Random Amplified Polymorphic DNA Types Research Articles

Capsular gene distribution and RAPD typing of Streptococcus agalactiae isolated from pregnant women

Streptococcus agalactiae has different virulence factors, from which the capsule has the most significant role in the pathogenesis of this organism. We aimed to investigate the distribution of more prevalent capsular genes among different Random Amplified Polymorphic DNA (RAPD) types of S. agalactiae isolated from pregnant women. A total of 106 isolates were collected from 420 vaginal and rectal swabs obtained from pregnant women. The specimens were transferred using Todd Hewitt Broth and were cultured on a blood agar containing antibiotics. The S. agalactiae isolates were identified by the standard microbiological and biochemical tests. The genomic DNAs of S. agalactiae isolates were extracted using an extraction kit. Then, the PCR method was used to detection of the capsular genes. Moreover, The RAPD PCR was used to genotyping of the isolates. The colonization rate of the pregnant women was 25.23%, and there was a statistically significant correlation between the weeks of gestation and the probability of colonization (p-value < 0.05). Also, 31 (29.24%) and 18 (16.98%) pregnant women had a history of abortion and membrane rupture, respectively. In addition, 20 (18.86%), 32 (30.18%), 4 (3.77%), and 6 (5.66%) isolates carried genes encoding capsular types Ia, Ib, III, and V, respectively. None isolates had the type II capsular gene, and other 44 isolates were non-typeable. Nine clones (clusters) of S. agalactiae were observed in the present study with 70% similarity, and 53 different types were identified among the isolates. Except for capsular types III and V that belonged to clones 3, 5, 7, and 9, other capsular types were detected in different RAPD types. We found that the capsular types Ib and Ia were predominant among pregnant women in this area, indicating their significance for vaccine designation. Also, our isolates showed a lower genotypic diversity in RAPD typing. This may be due to the same sources of most isolates.

Genotypic and antimicrobial susceptibility of Streptococcus agalactiae causing bovine mastitis in the central region of Thailand.

Streptococcus agalactiae is a highly contagious pathogen that causes bovine mastitis, leading to significant economic losses. This study aimed to (1) identify and characterize S. agalactiae strains responsible for bovine mastitis by examining their phenotypic and genotypic characteristics in Thai dairy-intensive farming areas and (2) determine their susceptibility profiles to antimicrobial agents. In total, 100 S. agalactiae isolates obtained from clinical and subclinical mastitis cases from 13 dairy herds located in the central region of Thailand were examined. To confirm the identity of the bacterial pathogens, conventional microbiological procedures recommended by the National Mastitis Council (NMC) and the VITEK® 2 system were employed. All 100 isolates were successfully identified as S. agalactiae using the NMC procedure, whereas 94 isolates were identified as S. agalactiae using the VITEK® 2 system. Finally, the S. agalactiae-specific gene dlt S was identified in all the examined isolates using polymerase chain reaction. Capsular polysaccharide (CPS) typing revealed that all strains belonged to CPS type Ia. Multilocus sequence typing identified 33 selected isolates as sequence type 103. Random amplified polymorphic DNA (RAPD) typing yielded 43 RAPD types, with 6 RAPD clusters identified. These results demonstrated a high level of genetic diversity among S. agalactiae within the studied herds. RAPD analysis suggested that specific S. agalactiae strains could persist in dairy farms for 2-12 months. Furthermore, antimicrobial susceptibility testing was performed using the broth microdilution method. Most strains demonstrated susceptibility to ampicillin, penicillin, penicillin/novobiocin, cephalothin, oxacillin, ceftiofur, and erythromycin. This study revealed the phenotypic and genotypic characteristics of S. agalactiae isolates responsible for bovine mastitis in the central region of Thailand. The rapid identification of S. agalactiae and application of molecular typing methods can provide valuable epidemiological information regarding S. agalactiae causing mastitis in dairy farms. The antimicrobial susceptibility of S. agalactiae indicates that antimicrobial treatment for control and eradication could be a successful protocol. Our findings revealed that a single clonal strain of S. agalactiae affected the 13 studied farms. Further research is needed to explore the feasibility of vaccine development and application.

