Clonality and antimicrobial resistance gene profiles of multidrug- resistant Salmonella enterica serovar infantis isolates from four public hospitals in Rio de Janeiro, Brazil

CRISPR and CRISPR-MVLST reveal conserved spacer distribution and high similarity among Salmonella enterica serovar Infantis genomes from Brazil and other countries

Salmonella enterica serovar Infantis (S. Infantis) is a globally distributed non-typhoid serovar infecting humans and food-producing animals. Considering the zoonotic potential and public health importance of this serovar, strategies to characterizing, monitor and control this pathogen are of great importance. This study aimed to determine the genetic relatedness of 80 Brazilian S. Infantis genomes in comparison to 40 non-Brazilian genomes from 14 countries using Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-Multi-Locus Virulence Sequence Typing (CRISPR-MVLST). CRISPR spacers were searched using CRISPR-Cas++ and fimH and sseL alleles using BLAST and MEGA X. Results were analyzed using BioNumerics 7.6 in order to obtain similarity dendrograms. A total of 23 CRISPR1 and 11 CRISPR2 alleles formed by 37 and 26 types of spacers, respectively, were detected. MVLST revealed the presence of five fimH and three sseL alleles. CRISPR's similarity dendrogram showed 32 strain subtypes, with an overall similarity ≥ 78.6. The CRISPR-MVLST similarity dendrogram showed 37 subtypes, with an overall similarity ≥ 79.2. In conclusion, S. Infantis strains isolated from diverse sources in Brazil and other countries presented a high genetic similarity according to CRISPR and CRISPR-MVLST, regardless of their source, year, and/or place of isolation. These results suggest that both methods might be useful for molecular typing S. Infantis strains using WGS data.

Salmonella enterica serovars linked with poultry in India: antibiotic resistance profiles and carriage of virulence genes

Salmonella is an important poultry pathogen with zoonotic potential. Being a foodborne pathogen, Salmonella-contaminated poultry products can act as the major source of infection in humans. In India, limited studies have addressed the diversity of Salmonella strains of poultry origin. This study represented 26 strains belonging to Salmonella serovars Typhimurium, Infantis, Virchow, Kentucky, and Agona. The strains were tested for resistance to 14 different antimicrobial agents using the Kirby-Bauer disk-diffusion assay. The presence of the invA, hilA, agfA, lpfA, sopE, and spvC virulence genes was assessed by polymerase chain reaction (PCR), and the genetic diversity was assessed by Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR). The highest resistance to tetracycline (n = 17; 65.38%) followed by nalidixic acid (n = 16; 61.53%) was detected among the strains. Among the strains (n = 17) phenotypically resistant to tetracycline, 94% (n = 16) were also positive for the tetA gene. Based on the presence of virulence genes, the strains were characterized into three virulence profiles (PI, P2, and P3). Among the investigated virulence genes, invA, hilA, agfA, and lpfA were present in all strains. The sopE gene was mostly associated with serovars Virchow (n = 3; 100%) and Typhimurium (n = 8; 80%), whereas spvC gene was exclusive for two Typhimurium strains that lacked sopE gene. ERIC-PCR profiling indicated clusters correlating their serovar, geographical, and farm origins. These results demonstrate that Salmonella isolates with a wide genetic range, antibiotic resistance, and virulence characteristics can colonize poultry. The presence of such strains is crucial for both food safety and public health.

Antimicrobial Resistance and Virulence of Non-Typhoidal Salmonella from Retail Foods Marketed in Bangkok, Thailand

Nontyphoidal-Salmonella bacteria cause foodborne gastroenteritis that may lead to fatal bacteremia, osteomyelitis, and meningitis if not treated properly. The emergence of multidrug-resistant Salmonella strains is a global public health threat. Regular monitoring of genotypes and phenotypes of Salmonella isolated from humans, animals, foods, and environments is mandatory for effective reduction and control of this food-borne pathogen. In this study, antimicrobial-resistant and virulent genotypes and phenotypes of Salmonella isolated from retail food samples in Bangkok, Thailand, were investigated. From 252 raw food samples, 58 Salmonella strains that belonged only to serotype Enteritidis were isolated. Disc diffusion method showed that all isolates were still sensitive to amikacin and carbapenems. More than 30% of the isolates were resistant to ampicillin, tetracycline, and ciprofloxacin. Twenty isolates resist at least three antibiotic classes. Minimum inhibitory concentration tests showed that 12.07% of the isolates produced extended-spectrum β-Lactamase. Polymerase chain reaction indicated that 32.76, 81.03, 39.66, and 5.17% of the isolates carried bla_TEM-1, tetA, sul2, and dfrA7, respectively. All isolates were positive for invasion-associated genes. Effective prevention and control of Salmonella (as well as other food-borne pathogens) is possible by increasing public awareness and applying food hygienic practices. Active and well harmonised “One Health” co-operation is required to effectively control food-borne zoonosis.

Genomic characterization and antimicrobial resistance profiles of Salmonella enterica serovar Infantis isolated from food, humans and veterinary-related sources in Brazil

AIMS

To characterize the genetic relatedness, phenotypic and genotypic antimicrobial resistance and plasmid content of 80 Salmonella Infantis strains isolated from food, humans and veterinary sources from 2013 to 2018 in Brazil.

