Antimicrobial susceptibility, virulence gene profiles and molecular subtypes of Salmonella Newport isolated from humans and other sources

Multi-locus sequence typing, antimicrobials resistance and virulence profiles of Salmonella enterica isolated from bovine carcasses in Minas Gerais state, Brazil

The aim of this study was to identify virulence and antimicrobial resistance profiles and determine the sequence type (ST) by multilocus sequence typing (MLST) of Salmonella enterica isolates from bovine carcasses from slaughterhouse located in Minas Gerais state, Brazil, and its relationship with bovine isolates obtained on the American continent based on sequence type profile. The MLST results were compared with all Salmonella STs associated with cattle on American continent, and a multi-locus sequence tree (MS tree) was built. Among the 17 S. enterica isolates, five ST profiles identified, and ST10 were the most frequent, grouping seven (41.2%) isolates. The isolates presented 11 different profiles of virulence genes, and six different antibiotics resistance profiles. The survey on Enterobase platform showed 333 Salmonella STs from American continent, grouped into four different clusters. Most of the isolates in the present study (13/17), were concentrated in a single cluster (L4) composed by 74 STs. As a conclusion, five different STs were identified, with ST10 being the most common. The isolates showed great diversity of virulence genes and antibiotics resistance profiles. Most of the isolates of this study were grouped into a single cluster composed by 74 STs formed by bovine isolates obtained on the American continent.

Virulence gene profiles and antimicrobial susceptibility of Salmonella Brancaster from chicken

BACKGROUND

The current conventional serotyping based on antigen-antisera agglutination could not provide a better understanding of the potential pathogenicity of Salmonella enterica subsp. enterica serovar Brancaster. Surveillance data from Malaysian poultry farms indicated an increase in its presence over the years.

OBJECTIVE

This study aims to investigate the virulence determinants and antimicrobial resistance in S. Brancaster isolated from chickens in Malaysia.

METHODS

One hundred strains of archived S. Brancaster isolated from chicken cloacal swabs and raw chicken meat from 2017 to 2022 were studied. Two sets of multiplex polymerase chain reaction (PCR) were conducted to identify eight virulence genes associated with pathogenicity in Salmonella (invasion protein gene [invA], Salmonella invasion protein gene [sipB], Salmonella-induced filament gene [sifA], cytolethal-distending toxin B gene [cdtB], Salmonella iron transporter gene [sitC], Salmonella pathogenicity islands gene [spiA], Salmonella plasmid virulence gene [spvB], and inositol phosphate phosphatase gene [sopB]). Antimicrobial susceptibility assessment was conducted by disc diffusion method on nine selected antibiotics for the S. Brancaster isolates. S. Brancaster, with the phenotypic ACSSuT-resistance pattern (ampicillin, chloramphenicol, streptomycin, sulphonamides, and tetracycline), was subjected to PCR to detect the corresponding resistance gene(s).

RESULTS

Virulence genes detected in S. Brancaster in this study were invA, sitC, spiA, sipB, sopB, sifA, cdtB, and spvB. A total of 36 antibiogram patterns of S. Brancaster with a high level of multidrug resistance were observed, with ampicillin exhibiting the highest resistance. Over a third of the isolates displayed ACSSuT-resistance, and seven resistance genes (β-lactamase temoneira [blaTEM], florfenicol/chloramphenicol resistance gene [floR], streptomycin resistance gene [strA], aminoglycoside nucleotidyltransferase gene [ant(3″)-Ia], sulfonamides resistance gene [sul-1, sul-2], and tetracycline resistance gene [tetA]) were detected.

CONCLUSION

Multidrug-resistant S. Brancaster from chickens harbored an array of virulence-associated genes similar to other clinically significant and invasive non-typhoidal Salmonella serovars, placing it as another significant foodborne zoonosis.