Genetic diversity and iron metabolism of Staphylococcus hominis isolates originating from bovine quarter milk, rectal feces, and teat apices.

Staphylococcus hominis, a member of the non-aureus staphylococci (NAS) group, is part of the human and animal microbiota. Although it has been isolated from multiple bovine-associated habitats, its relevance as a cause of bovine mastitis is currently not well described. To successfully colonize and proliferate in the bovine mammary gland, a bacterial species must be able to acquire iron from host iron-binding proteins. The aims of this study were (1) to assess the genetic diversity of S. hominis isolated from bovine quarter milk, rectal feces, and teat apices, and (2) to investigate the capacity of bovine S. hominis isolates belonging to these different habitats to utilize ferritin and lactoferrin as iron sources. To expand on an available collection of bovine S. hominis isolates (2 from quarter milk, 8 from rectal feces, and 19 from teat apices) from one commercial dairy herd, a subsequent single cross-sectional quarter milk sampling (n = 360) was performed on all lactating cows (n = 90) of the same herd. In total, 514 NAS isolates were recovered and identified by MALDI-TOF mass spectrometry; the 6 most prevalent NAS species were S. cohnii (33.9%), S. sciuri (16.7%), S. haemolyticus (16.3%), S. xylosus (9.6%), S. equorum (9.4%), and S. hominis (3.5%). A random amplified polymorphic DNA (RAPD) analysis was performed on 46 S. hominis isolates (19 from quarter milk, 8 from rectal feces, and 19 from teat apices). Eighteen distinct RAPD fingerprint groups were distinguished although we were unable to detect the presence of the same RAPD type in all 3 habitats. One S. hominis isolate of a distinct RAPD type unique to a specific habitat (8 from quarter milk, 3 from rectal feces, and 4 from teat apices) along with the quality control strain Staphylococcus aureus ATCC 25923 and 2 well-studied Staphylococcus chromogenes isolates ("IM" and "TA") were included in the phenotypical iron test. All isolates were grown in 4 types of media: iron-rich tryptic soy broth, iron-rich tryptic soy broth deferrated by 2,2'-bipyridyl, and deferrated tryptic soy broth supplemented with human recombinant lactoferrin or equine spleen-derived ferritin. The growth of the different strains was modified by the medium in which they were grown. Staphylococcus chromogenes TA showed significantly lower growth under iron-deprived conditions, and adding an iron supplement (lactoferrin or ferritin) resulted in no improvement in growth; in contrast, growth of S. chromogenes IM was significantly recovered with iron supplementation. Staphylococcus hominis strains from all 3 habitats were able to significantly utilize ferritin but not lactoferrin as an iron source to reverse the growth inhibition, in varying degrees, caused by the chelating agent 2,2'-bipyridyl.

Randomly amplified polymorphic DNA analysis of Staphylococcus chromogenes isolated from bovine and bubaline mastitis in Karnataka.

Background and Aim:In recent times, non-aureus staphylococci (NAS) have emerged as the major organisms isolated from mastitis cases in dairy animals, with a predominance of Staphylococcus epidermidis and Staphylococcus chromogenes. As compared to Staphylococcus aureus, much less is known about the molecular types or the spatiotemporal epidemiology of these NAS species. In the present study, randomly amplified polymorphic DNA (RAPD) was employed to detect genetic polymorphisms, intraspecies diversity, and epidemiology of S. chromogenes strains (n=37) isolated from bovine and bubaline mastitis cases in the state of Karnataka.Materials and Methods:Thirty-seven S. chromogenes isolates (14 from bovines and 23 from bubaline) isolated from subclinical mastitis cases, from organized and unorganized sectors, were subjected to RAPD typing. Further, methicillin resistance was determined by cefoxitin disk diffusion method.Results:The amplified DNA fragments ranged from 150 to 3000 base pairs and yielded several RAPD profiles. Further analysis using Digital Image Correlation Engine correlation coefficient and UPGMA method showed that the 37 isolates could be classified into 12 distinct RAPD types (A to L) at 62% similarity (D=0.889). Four of the most predominant RAPD types, B, A, C, and E, in that order, and together, represented 65% of the isolates. High diversity was observed among the isolates both within farms and between geographic locations. Most of the isolates exhibited methicillin resistance. This is the first such report from India.Conclusion:In the absence of defined multilocus sequence type protocols or sufficient sequences available in the public domain, RAPD can be employed to determine genetic diversity of S. chromogenes isolates.