METHODS AND RESULTS

Pulsed-field gel electrophoresis and single-nucleotide polymorphism analysis showed major clusters containing 50% and 38.8% of the strains studied respectively. Multilocus sequence typing assigned all strains to ST32. Disk-diffusion revealed that 90% of the strains presented resistant or intermediate resistant profiles and 38.8% displayed multidrug resistance. Resistance genes for aminoglycosides (aac(6')-Iaa; aadA12; aph(3″-Ib; aph(6)-Id), β-lactams (bla_TEM-1 ; bla_CTX-M-8 ; bla_CMY-2 ), trimethoprim (dfrA8), tetracycline (tet(A)), amphenicols (floR), sulfonamide (sul2), efflux pumps (mdsA; mdsB), chromosomal point mutations in gyrB, parC, acrB and pmrA were detected. Strains harboured IncI, IncF, IncX, IncQ, IncN and IncR plasmids.

CONCLUSIONS

The presence of a prevalent S. Infantis subtype in Brazil and the high antimicrobial resistance rates reinforced the potential hazard of this serovar for the public health and food safety fields.

SIGNIFICANCE AND IMPACT OF THE STUDY

This is the first study characterizing a large set of S. Infantis from Brazil by whole-genome sequencing, which provided a better local and global comprehension about the distribution and characteristics of this serovar of importance in the food, human and veterinary fields.

Investigation of the Genes Involved in the Outbreaks of Escherichia coli and Salmonella spp. in the United States

Salmonella spp. and Escherichiacoli (E. coli) are two of the deadliest foodborne pathogens in the US. Genes involved in antimicrobial resistance, virulence, and stress response, enable these pathogens to increase their pathogenicity. This study aims to examine the genes detected in both outbreak and non-outbreak Salmonella spp. and E. coli by analyzing the data from the National Centre for Biotechnology Information (NCBI) Pathogen Detection Isolates Browser database. A multivariate statistical analysis was conducted on the genes detected in isolates of outbreak Salmonella spp., non-outbreak Salmonella spp., outbreak E. coli, and non-outbreak E. coli. The genes from the data were projected onto a two-dimensional space through principal component analysis. Hierarchical clustering was then used to quantify the relationship between the genes in the dataset. Most of the outlier genes identified in E. coli isolates are virulence genes, while outlier genes identified in Salmonella spp. are mainly involved in stress response. Gene epeA, which encodes a high-molecular-weight serine protease autotransporter of Enterobacteriaceae (SPATE) protein, along with subA and subB that encode cytotoxic activity, may contribute to the pathogenesis of outbreak E. coli. The iro operon and ars operon may play a role in the ecological success of the epidemic clones of Salmonella spp. Concurrent relationships between esp and ter operons in E. coli and pco and sil operons in Salmonella spp. are found. Stress-response genes (asr, golT, golS), virulence gene (sinH), and antimicrobial resistance genes (mdsA and mdsB) in Salmonella spp. also show a concurrent relationship. All these findings provide helpful information for experiment design to combat outbreaks of E. coli and Salmonella spp.

Genetic Profiles and Antimicrobial Resistance Patterns of Salmonella Infantis Strains Isolated in Italy in the Food Chain of Broiler Meat Production

This work aimed to evaluate the antimicrobial susceptibility of 87 Salmonella Infantis strains isolated in Italy from 2016 to 2019 along the food chain of broiler meat production and in humans and to determine the genetic profiles of the strains in order to establish a possible correlation with the antimicrobial pattern. All isolates were tested by the disk diffusion method to evaluate antimicrobial susceptibility toward sixteen antimicrobials, and the broth microdilution method was used to confirm extended spectrum β-lactamase (ESBL) production. PCR and pulsed field gel electrophoresis (PFGE) were applied to characterize ESBL-encoding and AmpC β-lactamase genes and to analyze the S. Infantis strains genetic profiles respectively. S. Infantis isolates showed high prevalence of resistance, in particular toward nalidixic acid (97.7%), tetracycline (96.5%), sulphamethoxazole/trimethoprim (91%) and cefepime (72.4%). The 80.5% of isolates were ESBL, cefotaxime-resistant, carrying the bla_CTX-M1 gene. The most prevalent PFGE profile was XbaI.0126 (35.6%). The remaining strains had a genetic homology from 81% to 97% with the XbaI.0126 profile. The strains belonging to these profiles were isolated from different matrices collected along the broiler food chain independently on the year and from the region and there was no correlation between the PFGE profiles and resistance patterns. We found two ESBL-producing S. Infantis strains with the same XbaI.2621 profile isolated from humans and from poultry feces, not yet reported in Italy. Our findings confirmed the diffusion of ESBL-multi drug resistant (MDR) S. Infantis along the broiler food chain and in humans and underlined the importance of continuous monitoring to control and to reduce the prevalence of this bacterium, applying a global One Health approach.

Molecular identification and antibiotic resistance profiling of Salmonella species isolated from chickens in eastern Turkey

BACKGROUND

The aim of this study was to obtain quantitative data about the frequency, genotypic characterization and antibiotic resistance profiling of Salmonella agents in chicken flocks located in eastern Turkey.

