Elucidation of global and national genomic epidemiology of Salmonella enterica serovar Enteritidis through multilevel genome typing

Luo, Lijuan; Payne, Michael; Kaur, Sandeep; Hu, Dalong; Cheney, Liam; Octavia, Sophie; Wang, Qinning; Tanaka, Mark M.; Sintchenko, Vitali; Lan, Ruiting

doi:10.1099/mgen.0.000605

Cited by 11 publications

(63 citation statements)

References 69 publications

(184 reference statements)

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“…Examples of host selection pressure narrowing genomic variability for S. enterica include the relative clonality of egg-contaminating S. enteritidis in comparison to other prevalent foodborne serotypes and clonality of the typhoidal S. enterica subspecies I of humans, namely S. typhi and S. paratyphi . In these instances, WGS, or approaches based on knowledge of WGS, is required to detect and characterize SNPs associated with evolutionary trends [ 30 , 31 , 32 , 33 , 34 ].…”

Section: Speciation As An Inherent Contributor To Salmonell...mentioning

confidence: 99%

Through the Looking Glass: Genome, Phenome, and Interactome of Salmonella enterica

Guard

2022

Pathogens

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This review revisits previous concepts on biological phenomenon contributing to the success of the Salmonella enterica subspecies I as a pathogen and expands upon them to include progress in epidemiology based on whole genome sequencing (WGS). Discussion goes beyond epidemiological uses of WGS to consider how phenotype, which is the biological character of an organism, can be correlated with its genotype to develop a knowledge of the interactome. Deciphering genome interactions with proteins, the impact of metabolic flux, epigenetic modifications, and other complex biochemical processes will lead to new therapeutics, control measures, environmental remediations, and improved design of vaccines.

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Section: Speciation As An Inherent Contributor To Salmonell...mentioning

confidence: 99%

Through the Looking Glass: Genome, Phenome, and Interactome of Salmonella enterica

Guard

2022

Pathogens

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“…We previously identified MDR associated STs within which there was a high proportion of predicted MDR genomes (>= 80%) at different MGT levels [17] S5). Except for IncFII(S) and IncFIB(S), more than 85% of the isolates with IncX1 (IncX1_1 or IncX1_4) plasmid types were found to carry AMR genes (Figure S5).…”

Section: Presence Of Amr Genes In Australian S Enteritidismentioning

confidence: 99%

“…A unified global genomic surveillance system would contribute to tracking and controlling the spread of outbreak clusters and MDR clones in Australia. Multilevel genome typing (MGT) for S. Enteritidis [17] is a recently defined and publicly accessible whole genome sequencing (WGS) typing scheme (https://mgtdb.unsw.edu.au/enteritidis/). The key benefit of MGT is the provision of multiple resolution typing levels with sequence types (STs) assigned at each level [25].…”

Section: Introductionmentioning

confidence: 99%

“…The exact comparison based STs can avoid the drawbacks of clusters merging using the single linkage clustering algorithm, which enhances the stability of the ST assignments [25]. The STs from different resolution levels have been found useful in investigating the epidemiological distribution of S. Enteritidis and tracking MDR clones [17]. Moreover, the core genome multilocus sequence typing (cgMLST) level MGT9, which includes the serovar core genes and core intergenic regions, offered the highest resolution of typing for outbreak investigations [17,26].…”

Section: Introductionmentioning

confidence: 99%

“…The global S. Enteritidis MGT database [17] processes new publicly available genomes and metadata regularly making it useful for national and international surveillance of S. Enteritidis. In this study, 573 newly sequenced genomes from two states of Australia, Queensland (QLD) and New South Wales (NSW) were investigated using S. Enteritidis MGT.…”

Section: Introductionmentioning

confidence: 99%

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Genomic epidemiology and multilevel genome typing of Australian Salmonella enterica serovar Enteritidis