Microbial characterization of an artisanal production of Robiola di Roccaverano cheese

Robiola di Roccaverano, from the Piedmont region of Italy, is a Protected Designation of Origin soft cheese made with raw goat milk. The peculiarity of this cheese is that during the manufacturing process, a natural starter culture (NC) is added to raw milk. This study examined the viable microorganisms of technological interest, including lactic acid bacteria and fungal populations, in samples of raw milk, NC, and fresh and ripened cheese collected from one dairy using culture-dependent techniques. First, the isolated colonies were analyzed using random amplification of polymorphic DNA (RAPD) PCR, and strains with similar fingerprints were clustered together. Further, representative isolates of each group were subjected to 16S or 26S ribosomal DNA sequencing. Finally, species-specific PCR was conducted to distinguish the Lactococcus lactis ssp. lactis and Lc. lactis ssp. cremoris. Among the studied lactic acid bacteria, 13 RAPD profiles were obtained, corresponding to 9 different bacterial species or subspecies. Concerning mold and yeast isolates, 5 species were found that coincided with 5 RAPD types. Observing the strains isolated in the study, Lc. lactis was the most prevalent species in raw milk and NC samples, and Leuconostoc mesenteroides was the predominant species identified in 5- and 15-d cheese isolates. Furthermore, whereas only these 2 species were detected in NC, Enterococcus and Lactobacillus genera were found in raw milk and cheese, respectively. Concerning the mold and yeast isolates, in NC Kluyveromyces spp. was mainly found, and in cheese samples the representative species were Geotrichum candidum and Yarrowia lipolytica. Finally, raw milk and cheese safety were evaluated, and the samples complied with the standard required by European Commission regulation number 2073/2005.

Corneal ulcer/keratitis derived Aspergillus flavus &Aspergillus tamarii and their RAPD-PCR typing

The aim of the study was investigate the DNA polymorphisms of Aspergillus flavus and Aspergillus tamarii isolated from regional fungal keratitis cases based on random amplified polymorphic DNA (RAPD) analyses. Thirty-two A. flavus and six A. tamarii isolates were identified using conventional macroscopic and microscopic features. Five decamer primers were used to amplify the genomic DNA sequences of the test isolates, and 140 total RAPD patterns were generated among them. From each of the 38 isolates, a range of 15–30 RAPD types were revealed. All of these were isolated from male farmers from Tamil Nadu. In the future, RAPD analyses could be employed as a reliable and rapid technique to differentiate among keratitis isolates of fungal pathogens.

Phenotypic and Genotypic Characteristics of Clostridium difficile Isolates in Patients with Type 2 Diabetes in Iran.

PurposeThis study aimed to investigate the phenotypic and genotypic characterization of Clostridium difficile isolates in type 2 diabetes patients with hospital-acquired diarrhea in four teaching hospitals in Isfahan, Iran.Patients and MethodsA total of 104 hospitalized patients with type 2 diabetes and nosocomial diarrhea were included in the current study over a 2-year period (2015–2017). C. difficile isolates were characterized by conventional microbiological methods including the presence of toxin genes, antibiotic resistance testing and molecular methods including multilocus sequence typing (MLST) and random amplification of polymorphic DNA (RAPD).ResultsAll 21 C. difficile isolates (20.2%) were detected from 104 studied patients. All isolates were susceptible to metronidazole and vancomycin. The antimicrobial resistance rates were distinctly higher for clindamycin and for moxifloxacin. Based on PCR amplification of tcdA and tcdB, 13 isolates (12.5%) carried both of these genes and were considered toxigenic. Thirteen toxigenic C. difficile strains were classified into two sequence types (STs), that is, ST54 and ST2 types. The RAPD-PCR amplification patterns of the detected toxigenic C. difficile revealed three distinct but related RAPD clusters. RAPD cluster 1 had the highest similarity with RAPD types 2 and 3.ConclusionA relatively high rate of CDI was observed in patients with type 2 diabetes and was associated with poorer health outcomes. These patients were exposed to multiple antibiotics and other therapeutic agents. We recommend close screening for the coexistence of CDI and type 2 diabetes in patients with diarrhea using a combination of conventional and molecular methods.