RESULTS

Feces samples representing at least 20% of the flock area were collected via sock swabs from commercial poultry flocks in the study region in addition to internal organs (liver, spleen, intestine) collected at necropsy of suspected chickens belonging to small family enterprises. The samples were analyzed by conventional bacteriological methods (ISO 6579:2002/A1:2007) for isolation, and genus specific (invA) PCR for the identification of Salmonella spp. Then, two mPCR were set up to determine Salmonella serotypes and genotypic resistance status of the field isolates against ampicillin, tetracycline, trimethoprim-sulfamethoxazole and chloramphenicol antibiotics. In the PCR analysis of the suspected colonies, 98.5% were confirmed as Salmonella spp., and, the most prevalent serotype was identified as S. Infantis with the proportion of 26.6% (17/64), followed by S. Enteritidis with 21.9% (14/64) and S. Typhimurium with 9.4% (6/64). The findings related to antibiotic resistance genes revealed that the most frequently determined gene was sul1 with approximately 58%, while the blaTEM gene was detected at the lowest proportion with 20%, among Salmonella isolates.

CONCLUSIONS

The results indicated that Salmonella infections constitute a potential risk for chicken flocks in the country and that genotypic resistance rates against various antibiotics should draw particular attention in terms of both human and animal health.

Antimicrobial Resistance in Nontyphoidal Salmonella Isolates from Human and Swine Sources in Brazil: A Systematic Review of the Past Three Decades

Salmonella is the leading cause of foodborne illnesses worldwide. The widespread use of antimicrobials as prophylactic, therapeutic, and growth promoters in both livestock and human medicine has resulted in selective pressure regarding antimicrobial-resistant (AMR) bacteria. This systematic review summarizes phenotypic antimicrobial resistance profiles in Salmonella isolates from human and swine sources between 1990 and 2018 in Brazil. The 20 studies that matched the eligibility criteria-isolates from pigs and humans from Brazil, between 1990 and 2016, containing information on the number of Salmonella isolates, and applying the disk diffusion susceptibility method-were included. During the assessed period, Salmonella strains isolated from swine sources displayed the highest resistance rates for tetracycline (20.3%) and sulfonamides (17.4%). In contrast, human isolates displayed the highest resistance rates against ampicillin (19.8%) and tetracycline (17%). Salmonella Typhimurium was the most frequent AMR isolate from both swine and human sources, corresponding to 67% of all isolates. From 2001 to 2005, tetracycline and ampicillin were the top antimicrobial resistance compounds, and the most frequently detected in swine and human sources, respectively. A total of 63 and 58 multiple drug resistance profiles were identified in swine and human isolates, respectively. Antimicrobial resistance has decreased throughout the 1990-2016 period, except for gentamicin and nalidixic acid in swine and human isolates, respectively. The results indicate that Salmonella isolated from human and swine display resistance against clinically important antimicrobials, indicating that swine are possibly one of the main vectors for spreading human salmonellosis in Brazil.

Draft Genome Sequences of 26 Salmonella Isolates Associated with Multiple Outbreaks in Brazil

Salmonella enterica subsp. enterica isolates are the leading cause of foodborne illness worldwide. Here, we report the draft genomes of 26 Salmonella isolates of food and clinical origin, belonging to four serovars, associated with outbreaks from 1999 to 2006 in the south of Brazil.

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.

Phenotypic and genotypic drug resistance profile of Salmonella serovars isolated from poultry farm and processing units located in and around Mumbai city, India

BACKGROUND AND AIM

The extensive use of antimicrobials in poultry has led to an increase in bacterial multidrug resistance, and the emergence of multidrug-resistant nontyphoidal Salmonella is a global problem. This study was performed to detect antibiotic-resistant Salmonella serovars in poultry farming and processing environment.

MATERIALS AND METHODS

A total of 956 various samples, comprising 432 farm origin, 324 poultry processing stage wise and environmental, and 154 product processing stages and environmental samples, were collected from poultry farms and processing units located in and around Mumbai city. Of a total of 71 recovered isolates, 42 randomly selected Salmonella isolates were subjected for antibiotic susceptibility testing by disk diffusion method and serotyping. A total of 31 serotypically confirmed isolates were characterized for the presence of tetA, tetB, bla TEM, and CTX-M gene.

RESULTS

Higher resistance was recorded against Doxycycline (100%), followed by Oxytetracycline (97.62%), Neomycin (88.10%), Erythromycin (83.33%), Tetracycline (78.57%), and Ceftizoxime (35.71%). Resistance from 0.00 to 26.19 percent was found to antimicrobials, namely Norfloxacin (26.19%), Ampicillin (21.43%), Azithromycin (21.43%), Ciprofloxacin (19.05%), Colistin (4.76%), Streptomycin (16.67%), Cefotaxime (14.19%), Enrofloxacin (14.29%), Amoxyclav (14.29%), Gentamicin (7.14%), Chloramphenicol (4.76%), Amikacin (4.76%), and Ceftazidime (0.0%). Results demonstrate that the Salmonella Virchow dominated and all serotypes were found to carry Tetracycline resistance gene tetA, 5 isolates were found to be positive for blaTEM , whereas none of the isolates were carrying tetB and CTX-M gene.

CONCLUSION

This study revealed that there is a significant rise of Tetracycline resistance with the presence of tetA gene in Salmonella spp. which indicates selective pressure for adopting resistance against tetracycline group of antibiotics.

Detection of common clones of Salmonella enterica serotype Infantis from human sources in Tehran hospitals

AIM

The aims of this study were to investigate antibiotic resistance pattern and molecular characterization of Salmonella Infantis strains, isolated from human sources in Tehran hospitals from 2008 to 2010.

