Phylogenomic analysis of Salmonella Indiana ST17, an emerging MDR clonal group in China

Co-occurrence of qacEΔ1 disinfectant resistance gene and ARGs among Salmonella Indiana and its correlation with resistance to sodium hypochlorite

Sodium hypochlorite (SHC) is the most commonly utilized carcass and equipment disinfectant in the poultry industry. However, prolonged exposure to SHC can result in the development of bacterial tolerance and exert co-selection on antimicrobial resistance. This study investigated the co-resistance to SHC and multiple antimicrobial agents among Salmonella enterica serovar Indiana (S. Indiana), with a specific focus on the co-occurrence of disinfectant resistance gene qacEΔ1 and the antimicrobial resistance genes (ARGs) revealed by whole genome sequencing (WGS). Additionally, the study examined the transcriptional response of qacEΔ1 and its closely associated ARGs under SHC pressure. Moreover, the study determined the optimal SHC concentration for the decontamination of multidrug-resistant (MDR) S. Indiana on chicken. The results indicated that S. Indiana exhibited a resistance rate of 73.31 % to SHC, and varying levels of resistance to 13 antimicrobial agents. Furthermore, the analysis revealed a significant correlation between the qacEΔ1 gene and ARGs, including catB3, sul1, arr-3 and blaOXA-1. The genetic contexts surrounding the qacEΔ1 gene demonstrated a high degree of homology, allowing for the categorization into 11 distinct genetic context types, among which the gene cluster aacA4-blaOXA-1-catB3-arr-3-qacEΔ1-sul1 was the most prevalent. Further analysis of the MDR IndS97 strain using PacBio SMRT sequencing revealed that the qacEΔ1 gene was located on plasmid pLKQY01, with IS26 and ISRle7 positioned at the flanks of the composite transposon aacA4-blaOXA-1-catB3-arr-3-qacEΔ1-sul1. The transcription levels of qacEΔ1, arr-3 and sul1 genes in response to SHC stress initially increased, followed by a decline as SHC concentrations rose. At an SHC concentration of 0.5 MIC, the transcription levels of these genes were notably low, and the results indicated a decontamination efficacy of 86.51 % against Salmonella contamination while relatively preserving the freshness of the chicken. This study enhanced the understanding of disinfectant effects on the antimicrobial resistance of S. Indiana and provided evidence to support the regulated use of disinfectants.

Stool carriage of CTX-M/CMY-producing Salmonella enterica in a Chinese tertiary hospital in Shenzhen, China

Salmonellosis, caused by non-typhoidal Salmonella, is a common foodborne gastrointestinal infection. Third-generation cephalosporins are recommended as the first-line treatment for Salmonella infections. Our study aimed to investigate the molecular epidemiology, antimicrobial resistance, and the transmission of extended-spectrum β-lactamases (ESBL) genes in 96 clinical Salmonella isolates collected between 2020 and 2022 at a tertiary hospital in Shenzhen, China. We performed antimicrobial susceptibility testing and whole-genome sequencing to identify serotypes, multilocus sequence typing, antimicrobial resistance genes in these isolates, and the genetic structures of the bla CTX-M/bla CMY genes. Seventeen Salmonella serotypes were identified, with S. 4,[5],12:i:- (37.5%) being the most common, followed by S. Enteritidis (15.63%), S. Typhimurium (14.58%), S. London (7.29%), and S. Rissen (5.21%). MLST analysis revealed 19 distinct sequence types (STs), with ST34 being the most prevalent (36.46%), followed by ST11 (15.63%) and ST19 (13.54%). Antimicrobial resistance testing showed those isolates had high levels of resistance to ampicillin (72.92%) and tetracycline (71.88%), with 70.83% of isolates as multidrug-resistant (MDR). Three bla CTX-M genes (bla CTX-M-14, bla CTX-M-55, and bla CTX-M-65) and bla CMY-2 were identified among 18 cefotaxime-resistant strains, of which one and 12 isolates successfully transferred bla CMY or bla CTX-M to E. coli C600 via conjugation, respectively. The bla CTX-M/bla CMY-2-carrying contigs in nine Salmonella isolates ranged from 2,156 to 164,862 bp, were located either on the chromosome (n=1) or plasmids (IncI1, IncK1, IncA/C) (n=9), and the bla CTX-M/bla CMY-2 genes were associated with ISEcp1. Our study demonstrates the diversity of MDR Salmonella serotypes in clinical isolates, and highlights the role of plasmids and mobile genetic elements in the horizontal transfer of bla CTX-M/bla CMY, emphasizing the need for continuous surveillance of Salmonella in clinical samples.