Genotyping and antimicrobial resistance of Streptococcus uberis isolated from bovine clinical mastitis.

A genotypic characterization of Streptococcus uberis isolated from clinical mastitis (CM) in dairy cows, and the association of Strep. uberis genotypes and antimicrobial susceptibility (AMS) was performed. A total of 89 isolates identified as Strep. uberis from 86 dairy cows with CM in 17 dairy herds of Southeastern Brazil were genotyped using random amplified polymorphic DNA (RAPD) analysis. After genotyping, two clusters (I and II) were created according to RAPD types. A commercial broth microdilution test was used to determine the susceptibility of Strep. uberis isolates to 8 antimicrobials (ampicillin, ceftiofur, cephalothin, erythromycin, penicillin, penicillin+novobiocin, pirlimycin and tetracycline). For each antimicrobial, we determined the minimal inhibitory concentrations that inhibit 50% (MIC50) and 90% (MIC90) of Strep. uberis strains. Differences in AMS among genotypic clusters were evaluated using mixed regression models. Overall, a great polymorphism (56 RAPD-types) was found among Strep. uberis isolates, although a higher genetic similarity (based on the PCR bands features) was observed within herds after genotypic clustering. No differences in AMS were observed among clusters. Strep. uberis isolated from bovine CM were resistant to most antimicrobials, with the exception of cephalothin and penicillin+novobiocin.

Molecular epidemiology and distribution of antimicrobial resistance genes of Staphylococcus species isolated from Chinese dairy cows with clinical mastitis

Staphylococcus species, categorized into Staphylococcus aureus and non-aureus staphylococci (NAS), are frequent causes of mastitis in dairy cattle around the world. Current treatments using antimicrobials are under increasing scrutiny due to rising prevalence of multi-drug resistance in S. aureus. Objectives of this study were to determine: (1) genetic diversity of Staphylococcus species isolated from clinical mastitis in cows from large Chinese dairy farms; and (2) prevalence and distribution of antimicrobial resistance genes (ARG) in these isolates. Staphylococcus aureus (n = 96) were isolated from 26 herds located in 12 provinces of China, whereas NAS (n = 112) were isolated from 59 herds located in 18 provinces of China. The NAS were identified at the species level using a partial 16S rRNA sequencing method, whereas random amplification of polymorphic DNA (RAPD) PCR was done to determine genetic relationships of isolates. Finally, PCR was used to detect resistance and biofilm formation genes. Staphylococcus chromogenes (33%) was the most common NAS species, followed by Staphylococcus sciuri (17%) and Staphylococcus epidermidis (8%). Staphylococcus aureus was grouped in 12 genotypes, of which 2 types represented 56% of isolates. Staphylococcus chromogenes (n = 37) clustered into 8 RAPD types, with 2 prevalent types containing 73% of isolates. The most prevalent ARG in S. aureus isolates was blaZ (95%), followed by tetM (33%), tetK (31%), ermT (26%), and aacA-aphD (23%). The mecA and vanA were detected in 16 and 4% of isolates, respectively. In NAS, blaZ (100%), mecA (73%), tetK (79%), tetM (96%), mphC (63%), and msrA (54%) were frequently detected. Antimicrobial resistance genes mecA, tetK, tetL, tetM, dfrG, ermB, msrA, mphC, aadD, and aphA3 were more commonly detected in NAS than in S. aureus. Biofilm formation genes (icaA and icaD) were frequently detected in staphylococci isolated from bovine clinical mastitis. The existence of predominant RAPD types in S. aureus and S. chromogenes isolates across Chinese dairy farms indicated that specific genotypes had disseminated within herds and become more udder-adapted. High prevalence of ARG, especially in NAS, highlighted the risk of selection of multi-drug resistant staphylococci with potential as a reservoir of ARG.