BACKGROUND

Infection caused by Salmonella is one of the major public health problems. Despite the clinical importance of Salmonella enteric subsp. enteric serovar Infantis in humans, there is no information available about the common clones of Salmonella Infantis in clinical isolates in Iran.

METHODS

S. Infantis strains were identified by conventional microbiological and serological testing. The antimicrobial susceptibility of the S.Infantis isolates was determined using the disk diffusion method. The genetic relatedness and the dominant clones of S. Infantis strains were detected by the Multi Locus Sequence Typing (MLST) and pulsed-field gel electrophoresis (PFGE) techniques.

RESULTS

More than 80% of the S. Infantis isolates represented multidrug-resistant patterns. PFGE revealed high genetic similarity among S. Infantis strains. While, MLST indicated high-clonal similarity among strains, where all S. Infantis strains were assigned to the ST32 sequence type.

CONCLUSION

This is the first study in Iran conducted to determine the sequence types of S. Infantis in clinical isolates using MLST. The genetically closed MDR S. Infantis clones were responsible for the apparent endemic occurrence of salmonellosis, caused by this Salmonella serovar, in Tehran.

Multiple clones and low antimicrobial resistance rates for Salmonella enterica serovar Infantis populations in Greece

All the Salmonella enterica ser. Infantis strains isolated under official control programs in Greece during a four year period were studied, 23 of human origin, 16 from food animals and one from food. Molecular analyses (PFGE) in combination with antimicrobial susceptibility testing were used to study whether the occurrence S. Infantis in Greece resulted from different biotypes or a successful spread of one clone. Low rates of antimicrobial resistance were observed, except for streptomycin among human isolates (48%), indicating that selective pressure due to consumption of antimicrobials has not resulted the spread of dominant clones. Pulsed Field Gel Electrophoresis revealed 31 XbaI distinct pulsotypes among the 40 strains with 60% overall similarity reflecting diversity. Four main clusters were constructed, using an 85% cut off value, clusters A, B, C and D consisting of 14, 6, 8 and 8 isolates respectively. Point source of transmission was not hypothesized as multiple reservoirs of the serovar seem to be present in Greece during the study period.

Epidemiological, molecular characterization and antibiotic resistance of Salmonella enterica serovars isolated from chicken farms in Egypt

BACKGROUND

Salmonella is one of major causes of foodborne outbreaks globally. This study was conducted to estimate the prevalence, typing and antibiotic susceptibilities of Salmonella enterica serovars isolated from 41 broiler chicken farms located in Kafr El-Sheikh Province in Northern Egypt during 2014-2015. The clinical signs and mortalities were observed.

RESULTS

In total 615 clinical samples were collected from broiler flocks from different organs (liver, intestinal content and gall bladder). Salmonella infection was identified in 17 (41%) broiler chicken flocks and 67 Salmonella isolates were collected. Recovered isolates were serotyped as 58 (86.6%) S. enterica serovar Typhimurium, 6 (9%) S. enterica serovar Enteritidis and 3 (4.5%) were non-typable. The significant high mortality rate was observed only in 1-week-old chicks. sopE gene was detected in 92.5% of the isolates which indicating their ability to infect humans. All S. enterica serovar Enteritidis isolates were susceptible to all tested antimicrobials. The phenotypically resistant S. enterica serovar Typhimurium isolates against ampicillin, tetracycline, sulphamethoxazole and chloramphenicol were harbouring BlaTEM, (tetA and tetC), (sul1 and sul3) and (cat1 and floR), respectively. The sensitivity rate of S. enterica serovar Typhimurium to gentamycin, trimethoprim/sulphamethoxazole and streptomycin were 100, 94.8, 89.7%, respectively. The silent streptomycin antimicrobial cassettes were detected in all Salmonella serovars. A class one integron (dfrA12, orfF and aadA2) was identified in three of S. enterica serovar Typhimurium strains.

CONCLUSIONS

To the best of our knowledge, this study considered first report discussing the prevalence, genotyping, antibiotic susceptibility and public health significance of S. enterica serovars in broilers farms of different ages in Delta Egypt. Further studies are mandatory to verify the location of some resistance genes that are within or associated with the class one integron.

Antimicrobial Resistance in Nontyphoidal Salmonella Isolated from Human and Poultry-Related Samples in Brazil: 20-Year Meta-Analysis

Nontyphoidal Salmonella are one of the leading causes of foodborne diseases in the world. As poultry products are recognized as main sources of human salmonellosis, nontyphoidal Salmonella control has become a global issue for the poultry industry. The increasing antimicrobial resistance in poultry-related nontyphoidal Salmonella serovars is a global matter of concern. By monitoring the evolution of antimicrobial resistance, alternative treatments can be identified and possible restrictions in the treatment of systemic human salmonellosis foreseen. A meta-analysis was conducted to assess the profile and temporal evolution of the antimicrobial resistance of nontyphoidal Salmonella of poultry and human origin in Brazil, isolated in the period from 1995 to 2014. Four databases were researched; twenty-nine articles met the eligibility criteria and were included in the meta-analysis. In the nontyphoidal isolates of poultry origin, the highest levels of antimicrobial resistance were verified for sulfonamides (44.3%), nalidixic acid (42.5%), and tetracycline (35.5%). In the human-origin isolates, the resistance occurred mainly for sulfonamides (46.4%), tetracycline (36.9%), and ampicillin (23.6%). Twenty-two articles described results of antimicrobial resistance specifically for Salmonella Enteritidis, also enabling the individual meta-analysis of this serovar. For most antimicrobials, the resistance levels of Salmonella Enteritidis were lower than those found when considering all the nontyphoidal serovars. In the poultry-origin isolates, a quadratic temporal distribution was observed, with reduced resistance to streptomycin in Salmonella Enteritidis and in all nontyphoidal serovars, and a linear increase of resistance to nalidixic acid in Salmonella Enteritidis. In the human-origin isolates, a linear increase was identified in the resistance to nalidixic acid in Salmonella Enteritidis and in all the nontyphoidal isolates, and to gentamicin in Salmonella Enteritidis. Continuous monitoring of the development and spread of antimicrobial resistance could support the measurement of the consequences on poultry and human health.

