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

2019 ◽  
Vol 63 (7) ◽  
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.

scholarly journals Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility

2021 ◽  
Vol 7 (9) ◽  
Author(s):  
Rebecca J. Hall ◽  
Fiona J. Whelan ◽  
Elizabeth A. Cummins ◽  
Christopher Connor ◽  
Alan McNally ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Complex Network ◽  
Type Species ◽  
Core Genome ◽  
Mobile Genetic Elements ◽  
Dynamic Nature ◽  
Content Type ◽  
Accessory Genome ◽  
The Core ◽  
Sequence Types

The pangenome contains all genes encoded by a species, with the core genome present in all strains and the accessory genome in only a subset. Coincident gene relationships are expected within the accessory genome, where the presence or absence of one gene is influenced by the presence or absence of another. Here, we analysed the accessory genome of an Escherichia coli pangenome consisting of 400 genomes from 20 sequence types to identify genes that display significant co-occurrence or avoidance patterns with one another. We present a complex network of genes that are either found together or that avoid one another more often than would be expected by chance, and show that these relationships vary by lineage. We demonstrate that genes co-occur by function, and that several highly connected gene relationships are linked to mobile genetic elements. We find that genes are more likely to co-occur with, rather than avoid, another gene in the accessory genome. This work furthers our understanding of the dynamic nature of prokaryote pangenomes and implicates both function and mobility as drivers of gene relationships.

scholarly journals Serotyping, MLST, and Core Genome MLST Analysis of Salmonella enterica From Different Sources in China During 2004–2019

2021 ◽  
Vol 12 ◽  
Author(s):  
Shigan Yan ◽  
Wencheng Zhang ◽  
Chengyu Li ◽  
Xu Liu ◽  
Liping Zhu ◽  
...  
Keyword(s):  
Salmonella Enterica ◽  
Core Genome ◽  
Foodborne Pathogen ◽  
Food Poisoning ◽  
Human Infection ◽  
Temporal And Spatial Distribution ◽  
Typing Method ◽  
Bacterial Typing ◽  
Mlst Analysis ◽  
Sequence Types

Salmonella enterica (S. enterica) is an important foodborne pathogen, causing food poisoning and human infection, and critically threatening food safety and public health. Salmonella typing is essential for bacterial identification, tracing, epidemiological investigation, and monitoring. Serotyping and multilocus sequence typing (MLST) analysis are standard bacterial typing methods despite the low resolution. Core genome MLST (cgMLST) is a high-resolution molecular typing method based on whole genomic sequencing for accurate bacterial tracing. We investigated 250 S. enterica isolates from poultry, livestock, food, and human sources in nine provinces of China from 2004 to 2019 using serotyping, MLST, and cgMLST analysis. All S. enterica isolates were divided into 36 serovars using slide agglutination. The major serovars in order were Enteritidis (31 isolates), Typhimurium (29 isolates), Mbandaka (23 isolates), and Indiana (22 isolates). All strains were assigned into 43 sequence types (STs) by MLST. Among them, ST11 (31 isolates) was the primary ST. Besides this, a novel ST, ST8016, was identified, and it was different from ST40 by position 317 C → T in dnaN. Furthermore, these 250 isolates were grouped into 185 cgMLST sequence types (cgSTs) by cgMLST. The major cgST was cgST235530 (11 isolates), and only three cgSTs contained isolates from human and other sources, indicating a possibility of cross-species infection. Phylogenetic analysis indicated that most of the same serovar strains were putatively homologous except Saintpaul and Derby due to their multilineage characteristics. In addition, serovar I 4,[5],12:i:- and Typhimurium isolates have similar genomic relatedness on the phylogenetic tree. In conclusion, we sorted out the phenotyping and genotyping diversity of S. enterica isolates in China during 2004–2019 and clarified the temporal and spatial distribution characteristics of Salmonella from different hosts in China in the recent 16 years. These results greatly supplement Salmonella strain resources, genetic information, and traceability typing data; facilitate the typing, traceability, identification, and genetic evolution analysis of Salmonella; and therefore, improve the level of analysis, monitoring, and controlling of foodborne microorganisms in China.