Inhibitory spectrum of diverse guaiacol-producing Alicyclobacillus acidoterrestris by poly dimethyl ammonium chloride disinfectant

Alicyclobacillus acidoterrestris is a soil-borne, thermo-acidophilic, endospore-forming bacterium which causes the spoilage of pasteurized fruit juices with the production of guaiacol taints. In this study the antimicrobial activity of poly dimethyl ammonium chloride (PDAC), an emerging disinfectant, against A. acidoterrestris was investigated. Initially, four bacteria isolates obtained from orchard soils were identified as A. acidoterrestris by 16S ribosomal RNA (rRNA) gene sequencing followed by analysis of random amplified polymorphic DNA (RAPD) fragments, which grouped the isolates into two genotypes. High performance liquid chromatographic (HPLC) analysis revealed the activity of vanillic-acid decarboxylase (vdc) in the A. acidoterrestris strains, as measured by the production of guaiacol from vanillic acid (VA), indicating the isolates’ spoilage potential. Subsequently, representative strains from the two RAPD types of A. acidoterrestris were treated with PDAC. Disc diffusion assay on YSG agar revealed that A. acidoterrestris strains ULAG14, ULAG15 and the type strain DSM 3922T were sensitive to PDAC at concentrations ranging from 0.5% to 20% and inhibition of endospore germination was observed after 5 min exposure. PDAC has an inhibitory effect against the vegetative cells and endospores of A. acidoterrestris under laboratory conditions; it may be potentially useful for industrial application in cleaning of fruits and production surfaces for quality control during the processing of tropical fruit juices.

Genotype Diversity and Evaluation of Biofilm Formation in sasX Positive Methicillin-Resistant Staphylococcus aureus

Objectives: Staphylococcus aureus surface protein X (sasX) is a newly described protein that has different roles in virulence, such as biofilm formatin, as a bacterial approach for pathogenesis. SasX gene was initially found in eastern Asian countries, yet, studiese have shown spreading of this gene to other strains. Because there is no report on this gene in Iran, the current study aimed at determining the prevalence, genotype diversity, and evaluation of biofilm formation in sasX positive methicillin-resistant Staphylococcus aureus (MRSA). Methods: This experimental study was conducted on strains isolated from inpatients during 2014 to 2015. Cultivation, identification, and confirmation of MRSA isolates were performed. The evaluation of biofilm production, sasX gene detection, and Random amplified polymorphic DNA (RAPD)-polymerase chain reaction (PCR) were done. Data collection and comparison were performed by SPSS and gelcompare softwares. Results: Overall, 140 isolates (77.8%) formed a biofilm and 23 (12.6%) isolates were sasX positive. Amongst 23 sasX+ strains, 21 (91.3%) isolates created a biofilm. The RAPD-PCR analysis of 23 sasX positive isolates showed 19 RAPD types with 4 common types (CT) and 15 single types (ST). Conclusions: Frequency of sasX gene was somewhat similar to another study in eastern countries and the ability of biofilm formation in sasX+ strains compared to all of MRSA isolates were not significant (P value > 0.05) and a correlation was not found between RAPD type and biofilm grade.