Association between Phenotypes of Antimicrobial Resistance, ESBL Resistance Genes, and Virulence Genes of Salmonella Isolated from Chickens in Sichuan, China

The aim of this study was to explore the association between antimicrobial resistance, ESBL genes, and virulence genes of Salmonella isolates. From 2019 to 2021, a total of 117 Salmonella isolates were obtained from symptomatic chickens in Sichuan Province, China. The strains were tested for antimicrobial resistance and the presence of ESBL according to the Clinical and Laboratory Standards Institute (CLSI) instructions. The presence of ESBL genes and genes for virulence was determined using Polymerase Chain Reaction (PCR). In addition, Multilocus Sequence Typing (MLST) was applied to confirm the molecular genotyping. Moreover, the mechanism of ESBL and virulence gene transfer and the relationships between the resistance phenotype, ESBL genes, and virulence genes were explored. The isolates exhibited different frequencies of resistance to antibiotics (resistance rates ranged from 21.37% to 97.44%), whereas 68.38% and 41.03% of isolates were multi-drug resistance (MDR) and ESBL-producers, respectively. In the PCR analysis, blaCTX-M was the most prevalent ESBL genotype (73.42%, 58/79), and blaCTX-M-55 showed the most significant effect on the resistance to cephalosporins as tested by logistic regression analysis. Isolates showed a high carriage rate of invA, avrA, sopB, sopE, ssaQ, spvR, spvB, spvC, stn, and bcfC (ranged from 51.28% to 100%). MLST analysis revealed that the 117 isolates were divided into 11 types, mainly ST92, ST11, and ST3717. Of 48 ESBL-producers, 21 transconjugants were successfully obtained by conjugation. Furthermore, ESBL and spv virulence genes were obtained simultaneously in 15 transconjugants. These results highlighted that Salmonella isolates were common carriers of ESBLs and multiple virulence genes. Horizontal transfer played a key role in disseminating antimicrobial resistance and pathogenesis. Therefore, it is necessary to continuously monitor the use of antimicrobials and the prevalence of AMR and virulence in Salmonella from food animals and to improve the antibiotic stewardship for salmonellosis.

Study of Virulence Genes, Antimicrobial Resistance, and Genetic Relatedness of Foodborne Salmonella Isolates from Tunisia

ABSTRACT

Nontyphoidal Salmonella strains are among the major foodborne pathogens with emerging multidrug-resistant phenotypes. In this study, antimicrobial susceptibility testing of a collection of Salmonella isolates (n = 54) recovered from poultry and bivalve molluscs was performed. The study also investigated profiling of virulence and resistance genes as well as phylogenetic relationships through pulsed-field gel electrophoresis (PFGE) and enterobacterial repetitive intergenic consensus (ERIC)-PCR fingerprinting. Results revealed the presence of multiple virulence genes among Salmonella isolates. Salmonella intestinal infection A (siiA), Salmonella outer protein (sopB and sopE), putative 4-hydroxybutyrate coenzyme A transferase (cat2), Salmonella atypical fimbria C (safC), and Salmonella Enteritidis fimbria B (sefB) were present in most (83.32 to 100%) of the isolates, whereas the remaining tested genes (Salmonella plasmid virulence [spvC and spvB]), and the sopE gene, were exclusively detected within the serotype Enteritidis. The highest resistance rates were observed for oxacillin (94.4%), ampicillin (37%), and nalidixic acid (27.7%), followed by cefotaxime and amoxicillin-clavulanic acid (14.8%), trimethoprim-sulfamethoxazole (9.3%), and ciprofloxacin (5.5%). The results indicate that the Salmonella Enteritidis serotype possessed the widest range of virulence determinants and increasing levels of resistance. Such high-risk clones should be particularly controlled in Tunisia. Overall, increased resistance and virulence confer a selective advantage for the evolution of these bacteria and represent an alarming problem for global public health. The genetic study via PFGE and ERIC-PCR showed the high diversity of the clonal origins of these bacteria and the sources of contamination and revealed the great capacity of Salmonella to diversify within food-producing animals.

