Genome-Based Assessment of Antimicrobial Resistance and Virulence Potential of Isolates of Non-Pullorum/Gallinarum Salmonella Serovars Recovered from Dead Poultry in China

Abstract

Avian salmonellosis is one of the leading global causes of poultry death, resulting in substantial economic losses in China (constituting 9% of overall financial losses). In Shandong province, a top poultry producer (30% of the overall production in China, with 15% being exported to the world), extensive outbreaks of avian salmonellosis have been reported in the past decade where the causal agents or exact types remain rarely addressed.

Antimicrobial resistance and genomic investigation of non-typhoidal Salmonella isolated from outpatients in Shaoxing city, China

“…All bioinformatic analyses were conducted on our in-house Galaxy platform as previously described ( 20 ). On the other hand, the association between antimicrobial resistance genes and the corresponding plasmid replicons has been investigated according to the method described previously ( 18 ).…”

“…To date, more than 2,600 Salmonella serovars have been described ( 7 ), where only some of them were reported to cause human salmonellosis ( 8 – 17 ). The digestive tract of vertebrates is considered the main reservoir of Salmonella species, and animal farms are the primary source for the development and dissemination ( 6 , 18 – 22 ). Salmonella might contaminate animal carcasses during transport, slaughtering, and then transmitted to humans via the farm-to-fork route ( 23 – 30 ), causing severe infections and threatening public health systems.…”

“…Currently, the third-generation cephalosporins and quinolones are used as the last line of defense to treat salmonellosis in both adult and young patients, while polymyxins are used to treat the cases of multidrug resistance Enterobacteriaceae ( 31 , 32 ). However, recent investigations have reported the resistance of Salmonella isolates recovered from animal farms, food chain processes, foods, and humans to different antibiotics, including the third-generation cephalosporins, quinolones, polymyxins, aminoglycosides, and others ( 18 , 31 , 33 ), with the usual detection of superbug isolates which further complicates the epidemiological situation and is considered a serious threat to public health by limiting choices for therapeutic treatment of patients ( 34 ).…”

Prevalence and antimicrobial-resistant characterization of Bacillus cereus isolated from ready-to-eat rice products in Eastern China

“…The breakpoint for ceftriaxone was from CLSI documents M45-A2 ( Clinical and Laboratory Standards Institute, 2010 ). The isolates resistant to three or more types of antimicrobial classified into different antimicrobial categories were defined as multi-drug resistant ( Li et al, 2022b ). Staphylococcus aureus ATCC 29213 was used as a positive control.…”

Paving the way for precise diagnostics of antimicrobial resistant bacteria

“…With decreasing sequencing costs and advancements in bioinformatics toolkits, whole-genome sequencing (WGS) for AMR diagnosing has been considered an efficient avenue for combating AMR (Schurch and van Schaik, 2017). The genotypebased alternative promises a quicker AMR detection than phenotypic AST by bypassing routine culturing for early detection and providing genomic insights into the mechanisms of AMR action, as well as critical clinical information, including pathogen species and virulence factors (Li et al, 2022). Utilizing the increasing WGS data and robust computerized analysis, machine learning has emerged to address the global AMR increase (Ren et al, 2021).…”