Genomic Characterization of New Variant of Hydrogen Sulfide (H2S)-Producing Escherichia coli with Multidrug Resistance Properties Carrying the mcr-1 Gene in China

Biswas, Sanket; Elbediwi, Mohammed; Gu, Guimin; Yue, Min

doi:10.3390/antibiotics9020080

Cited by 22 publications

(21 citation statements)

References 26 publications

(35 reference statements)

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“…MS-102-2002). High-throughput genome sequencing was accomplished by the Illumina Miseq sequencing platform, as previously described ( Paudyal et al, 2019 ; Biswas et al, 2020 ; Yu et al, 2020 ).…”

Section: Methodsmentioning

confidence: 99%

Genomic Characterization of mcr-1-carrying Salmonella enterica Serovar 4,[5],12:i:- ST 34 Clone Isolated From Pigs in China

Elbediwi

Pan

et al. 2020

Front. Bioeng. Biotechnol.

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Salmonella enterica serovar 4,[5],12:i:-, so-called Typhimurium monophasic variant, has become one of the most frequently isolated serovars both in humans and in animals all over the world. The increasing prevalence of mcr-1-carrying Salmonella poses significant global health concerns. However, the potential role of Salmonella 4,[5],12:i:-in mcr-1 gene migration through the food chain to the human remains obscure. Here, we investigated 337 Salmonella isolates from apparently healthy finishing pigs, which is rarely studied, obtained from pig farms and slaughterhouses in China. The mcr-1 gene was found in four colistin-resistant S. enterica 4,[5],12:i:-isolates. Notably, all four isolates belonged to sequence type 34 (ST34) with multidrug resistance phenotype. Further genomic sequencing and antimicrobial resistance characterization confirmed that mcr was responsible for the colistin resistance, and the conjugation assay demonstrated that three of four isolates carried mcr-1 in IncHI2 plasmid. Importantly, mcr-1 and class-1 integron were found to co-localize in two strains with IncHI2 plasmid. By collecting all the mcr-1-carrying Typhimurium and monophasic variant strains across the food chain (farm animals, animal-origin food, and humans), our phylogenomic analysis of available 66 genomes, including four strains in this study, demonstrated an independent phylogenetic cluster of all eight Chinese swine-originated isolates and one human isolate. Together, this study provides direct evidence for clonal and pork-borne transmission of mcr-1 by Salmonella 4,[5],12:i:-ST34 in China and highlighted a domestication pathway by acquisition of additional antimicrobial resistance determinants in Chinese ST34 isolates.

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Section: Methodsmentioning

confidence: 99%

Genomic Characterization of mcr-1-carrying Salmonella enterica Serovar 4,[5],12:i:- ST 34 Clone Isolated From Pigs in China

Elbediwi

Pan

et al. 2020

Front. Bioeng. Biotechnol.

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“…The genomic DNA library was constructed using Nextera XT DNA library construction kit (Illumina, USA, no: FC-131-1024), followed by genomic sequencing using Miseq Reagent Kit v2 300cycle kit (Illumina, USA, No: MS-102-2002). High-throughput genome sequencing was achieved by the Illumina Miseq sequencing platform, as previously described [ 26 , 27 , 28 ]. The quality of sequencing was checked with FastQC toolkit, while low-quality sequences and joint sequences were removed with trimmomatic [ 29 ].…”

Section: Methodsmentioning

confidence: 99%

Characterization of Multidrug Resistance Patterns of Emerging Salmonella enterica Serovar Rissen along the Food Chain in China