HIGHLIGHTS

Detection, quantification, and characterization of Salmonella enterica in mango, tomato, and raw chicken purchased in the central region of Mexico

To estimate human exposure to Salmonella enterica, it is essential to understand the pathogen distribution and characteristics. Prevalence and concentration of S. enterica were determined in mango, tomato, and raw chicken samples purchased in three states (Aguascalientes, Querétaro, and Guadalajara) located in the central region of Mexico during two seasons. In addition, S. enterica isolates were characterized by absence/presence of 13 virulence genes (chromosomal, prophage, and plasmid) and resistance to 14 antibiotics. A total of 300 samples of mango, 272 of tomato, and 354 of raw chicken were analyzed. The mean of the prevalence (24.9%) and concentration (-0.61 Log MPN/g) of S. enterica in chicken was higher than in mango (1.3%, -1.7 Log MPN/g) and tomato (1.1%, -1.7 Log MPN). Among S. enterica isolates (284), there were 7 different virulotypes, belonging 68.7% of isolates to V2; there was high variability in the presence of mobile genetic elements. The occurrence of specific mobile elements ranged from 81.4% to 11.3% among isolates. Among the isolates, 91.5% were resistant to at least one antibiotic with ampicillin being the most frequent; 54.9% of isolates were multidrug resistant. Data from this study can be used for quantitative microbial risk assessment of S. enterica related to mango, tomato, and raw chicken consumption in the central region of Mexico. PRACTICAL APPLICATION: Data on the prevalence and concentration of Salmonella enterica obtained in this study can be used to estimate the exposure assessment for the consumption of mango, tomato, and chicken in the central region of Mexico. In addition, the characteristics of the S. enterica isolates could be used to select representative strains for future studies to evaluate the intraspecies variability.

Association of Virulence and Antibiotic Resistance in Salmonella-Statistical and Computational Insights into a Selected Set of Clinical Isolates

The acquisition of antibiotic resistance (AR) by foodborne pathogens, such as Salmonella enterica, has emerged as a serious public health concern. The relationship between the two key survival mechanisms (i.e., antibiotic resistance and virulence) of bacterial pathogens is complex. However, it is unclear if the presence of certain virulence determinants (i.e., virulence genes) and AR have any association in Salmonella. In this study, we report the prevalence of selected virulence genes and their association with AR in a set of phenotypically tested antibiotic-resistant (n = 117) and antibiotic-susceptible (n = 94) clinical isolates of Salmonella collected from Tennessee, USA. Profiling of virulence genes (i.e., virulotyping) in Salmonella isolates (n = 211) was conducted by targeting 13 known virulence genes and a gene for class 1 integron. The association of the presence/absence of virulence genes in an isolate with their AR phenotypes was determined by the machine learning algorithm Random Forest. The analysis revealed that Salmonella virulotypes with gene clusters consisting of avrA, gipA, sodC1, and sopE1 were strongly associated with any resistant phenotypes. To conclude, the results of this exploratory study shed light on the association of specific virulence genes with drug-resistant phenotypes of Salmonella. The presence of certain virulence genes clusters in resistant isolates may become useful for the risk assessment and management of salmonellosis caused by drug-resistant Salmonella in humans.

Persistent Asymptomatic Human Infections by Salmonella enterica Serovar Newport in China

Human infections caused by Salmonella Newport generally lead to gastrointestinal diseases. These infections are normally self-limiting; however, in certain cases, broad-spectrum antimicrobials are prescribed for the treatment. The Chinese National Foodborne Disease Surveillance Network has reported a gradual increase in the incidence of multidrug-resistant S. Newport infections in humans. After careful evaluation of the dynamic relationship among the clinical findings, the age group, and the genomic sequence data, it was found that young patients represented the major group with persistent diarrhea, whereas adults were either asymptomatic or diarrheic. Furthermore, all these strains contained multiple acquired antimicrobial resistance determinants, which limited the use of antimicrobials for human patients of all age groups. This analysis of the laboratory-confirmed cases, coupled with genetic analysis of the corresponding pathogen, revealed that antimicrobial treatment of persistent infections by S. Newport in infants and toddlers, and in asymptomatic or diarrheic adults, may not be successful. If the antimicrobials must be prescribed at all, they must be used with caution because of the presence of multiple acquired antimicrobial resistance determinants in such strains.