Genomic insights into a clinical Salmonella Typhimurium isolate carrying plasmid-mediated blaNDM-5

OBJECTIVE

Highly carbapenem-resistant Salmonella has emerged worldwide in recent years and is largely associated with the multiform transmission of resistance genes, which poses a huge challenge in clinical practice. Our study delves into the resistance mechanisms and epidemiology of blaNDM-carrying plasmids.

METHODS

Whole-genome sequencing was utilised to analyse the molecular characteristics and antimicrobial resistance mechanisms of Salmonella isolates recovered from the faeces of a paediatric patient at the Children's Hospital of Nanjing Medical University. Moreover, we conducted an epidemiologic analysis and focused on studying the mechanisms of plasmid-mediated blaNDM transmission, incorporating genomes deposited in the NCBI Pathogen Detection database.

RESULTS

The clinical isolate 23S9 belonged to serovar Typhimurium, antigenic profile 4:i:-, ST34, and carried pNDM_23S9 harbouring several antimicrobial resistance genes, including aac(6')-Ib-cr6, OXA-1, catB3, arr-3, qacEdeltal and blaNDM. Comparative analysis revealed that blaNDM-5 can exist in different plasmids of different isolates, proving its transmission through plasmids. Furthermore, blaNDM-carrying isolates are mostly resistant to beta-lactams, aminoglycosides, sulphonamide, macrolides, and trimethoprim.

CONCLUSIONS

These findings provided thorough and intuitive insights into the intercontinental spread of blaNDM-carrying Salmonella. Ongoing surveillance is essential for effectively monitoring the worldwide dissemination of this high-risk carbapenem-resistant Salmonella.

Antimicrobial Resistance Genes and Clonal Relationships of Duck-Derived Salmonella in Shandong Province, China in 2023

Salmonella is a major threat to both human and animal health. However, the diversity and antibiotic resistance of animal-derived Salmonella and their association with human infections remain largely unexplored. In this study, Salmonella strains were isolated, identified, and sequenced from dead embryos and cloacal swab samples obtained from 278 large-scale duck farms in 11 cities in Shandong Province. The results show that a total of 57 Salmonella strains were isolated, with the dominant sequence types (ST) being ST17 (15/57) and ST19 (9/57), while the dominant serotypes were S. Indiana (15/57) and S. Typhimurium (11/57). Furthermore, genomic analysis has revealed the presence of prevalent antibiotic resistance genes (ARGs), which are often associated with co-transfer mechanisms. Over 52.63% of the strains were observed to carry two or more ARGs, especially one Salmonella strain that carried twenty-eight distinct ARGs. Furthermore, core genome multilocus sequence typing analysis (cgMLST) indicated that the 57 Salmonella strains may have a close relationship, which could be clonally transmitted among different cities. The results demonstrated a close relationship between the Salmonella strains identified in diverse geographical regions, suggesting that these strains may have been widely disseminated through clonal transmission. The mutation analysis reveals significant mutations at parC (T57S), gyrA (S83F), parC (S80R), gyrA (D87N), and gyrA (S83Y). These findings emphasize the necessity for monitoring and controlling Salmonella infections in animals, as they may serve as a reservoir for ARGs with the potential to affect human health or even be the source of pathogens that infect humans.

