Genomes-based MLST, cgMLST, wgMLST and SNP analysis of Salmonella Typhimurium from animals and humans

Yan, Shigan; Jiang, Zhaoxu; Zhang, Wencheng; Liu, Zhenhai; Dong, Xiaohu; Li, Donghui; Liu, Zijun; Li, Chengyu; Liu, Xu; Zhu, Liping

doi:10.1016/j.cimid.2023.101973

Cited by 7 publications

(1 citation statement)

References 44 publications

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“…Cluster 3 is the most diverse, comprising eleven different cgST Cplx isolates, belonging to phylogroups A, B2, D, E, F, and G from human isolates. The only isolate of phylogroup A, analyzed under the cgMLST scheme, belongs to a different cgST Cplx than the isolates of cluster 1, showing a higher level of discrimination of this scheme [52,53]. Therefore, the swine E. coli isolates analyzed in this study were not grouped into phylogroups other than A and B1 [40].…”

Section: Discussionmentioning

confidence: 78%

Genomic Profiling of Multidrug-Resistant Swine Escherichia coli and Clonal Relationship to Human Isolates in Peru

Alvarez,

Carhuaricra,

Palomino-Farfan

et al. 2023

Antibiotics

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The misuse of antibiotics is accelerating antimicrobial resistance (AMR) in Escherichia coli isolated from farm animals. The genomes of ten multidrug-resistant (MDR) E. coli isolates from pigs were analyzed to determine their sequence types, serotypes, virulence, and AMR genes (ARGs). Additionally, the relationship was evaluated adding all the available genomes of Peruvian E. coli from humans using the cgMLST + HierCC scheme. Two aEPEC O186:H11-ST29 were identified, of which H11 and ST29 are reported in aEPEC isolates from different sources. An isolate ETEC-O149:H10-ST100 was identified, considered a high-risk clone that is frequently reported in different countries as a cause of diarrhea in piglets. One ExPEC O101:H11-ST167 was identified, for which ST167 is an international high-risk clone related to urinary infections in humans. We identified many ARGs, including extended-spectrum β-lactamase genes, and one ETEC harboring the mcr-1 gene. CgMLST + HierCC analysis differentiated three clusters, and in two, the human isolates were grouped with those of swine in the same cluster. We observed that Peruvian swine MDR E. coli cluster with Peruvian E. coli isolates from healthy humans and from clinical cases, which is of great public health concern and evidence that AMR surveillance should be strengthened based on the One Health approach.

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Section: Discussionmentioning

confidence: 78%

Genomic Profiling of Multidrug-Resistant Swine Escherichia coli and Clonal Relationship to Human Isolates in Peru

Alvarez,

Carhuaricra,

Palomino-Farfan

et al. 2023

Antibiotics

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A secure visualization platform for pathogenic genome analysis with an accurate reference database

Fan,

Guo,

Zhang

et al. 2024

Biosafety and Health

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Origin tracking of Brucella strain B. melitensics bv.3 ARQ-070 using biochemical and genomic studies

Ta,

Zuo,

Gao

et al. 2024

FEMS Microbiology Letters

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Objective To conduct an origin tracking and genomic study of the Brucella strain B. melitensis bv.3 ARQ-070, with the aim of addressing the challenges posed by the highly conserved genome of Brucella to conventional typing methods and to gain an understanding of the geographic distribution and interspecies transmission of this pathogen in China. Methods Differentiation and genotyping were established via biochemical profiles and polymerase chain reaction (AMOS-PCR). Illumina MiSeq® was applied to sequence the Brucella isolates. Using multilocus sequence typing (MLST) multilocus sequence typing and Fisher's exact test was used for the KEGG enrichment analysis of differential genes. Differential gene protein PPI network analysis was conducted using the STRING database and visualisation was performed using. Results According to the final identification results of an A/M serum agglutination test. ARQ-070 was identified as the No. 3 white spirulina biological variety, and mM was identified as the No. 1 white Spirulina biological variety. The genetic information of this strain is very close to that of the M5 vaccine strain, suggesting possible vaccine-escape infection. In the comparative genomics analysis with B. melitensis bv.1 16 M, the main differences between the B. melitensis strains were found to be concentrated in the genes related to amino acid metabolism and environmental perception. A base mutation was found in the Brucella gene virB9, which is associated with the key virulence factor of the type IV secretion system (T4SS), but this mutation did not lead to changes in the protein's tertiary structure, and the strain did not lose its infectivity. Conclusion The study discovered a base mutation in the virB9 gene of Brucella, which is linked to T4SS but does not affect the protein's structure or the strain's infectivity. This mutation could influence public health approaches to detecting and preventing Brucella transmission. Future research aims to analyse a wider range of Brucella strains for a deeper understanding of their epidemiology.

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Genomes-based MLST, cgMLST, wgMLST and SNP analysis of Salmonella Typhimurium from animals and humans

Cited by 7 publications

References 44 publications

Genomic Profiling of Multidrug-Resistant Swine Escherichia coli and Clonal Relationship to Human Isolates in Peru

Genomic Profiling of Multidrug-Resistant Swine Escherichia coli and Clonal Relationship to Human Isolates in Peru

A secure visualization platform for pathogenic genome analysis with an accurate reference database

Origin tracking of Brucella strain B. melitensics bv.3 ARQ-070 using biochemical and genomic studies

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