Salmonella enterica serovar Newport (S. Newport) infections are gradually on the rise in China from the last decade. For humans’ infections, S. Newport has been ranked among the top five serovars responsible for persistent infections, globally. A total of 290 S. Newport strains with their relevant clinical metadata were analyzed, and the strains were subjected to whole-genome sequence analysis. Among these, 62.4% (n = 181) were from diarrheic patients and 28.9% (n = 84) were from asymptomatic individuals (including adults and youngsters) while 8.6% (n = 25) were from cases of persistent diarrhea in infants (28%, n = 7) and toddlers (72%, n = 18). The association between the sequence types (STs) and the variations in the clinical presentation was statistically significant (P = 0.0432), with ST46 causing diarrhea or representing asymptomatic patients and ST31 or ST68 causing persistent diarrhea. Genomic analysis revealed that the highest proportion of the isolates (98.5%, n = 279), primarily from patients with or without diarrhea rather than from asymptomatic individuals, carried antimicrobial resistance determinants corresponding to the aminoglycosides and beta-lactams, highlighting the need for cautionary usage of antimicrobials in such patients. These findings also suggest that cases of nontyphoidal Salmonella infection with symptoms of acute diarrhea or persistent diarrhea caused by S. Newport should be handled with caution, due to the high chance of development of an antimicrobial resistance phenotype that might lead to therapeutic failures. Together, S. Newport ST31 and ST46, which have the highest frequency of carriage of multidrug resistance, are potentially responsible for antimicrobial-resistant diarrhea/persistent diarrhea in infants and children, while adult humans are more likely to be (asymptomatic) carriers of the S. Newport strains.

IMPORTANCE Human infections caused by Salmonella Newport generally lead to gastrointestinal diseases. These infections are normally self-limiting; however, in certain cases, broad-spectrum antimicrobials are prescribed for the treatment. The Chinese National Foodborne Disease Surveillance Network has reported a gradual increase in the incidence of multidrug-resistant S. Newport infections in humans. After careful evaluation of the dynamic relationship among the clinical findings, the age group, and the genomic sequence data, it was found that young patients represented the major group with persistent diarrhea, whereas adults were either asymptomatic or diarrheic. Furthermore, all these strains contained multiple acquired antimicrobial resistance determinants, which limited the use of antimicrobials for human patients of all age groups. This analysis of the laboratory-confirmed cases, coupled with genetic analysis of the corresponding pathogen, revealed that antimicrobial treatment of persistent infections by S. Newport in infants and toddlers, and in asymptomatic or diarrheic adults, may not be successful. If the antimicrobials must be prescribed at all, they must be used with caution because of the presence of multiple acquired antimicrobial resistance determinants in such strains.

Emerging colistin resistance in Salmonella enterica serovar Newport isolates from human infections

Worldwide emergence of Salmonella enterica serovar Newport (S. Newport) infection in humans, in parallel with a significant increasing prevalence of antimicrobial resistance (AR), is a serious public health concern. However, the prevalence of S. Newport resistance in China remains largely unknown. A retrospective study of 287 S. Newport clinical isolates collected during 1997-2018 was undertaken for characterization of AR profiles using the micro-dilution assay. We found a recent emergence of colistin resistance in four Chinese clinical isolates, including mcr-1-positive isolates. Importantly, phylogenomic and microbiological investigations indicate multiple independent clonal transmission of colistin-resistant S. Newport isolates of different seafood origins. Our study highlights potential reservoirs for transmission of colistin resistance and suggests that the global food supply chain may facilitate this dissemination.

Molecular Detection Of Multidrug-Resistant Salmonella Isolated From Livestock Production Systems In South Africa

BACKGROUND

Antibiotic-resistant bacterial pathogens associated with livestock remain a major concern worldwide as they get transmitted from animals to humans and cause foodborne and zoonotic diseases.

METHODS

Antimicrobial resistance in livestock-associated Salmonella spp in South Africa was investigated using molecular DNA methods. Three hundred and sixty-one environmental faecal samples were randomly collected from avian (chicken and ducks), cows, pigs, goats, and sheep. Salmonella spp. were isolated on selective media and were confirmed using the polymerase chain reaction. Antimicrobial susceptibility testing against ampicillin, chloramphenicol, ciprofloxacin, ceftriaxone, azithromycin, tetracycline, amoxicillin-clavulanate and trimethoprim-sulfamethoxazole was determined using the Kirby-Bauer disk diffusion method. Isolates were screened for the presence of blaTEM-1, blaCMY-2, tetA, tetC, sul2 and dfrA7 resistance genes by PCR.