Niche-specific evolution and gene exchange of Salmonella in retail pork and chicken

Salmonella exhibits extensive genetic diversity, facilitated by horizontal gene transfer occurring within and between species, playing a pivotal role in this diversification. Nevertheless, most studies focus on clinical and farm animal isolates, and research on the pangenome dynamics of Salmonella isolates from retail stage of the animal food supply chain is limited. Here, we investigated the genomes of 950 Salmonella isolates recovered from retail chicken and pork meats in seven provinces and one municipality of China in 2018. We observed a strong correlation between Salmonella sublineage diversity and the accessory genome with meat type, revealing reduced diversity associated with increased resistance. Importantly, genes associated with antibiotic, biocide, and heavy metal resistance were unevenly distributed in Salmonella from retail chicken and pork. Pork Salmonella isolates showed a higher prevalence of copper and silver resistance genes, while chicken Salmonella isolates displayed a significant predominance of genetic determinants associated with cephalosporin and ciprofloxacin resistance. Moreover, co-occurrence patterns of resistance determinants and their interaction with mobile genetic elements also correlated with meat type. In summary, our findings shed light on how Salmonella achieves their ecological niche success driven by evolution and gene changes in the retail stage of the animal food supply chain.

Antimicrobial resistance and population genomics of emerging multidrug-resistant Salmonella 4,[5],12:i:- in Guangdong, China

Salmonella 4,[5],12:i:-, a monophasic variant of Salmonella Typhimurium, has emerged as a global cause of multidrug-resistant salmonellosis and has become endemic in many developing and developed countries, especially in China. Here, we have sequenced 352 clinical isolates in Guangdong, China, during 2009-2019 and performed a large-scale collection of Salmonella 4,[5],12:i:- with whole genome sequencing (WGS) data across the globe, to better understand the population structure, antimicrobial resistance (AMR) genomic characterization, and transmission routes of Salmonella 4,[5],12:i:- across Guangdong. Salmonella 4,[5],12:i:- strains showed broad genetic diversity; Guangdong isolates were found to be widely distributed among the global lineages. Of note, we identified the formation of a novel Guangdong clade (Bayesian analysis of population structure lineage 1 [BAPS1]) genetically diversified from the global isolates and likely emerged around 1990s. BAPS1 exhibits unique genomic features, including large pan-genome, decreased ciprofloxacin susceptibility due to mutation in gyrA and carriage of plasmid-mediated quinolone resistance (PMQR) genes, and the multidrug-resistant IncHI2 plasmid. Furthermore, high genetic similarity was found between strains collected from Guangdong, Europe, and North America, indicating the association with multiple introductions from overseas. These results suggested that global dissemination and local clonal expansion simultaneously occurred in Guangdong, China, and horizontally acquired resistance to first-line and last-line antimicrobials at local level, underlying emergences of extensive drug and pan-drug resistance. Our findings have increased the knowledge of global and local epidemics of Salmonella 4,[5],12:i:- in Guangdong, China, and provided a comprehensive baseline data set essential for future molecular surveillance.IMPORTANCESalmonella 4,[5],12:i:- has been regarded as the predominant pandemic serotype causing diarrheal diseases globally, while multidrug resistance (MDR) constitutes great public health concerns. This study provided a detailed and comprehensive genome-scale analysis of this important Salmonella serovar in the past decade in Guangdong, China. Our results revealed the complexity of two distinct transmission modes, namely global transmission and local expansion, circulating in Guangdong over a decade. Using phylogeography models, the origin of Salmonella 4,[5],12:i:- was predicted from two aspects, year and country, that is, Salmonella 4,[5],12:i:- emerged in 1983, and was introduced from the UK, and subsequently differentiated into the local endemic lineage circa 1991. Additionally, based on the pan-genome analysis, it was found that the gene accumulation rate in local endemic BAPS 1 lineage was higher than in other lineages, and the horizontal transmission of MDR IncHI2 plasmid associated with high resistance played a major role, which showed the potential threat to public health.

