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 3 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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Antimicrobial Resistance and Genomic Characterization of Salmonella Isolated from Pigeons in China

Zhang,

Lu,

Zhao

et al. 2024

Transboundary and Emerging Diseases

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Salmonellosis is one of the important bacterial infectious diseases affecting the health of pigeons. Heretofore, the epidemiological characteristics of Salmonella in pigeon populations in China remain largely unclear. The present study investigated the antimicrobial resistance and genomic characteristics of Salmonella isolates in pigeons in different regions of China from 2022 to 2023. Thirty-two Salmonella isolates were collected and subjected to 24 different antimicrobial agents, representing nine categories. The results showed that these isolates were highly resistant to cefazolin (100%), gentamicin (100%), tobramycin (100%), and amikacin (100%). Three or more types of antimicrobial resistance were present in 90.62% of the isolates, indicating multidrug resistance. Furthermore, using whole genome sequencing technology, we analyzed the profiles of serotypes, multilocus sequence typing, virulence genes, antimicrobial resistance genes, and plasmid replicons and constructed phylogenetic genomics to determine the epidemiological correlation among these isolates. All strains belonged to Salmonella Typhimurium var. Copenhagen and exhibited five antimicrobial resistance genes and more than 150 Salmonella virulence genes. Moreover, each isolate contained both the IncFIB(S) and IncFII(S) plasmids. In addition, phylogenetic analysis showed that all isolates were very close to each other, and isolates from the same region clustered in the same branch. Overall, our findings provide the first evidence for the epidemiological characteristics of Salmonella in pigeons of China, highlighting the importance of preventing salmonellosis in pigeons.

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

Cited by 3 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

Antimicrobial Resistance and Genomic Characterization of Salmonella Isolated from Pigeons in China

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