RESULTS

Most of the isolates were resistant to ampicillin (64%), tetracycline (63%), amoxicillin-clavulanate (49%), trimethoprim-sulfamethoxazole (38%), and ceftriaxone (20%). Eight percent of the tested isolates were ciprofloxacin-resistant Salmonella spp. Multidrug resistance was observed with the mean multiple antibiotic resistance (MAR) index of 0.31. The study demonstrated that 43% of the isolates were multiple drug resistant. The prevalence rates of resistance genes were 44% for blaTEM-1 , 35% for blaCMY-2 , 21% for sul2, 18% for tetC, 14% for dfrA7 and 8% for tetA.

CONCLUSION

Resistance to ceftriaxone, detection of blaCMY-2 gene and the high level of intermediate susceptibility (33%) against ciprofloxacin suggested that livestock carry problematic Salmonella spp. This study used the global one-health initiative to report the potential public health risks of livestock-associated pathogens and highlights the importance of monitoring the trends of antimicrobial resistance for sustainability of antibiotics.

Worldwide Epidemiology of Salmonella Serovars in Animal-Based Foods: a Meta-analysis

Salmonella spp. are among the most important foodborne pathogens and the third leading cause of human death among diarrheal diseases worldwide. Animals are the primary source of this pathogen, and animal-based foods are the main transmission route to humans. Thus, understanding the global epidemiology of Salmonella serovars is key to controlling and monitoring this bacterium. In this context, this study aimed to evaluate the prevalence and diversity of Salmonella enterica serovars in animal-based foods (beef, pork, poultry, and seafood) throughout the five continents (Africa, the Americas [North and Latin America], Asia, Europe, and Oceania). The meta-analysis consisted of a chemometric assessment (hierarchical cluster analysis and principal component analysis) to identify the main epidemiological findings, including the prevalence and diversity of the Salmonella serovars in each matrix. Regarding the serovar distribution, S Typhimurium presented a cosmopolitan distribution, reported in all four assessed matrices and continents; poultry continues to play a central role in the dissemination of the Enteritidis serovar to humans, and Anatum and Weltevreden were the most frequently found in beef and seafood, respectively. Additionally, we recommended careful monitoring of certain serovars, such as Derby, Agona, Infantis, and Kentucky. Finally, given the scientific data regarding the most frequently reported serovars and which matrices constitute the main vehicles for the transmission of this pathogen, control programs may be improved, and specific interventions may be implemented in an attempt to reduce the risk of this pathogen reaching humans.IMPORTANCE Salmonellosis is caused by Salmonella spp. and is the third leading cause of death among food-transmitted diseases. This pathogen is commonly disseminated in domestic and wild animals, and the infection's symptoms are characterized by acute fever, nausea, abdominal pain, and diarrhea. The animals are the primary source of salmonellae, and animal-based foods are the main transmission route to humans. Therefore, data collected from these sources could contribute to future global interventions for effective control and surveillance of Salmonella along the food chain. In light of this, the importance of our research is in identifying the prevalence of Salmonella serovars in four animal-based food matrices (pork, poultry, beef, and seafood) and to evaluate the importance that each matrix has as the primary source of this pathogen to humans.

Diversified sources for human infections by Salmonella enterica serovar newport

Salmonella enterica Newport (S. Newport), with phylogenetic diversity feature, contributes to significant public health concerns. Our previous study suggested that S. Newport from multiple animal-borne routes, with distinct antibiotic resistant pattern, might transmit to human. However, their genetic information was lacking. As a complement to the earlier finding, we investigate the relationship between each other among the hosts, sources, genotype and antibiotic resistance in S. Newport. We used the multilocus sequence typing (MLST) in conjunction with minimum inhibitory concentration of 16 antibiotics of globally sampled 1842 S. Newport strains, including 282 newly contributed Chinese strains, to evaluate this association. Our analysis reveals that sequence types (STs) are significantly associated with different host sources, including livestock (ST45), birds (ST5), contaminated water and soil (ST118), reptiles (ST46) and seafood (ST31). Importantly, ST45 contained most of (344/553) the multi-drug resistance (MDR) strains, which were believed to be responsible for human MDR bacterial infections. Chinese isolates were detected to form two unique lineages of avian (ST808 group) and freshwater animal (ST2364 group) origin. Taken together, genotyping information of S. Newport could serve to improve Salmonella source-originated diagnostics and guide better selection of antibiotic therapy against Salmonella infections.