Multiple-locus variable-number tandem repeat analysis (MLVA) for genotyping of Salmonella enterica subspecies enterica serotype Infantis isolated from human sources

Salmonella is an important cause of food-borne infection worldwide. Detection of outbreaks caused by Salmonella spp. relies on suitable and robust methods for genotyping. Little is known about the genetic diversity of the Salmonella enterica subspecies enterica serotype Infantis strains isolated from human sources in Iran. In this study, 40 isolates of S. Infantis, which were previously recovered from patients with gastroenteritis or diarrhea in Tehran between years 2007 and 2009, were subjected to multiple-locus variable-number of tandem repeat (VNTR) analysis (MLVA), pulsed-field gel electrophoresis (PFGE), and ERIC-PCR. Using MLVA method, 31 types were identified. The MLVA clustering of the isolates by the unweighted pair group method with arithmetic mean (UPGMA) revealed the presence of two major clusters. The discriminatory power of MLVA was superior to that of PFGE and ERIC-PCR. Overall, our data showed that MLVA assay could effectively differentiate closely related strains. It is technically simple and inexpensive to perform. Furthermore, MLVA can be used as a helpful method for epidemiological investigations.

Antimicrobial Susceptibility of Bordetella bronchiseptica Isolates from Swine and Companion Animals and Detection of Resistance Genes

Bordetella bronchiseptica causes infections of the respiratory tract in swine and other mammals and is a precursor for secondary infections with Pasteurella multocida. Treatment of B. bronchiseptica infections is conducted primarily with antimicrobial agents. Therefore it is essential to get an overview of the susceptibility status of these bacteria. The aim of this study was to comparatively analyse broth microdilution susceptibility testing according to CLSI recommendations with an incubation time of 16 to 20 hours and a longer incubation time of 24 hours, as recently proposed to obtain more homogenous MICs. Susceptibility testing against a panel of 22 antimicrobial agents and two fixed combinations was performed with 107 porcine isolates from different farms and regions in Germany and 43 isolates obtained from companion animals in Germany and other European countries. Isolates with increased MICs were investigated by PCR assays for the presence of resistance genes. For ampicillin, all 107 porcine isolates were classified as resistant, whereas only a single isolate was resistant to florfenicol. All isolates obtained from companion animals showed elevated MICs for β-lactam antibiotics and demonstrated an overall low susceptibility to cephalosporines. Extension of the incubation time resulted in 1-2 dilution steps higher MIC50 values of porcine isolates for seven antimicrobial agents tested, while isolates from companion animals exhibited twofold higher MIC50/90 values only for tetracycline and cefotaxime. For three antimicrobial agents, lower MIC50 and MIC90 values were detected for both, porcine and companion animal isolates. Among the 150 isolates tested, the resistance genes blaBOR-1 (n = 147), blaOXA-2, (n = 4), strA and strB (n = 17), sul1 (n = 10), sul2 (n = 73), dfrA7 (n = 3) and tet(A) (n = 8) were detected and a plasmid localisation was identified for several of the resistance genes.

Molecular identification of Salmonella Infantis isolated from backyard chickens and detection of their resistance genesby PCR

This study aims at molecular identification of Salmonella Infantis isolated from backyard chickens and the detection of their antibiotic resistance genes. A total of 46 Salmonella-suspected samples isolated from backyard chickens of northern Iran were collected. Serotyping was done by the traditional method and then confirmed by PCR. Antimicrobial susceptibility of the isolates against 13 antimicrobial agents was determined by the standard disk diffusion method. There were 44 samples identified as Salmonella. Serotyping results showed that all 44 isolates belonged to serogroup C1 and serovar Infantis. The most resistance observed was to tetracycline and doxycycline (100%), chloramphenicol (79%) and florfenicol (72%). The floR, catI, tetA and tetG genes were used for the detection of florfenicol chloramphenicol and tetracycline resistance. In order to identify the phenotypic resistance in strains which showed resistance genes by PCR, colony PCR and culture on plates each containing antibiotic was performed simultaneously. All the Salmonella Infantis resistant to florfenicol and chloramphenicol harbored floR and catI. None of the Salmonella resistant to tetracycline carried tetA or tetG. The result of colony PCR and culture in antibiotic medium confirmed the results of PCR and indicated phenotypic resistance in these samples.

Quantification and characterization of Salmonella spp. isolates in sewage sludge with potential usage in agriculture

Background

This study aims to scrutinize Salmonella spp. and its serotypes in sewage sludge samples from wastewater treatment plants, and assesses the presence of virulence genes and antibiotics resistant to the profile. Samples (n = 54) were collected and analyzed in accordance with the EPA Method 1682/2006. For positive serological reaction, 40 strains were selected for PCR analyses and detection of spvC, invA and sseL virulence genes, plasmid presence and resistance to antibiotics.