Relationships among superantigen toxin gene profiles, genotypes, and pathogenic characteristics of Staphylococcus aureus isolates from bovine mastitis

Staphylococcus aureus is one of the major etiological agents of bovine mastitis, harboring a wide variety of staphylococcal superantigen (SAg) toxin genes. The SAg toxin genes are reported to be closely associated with the pathogenicity of the Staph. aureus causing the bovine mastitis. This study was conducted to investigate SAg toxin gene profiles and to assess the relationships among SAg toxin genes, genotypes of Staph. aureus, and their pathogenic properties. A total of 327 quarter milk samples were collected from bovine mastitis cases for isolation and identification of pathogens. In total, 35 isolates were identified as Staph. aureus, and the prevalence of Staph. aureus in milk samples was 13.6% (35/256). Polymerase chain reaction (PCR) and randomly amplified polymorphic DNA (RAPD) assays were used to detect the SAg toxin genes and to genotype Staph. aureus strains isolated from milk samples of bovine mastitis in 10 dairy herds located in Ningxia, China, respectively. The results showed that among the Staph. aureus isolates (n = 35), 71.4% (n = 25) of isolates carried at least one SAg toxin gene. In total, 18 SAg genes and 21 different gene combination patterns were detected among these isolates. The most common SAg genes in Staph. aureus isolates were sei, sen, and seu (44.0% each), followed by seo, tst, and etB (28.0% each), etA (24.0%), sem and sep (16.0% each), seb, sec, sed, and sek (12.0% each), and sea and seh genes (8.0% each); the seg, sej, and ser genes were present in 4.0% of the isolates. Three gene combinations were found to be related to mobile genetic elements that carried 2 or more genes. The egc-cluster of the seg-sei-sem-sen-seo genes, located on the pathogenicity island Type I υSaβ, was detected in 16% of isolates. Interestingly, we observed 6 RAPD genotypes (I to VI) in Staph. aureus isolates, and 2 of these genotypes were strongly associated with the severity of bovine mastitis; there was a close relationship between the RAPD genotypes and SAg genes. Isolates of RAPD type III were more frequently associated with clinical and subclinical mastitis, whereas strains of type VI were mostly related to subclinical mastitis. In addition, SAg genes were related to severity of bovine mastitis. We conclude that an obvious relationship exists among RAPD genotypes, SAg toxin genes, and severity of bovine mastitis.

Typing of Indigenous Campylobacter spp. From Serbia by M-PCR and RAPD

Abstract Campylobacteriosis is an infectious human disease caused by thermophilic Campylobacter species, mainly C. jejuni and C. coli. It is the leading cause of human gastroenteritis today with the number of cases surpassing the number of Salmonella poisoning cases. The epidemiology of the agent is not completely clear, but a number of investigations indicate an important role of broiler meat in human infections. The purpose of this study was to investigate the diversity of Campylobacter jejuni strains present in the Republic of Serbia and to determine a fast and reliable system for the confirmation and typing of the isolated strains. Samples taken at slaughterhouses, broiler farms, as well as two human isolates of Campylobacter species have been investigated. Strain identification was performed by multiplex-PCR. Genotyping was performed by Random Amplified Polymorphic DNA (RAPD) with multiple primers. Using several unusual primers and a newly designed one (DJP17), we report on the RAPD types of indigenous Campylobacter species. RAPD profiles showed different levels of discrimination between the isolates, depending on the primer: SPH1 and AG15 were informative only in part and better results were obtained with AP10, AK16 and DJP17.

Application of the Random Amplified Polymorphic DNA (RAPD) Fingerprinting to Analyze Genetic Variation in Community Associated-Methicillin Resistant Staphylococcus Aureus (CA-MRSA) Isolates in Iran.

The aim of this study was to apply RAPD technique to analyze the genetic variability among the Iranian CA-MRSA isolates.The RAPD amplification was implemented on 25 strains isolated from the anterior nares of 410 healthy children using four randomly selected oligonucleotide primers from the stocks available in our laboratory, including the primers 1254, GE6, OLP6 and OLP13 from our stock. The amplified PCR products were detected on a 1.5% agarose gel and subjected to further analysis to establish the band profiles and genetic relationships using the Gel Compar® program.The Iranian CA-MRSA isolates produced distinct RAPD patterns which varied based on the primer used, however, the primer 1254 revealed highly polymorphic patterns consisting 5 discernable RAPD types (RT), “RT1” (12, 48%), “RT2” (8, 32%), “RT3” (3, 12%), and “RT4 and RT5”, (a single RAPD type each, 4%). Phylogenetic analysis based on RAPD profiles divided most of the CA-MRSA isolates into 2 distinct but related RAPD clusters, a small group and two single unrelated RAPD types.This study shows that the simple and cost-effective but rather difficult to optimize RAPD fingerprinting could be used to evaluate genetic and epidemiological relationships of CA-MRSA isolates on condition that the patterns are obtained from carefully optimized laboratory tests.

