Molecular characterisation of antimicrobial resistance determinants and class 1 integrons of Salmonella enterica subsp. enterica serotype Enteritidis strains from retail food in China

Clonal Spread and Genetic Mechanisms Underpinning Ciprofloxacin Resistance in Salmonella enteritidis

Salmonella enteritidis is a major cause of foodborne illness worldwide, and the emergence of ciprofloxacin-resistant strains poses a significant threat to food safety and public health. This study aimed to investigate the prevalence, spread, and mechanisms of ciprofloxacin resistance in S. enteritidis isolates from food and patient samples in Shanghai, China. A total of 1625 S. enteritidis isolates were screened, and 34 (2.1%) exhibited resistance to ciprofloxacin. Pulsed-field gel electrophoresis (PFGE) results suggested that clonal spread might have persisted among these 34 isolates in the local area for several years. Multiple plasmid-mediated quinolone resistance (PMQR) genes, GyrA mutations in the quinolone resistance-determining region (QRDR), and overexpression of RND efflux pumps were identified as potential contributors to ciprofloxacin resistance. PMQR genes oqxAB, qnrA, qnrB, and aac(6')-Ib-cr as well as GyrA mutations S83Y, S83R, D87Y, D87G, D87N, and S83Y-D87Y were identified. The co-transfer of the PMQR gene oqxAB with the ESBL gene blaCTX-M-14/55 on an IncHI2 plasmid with a size of ~245 kbp was observed through conjugation, highlighting the role of horizontal gene transfer in the dissemination of antibiotic resistance. Sequencing of the oqxAB-bearing plasmid p12519A revealed a 248,746 bp sequence with a typical IncHI2 backbone. A 53,104 bp multidrug resistance region (MRR) was identified, containing two key antibiotic resistance determinants: IS26-oqxR-oqxAB-IS26 and IS26-ΔISEcp1-blaCTX-M-14-IS903B. The findings of this study indicate that ciprofloxacin-resistant S. Enteritidis poses a significant threat to food safety and public health. The persistence of clonal spread and the horizontal transfer of resistance genes highlight the need for enhanced surveillance and control measures to prevent the further spread of antibiotic resistance.

Comparative genomics analysis of Salmonella Enteritidis isolated from clinical cases associated with chicken

Salmonella Enteritidis is a major foodborne pathogen, and the emergence of multidrug-resistant (MDR) S. Enteritidis poses a serious public health challenge. In this study, we report the genomic characterization of five S. Enteritidis isolates from clinical. These isolates exhibited resistance to seven classes of antimicrobials with four of the five characterized as MDR. Isolate 33 A exhibited resistance to colistin and polymyxin B, while no associated antimicrobial resistance genes (ARGs) were identified in its genome. Isolate 21 A and 44 A were extended-spectrum beta-lactamases-producing (ESBLs). Whole genome sequencing analysis revealed the presence of multiple mobile genetic elements (MGEs), including plasmids, prophages, and genomic islands, which may have facilitated the acquisition and dissemination of ARGs. Notably, several ARGs, including blaCTX-M-55, blaTEM-141, blaTEM-1B, aph(3')-IIa, aph(3'')-Ib, aph(6)-Id, tet(A), floR, fosA3, and sul2, were identified on plasmids. In addition, chromosomal point mutations in gyrA (D87G and D87Y) and acrB (F28L and L40P) were also observed in each isolate. Multiple virulence genes associated with the type III secretion system were identified on Salmonella pathogenicity islands (SPIs) SPI-1 and SPI-2. Phylogenetic analysis revealed that the five isolates, along with a clinical and chicken origin isolates in the database, clustered together, suggesting a probable common source of infection. Our findings highlight the intricate genetic mechanisms behind MDR in S. Enteritidis, emphasizing the ongoing necessity for surveillance and appropriate antimicrobial usage. This contributes to our understanding of S. Enteritidis transmission within the food chain.

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.