Biswas

et al. 2020

Antibiotics

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Salmonella spp. are recognized as important foodborne pathogens globally. Salmonella enterica serovar Rissen is one of the important Salmonella serovars linked with swine products in numerous countries and can transmit to humans by food chain contamination. Worldwide emerging S. Rissen is considered as one of the most common pathogens to cause human salmonellosis. The objective of this study was to determine the antimicrobial resistance properties and patterns of Salmonella Rissen isolates obtained from humans, animals, animal-derived food products, and the environment in China. Between 2016 and 2019, a total of 311 S. Rissen isolates from different provinces or province-level cities in China were included here. Bacterial isolates were characterized by serotyping and antimicrobial susceptibility testing. Minimum inhibitory concentration (MIC) values of 14 clinically relevant antimicrobials were obtained by broth microdilution method. S. Rissen isolates from humans were found dominant (67%; 208/311). S. Rissen isolates obtained from human patients were mostly found with diarrhea. Other S. Rissen isolates were acquired from food (22%; 69/311), animals (8%; 25/311), and the environment (3%; 9/311). Most of the isolates were resistant to tetracycline, trimethoprim-sulfamethoxazole, chloramphenicol, streptomycin, sulfisoxazole, and ampicillin. The S. Rissen isolates showed susceptibility against ceftriaxone, ceftiofur, gentamicin, nalidixic acid, ciprofloxacin, and azithromycin. In total, 92% of the S. Rissen isolates were multidrug-resistant and ASSuT (27%), ACT (25%), ACSSuT (22%), ACSSuTAmc (11%), and ACSSuTFox (7%) patterns were among the most prevalent antibiotic resistance patterns found in this study. The widespread dissemination of antimicrobial resistance could have emerged from misuse of antimicrobial agents in animal husbandry in China. These findings could be useful for rational antimicrobial usage against Salmonella Rissen infections.

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“…Salmonella in silico serotyping was conducted by SISTR web tool. Further, the sequence type, antimicrobial resistance genes (ARG) and plasmid types were detected using assemblies of the samples on the in-house Galaxy platform ( 27 – 29 ), combined with mlst v2.16.1 ( https://githubcom/tseemann/mlst2016 ) and abricate v0.8 ( 30 ), including CGE ResFinder database (updated in 2019-04-23) with a similarity cutoff of 90% for ARG and PlasmidFinder database (updated in 2019-04-23) with a similarity cutoff of 95% ( 31 ).…”

Section: Methodsmentioning

confidence: 99%

Characterization of Salmonella Resistome and Plasmidome in Pork Production System in Jiangsu, China

et al. 2020

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The prevalence of antimicrobial resistance in zoonotic Salmonella is a significant ongoing concern over the world. Several reports have investigated the prevalence of Salmonella infections in the farm animals in China; however, there is only limited knowledge about the Salmonella cross-contamination in the slaughterhouses. Moreover, the application of genomic approaches for understanding the cross-contamination in the food-animal slaughterhouses is still in its infancy in China. In the present study, we have isolated 105 Salmonella strains from pig carcasses and environment samples collected from four independent slaughterhouses in Jiangsu, China. All the Salmonella isolates were subjected to whole genome sequencing, bioinformatics analysis for serovar predictions, multi-locus sequence types, antimicrobial resistance genes, and plasmid types by using the in-house Galaxy platform. The antimicrobial resistance of Salmonella isolates was determined using a minimal inhibitory concentration assay with 14 antimicrobials. We found that the predominant serovar and serogroup was S. Derby and O:4(B), with a prevalence of 41.9 and 55%, respectively. All the isolates were multidrug-resistant and the highest resistance was observed against antimicrobials tetracycline (95.4%) and trimethoprim and sulfamethoxazole (90.9%). Additionally, the colistin-resistant determinant mcr-1 gene was detected in five (4.8%) strains. Our study demonstrated the prevalence of antimicrobial resistance in Salmonella strains isolated from pig slaughterhouses in China and suggested that the genomic platform can serve as routine surveillance along with the food-chain investigation.

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Genomic Characterization of New Variant of Hydrogen Sulfide (H2S)-Producing Escherichia coli with Multidrug Resistance Properties Carrying the mcr-1 Gene in China

Cited by 22 publications

References 26 publications

Genomic Characterization of mcr-1-carrying Salmonella enterica Serovar 4,[5],12:i:- ST 34 Clone Isolated From Pigs in China

Genomic Characterization of mcr-1-carrying Salmonella enterica Serovar 4,[5],12:i:- ST 34 Clone Isolated From Pigs in China

Characterization of Multidrug Resistance Patterns of Emerging Salmonella enterica Serovar Rissen along the Food Chain in China

Characterization of Salmonella Resistome and Plasmidome in Pork Production System in Jiangsu, China

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