Genotyping and study of the pauA and sua genes of Streptococcus uberis isolates from bovine mastitis

This study aimed to determine the clonal relationship among 137 Streptococcus uberis isolates from bovine milk with subclinical or clinical mastitis in Argentina and to assess the prevalence and conservation of pauA and sua genes. This information is critical for the rational design of a vaccine for the prevention of bovine mastitis caused by S. uberis. The isolates were typed by random amplified polymorphic DNA (RAPD) analysis and by pulsed-field gel electrophoresis (PFGE). The 137 isolates exhibited 61 different PFGE types and 25 distinct RAPD profiles. Simpson's diversity index was calculated both for PFGE (0.983) and for RAPD (0.941), showing a high discriminatory power in both techniques. The analysis of the relationship between pairs of isolates showed 92.6% concordance between both techniques indicating that any given pair of isolates distinguished by one method tended to be distinguished by the other. The prevalence of the sua and pauA genes was 97.8% (134/137) and 94.9% (130/137), respectively. Nucleotide and amino acid sequences of the sua and pauA genes from 20 S. uberis selected isolates, based on their PFGE and RAPD types and geographical origin, showed an identity between 95% and 100% with respect to all reference sequences registered in GenBank. These results demonstrate that, in spite of S. uberis clonal diversity, the sua and pauA genes are prevalent and highly conserved, showing their importance to be included in future vaccine studies to prevent S. uberis bovine mastitis.

English

Twenty three isolates of Salmonella enterica representing two serovars, Salmonella Typhimurium and Salmonella Enteritidis isolated from three hospitals in Taif province, Kingdom of Saudi Arabia, were allocated to 23 genomic types using random amplified polymorphic DNA RAPD-PCR employing four 10-mer arbitrary primers. Jaccard's similarity coefficients were used to reveal the genetic diversity among isolates. Random amplified polymorphic DNA-polymerase chain reactioin (RAPD-PCR) amplified a total of 55 distinct bands (54 polymorphic bands or 98%). Cluster analysis based on the combined data from the four primers indicated that each of the S. Enteritidis or S. Typhimurium isolates had a distinct RAPD type. Principal component analysis (PCA) showed that the first three components explained about 65 and 33% of the total variability among RAPD types belonging to serovars Enteritidis and Typhimurium, respectively. The isolates belonging to serovar Enteritidis exhibited considerable genetic variation between locations, while those belonging to serovar Typhimurium exhibited considerable genetic variation both within and between locations. RAPD-PCR yielded highly reproducible results that demonstrated the high genetic heterogeneity of Salmonella isolates. Several genovars were present among Salmonella serovars and no specific RAPD type (or genovar) was found to be predominantly circulating in Taif province. The results presented here indicated that RAPD analysis has a great discriminatory power for the differentiation of Salmonella isolates and, therefore, can be a useful tool for the analysis of Salmonella genovars. Key words: Salmonella genovars, Taif province, random amplified polymorphic DNA (RAPD) proi¬les, RAPD types, discrimination index, cluster analysis, principal component analysis.