High-levels of resistance to quinolone and cephalosporin antibiotics in MDR-ACSSuT Salmonella enterica serovar Enteritidis mainly isolated from patients and foods in Shanghai, China

In this study, 2887 Salmonella strains were mainly obtained from patients and foods in Shanghai from 2006 to 2014 in order to assess the susceptibility to 16 antibiotics. Among them, 3.8% (110/2887) S. Enteritidis isolates were shown to have an ACSSuT (ampicillin, chloramphenicol, streptomycin, sulfamethoxazole, and tetracycline) resistance pattern. The resistance genes of ACSSuT included sul2 (74.55%), flo (67.27%), tetA (49.09%), and aph(3)-IIa (46.36%). In addition, class 1 integron profiles were detected in 9 isolates, and 55.6% (5/9) were shown to carry resistant genes against aminoglycosides and sulfonamides. Moreover, these isolates had a high rate of resistance to nalidixic acid (95.29%), cefotaxime (70.64%), cefepime (58.72%), and ceftazidime (48.62%). Detection of quinolone genes showed that 93.64% (103/110) of the strains had gyrA single mutations (D87G, D87Y, D87N, S83Y, and S83F), where D87G was the dominant mutation in 55.45% isolates. 19.1% (21/110) isolates carried plasmid-mediated quinolone resistance (PMQR) genes (qnrB and aac(6')-Ib-cr), and the most prevalent was qnrB. Furthermore, we also detected ESBLS genes. The most common were bla_CTX-M-55 (57.27%) followed by bla_TEM (23.6%) and bla_OXY (4.55%). Mart, prot6E, steB, fimA, and sopE2 genes (100%) were the most in these isolates. The strains in the dominant PFGE profiles of G1 were all co-resistant to quinolones, cephalosporins, and ACSSuT, and were isolated from different sources. This suggests that existence of these genes lead to the emergence of high-levels of resistance to quinolone and cephalosporin in these ACSSuT resistance pattern isolates. And these isolates are transmitted between humans and food.

Phenotypic Characteristics and Genetic Diversity of Salmonella enterica Serotype Derby Isolated from Human Patients and Foods of Animal Origin

Salmonella enterica serotype Derby is among the three most common serotypes of nontyphoidal Salmonella isolated from patients with diarrhea in China. In this study, 133 Salmonella Derby isolates from human patients (n = 74) and foods of animal origin (n = 59) in Shanghai, China, between September 2013 and December 2014, were selected to study its phenotypic characteristics and genetic diversity. The isolates were subjected to antimicrobial susceptibility testing, plasmid replicon typing, virulence profile determination, and molecular subtyping by pulsed-field gel electrophoresis (PFGE). Isolates were frequently resistant to tetracycline (87.22%), sulfisoxazole (74.44%), and streptomycin (62.41%), and a low frequency of resistance was found toward ofloxacin (3.01%), ceftazidime (2.26%), and cefepime (1.50%); in addition, 93 (69.92%) isolates were multidrug resistant. The most common plasmid incompatibility replicon types were the IncF family (FIA, 51.31%; FIC, 27.82%; and FIB, 21.80%) and IncP types (35.34%): these plasmid types may be associated with the spread of antibiotic resistance and virulence genes. All isolates were positive for the Salmonella pathogenicity island (SPI) gene avrA and the fimbrial gene bcfC from among the 10 virulence genes detected, and most of them carried ssaQ (99.25%), mgtC (97.74%), siiD (98.50%), sopB (97.74%), and sopE (96.99%). PFGE showed 68 patterns in nine main clusters at an 85% similarity threshold. Most of the isolates from different sources possessed the same fingerprints or molecular profiles in each cluster, which strongly suggests the possibility that foods of animal origin, especially pork, serve as an important source for human infection. Moreover, this diversity may suggest strains originating from multiple clones. Therefore, surveillance on this serotype should be strengthened to prevent transmission of Salmonella Derby from foods of animal origin, especially pork, to humans.