The Study of Genetic Relationship Among Third Generation Cephalosporin-resistant Salmonella enterica Strains by ERIC-PCR

Molecular Typing of Different Salmonella Serotypes by Multiple-Locus Analysis of Tandem Repeats

Salmonella enterica subspecies enterica causes salmonellosis in humans and animals and is an important cause of food infections worldwide. In recent years, the multiple-locus variable-number of tandem repeat (VNTR) analysis (MLVA), a fast molecular typing method with strong epidemiological discrimination, has facilitated the effective control of diverse infections. This study aimed at the typing of 28 human origined Salmonella enteritidis, Salmonella infantis, and Salmonella typhimurium strains by using a single MLVA protocol. Previously these strains have been identified by pulsed field gel electrophoresis (PFGE) method and it has been shown that each strain produced a distinct PFGE banding profile. One MLVA protocol was tested on 3 serotypes simultaneously and it produced three banding patterns specific to each of the three common Salmonella serotypes. MLVA also constitute a relatively more cost-effective and faster method than PFGE.

The Frequency of Resistance Genes in Salmonella enteritidis Strains Isolated from Cattle

BACKGROUND

Salmonella enteritidis causes infections in humans and animals. Antibiotics are used to eliminate bacterial infections, which become resistant to antibiotics after a while. This study aimed to isolate S. enteritidis from cattle feces samples and also to evaluate the frequency of genes associated with multi-drug resistance (MDR).

METHODS

One hundred ten fecal samples of cattle were collected from Jul to Dec, 2017 in Khuzestan Province, southern Iran. Bacterial culture and molecular methods were used to isolate and identify S. enteritidis. Disk diffusion method was used to assess antibiotic susceptibility. Then Polymerase chain reaction (PCR), assay was used for definitive diagnosis of S. enteritidis and resistance genes.

RESULTS

Overall, 101 (91.81%) samples were detected to be contaminated with Salmonella genus and 86 samples (85.14%) were identified as S. enteritidis. The highest and lowest antibiotic resistance were belonged to gentamicin (n=70, 81.39%), and tetracycline (n=6, 6.97%). Besides, 64 samples (74.42%) had 2-10 drugs resistance patterns. Moreover, the highest and the least resistance were related to bla_IMP-1 (n=73, 84.88%) and tet(B) (n=49, 56.97%) genes respectively.

CONCLUSION

The drug-induced genes in S. enteritidis have a high frequency. Therefore, antibiotic resistance and high MDR to antibiotics can be due to the incorrect use of antibiotics and the lack of health monitoring in Cattle farms.

Study on antibiotic susceptibility of Salmonella typhimurium L forms to the third and forth generation cephalosporins

Salmonella typhimurium is a pathogenic gram-negative bacterium, which is found primarily in the intestinal lumen. It often causes diarrhea in infants and young children and leads to food poisoning. Drug resistance of Salmonella typhimurium presented serious complications in clinical patients. In this study, we investigated the antibiotic susceptibility of Salmonella typhimurium standard strain L forms to the third and forth generation cephalosporins, in order to control and eliminate Salmonella typhimurium L forms in infection treatment. Salmonella typhimurium L forms were induced by β-lactam antibiotic cefazolin in the culture medium of bacterial L forms. The antibiotic susceptibility of Salmonella typhimurium L forms was analyzed by K-B drug susceptibility testing. The change trend of drug susceptibility and resistance of Salmonella typhimurium L forms was obtained in accordance with USA clinical and laboratory standards institute (CLSI) evaluation data and statistical analysis. Drug resistance of Salmonella typhimurium L forms showed little increasing trend compared with their parent bacteria. The L form inhibition zone was smaller than in the parent bacteria. However, the drug susceptibility of L forms of Salmonella typhimurium to the third and forth generation cephalosporins remained sensitive.The antibiotic susceptibility of Salmonella typhimurium L forms to the third and forth generation cephalosporins remains sensitive, and the combined use of multi-antibiotics is a convenient and effective method to reduce Salmonella typhimurium L forms occurrence.

Distribution of extended-spectrum β-lactamases (ESBLs) among Salmonella serogroups isolated from pediatric patients

BACKGROUND AND OBJECTIVES

Extended-spectrum β-lactamases (ESBLs) and fluoroquinolones are generally used to treat invasive Salmonella infections, but emergence of antibiotic-resistant strains are increasing worldwide. This study was aimed to investigate the distribution of ESBLs among Salmonella serogroups isolated from pediatric patients in Tehran, Iran.