Results

Salmonella spp. was detected in 38.9% of the samples collected (<0.006473 to 12.19 MPN/gTS). The most prevalent serotype was Salmonella Infantis. All Salmonella spp. (n = 35) presented at least one of the three virulence genes mentioned above and 40% harboured plasmids. Salmonella Typhimurium strains were isolated harbouring at least one of the following virulence genes: spvC, invA or sseL. Four Salmonella spp. isolates were resistant to tetracycline; three were resistant to trimethoprim-sulfamethoxazole, and one isolate was resistant to ciprofloxacin. Two Salmonella spp. strains presented multi resistance to antimicrobial agents.

Conclusions

The results obtained demonstrated that Salmonella spp. have been found in sewage sludge, thus it is essential to set measures to mitigate human health risks when it is intended to be applied on agricultural soils.

Plasmid profile and pulsed-field gel electrophoresis analysis of Salmonella enterica isolates from humans in Turkey

This study was conducted for typing Salmonella enterica subspecies enterica strains in Turkey using pulsed–field gel electrophoresis (PFGE) and plasmid DNA profile analysis. Fourty-two strains were isolated from clinical samples obtained from unrelated patients with acute diarrhea. The samples were collected from state hospitals and public health laboratories located at seven provinces in different regions of Turkey at different times between 2004 and 2010. The strains were determined to belong to 4 different serovars. The Salmonella enterica strains belonged to the serovars Salmonella Enteritidis (n = 23), Salmonella Infantis (n = 14), Salmonella Munchen (n = 2), and Salmonella Typhi (n = 3). Forty-two Salmonella enterica strains were typed with PFGE methods using XbaI restriction enzyme and plasmid analysis. At the end of typing, 11 different PFGE band profiles were obtained. Four different PFGE profiles (type 1, 4, 9, and 10) were found among serotype S. Enteritidis species, 3 different PFGE profiles (type 3, 5, 6) were found among S. Infantis species, 2 different PFGE profiles were found among S. Typhi species (type 2 and 11), and 2 different PFGE profiles were found among S. Munchen species (type 7, 8). The UPGMA dendrogram was built on the PFGE profiles. In this study, it was determined that 4 strains of 42 Salmonella enterica strains possess no plasmid, while the isolates have 1–3 plasmids ranging from 5.0 to 150 kb and making 12 different plasmid profiles (P1–P12). In this study, we have applied the analysis of the PFGE patterns and used bioinformatics methods to identify both inter and intra serotype relationships of 4 frequently encountered serotypes for the first time in Turkey.

Clonal spread of Salmonella enterica serovar Infantis in Serbia: acquisition of mutations in the topoisomerase genes gyrA and parC leads to increased resistance to fluoroquinolones

Quinolone-resistant Salmonella Infantis (n = 64) isolated from human stool samples, food and poultry during the years 2006-2011 were analysed for their resistance phenotypes, macrorestriction patterns and molecular mechanisms of decreased susceptibility to fluoroquinolones. Minimum inhibitory concentrations (MICs) of nalidixic acid (NAL) and ciprofloxacin (CIP) were determined by the agar dilution procedure, and the susceptibility to additional antimicrobial agents was determined by the disc diffusion method. To assess the influence of enhanced efflux activity, MICs were determined in the presence and absence of the inhibitor PAβN. The results of pulsed-field gel electrophoresis (PFGE) typing revealed that quinolone-resistant S. Infantis in Serbia had similar or indistinguishable PFGE profiles, suggesting a clonal spread. All S. Infantis showed combined resistance to NAL and tetracycline, whereas multiple drug resistance to three or more antibiotic classes was rare (2 isolates of human origin). The MICs ranged between 512 and 1024 μg/mL for NAL and 0.125-2 μg/mL for CIP. A single-point mutation in the gene gyrA leading to a Ser83→Tyr exchange was detected in all isolates, and a second exchange (Ser80→Arg) in the gene parC was only present in eight S. Infantis isolates exhibiting slightly higher MICs of CIP (2 μg/mL). The inhibitor PAβN decreased the MIC values of CIP by two dilution steps and of NAL by at minimum 3-6 dilution steps, indicating that enhanced efflux plays an important role in quinolone resistance in these isolates. The plasmid-mediated genes qnr, aac(6')-lb-cr and qepA were not detected by PCR assays.

Evaluation of virulence and antimicrobial resistance in Salmonella enterica serovar Enteritidis isolates from humans and chicken- and egg-associated sources