Class 1 integron carrying qacEΔ1 gene confers resistance to disinfectant and antibiotics in Salmonella

Salmonella has presented increasingly alarming rates of antimicrobial resistance believed to be a result of a high prevalence of integrons. It is speculated that disinfectant-resistant isolates are due to the expression of qacEΔ1, an efflux pump located in the 3' conserved sequence (3'CS) of class 1 integrons. With this concern, we tested the antibiotic and disinfectant resistance of 581 Salmonella strains collected from different sources, and characterized their integron structures. Gene expression and induction experiments were also performed. Results showed that Salmonella have high resistance to antimicrobials, especially to sulfonamides (SAs, 78.83 %), tetracyclines (TCs, 75.04 %) and benzalkonium chloride (BC, 87.26 %). The multi-drug resistance (MDR) frequency reached up to 63.17 %, and the prevalence of intI1 was 45.78 %. Molecular characterization of class 1 integrons exhibited nine different gene cassette arrays, of these, dfrA12-orf-aadA2 (n = 75), EstX (n = 25) and aadA2 (n = 14) were the most frequent. Importantly, 74.06 % of intI1-positive isolates were carrying qacEΔ1-sul1 genes in the 3'CS. This study also demonstrated that phenotypic resistance to both antibiotics and disinfectants was significantly correlated with the emergence of intI1 (p < 0.05). 91.37 % of qacEΔ1-sul1 positive Salmonella were found with disinfectant resistance. Additionally, expression of qacEΔ1 gene in Escherichia coli confirmed qacEΔ1 is predominantly involved in conferring disinfectant resistance. Disinfectant induction experiments further implicated qacEΔ1 in disinfectant resistance. RT-qPCR revealed a disinfectant-mediated increase in the relative expression of antibiotic-resistant genes (ARGs), aadA2 and dfrA12 on the integron, and efflux pump genes (mdtH and acrD) indicating that disinfectant could trigger co or cross-resistance. Therefore, our study confirmed that using disinfectant could provide selection pressure for strains with acquired resistance to antibiotics, providing new insights into the public health impact of Salmonella and guide continued efforts in antimicrobial stewardship and prevention of antibiotic resistance.

Metagenomic Analysis of the Abundance and Composition of Antibiotic Resistance Genes in Hospital Wastewater in Benin, Burkina Faso, and Finland

Antibiotic resistance is a global threat to human health, with the most severe effect in low- and middle-income countries. We explored the presence of antibiotic resistance genes (ARGs) in the hospital wastewater (HWW) of nine hospitals in Benin and Burkina Faso, two low-income countries in West Africa, with shotgun metagenomic sequencing. For comparison, we also studied six hospitals in Finland. The highest sum of the relative abundance of ARGs in the 68 HWW samples was detected in Benin and the lowest in Finland. HWW resistomes and mobilomes in Benin and Burkina Faso resembled each other more than those in Finland. Many carbapenemase genes were detected at various abundances, especially in HWW from Burkina Faso and Finland. The bla_GES genes, the most widespread carbapenemase gene in the Beninese HWW, were also found in water intended for hand washing and in a puddle at a hospital yard in Benin. mcr genes were detected in the HWW of all three countries, with mcr-5 being the most common mcr gene. These and other mcr genes were observed in very high relative abundances, even in treated wastewater in Burkina Faso and a street gutter in Benin. The results highlight the importance of wastewater treatment, with particular attention to HWW. IMPORTANCE The global emergence and increased spread of antibiotic resistance threaten the effectiveness of antibiotics and, thus, the health of the entire population. Therefore, understanding the resistomes in different geographical locations is crucial in the global fight against the antibiotic resistance crisis. However, this information is scarce in many low- and middle-income countries (LMICs), such as those in West Africa. In this study, we describe the resistomes of hospital wastewater in Benin and Burkina Faso and, as a comparison, Finland. Our results help to understand the hitherto unrevealed resistance in Beninese and Burkinabe hospitals. Furthermore, the results emphasize the importance of wastewater management infrastructure design to minimize exposure events between humans, HWW, and the environment, preventing the circulation of resistant bacteria and ARGs between humans (hospitals and community) and the environment.

