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

Yan, Shigan; Zhang, Wencheng; Li, Chengyu; Xu, Li; Zhu, Liping; Chen, Leilei; Yang, Baowei

doi:10.3389/fmicb.2021.688614

Cited by 33 publications

(34 citation statements)

References 57 publications

(71 reference statements)

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“…In a recent study showing 250 S . enterica were isolated from different sources covering nine provinces of China from 2004 to 2019, all strains were assigned into 36 serovars and 43 sequence types (STs) ( Yan et al, 2021 ). Antibiotics are used to treat severe Salmonella infections.…”

Section: Introductionmentioning

confidence: 99%

Whole-Genome Sequencing Provides Insight Into Antimicrobial Resistance and Molecular Characteristics of Salmonella From Livestock Meat and Diarrhea Patient in Hanzhong, China

Gu²,

Zhang³

et al. 2022

Front. Microbiol.

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Salmonella is a major zoonotic pathogen, which usually contaminates food resulting in salmonellosis in humans. Exploring the characteristics and origins of Salmonella is essential in formulating prevention and control measures for Salmonella infection. We used slide agglutination, antimicrobial susceptibility testing, and whole-genome sequencing to analyze and compare Salmonella’s phenotype, genotyping diversity, and genetic relatedness from livestock meat and diarrhea patients in Hanzhong, China, from 2018 to 2020. Totally 216 Salmonella enterica isolates were screened from frozen whole chicken carcasses (44.3%, 70/158), frozen raw ground pork (36.2%, 59/163), and diarrhea patients (4.4%, 87/1964). Salmonella Typhimurium was the dominant serotype. Notably, compared with other sources, isolates obtained from frozen whole chicken carcasses showed significant resistance to third-generation cephalosporin and fluoroquinolones (p < 0.05). All strains were assigned into 36 sequence types (STs) and two novel STs, and an excellent consistency was observed between ST and serotype. Genomic data revealed that extended-spectrum β-lactamase genes were responsible for third-generation cephalosporin resistance in 52 Salmonella strains, and the most predominant resistance determinant was blaCTX–M. Furthermore, of the 60 ciprofloxacin-resistant isolates, five single-base mutations in quinolone resistance-determining regions were identified in gyrA or parC, and the plasmid-mediated quinolone resistance gene aac(6’)Ib-cr was most often detected. The cgMLST clusters show that five clusters among four serotypes (including S. Typhimurium, S. London, S. Derby, and S. Agona) cover samples from diarrhea patients and livestock meat pathway isolate, indicating a possibility of cross-host transmission. In conclusion, the livestock meat isolates have a higher level of resistance than diarrhea patients’ isolates and could be an essential source of human Salmonella infection.

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Section: Introductionmentioning

confidence: 99%

Whole-Genome Sequencing Provides Insight Into Antimicrobial Resistance and Molecular Characteristics of Salmonella From Livestock Meat and Diarrhea Patient in Hanzhong, China

Gu²,

Zhang³

et al. 2022

Front. Microbiol.

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“…Although ST40, ST39, and ST682 have been reported to be predominantly associated with swine, a strong link has been suggested between ST71 and poultry based on previous reports and the Enterobase database; these poultry-specific ST71 strains were mainly isolated in Europe, including France and Germany [6][7][8]. In China, ST40 and ST71 were the two main MLST profiles associated with S. Derby [9]. ST40-affiliated strains identified in China were mainly isolated from swine-associated samples, which was consistent with previous findings in Europe and other geographic locations.…”

Section: Introductionmentioning

confidence: 99%

“…In China, ST40 and ST71 were the two main MLST profiles associated with S . Derby [ 9 ]. ST40-affiliated strains identified in China were mainly isolated from swine-associated samples, which was consistent with previous findings in Europe and other geographic locations.…”