MATERIALS AND METHODS

The study included all Salmonella isolates recovered from pediatric patients admitted to Children's Medical Center, Tehran, Iran during 2015-2016. Bacterial isolation and identification were performed by standard biochemical and agglutination tests. Antimicrobial susceptibility testing was done according to the Clinical and Laboratory Standards Institute (CLSI). Polymerase chain reaction was used to identify the genetic determinants responsible for ESBL phenotypes.

RESULTS

A total of 138 S. enterica serovars were isolated from stool specimens, including serogroup A (1), serogroup B (18), serogroup C (41) and serogroup D (78). Forty isolates out of 138 Salmonella strains had shown ESBL-positive phenotype. All ESBL-positive isolates showed multiple resistant phenotype. Resistance to more than 3 antimicrobial agents was observed among ESBL-positive strains. The frequency of Salmonella strains carrying the bla _CTX, bla _TEM and bla _SHV genes was 17 (12.3%), 40 (29.9%) and 4 (2.89%) respectively.

CONCLUSION

The high rates of ESBLs positive-Salmonella strains recovered from pediatric patients is alarming and indicates a necessity to substitute the cephalosporins with a proper alternative.

The Frequency of Antibiotic Resistance and ESBLs Among Clinically Acinetobacter baumannii Strains Isolated from Patients in a Major Hospital in Tehran, Iran

Background:

Bacterial resistance to antibiotics limits treatment options, increases morbidity and mortality, and raises the risk of antibiotic-associated adverse events. Antibacterial resistance emerges rapidly following an increase in the consumption of antibiotics against infectious diseases. The spread of ESBL producing strains has a limiting factor based on antibiotic function for the treatment of infections particularly caused by Acinetobacter baumannii (A. baumannii).

Objective:

This study was conducted to evaluate the prevalence of antimicrobial resistance and distribution of bla_TEM, bla_CTX, and bla_SHV genes among A. baumannii strains isolated from clinical samples at a major hospital in Teheran, Iran.

Methods:

A. baumannii strains were isolated and identified using standard microbiological methods. The disc diffusion and combined discs methods were used for testing antimicrobial susceptibility and to identify the strains producing Extended-Spectrum Beta-Lactamases (ESBL), respectively. DNA extraction was done by boiling method. Finally, the frequency of resistant genes including bla_TEM, bla_CTX, and bla_SHV in ESBL producing isolates was studied by PCR.

Results:

Gender distribution in this study was 53 (53%) samples for men and 47 (47%) for women. Totally, one hundred A. baumannii strains were isolated. More than 93% of the isolates were multi drug resistant. The highest to lowest antibiotic resistance was observed against amoxicillin/clavulanic acid (98%), ceftriaxone (96%), cefotaxime (94%), and ceftazidime (93%), respectively. The frequency of positive phenotypic test of ESBL was 19% and 16% for CAZ-C and CTX-C, respectively. The frequency of bla_TEM, bla_CTX, and bla_SHV genes was 52.1, 43.4, and 21.7, respectively.

Conclusion:

A. baumannii isolates exhibited an extremely worrying level of antibiotic resistance, and a high percentage of the isolates showed MDR in this study. This is a serious warning because ESBLs are a major threat to the effectiveness of antibiotics that are currently available for medical uses. The frequency of genes encoded ESBL isolates of A. baumannii may be due to overuse and misuse of antibiotics.

Genetic Investigation of Beta-Lactam Associated Antibiotic Resistance Among Escherichia Coli Strains Isolated from Water Sources

Background:

Antimicrobial resistance is an important factor threatening human health. It is widely accepted that antibiotic resistant bacteria such as Escherichia coli (E. coli) released from humans and animals into the water sources, can introduce their resistance genes into the natural bacterial community.

Objective:

The aim of this study was to investigate the prevalence of bla_TEM, bla_CTX, bla_SHV, bla_OXA and bla_VEB associated-antibiotic resistance among E. coli bacteria isolated from different water resources in Iran.

Methods:

The study contained all E. coli strains segregated from different surface water sources. The Kirby-Bauer method and combined discs method was determined in this study for testing antimicrobial susceptibility and strains that produced Extended-Spectrum Beta Lactamases (ESBL), respectively. DNA extraction kit was applied for genomic and plasmid DNA derivation. Finally the frequency of resistant genes including bla_TEM, bla_CTX, bla_SHV, bla_OXA and bla_VEB in ESBL producing isolates were studied by PCR.