Uncoupling between core genome and virulome in extraintestinal pathogenic Escherichia coli

2015 ◽  
Vol 61 (9) ◽  
pp. 647-652 ◽  
Author(s):  
Natalia Fernández-Romero ◽  
María Pilar Romero-Gómez ◽  
Marta Mora-Rillo ◽  
Jesús Rodríguez-Baño ◽  
Lorena López-Cerero ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Core Genome ◽  
Virulence Gene ◽  
Bloodstream Infections ◽  
Opportunistic Pathogens ◽  
Single Nucleotide ◽  
The Core ◽  
Gene Profiles ◽  
Pathogenic Escherichia Coli ◽  
Sequence Types

Extraintestinal pathogenic Escherichia coli (ExPEC) are among the most frequently isolated bacterial pathogens in hospitals. They are considered opportunistic pathogens and are found mostly in urinary and bloodstream infections. They are genetically diverse, and many studies have sought associations between genotypes or virulence genes and infection site, severity, or outcome, with varied, often contradictory, results. To understand these difficulties, we have analyzed the diversity patterns in the core genomes and virulomes of more than 500 ExPEC isolates from 5 different collections. The core genome was analyzed using a multilocus sequence type-based single-nucleotide polymorphism (SNP) pyrosequencing approach, while the virulence gene content (the virulome) was studied by polymerase chain reaction detection of 25 representative genes. SNP typing showed a similar population structure in the different collections: half of the isolates belong to a few sequence types (5 to 8), while the other half is composed of a large diversity of sequence types that are found once or twice. Sampling analysis by rarefaction plots of SNP profiles showed saturation curves indicative of a limited diversity. Contrary to this, the virulome shows an extremely high diversity, with almost as many gene profiles as isolates, and linear, nonsaturating, rarefaction plots, even within sequence types. These data show that genetic exchange rates are very heterogeneous along the chromosome, being much higher in the virulome fraction of the genome than in the core genome.

scholarly journals Gene-gene relationships in an Escherichia coli accessory genome are linked to function and mobility

2021 ◽  
Author(s):  
Rebecca J Hall ◽  
Fiona J Whelan ◽  
Elizabeth A Cummins ◽  
Christopher Connor ◽  
Alan McNally ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Complex Network ◽  
Core Genome ◽  
Mobile Genetic Elements ◽  
Dynamic Nature ◽  
Accessory Genome ◽  
Genetic Elements ◽  
The Core ◽  
Sequence Types

The pangenome contains all genes encoded by a species, with the core genome present in all strains and the accessory genome in only a subset. Coincident gene relationships are expected within the accessory genome, where the presence or absence of one gene is influenced by the presence or absence of another. Here, we analysed the accessory genome of an Escherichia coli pangenome consisting of 400 genomes from 20 sequence types to identify genes that display significant co-occurrence or avoidance patterns with one another. We present a complex network of genes that are either found together or that avoid one another more often than would be expected by chance, and show that these relationships vary by lineage. We demonstrate that genes co-occur by function, and that several highly connected gene relationships are linked to mobile genetic elements. We find that genes are more likely to co-occur with, rather than avoid, another gene, suggesting that cooperation is more common than conflict in the accessory genome. This work furthers our understanding of the dynamic nature of prokaryote pangenomes and implicates both function and mobility as drivers of gene relationships.

EFECTO INHIBITORIO DE EXTRACTOS DE Vitex mollis Kunth CONTRA BACTERIAS Y ESPECIES DE Fusarium DE IMPORTANCIA HUMANA Y AGRÍCOLA

2018 ◽  
Vol 41 (4) ◽  
pp. 353-363
Author(s):  
Alberto J. Valencia-Botin ◽  
Melesio Gutiérrez-Lomelí ◽  
Juan A. Morales-Del-Río ◽  
Pedro J. Guerrero-Medina ◽  
Miguel A. Robles-García ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Staphylococcus Aureus ◽  
Salmonella Enterica ◽  
Micrococcus Luteus ◽  
E Coli

Actualmente existe la necesidad de hacer frente al problema de la resistencia a los antibióticos y al uso indiscriminado de fungicidas químicos en la agricultura. El objetivo de este trabajo fue evaluar el efecto inhibitorio de extractos acuosos, metanólicos, acetónicos y hexánicos de hoja y tallo de Vitex mollis Kunth (Lamiaceae) contra diferentes bacterias (Escherichia coli, Micrococcus luteus, Salmonella enterica y Staphylococcus aureus) y especies del hongo Fusarium (F. verticillioides, F. oxysporum, F. tapsinum y F. oxysporum f.sp. lycopersici) de importancia en la salud y en la agricultura, así como determinar su composición química general. Se determinaron las concentraciones inhibitorias mínimas (CIM) de todos los extractos por la técnica de microdilución, excepto del hexánico, que no presentó inhibición en las bacterias estudiadas. S. enterica fue la bacteria que mostró mayor sensibilidad al extracto metanólico de tallo (CIM = 28 μg mL-1), le siguieron M. luteus (CIM = 32 μg mL-1), S. aureus (CIM = 75 μg mL-1) y E. coli (CIM = 80 μg mL- 1). Los extractos metanólicos y acuosos de tallo presentaron mayor porcentaje de inhibición contra los diferentes tipos de Fusarium evaluados por el método de dilución en agar. Los extractos de V. mollis inhibieron a F. verticillioides entre 62 y 91 % con 120 μg mL-1 de extracto. El orden de las especies de hongos inhibidas por los extractos fue: F. verticillioides > F. oxysporum > F. tapsinum > F. oxysporum f.sp. lycopersici. La composición química de las especies se determinó mediante pruebas para fenoles, taninos, flavonoides, triterpenos, alcaloides, cumarinas y saponinas. Ninguno de los extractos presentó alcaloides y saponinas. Los fenoles (37.1 mg EAG/g muestra seca) y flavonoides (26.8 mg EQ/g muestra seca) fueron los compuestos mayoritarios en los extractos metanólicos y acuosos. En conclusión, se requieren cantidades muy pequeñas de extracto para la inhibición de bacterias y de Fusarium; por lo tanto, V. mollis puede ser considerada una fuente de metabolitos para este fin y en la agricultura como control alternativo dentro de un manejo integrado de enfermedades.