Salmonella enterica serovar Enteritidis is a leading cause of salmonellosis throughout the world and is most commonly associated with the consumption of contaminated poultry and egg products. Salmonella Enteritidis has enhanced ability to colonize and persist in extraintestinal sites within chickens. In this study, 54 Salmonella Enteritidis isolates from human patients (n=28), retail chicken (n=9), broiler farms (n=9), and egg production facilities (n=8) were characterized by antimicrobial susceptibility testing, plasmid analysis, genetic relatedness using XbaI and AvrII pulsed-field gel electrophoresis (PFGE), and the presence of putative virulence genes. Nine isolates were evaluated for their abilities to invade and survive in intestinal epithelial and macrophage cell lines. Overall, 56% (n=30) of isolates were resistant to at least one antimicrobial agent tested, yet no isolates showed resistance to more than three antimicrobials. All isolates carried a common ∼55-kb plasmid, with some strains containing additional plasmids ranging from 3 to 50 kb. PFGE analysis revealed five XbaI and AvrII clusters. There were significant overlaps in the PFGE patterns of the isolates from human, chicken, and egg houses. All isolates tested PCR positive for iacP, purR, ttrB, spi4H, rmbA, sopE, invA, sopB, spvB, pagC, msgA, spaN, orgA, tolC, and sifA, and negative for iss, virB4, and sipB. Of the isolates selected for virulence testing, those containing the iron acquisition genes, iutA, sitA, and iucA, and ∼50-kb plasmids demonstrated among the highest levels of macrophage and epithelial cell invasion, which may indicate their importance in pathogenesis.

Molecular epidemiology and virulence markers of Salmonella Infantis isolated over 25 years in São Paulo State, Brazil

Infection of humans and animals caused by Salmonella is a major public health problem worldwide. Among the more than 2500 serovars, S. Infantis has been one of the 15 most isolated serovars in the world. Despite its clinical importance, little is known about the molecular characteristics of S. Infantis strains from Brazil. The aims of this study were to type S. Infantis isolates of this country and to assess their pathogenic potential. The molecular epidemiology of 35 S. Infantis strains, isolated from human sources (25) and food items (10) between 1984 and 2009 in São Paulo State, Brazil, were investigated using ERIC-PCR, PFGE and MLST. Furthermore, the presence of some virulence markers from Salmonella pathogenicity islands (SPIs) SPI-1 and SPI-2 and from the virulence plasmid was assessed by PCR. Using ERIC-PCR, 34 S. Infantis strains exhibited a high genetic similarity (≥ 93.7%) and using PFGE, 32 strains exhibited a similarity ≥ 80.6%. Additionally, MLST showed a high clonal similarity among strains that all presented the same ST32. Thirty-two isolates under investigation contained the virulence markers invA, sopB, sopD, sipA, sipD, ssaR, sifA, flgK, fljB and flgL. In conclusion, the S. Infantis strains studied were genetically similar, suggesting that a prevalent subtype has been causing disease and food contamination during a 25year period in São Paulo State, an important metropolitan region in Brazil. Furthermore, the contamination between strains from food items and sick humans indicates that better control measures for S. Infantis may be needed in this country.

Typing ofSalmonella entericaserovar Infantis isolates from 51 outbreaks in Germany between 1974 and 2009 by a novel phage-typing scheme

We developed a new phage-typing method and evaluated its application in combination withXbaI macrorestriction analysis by pulsed-field gel electrophoresis (PFGE) as a useful tool for the long-term epidemiology ofSalmonella entericaserovar Infantis. In this study, we investigated 1008S.Infantis isolates recovered from humans, various animal species and food products from 1973 to 2009. The typing scheme is based on 17 typing phages, defining 61 different patterns within the strain collection. The experiments showed that phage typing is a reliable method for differentiation of outbreaks and sporadic clinical cases as well as for elucidation of chains of transmission. The combined analysis of phage typing and PFGE revealed the existence of epidemic clones with a high stability over time like PT29/XB27 which was identified in nosocomial salmonellosis, community outbreaks as well as in broiler chickens from 2002 to 2009.

Diversity of integron- and culture-associated antibiotic resistance genes in freshwater floc

Clinically important antibiotic resistance genes were detected in culturable bacteria and class 1 integron gene cassettes recovered from suspended floc, a significant aquatic repository for microorganisms and trace elements, across freshwater systems variably impacted by anthropogenic activities. Antibiotic resistance gene cassettes in floc total community DNA differed appreciably in number and type from genes detected in bacteria cultured from floc. The number of floc antibiotic resistance gene cassette types detected across sites was positively correlated with total (the sum of Ag, As, Cu, and Pb) trace element concentrations in aqueous solution and in a component of floc readily accessible to bacteria. In particular, concentrations of Cu and Pb in the floc component were positively correlated with floc resistance gene cassette diversity. Collectively, these results identify suspended floc as an important reservoir, distinct from bulk water and bed sediment, for antibiotic resistance in aquatic environments ranging from heavily impacted urban sites to remote areas of nature reserves and indicate that trace elements, particularly Cu and Pb, are geochemical markers of resistance diversity in this environmental reservoir. The increase in contamination of global water supplies suggests that aquatic environments will become an even more important reservoir of clinically important antibiotic resistance in the future.

The establishment of Enterobacteriaceae and Salmonella London in a new dairy farm environment