Results:

One hundred E. coli strains were isolated and entered in the study. The highest antibiotic resistance was observed on clindamycin (96%). Moreover, 38.5% isolates were ESBL producers. The frequency of different ESBLs genes were 37%, 27%, 27%, and 25% for bla_TEM, bla_CTX, bla_SHV, and bla_OXA, respectively. The bla_VEB wasn’t found in any isolates.

Conclusion:

The study revealed a high prevalence of CTX-M, TEM, SHV and OXA genes among E. coli strains in surface water resources. In conclusion, these results raised a concern regarding the presence and distribution of these threatening factors in surface water sources and its subsequent outcomes.

The Molecular Study of Antibiotic Resistance to Quinolones in Salmonella enterica Strains Isolated in Tehran, Iran

Introduction:

Salmonella is known as one of the most important causes of gastrointestinal disease in the world. Quinolones and fluoroquinolones are used successfully in the treatment of salmonellosis particularly for infections that have become resistant to several antibiotics. But non-susceptible isolates to quinolones have been reported in several countries. The data are limited about the prevalence of quinolone-resistant isolates in our country. Therefore, this study investigated the plasmid-mediated quinolone resistance genes in Salmonella enterica isolated in Children's Medical Center in Tehran during 2014-2015.

Methods and Materials:

Salmonella isolates were isolated and identified using standard microbiological methods. Antibiotic susceptibility testing and screening of Salmonella strains resistant to quinolones were performed according to the CLSI guidelines. The molecular investigation was done using specific primers for detection of qnr genes including: qnrA, qnrB and qnrS, by polymerase chain reaction.

Results:

Overall, 92 (66.6%) strains were resistant to nalidixic acid. None of the strains showed resistance to ciprofloxacin. Out of the 92 nalidixic acid resistant strains, 52 (56.52%) harbored qnrS genes, 15 strains (16.30%) had both qnrA and qnrS genes. Two (1.1%) isolates were positive for qnrB gene. Twenty four (26.08%) nalidixic acid resistant isolates did not have any qnr qens.

Conclusion:

The results of this study show high prevalence of resistance to nalidixic and qnr genes in Salmonella isolates. Plasmid nature of this type of resistance poses an increased risk of dissemination of quinolone resistance between Salmonella and non-Salmonella isolates circulating in hospitals environments.

Multilocus Sequence Typing of the Clinical Isolates of Salmonella Enterica Serovar Typhimurium in Tehran Hospitals

BACKGROUND

Salmonella enterica serovar Typhimurium is one of the most important serovars of Salmonella enterica and is associated with human salmonellosis worldwide. Many epidemiological studies have focused on the characteristics of Salmonella Typhimurium in many countries as well as in Asia. This study was conducted to investigate the genetic characteristics of Salmonella Typhimurium using multilocus sequence typing (MLST).

METHODS

Clinical samples (urine, blood, and stool) were collected from patients, who were admitted to 2 hospitals in Tehran between April and September, 2015. Salmonella Typhimurium strains were identified by conventional standard biochemical and serological testing. The antibiotic susceptibility patterns of the Salmonella Typhimurium isolates against 16 antibiotics was determined using the disk diffusion assay. The clonal relationship between the strains of Salmonella Typhimurium was analyzed using MLST.

RESULTS

Among the 68 Salmonella isolates, 31% (n=21) were Salmonella Typhimurium. Of the total 21 Salmonella Typhimurium isolates, 76% (n=16) were multidrug-resistant and showed resistance to 3 or more antibiotic families. The Salmonella Typhimurium isolates were assigned to 2 sequence types: ST19 and ST328. ST19 was more common (86%). Both sequence types were further assigned to 1 eBURST group.

CONCLUSION

This is the first study of its kind in Iran to determine the sequence types of the clinical isolates of Salmonella Typhimurium in Tehran hospitals using MLST. ST19 was detected as the major sequence type of Salmonella Typhimurium.