scholarly journals Presence of β-Lactamase-producing Enterobacterales and Salmonella Isolates in Marine Mammals

2021 ◽  
Vol 22 (11) ◽  
pp. 5905
Author(s):  
Olivia M. Grünzweil ◽  
Lauren Palmer ◽  
Adriana Cabal ◽  
Michael P. Szostak ◽  
Werner Ruppitsch ◽  
...  
Keyword(s):  
Escherichia Coli ◽  
Marine Mammals ◽  
Virulence Genes ◽  
Multidrug Resistant ◽  
Healthcare Sector ◽  
Whole Genome ◽  
E Coli ◽  
High Prevalence ◽  
Lactamase Gene ◽  
Sequence Types

Marine mammals have been described as sentinels of the health of marine ecosystems. Therefore, the aim of this study was to investigate (i) the presence of extended-spectrum β-lactamase (ESBL)- and AmpC-producing Enterobacterales, which comprise several bacterial families important to the healthcare sector, as well as (ii) the presence of Salmonella in these coastal animals. The antimicrobial resistance pheno- and genotypes, as well as biocide susceptibility of Enterobacterales isolated from stranded marine mammals, were determined prior to their rehabilitation. All E. coli isolates (n = 27) were screened for virulence genes via DNA-based microarray, and twelve selected E. coli isolates were analyzed by whole-genome sequencing. Seventy-one percent of the Enterobacterales isolates exhibited a multidrug-resistant (MDR) pheno- and genotype. The gene blaCMY (n = 51) was the predominant β-lactamase gene. In addition, blaTEM-1 (n = 38), blaSHV-33 (n = 8), blaCTX-M-15 (n = 7), blaOXA-1 (n = 7), blaSHV-11 (n = 3), and blaDHA-1 (n = 2) were detected. The most prevalent non-β-lactamase genes were sul2 (n = 38), strA (n = 34), strB (n = 34), and tet(A) (n = 34). Escherichia coli isolates belonging to the pandemic sequence types (STs) ST38, ST167, and ST648 were identified. Among Salmonella isolates (n = 18), S. Havana was the most prevalent serotype. The present study revealed a high prevalence of MDR bacteria and the presence of pandemic high-risk clones, both of which are indicators of anthropogenic antimicrobial pollution, in marine mammals.

scholarly journals Long-Term Experimental Evolution in Escherichia coli. IV. Targets of Selection and the Specificity of Adaptation

Genetics ◽  
1996 ◽  
Vol 143 (1) ◽  
pp. 15-26 ◽  
Author(s):  
Michael Travisano ◽  
Richard E Lenski
Keyword(s):  
Escherichia Coli ◽  
Experimental Evolution ◽  
Common Ancestor ◽  
The Novel ◽  
Physiological Mechanisms ◽  
Outer Membranes ◽  
Limiting Nutrient ◽  
Novel Environments ◽  
Uptake Mechanisms

Abstract This study investigates the physiological manifestation of adaptive evolutionary change in 12 replicate populations of Escherichia coli that were propagated for 2000 generations in a glucose-limited environment. Representative genotypes from each population were assayed for fitness relative to their common ancestor in the experimental glucose environment and in 11 novel single-nutrient environments. After 2000 generations, the 12 derived genotypes had diverged into at least six distinct phenotypic classes. The nutrients were classified into four groups based upon their uptake physiology. All 12 derived genotypes improved in fitness by similar amounts in the glucose environment, and this pattern of parallel fitness gains was also seen in those novel environments where the limiting nutrient shared uptake mechanisms with glucose. Fitness showed little or no consistent improvement, but much greater genetic variation, in novel environments where the limiting nutrient differed from glucose in its uptake mechanisms. This pattern of fitness variation in the novel nutrient environments suggests that the independently derived genotypes adapted to the glucose environment by similar, but not identical, changes in the physiological mechanisms for moving glucose across both the inner and outer membranes.

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