Salmonella spp. are important zoonotic pathogens in humans and animals. A longitudinal study was conducted at the Iowa State University's campus (at the Dairy/Animal Science Education and Discovery Facility) to observe change in Enterobacteriaceae (specifically Salmonella) before and after the placement of dairy livestock. To our knowledge, this is the first study that evaluated environmental changes of Gram-negative organisms in a new dairy farm environment. Environmental samples were taken using drag swabs and immediately processed in the laboratory using phenotypic methods (replica plating, the BBL Crystal Identification System for enteric/nonfermenter organisms™, and plating on specialized media/broths). Genotypic methods were also used (BAX PCR™ and pulsed-field gel electrophoresis). Organisms identified as Salmonella were sent to the National Veterinary Services Laboratory (Ames, IA) for confirmatory serotyping. Resistance to antibiotics (ampicillin, nalidixic acid, and tetracycline) was determined by replica plating of Enterobacteriaceae and Salmonella isolates using the guidelines of the National Antimicrobial Resistance Monitoring System and Clinical and Laboratory Standards Institute. The microflora of Enterobacteriaceae changed as cattle were introduced and as time progressed. Additionally, multidrug-resistant isolates began to appear immediately after cattle were introduced (multidrug-resistant isolates were rare prior to introduction of livestock). Variables such as temperature and humidity did not affect the proliferation of bacterial organisms. Seventeen Salmonella isolates were identified as Salmonella London and three isolates as Salmonella Montevideo. Based on pulsed-field gel electrophoresis-generated dendrograms, it is likely that 17 Salmonella London isolates and 3 Salmonella Montevideo isolates are clonal.

CTX-M-2-producing Salmonella Typhimurium isolated from pediatric patients and poultry in Brazil

Ten Salmonella enterica serovar Typhimurium isolates producing CTX-M-2 extended-spectrum beta-lactamase were identified from clinical and poultry sources in two distant cities in Brazil between 2003 and 2004. They included two isolates from pediatric patients and eight isolates from poultry or its environment. All isolates exhibited coresistance to non-beta-lactam antimicrobials including tetracycline and trimethoprim/sulfamethoxazole. The CTX-M-2 gene was located on transferable plasmids with sizes between 90 and 170 kb that also carried other resistance determinants in some isolates. By pulsed-field gel electrophoresis, the genetic similarity of the isolates including clinical and poultry ones ranged from 89% to 100%.

A comparison of three molecular typing methods for the discrimination of Salmonella enterica serovar Infantis

Seventy-six epidemiologically unrelated Salmonella enterica serovar Infantis (S. Infantis) isolates were typed by pulsed-field gel electrophoresis (PFGE), multiple amplification of phage loci typing (MAPLT) and multiple-locus variable-number tandem-repeat analysis (MLVA). PFGE, using the restriction endonuclease XbaI, generated 23 different profiles for the 76 isolates (DI=0.848). MAPLT was undertaken using a combination of 11 primer sets based on bacteriophage sequences and generated 28 different profiles (DI=0.938). By contrast, MLVA only produced nine profiles (DI=0.668) with 13 different primer sets, including the five primer sets routinely used for S. Typhimurium typing. Reducing the number of MAPLT primer sets to four still provided a diversity index of 0.838. All three typing methods revealed two distinct lineages of S. Infantis, with most isolates demonstrating genetic traits of either lineage but not both. The results demonstrate that MAPLT can potentially provide greater discrimination and separation of S. Infantis isolates than both PFGE and MLVA. Furthermore, MAPLT data can be generated much more rapidly and with reduced labour input than PFGE and without the need for expensive PFGE electrophoresis equipment, nor does it require capillary sequencing of PCR fragments to accurately determine PCR fragment lengths as is the case with MLVA.

Antimicrobial resistance genes associated with Salmonella enterica serovar newport isolates from food animals

Salmonella enterica serotype Newport is an important cause of salmonellosis, with strains increasingly being resistant to multiple antimicrobial agents. The increase is associated with the acquisition of multiple resistance genes. This study characterizes the genetic basis of resistance of serotype Newport isolates collected from veterinary sources by PCR and DNA sequencing analysis.

Weakening of salmonella with selected microbial metabolites of berry-derived phenolic compounds and organic acids

Gram-negative bacteria are important food spoilage and pathogenic bacteria. Their unique outer membrane (OM) provides them with a hydrophilic surface structure, which makes them inherently resistant to many antimicrobial agents, thus hindering their control. However, with permeabilizers, compounds that disintegrate and weaken the OM, Gram-negative cells can be sensitized to several external agents. Although antimicrobial activity of plant-derived phenolic compounds has been widely reported, their mechanisms of action have not yet been well demonstrated. The aim of our study was to elucidate the role of selected colonic microbial metabolites of berry-derived phenolic compounds in the weakening of the Gram-negative OM. The effect of the agents on the OM permeability of Salmonella was studied utilizing a fluorescence probe uptake assay, sensitization to hydrophobic antibiotics, and lipopolysaccharide (LPS) release. Our results show that 3,4-dihydroxyphenylacetic acid, 3-hydroxyphenylacetic acid, 3-(3,4-dihydroxyphenyl)propionic acid (3,4-diHPP), 3-(4-hydroxyphenyl)propionic acid, 3-phenylpropionic acid, and 3-(3-hydroxyphenyl)propionic acid efficiently destabilized the OM of Salmonella enterica subsp. enterica serovar Typhimurium and S. enterica subsp. enterica serovar Infantis as indicated by an increase in the uptake of the fluorescent probe 1-N-phenylnaphthylamine (NPN). The OM-destabilizing activity of the compounds was partially abolished by MgCl2 addition, indicating that part of their activity is based on removal of OM-stabilizing divalent cations. Furthermore, 3,4-dihydroxyphenylacetic acid, 3-hydroxyphenylacetic acid, and 3,4-diHPP increased the susceptibility of S. enterica subsp. enterica serovar Typhimurium strains for novobiocin. In addition, organic acids present in berries, such as malic acid, sorbic acid, and benzoic acid, were shown to be efficient permeabilizers of Salmonella as shown by an increase in the NPN uptake assay and by LPS release.