Evaluation of Antioxidant Activity and Growth Control Properties of Nonoscale Structure Produced from Aloe vera var. littoralis Extract on Clinical Isolates of Salmonella

The aim of the study was to examine antibacterial properties of microemulsion structure produced from Aloe vera var. littoralis extract as a new tool of nanoscale drug-like materials. Aloe vera var. littoralis (A. littoralis) extract was prepared by distillation method. A nonocarrier structure in the microemulsion system was prepared from the extract. Serial concentrations were prepared from 8 mg/mL extract and the nonocarrier containing 0.1 mg/mL pure extract and were evaluated by a disk diffusion method for 35 Salmonella clinical isolates. Minimum inhibitory concentration (MIC) and minimum bactericidal concentration (MBC) were determined by microbroth dilution assay using MTT (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide) method by an enzyme-linked immunosorbent assay(ELISA) Microplate Reader apparatus. Antioxidant activity of the extract was determined by measuring the ferric reducing ability of plasma (FRAP) assay. From 35 clinical isolates of Salmonella, 17 isolates-including resistant isolates of S.E.1103 and S.E.49-had a zone of inhibition (ZI) of 7 to 32 mm in 0.007 mg/mL of the extract. S.E.76 isolate exposed to 30 µg/mL ceftazidime disk had a ZI of 12 mm but had 10 mm in 7µg/mL of A. littoralis extract. The inhibitory effect of a nanocarrier at a concentration of 25 µg/mL by 20 mm ZI was comparable by the ceftazidime (30 µg/mL) effect. MIC50 was 0.25 mg/mL and MBC50 was 0.5 mg/mL by MTT method for the extract. It was shown that A.littoralis extract had antioxidant activity of 31.67 µM/mg that could be increased based on concentration. It was concluded that the nanocarrier had a significant effect on the studied isolates in comparison with ordinary antibiotics and had potential for use as a natural antioxidant and antimicrobial material in complementary medicine.

Molecular characterization of antimicrobial resistant non-typhoidal Salmonella from poultry industries in Korea

Background

Antimicrobial resistant Salmonella strains are a direct threat to human health when this resistance interferes with treatment and an indirect threat when resistance can be transferred to other human pathogens. The objective of the present study was to characterize antimicrobial resistant non-typhoidal Salmonella (NTS) isolates recovered from poultry industries, including a description of genetic diversity and virulence profiles.

Results

In total of 93 Salmonella isolates shown antimicrobial resistance to one or more drugs, all isolates exhibited common resistance to streptomycin, nalidixic acid and cephalothin but no ciprofloxacin resistance. Among 26 virulence gene profiling, 12 virulence genes, invA, orgA, prgH, sopB, tolC, sipB, gatC, msgA, pagC, spiA, sifA, and sitC were found in all antimicrobial-resistant NTS isolates. In comparing the data from ERIC-PCR clusters, virulence profiles and resistance profiles, some Salmonella isolates grouped into the same cluster were found to exhibit similar virulence and resistance patterns.

Conclusions

Virulence profiling combined with ERIC-PCR offered a rapid approach to characterize antimicrobial-resistant NTS.

Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) Genotyping of Escherichia coli Strains Isolated from Different Animal Stool Specimens

BACKGROUND

Escherichia coli is a commensal-pathogenic organism, which includes a wide range of strains. Despite several advanced molecular-genomic technologies for detecting and identifying different strains of E. coli, Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) technique is a quick, sharp and cost effective fingerprint method. The major purpose of the present study was to determine the distribution of ERICs within E. coli strains isolated from different healthy animal stool specimens including hens, sheep, and cows, as an appropriate and quick molecular-genomic tool.

METHODS

The animal stool samples were obtained during 1 year (October 2012 to October 2013), from animal husbandries around Tehran and Alborz provinces, Iran. After screening processes, the E. coli bacteria were isolated and cultured via standard microbiological methods. The DNA molecules of E. coli bacteria were harvested and Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) was applied for bacterial molecular genotyping. The ERIC-PCR products were run on 1% gel electrophoresis. The final images regarding gel electrophoresis banding patterns were used for dendrogram generation via the GelClust software.

RESULTS

Of 120 isolated samples, 115 different strains were recognized as E. coli. The fingerprint patterns involved 380 to 3280 bp bands. The predominant bands included 2900 bp, 1200 bp, and 1200 bp in stool samples of hens, sheep, and cows, respectively. The highest frequencies and diversities were seen among E. coli strains isolated from hens and sheep stool samples.

CONCLUSION

The DNA profiles were clearly detectable via specific fingerprint patterns. The ERIC-PCR seemed to be a good approach for molecular typing of E. coli strains isolated from different animal sources.