Prevalence, antibiotic resistance, virulence genes and molecular characteristics of Salmonella isolated from ducks and wild geese in China

Salmonella is a major foodborne pathogen and the cause of significant morbidity and mortality via consumption of contaminated meat and meat-products. The prevalence of Salmonella in ducks and wild geese in China are poorly characterized and these sources represent a potential pool that could be transferred to farm-reared fowl. In this study, we isolated 335 (18.3%) Salmonella from 1830 samples and identified 24 serotypes and most prevalent were Salmonella Indiana, Salmonella Kentucky and Salmonella Typhimurium. Whole genome sequencing revealed the presence of the dominant sequence types ST17, ST198 and ST19 for these three serotypes, respectively. In addition, these isolates were most likely clonally spread across different regions while S. Kentucky also crossed the species barrier. The majority of the Salmonella isolates possessed β-lactam and fluoroquinolone resistance and these were consistent with antibiotic resistance gene profiles. We also identified 8 plasmid replicon types and all isolates possessed virulence genes and the numbers were greatest for S. Enteritidis and S. Typhimurium isolates. This study provides novel insights concerning the epidemiology of Salmonella in ducks and wild geese and provides basic data for public health screening and management.

Antimicrobial resistance and genomic investigation of Salmonella isolated from retail foods in Guizhou, China

Introduction

Salmonella is a major foodborne pathogen worldwide that causes severe morbidity and mortality. It is mainly caused by consuming contaminated food, with retail food considered the primary source.

Methods

In Guizhou, China, 102 Salmonella strains isolated from 2016 to 2021 underwent phenotypic antimicrobial resistance testing and whole-genome sequencing (WGS) to understand Salmonella diversity, including serotypes, sequencing types (STs), antimicrobial genes, virulence genes, plasmid types, multi-locus sequence types (MLST), and core genome MLST (cgMLST).

Results and discussion

S.Typhimurium was the dominant serotype, and O:4(B) was the leading serogroup. The most prevalent genotype was ST40. Phenotypic antimicrobial resistance identified 66.7% of the sampled isolates as multi-drug resistant (MDR). S.Enteritidis (n = 7), S.Typhimurium (n = 1), S.Indiana (n = 1), S.Kentucky (n = 1), S.Uganda (n = 1), all of which were MDR, were resistant to Colistin. Resistance rates varied significantly across different strains and food types, particularly meat products exhibiting higher resistance. Notably, significant increases in resistance were observed from 2016 to 2021 for the following: ≥ 1 resistant (P = 0.001), MDR (P = 0.001), ampicillin (P = 0.001), tetracycline (P < 0.001), chloramphenicol (P = 0.030), and trimethoprim/sulfamethoxazole (P = 0.003). The marked escalation in drug resistance over the recent years, coupled with the varying resistance rates among food sources, underscores the growing public health concern. Our findings highlight the need for a coordinated approach to effectively monitor and respond to Salmonella infections in Guizhou, China.

Genomic Characterization of a Plasmid-Free and Highly Drug-Resistant Salmonella enterica Serovar Indiana Isolate in China

The emergence of multi-drug resistant (MDR) Salmonella enterica serovar Indiana (S. Indiana) strains in China is commonly associated with the presence of one or more resistance plasmids harboring integrons pivotal in acquiring antimicrobial resistance (AMR). This study aims to elucidate the genetic makeup of this plasmid-free, highly drug-resistant S. Indiana S1467 strain. Genomic sequencing was performed using Illumina HiSeq 2500 sequencer and PacBio RS II System. Prodigal software predicted putative protein-coding sequences while BLASTP analysis was conducted. The S1467 genome comprises a circular 4,998,300 bp chromosome with an average GC content of 51.81%, encompassing 4709 open reading frames (ORFs). Fifty-four AMR genes were identified, conferring resistance across 16 AMR categories, aligning closely with the strain's antibiotic susceptibility profile. Genomic island prediction unveiled an approximately 51 kb genomic island housing a unique YeeVU toxin-antitoxin system (TAS), a rarity in Salmonella species. This suggests that the AMR gene cluster on the S1467 genomic island may stem from the integration of plasmids originating from other Enterobacteriaceae. This study contributes not only to the understanding of the genomic characteristics of a plasmid-free, highly drug-resistant S. Indiana strain but also sheds light on the intricate mechanisms underlying antimicrobial resistance. The implications of our findings extend to the broader context of horizontal gene transfer between bacterial species, emphasizing the need for continued surveillance and research to address the evolving challenges posed by drug-resistant pathogens.

