obtain information regarding sequence type (ST) for each strain. For global phylogenetic analysis, a core genome ML-tree was constructed using genomic dataset for 265 C. fetus strains, isolated from various sources obtained from 20 countries. Results: The local core genome phylogenetic tree analysis described the presence of two major clusters (A and B) and one minor cluster (C). The occurrence of 82% of the strains in these three clusters suggested a clonal population structure for C. fetus. The MLST analysis for the local strains revealed that 31 strains were ST4 type and one strain was ST5 type. In addition, a new variant was identified that was assigned a novel ST, ST70. In the present case, ST4 was homogenously distributed across all the regions and clusters. The global analysis showed that most of the local strains clustered in the phylogenetic groups that comprised exclusively of the strains isolated from Argentina. Interestingly, three strains showed a close genetic relationship with bovine strains obtained from Uruguay and Brazil. The ST5 strain grouped in a distant cluster, with strains obtained from different sources from various geographic locations worldwide. Two local strains clustered in a phylogenetic group comprising intercontinental Campylobacter fetus venerealis strains. Conclusion: The results of the study suggested active movement of animals, probably due to economic trade between different regions of the country as well as with neighboring countries. MLST results were partially concordant with phylogenetic analysis. Thus, this method did not qualify as a reliable subtyping method to assess C. fetus diversity in Argentina. The present study provided a basic platform to conduct future research on C. fetus, both at local and international levels.

Download Full-text

A machine learning-based typing scheme refinement for Listeria monocytogenes core genome multilocus sequence typing with high discriminatory power for common source outbreak tracking

PLoS ONE ◽

10.1371/journal.pone.0260293 ◽

2021 ◽

Vol 16 (11) ◽

pp. e0260293

Author(s):

Yen-Yi Liu ◽

Chih-Chieh Chen

Keyword(s):

Listeria Monocytogenes ◽

Multilocus Sequence Typing ◽

Core Genome ◽

Search Time ◽

Discriminatory Power ◽

Common Source ◽

Whole Genome ◽

Gene Comparison ◽

Typing Methods ◽

Genome Assemblies

Background As whole-genome sequencing for pathogen genomes becomes increasingly popular, the typing methods of gene-by-gene comparison, such as core genome multilocus sequence typing (cgMLST) and whole-genome multilocus sequence typing (wgMLST), are being routinely implemented in molecular epidemiology. However, some intrinsic problems remain. For example, genomic sequences with varying read depths, read lengths, and assemblers influence the genome assemblies, introducing error or missing alleles into the generated allelic profiles. These errors and missing alleles might create “specious discrepancy” among closely related isolates, thus making accurate epidemiological interpretation challenging. In addition, the rapid growth of the cgMLST allelic profile database can cause problems related to storage and maintenance as well as long query search times. Methods We attempted to resolve these issues by decreasing the scheme size to reduce the occurrence of error and missing alleles, alleviate the storage burden, and improve the query search time. The challenge in this approach is maintaining the typing resolution when using fewer loci. We achieved this by using a popular artificial intelligence technique, XGBoost, coupled with Shapley additive explanations for feature selection. Finally, 370 loci from the original 1701 cgMLST loci of Listeria monocytogenes were selected. Results Although the size of the final scheme (LmScheme_370) was approximately 80% lower than that of the original cgMLST scheme, its discriminatory power, tested for 35 outbreaks, was concordant with that of the original cgMLST scheme. Although we used L. monocytogenes as a demonstration in this study, the approach can be applied to other schemes and pathogens. Our findings might help elucidate gene-by-gene–based epidemiology.

Download Full-text