Migration of antibiotic resistance genes and evolution of flora structure in the Xenopus tropicalis intestinal tract with combined exposure to roxithromycin and oxytetracycline

The intestinal flora is one of the most important environments for antibiotic resistance development, owing to its diverse mix of bacteria. An excellent medicine model organism, Xenopus tropicalis, was selected to investigate the spread of antibiotic resistance genes (ARGs) in the intestinal bacterial community with single or combined exposure to roxithromycin (ROX) and oxytetracycline (OTC). Seventeen resistance genes (tetA, tetB, tetE, tetM, tetO, tetS, tetX, ermF, msrA, mefA, ereA, ereB, mphA, mphB, intI1, intI2, intI3) were detected in the intestines of Xenopus tropicalis living in three testing tanks (ROX tanks, OTC tanks, ROX + OTC tanks) and a blank tank for 20 days. The results showed that the relative abundance of total ARGs increased obviously in the tank with single stress but decreased in the tank with combined stress, and the genes encoding the macrolide antibiotic efflux pump (msrA), phosphatase (mphB) and integron (intI2, intI3) were the most sensitive. With the aid of AFM scanning, DNA was found to be scattered short chain in the blank, became extended or curled and then compacted with the stress from a single antibiotic, and was compacted and then fragmented with combined stress, which might be the reason for the variation of the abundance of ARGs with stress. The ratio of Firmicutes/Bacteroides related to diseases was increased by ROX and OTC. The very significant correlation between intI2 and intI3 with tetS (p ≤ 0.001) hinted at a high risk of ARG transmission in the intestines. Collectively, our results suggested that the relative abundance of intestinal ARGs could be changed depending on the intestinal microbiome and DNA structures upon exposure to antibiotics at environmental concentrations.

In Silico Detection of Antimicrobial Resistance Integrons in Salmonella enterica Isolates from Countries of the Andean Community

Antimicrobial resistance genes are often associated with integrons, which promote their movement between and within DNA molecules. IntFinder 1.0 and I-VIP v1.2 were used for the detection of integrons and their associated resistance genes in assembled sequences and raw reads. A dataset comprising 1688 sequenced Salmonella enterica isolates from countries of the Andean Community was developed. A total of 749 and 680 integrons were identified by IntFinder 1.0 and I-VIP v1.2, respectively; class 2 integrons were the most abundant followed by class 1, whereas no class 3 integrons were detected. These elements were mainly associated with isolates from animal sources. S. Infantis ST32 contained the majority of integrons. Trimethoprim resistance genes (dfrA) were found in greater numbers than others, including aadA and bla genes. The presence of these resistance integrons may come as a response to antibiotic misuse, especially of co-trimoxazole. This represents a public health risk as novel resistant strains might appear due to gene dissemination. The information gathered from in silico studies not only contributes to our understanding of integron dynamics in pathogenic Salmonella, but also helps identify potential emergent patterns of resistance in the region, which is fundamental for developing pertinent antibiotic surveillance programs.

High Prevalence of ESBL and Plasmid-Mediated Quinolone Resistance Genes in Salmonella enterica Isolated from Retail Meats and Slaughterhouses in Egypt

The emergence and spread of multidrug-resistant Salmonella enterica (S. enterica) to humans through food of animal origin are considered a major global public health concern. Currently, little is known about the prevalence of important antimicrobial resistance genes in S. enterica from retail food in Africa. Therefore, the screening and characterization of the extended-spectrum β-lactamase (ESBL) and plasmid-mediated quinolone resistance (PMQR) genes in S. enterica isolated from retail meats and slaughterhouses in Egypt were done by using PCR and DNA sequencing techniques. Twenty-eight out of thirty-four (82.4%) non-duplicate S. enterica isolates showed multidrug-resistance phenotypes to at least three classes of antimicrobials, and fourteen (41.2%) exhibited an ESBL-resistance phenotype and harbored at least one ESBL-encoding gene. The identified β-lactamase-encoding genes included bla_CTX-M-1, bla_CTX-M-3, bla_CTX-M-13, bla_CTX-M-14, bla_CTX-M-15, and bla_SHV-12 (ESBL types); bla_CMY-2 (AmpC type); and bla_TEM-1 and bla_OXA-1 (narrow-spectrum types). PMQR genes (included qnrA, qnrB, qnrS, and aac(6′)-Ib-cr) were identified in 23 (67.6%) isolates. The presence of ESBL- and PMQR-producing S. enterica with a high prevalence rate in retail meats and slaughterhouses is considered a major threat to public health as these strains with resistance genes could be transmitted to humans through the food chain.