Genomic characterization of Salmonella isolated from retail chicken and humans with diarrhea in Qingdao, China

Salmonella, especially antimicrobial resistant strains, remains one of the leading causes of foodborne bacterial disease. Retail chicken is a major source of human salmonellosis. Here, we investigated the prevalence, antimicrobial resistance (AMR), and genomic characteristics of Salmonella in 88 out of 360 (24.4%) chilled chicken carcasses, together with 86 Salmonella from humans with diarrhea in Qingdao, China in 2020. The most common serotypes were Enteritidis and Typhimurium (including the serotype I 4,[5],12:i:-) among Salmonella from both chicken and humans. The sequence types were consistent with serotypes, with ST11, ST34 and ST19 the most dominantly identified. Resistance to nalidixic acid, ampicillin, tetracycline and chloramphenicol were the top four detected in Salmonella from both chicken and human sources. High multi-drug resistance (MDR) and resistance to third-generation cephalosporins resistance were found in Salmonella from chicken (53.4%) and humans (75.6%). In total, 149 of 174 (85.6%) Salmonella isolates could be categorized into 60 known SNP clusters, with 8 SNP clusters detected in both sources. Furthermore, high prevalence of plasmid replicons and prophages were observed among the studied isolates. A total of 79 antimicrobial resistant genes (ARGs) were found, with aac(6')-Iaa, blaTEM-1B, tet(A), aph(6)-Id, aph(3″)-Ib, sul2, floR and qnrS1 being the dominant ARGs. Moreover, nine CTX-M-type ESBL genes and the genes blaNMD-1, mcr-1.1, and mcr-9.1 were detected. The high incidence of MDR Salmonella, especially possessing lots of mobile genetic elements (MGEs) in this study posed a severe risk to food safety and public health, highlighting the importance of improving food hygiene measures to reduce the contamination and transmission of this bacterium. Overall, it is essential to continue monitoring the Salmonella serotypes, implement the necessary prevention and strategic control plans, and conduct an epidemiological surveillance system based on whole-genome sequencing.

A novel transposon Tn7540 carrying blaNDM-9 and fosA3 in chromosome of a pathogenic multidrug-resistant Salmonella enterica serovar Indiana isolated from human faeces

OBJECTIVES

Emergence of multidrug-resistant (MDR) Salmonella enterica serovar Indiana has raised global concern. Mobile genetic elements (MGEs) play vital roles in accelerating the dissemination of resistance genes in bacteria communities. The study aims to improve our understanding of the underlying resistance mechanisms and characterize the MGEs in a MDR S. Indiana isolate.

METHODS

Here, we report the characteristics of a MDR pathogenic S. Indiana isolate. The antimicrobial susceptibility pattern of S. Indiana QT6365 was determined. The genomic structure of the chromosome and the plasmid, serotype, and multi-locus sequence type were analysed by whole genome sequencing. The circular form derived from IS26-flanked transposon was confirmed by reverse polymerase chain reaction and sequencing.

RESULTS

S. Indiana QT6365 exhibited resistance to all tested antimicrobials except for aztreonam, amikacin, polymyxin, and tigecycline, was defined as MDR, and belonged to ST17. S. Indiana QT6365 was closely related with food resource S. Indiana C629 with similar resistance gene profiles. Multiple resistance genes are mainly carried by a novel transposon Tn7540 located on the chromosome and an IncHI2/HI2A/N plasmid. Sequence analysis and the formed circular intermediate suggested Tn7540 might be generated through homologous recombination by IS26-bounded translocatable units (IS26-fosA-IS26-intI1-dfrA12-aadA2-sul1-ISCR1-bla_NDM-9-IS26).

CONCLUSIONS

To the best of our knowledge, this is the first report of the novel chromosomal transposon possessing bla_NDM-9 and fosA3 in S. Indiana isolated from human specimen, which might facilitate the dissemination of resistance genes and should arouse serious awareness.