Section: Introductionmentioning

confidence: 99%

Prophage-mediated genome differentiation of the Salmonella Derby ST71 population

Wang

et al. 2022

Microbial Genomics

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Although Salmonella Derby ST71 strains have been recognized as poultry-specific by previous studies, multiple swine-associated S. Derby ST71 strains were identified in this long-term, multi-site epidemic study. Here, 15 representative swine-associated S. Derby ST71 strains were sequenced and compared with 65 (one swine-associated and 64 poultry-associated) S. Derby ST71 strains available in the NCBI database at a pangenomic level through comparative genomics analysis to identify genomic features related to the differentiation of swine-associated strains and previously reported poultry-associated strains. The distribution patterns of known Salmonella pathogenicity islands (SPIs) and virulence factor (VF) encoding genes were not capable of differentiating between the two strain groups. The results demonstrated that the S. Derby ST71 population harbours an open pan-genome, and swine-associated ST71 strains contain many more genes than the poultry-associated strains, mainly attributed to the prophage sequence contents in the genomes. The numbers of prophage sequences identified in the swine-associated strains were higher than those in the poultry-associated strains. Prophages specifically harboured by the swine-associated strains were found to contain genes that facilitate niche adaptation for the bacterial hosts. Gene deletion experiments revealed that the dam gene specifically present in the prophage of the swine-associated strains is important for S. Derby to adhere onto the host cells. This study provides novel insights into the roles of prophages during the genome differentiation of Salmonella .

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“…Multi-locus sequence typing (MLST) was developed in 1998 and provided high reproducibility in the characterization of isolates, enabling to identify the same clones within bacterial populations [ 2 ]. However, it lacks discrimination at the strain level [ 3 – 5 ]. With the advances in whole genome sequencing (WGS) [ 6 – 9 ], core genome MLST (cgMLST) tools and schemes have been proposed for several bacterial pathogens, expanding the advantages of MLST at the genomic scale and providing a high level of bacterial strain discrimination.…”

Section: Introductionmentioning

confidence: 99%

In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes

et al. 2022

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Background Whole genome sequencing analyzed by core genome multi-locus sequence typing (cgMLST) is widely used in surveillance of the pathogenic bacteria Listeria monocytogenes. Given the heterogeneity of available bioinformatics tools to define cgMLST alleles, our aim was to identify parameters influencing the precision of cgMLST profiles. Methods We used three L. monocytogenes reference genomes from different phylogenetic lineages and assessed the impact of in vitro (i.e. tested genomes, successive platings, replicates of DNA extraction and sequencing) and in silico parameters (i.e. targeted depth of coverage, depth of coverage, breadth of coverage, assembly metrics, cgMLST workflows, cgMLST completeness) on cgMLST precision made of 1748 core loci. Six cgMLST workflows were tested, comprising assembly-based (BIGSdb, INNUENDO, GENPAT, SeqSphere and BioNumerics) and assembly-free (i.e. kmer-based MentaLiST) allele callers. Principal component analyses and generalized linear models were used to identify the most impactful parameters on cgMLST precision. Results The isolate’s genetic background, cgMLST workflows, cgMLST completeness, as well as depth and breadth of coverage were the parameters that impacted most on cgMLST precision (i.e. identical alleles against reference circular genomes). All workflows performed well at ≥40X of depth of coverage, with high loci detection (> 99.54% for all, except for BioNumerics with 97.78%) and showed consistent cluster definitions using the reference cut-off of ≤7 allele differences. Conclusions This highlights that bioinformatics workflows dedicated to cgMLST allele calling are largely robust when paired-end reads are of high quality and when the sequencing depth is ≥40X.

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

Cited by 33 publications

References 57 publications

Whole-Genome Sequencing Provides Insight Into Antimicrobial Resistance and Molecular Characteristics of Salmonella From Livestock Meat and Diarrhea Patient in Hanzhong, China

Whole-Genome Sequencing Provides Insight Into Antimicrobial Resistance and Molecular Characteristics of Salmonella From Livestock Meat and Diarrhea Patient in Hanzhong, China

Prophage-mediated genome differentiation of the Salmonella Derby ST71 population

In vitro and in silico parameters for precise cgMLST typing of Listeria monocytogenes

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