Simultaneous Molecular Detection of Salmonella enterica Serovars Typhi, Enteritidis, Infantis, and Typhimurium

BACKGROUND

Salmonella enterica serovar Typhi, as causative agent of typhoid fever, is one of the most important endemic pathogens. Non-typhoidal Salmonella serovars, including Typhimurium, Infantis, and Enteritidis are amongst the most prevalent serotypes worldwide and in developing areas such as Iran. The aim of this study was to apply a uniplex PCR for rapid detection of Salmonella spp., and a multiplex PCR for the simultaneous detection of the four most common Salmonella serovars in Iran.

METHODS

Current research was done in 2010 at Molecular Biology Research Center, Baqiyatallah University of Medical Sciences, Tehran, Iran. For detection of Salmonella spp a pair of primers was used to replicate a chromosomal sequence. Four other sets of primers were also designed to amplify the target genes of four Salmonella species including S. typhi, and three non-typhoidal Salmonella spp (S. enteritidis, S. infantis, and S. typhimurium). The assay specificity was investigated by testing 15 different Salmonella serovars and 8 other additional non-Salmonella species.

RESULTS

The Salmonella genus-specific PCR yielded the expected DNA band of 404 bp in all Salmonella spp., strains tested. The uniplex and multiplex PCR assays produced also the expected fragments of 489 bp, 304 bp, 224 bp, and 104 bp for serovars Typhi, Enteritidis, Typhimurium, and Infantis, respectively. Each species-specific primer pair set did not show any cross-reactivity when tested on other Salmonella serovars or other non- but related- Salmonella strains.

CONCLUSION

Both uniplex and multiplex PCR protocols had a good specificity. They can provide an important tool for the rapid and simultaneous detection and differentiation of the four most prevalent Salmonella serovars in Iran.

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.

Molecular typing of uropathogenic E. coli strains by the ERIC-PCR method

Introduction

Escherichia coli (E. coli) is the most common cause of urinary infections in hospitals. The aim of this study was to evaluate the ERIC-PCR method for molecular typing of uropathogenic E. coli strains isolated from hospitalized patients.

Methods

In a cross sectional study, 98 E. coli samples were collected from urine samples taken from patients admitted to Baqiyatallah Hospital from June 2014 to January 2015. The disk agar diffusion method was used to determine antibiotic sensitivity. DNA proliferation based on repetitive intergenic consensus was used to classify the E. coli strains. The products of proliferation were electrophoresed on 1.5% agarose gel, and their dendrograms were drawn. The data were analyzed by online Insillico software.

Results

The method used in this research proliferated numerous bands (4–17 bands), ranging from 100 to 3000 base pairs. The detected strains were classified into six clusters (E1–E6) with 70% similarity between them.

Conclusion

In this study, uropathogenic E. coli strains belonged to different genotypic clusters. It was found that ERIC-PCR had good differentiation power for molecular typing of uropathogenic E. coli strains isolated from the patients in the study.

Acquisition of extended-spectrum cephalosporin- and colistin-resistant Salmonella enterica subsp. enterica serotype Newport by pilgrims during Hajj

Gatherings like the Hajj involving many people who travel from different parts of the world represent a risk for the acquisition and dissemination of infectious diseases. In this study, acquisition of multidrug-resistant (MDR) Salmonella spp. in 2013 Hajj pilgrims from Marseille, France, was investigated. In total, 267 rectal swabs were collected from 129 participants before their departure and after their return from the pilgrimage as well as during the pilgrimage from patients with diarrhoea. Samples were screened for the presence of Salmonella using quantitative real-time PCR and culture. Whole-genome sequencing was performed to characterise one of the isolates, and the mechanism leading to colistin resistance was investigated. Six post-Hajj samples and one sample collected during a diarrhoea episode in Hajj were positive for Salmonella by real-time PCR, with five Salmonella enterica belonging to several serotypes recovered by culture, whereas no pre-Hajj sample was positive. Two of the isolates belonged to the epidemic Newport serotype, were resistant to cephalosporins, gentamicin and colistin, and harboured the bla(CTX-M-2) gene and a 12-nucleotide deletion in the pmrB gene leading to colistin resistance. This study shows that pilgrims acquired Salmonella bacteria, including a novel MDR clone, during the Hajj pilgrimage. This calls for more improved public health surveillance during Hajj because Salmonella is one of the most common diarrhoea-causing bacteria worldwide. Therefore, returning pilgrims could disseminate MDR bacteria worldwide upon returning to their home countries.