Luo

Payne

Wang

et al. 2022

Preprint

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In Australia, Salmonella enterica serovar Enteritidis is the second prevalent cause of salmonellosis. It is mainly travel-related with only a few local outbreaks reported. However, a large-scale local outbreak occurred in 2018. This study aimed to characterise the genomic features of Australian S. Enteritidis and compare them with international strains using multilevel genome typing (MGT). A total of 573 S. Enteritidis isolates from two Australian states across two consecutive years were analysed using the S. Enteritidis MGT scheme and database (MGTdb) - which contained 40,390 publicly available genomes from 99 countries. The Australian S. Enteritidis strains were divided into three phylogenetic clades (A, B and C). Clade A and C represented 16.4% and 3.4% of the total isolates and were of local origin. Clade B accounted for 80.1% of the isolates which belonged to seven previously defined lineages but was dominated by the global epidemic lineage (MGT4-CC1). At MGT5 level, three out of five top sequence types (STs) in Australia were also top STs in Asia, suggesting that the Australian S. Enteritidis may be epidemiologically linked with Asian strains. The 2018 egg-associated large local outbreak was caused by a recently defined clade B lineage prevalent in Europe and was closely related but not directly linked to three international isolates from Europe. Additionally, antimicrobial-resistant genes were only found in Australian clade B isolates, with a predicted multidrug resistance (MDR) rate of 11.9%. Over half (55.8%) of the MDR isolates belonged to 10 MDR-associated MGT-STs, which were also frequent in Asian S. Enteritidis. IncX1 plasmids were frequently present in the Australian MDR isolates. Overall, this study investigated the genomic epidemiology and the first large outbreak of S. Enteritidis in Australia using MGT. The open MGT platform enables standardised and sharable nomenclature that can be effectively applied to public health agencies for unified surveillance of S. Enteritidis nationally and globally.

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Geography shapes the genomics and antimicrobial resistance of Salmonella enterica Serovar Enteritidis isolated from humans

Cao

Zhao

Kuang

et al. 2023

Sci Rep

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Multidrug-resistant (MDR) Salmonella has been a long-standing challenge in public health and food safety. The prevalence of MDR S. Enteritidis, especially isolated from humans, in China is significantly higher than those from the U.S. and other countries. A dataset of 197 S. Enteritidis genomes, including 16 sequenced clinical isolates from China and 181 downloaded genomes of human isolates from the U.S., Europe, and Africa, was analyzed for genomic diversity, virulence potential, and antimicrobial resistance (AMR). Phylogenomic analyses identified four major well-supported clades (I–IV). While AMR genotype in the majority of isolates in clades I and IV displayed as pan-susceptible, 81.8% (9/11) and 22.4% (13/58) of isolates in clades III and II were MDR, respectively. It is noted that 77% (10/13) of MDR isolates in clade II were from China. The most common antimicrobial resistance genes (ARGs) carried by the Chinese isolates were aph(3′)-IIa, blaCTX-M-55, and blaTEM-1B, whereas blaTEM-1B, sul1, sul2, drfA7, aph(3")-Ib/strA, and aph(6)-Id/strB were most often identified in those from Africa (clade III). Among the 14 plasmid types identified, IncX1 and IncFII(pHN7A8) were found exclusively in the Chinese MDR isolates, while IncQ1 was highly associated with the African MDR isolates. The spvRABCD virulence operon was present in 94.9% (187/197) of isolates tested and was highly associated with both the IncF (IncFII and IncFIB) plasmids. In addition, phylogenetic differences in distribution of Salmonella pathogenicity islands (SPIs), prophages and other accessory genes were also noted. Taken together, these findings provide new insights into the molecular mechanisms underpinning diversification of MDR S. Enteritidis.

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Elucidation of global and national genomic epidemiology of Salmonella enterica serovar Enteritidis through multilevel genome typing

Cited by 11 publications

References 69 publications

Through the Looking Glass: Genome, Phenome, and Interactome of Salmonella enterica

Through the Looking Glass: Genome, Phenome, and Interactome of Salmonella enterica

Genomic epidemiology and multilevel genome typing of Australian Salmonella enterica serovar Enteritidis

Geography shapes the genomics and antimicrobial resistance of Salmonella enterica Serovar Enteritidis isolated from humans

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