Determination of extended spectrum beta-lactamases, metallo-beta-lactamases and AmpC-beta-lactamases among carbapenem resistant Pseudomonas aeruginosa isolated from burn patients

BackgroundPseudomonas aeruginosa is an important cause of morbidity and mortality in patients with burns. MethodA total of 214 nonduplicated burn wound isolates of P. aeruginosa were recovered from burn patients. Identification of carbapenem resistant isolates and their antimicrobial susceptibility pattern was carried out using the phenotypic methods. The presence of genes encoding extended spectrum beta-lactamases (ESBLs) and metallo-beta-lactamases (MBLs) enzymes were determined by PCR. The genetic relationships between carbapenem resistant isolates were determined by Random Amplified Polymorphic DNA (RAPD)-PCR. ResultsOf 214 investigated P. aeruginosa isolates, 100 (46.7%) were carbapenem resistant. All carbapenem resistant P. aeruginosa were resistant to imipenem, meropenem, ertapenem, carbenicillin, aztreonam, gentamicin and ciprofloxacin but susceptible to polymyxin B. Among 100 carbapenem resistant P. aeruginosa isolates, 3%, 65% and 52% were identified as ESBLs, carbapenemase and AmpC overproduction positive isolates respectively. The most prevalent ESBLs and MBLs genes included blaOXA-10 (97%), blaTEM (61%), blaVIM (55%), blaPER (13%), blaIMP (3%) and blaAIM (1%). RAPD analysis yielded 13 distinct profiles among 92 isolates. A dominant RAPD type was designated as A that consisting of 80 isolates. ConclusionThis is the first report of Adelaide IMipenmase (AIM) MBLs producing P. aeruginosa from Iran and also of the high prevalence of AmpC overproduction isolates. According to the results of current study, P. aeruginosa isolates producing OXA-10, TEM, VIM, PER and IMP beta-lactamases are frequent and the population structures of these isolates are highly similar.

Emergence of Third Generation Cephalosporin Resistance and Typing by Randomly Amplified Polymorphic DNA (RAPD) among Clinical Salmonella Isolates from Lagos, Nigeria

Aims: To investigate emergence of cephalosporin resistance and clonal relatedness among clinical Salmonella isolates recovered from patients in Lagos, Nigeria. Study Design: It is an investigative study. A total of 300 patients who presented with various types of medical conditions at prominent referral public hospitals were recruited. Place and Duration of Study: Department of Microbiology, Lagos State University, Ojo, Lagos and Nigerian Institute of Medical Research, Yaba, Lagos, Nigeria from July 2011 to May 2012. Methodology: Salmonella identification was done using standard methods. The isolates were subjected to antimicrobial susceptibility by disk diffusion method. The isolates were further screened for plasmid DNA and blaCTX-M carriage on plasmid using alkaline lysis and PCR methods. Clonal relatedness of the isolates was assessed by RAPD PCR using genomic DNA as template for three RAPD primers (784, 1254 and OPA4). The resulting Original Research Article British Microbiology Research Journal, 4(6): 668-677, 2014 669 RAPD types were determined by visualization and discrimination index was measured using a discriminating index calculator. Results: Sixty three Salmonella isolates were recovered made up of five serovars. In all 49% of the isolates were resistant to cefuroxime, 46% to cefoxitin, 37% to cefriazone and 35% to ceftazidine. Interestingly 28(87.5%) of the 32 ESBL producing Salmonella isolates possessed at least one or more plasmids from five distinct sizes recorded 2.5; 4; 9; 15;23.5kb. Four distinct RAPD profiles were exhibited by the test strains. The total discriminatory power among the isolates was 0.77 (77%). Conclusion: Third generation cephalosporin resistance involving blaCTX-M has emerged among clinical Salmonella isolates in Lagos. RAPD elicits potential as a cost-effective and time saving tool for local discrimination of clinical Salmonella isolates for epidemiological purposes.

Differentiation of Avian Pathogenic &amp;lt;i&amp;gt;Escherichia coli&amp;lt;/i&amp;gt; Strains from Broiler Chickens by Multiplex Polymerase Chain Reaction (PCR) and Random Amplified Polymorphic (RAPD) DNA

We examined 50 Escherichia coli (E. coli) strains isolated from broiler chickens between January 2013 to March 2014 in order to evaluate the epidemiological prevalence of avian pathogenic E. coli (APEC) in Jordan by multiplex PCR and random amplification of polymorphic DNA (RAPD) tests. The multiplex polymerase chain reaction (PCR) which was used as tentative criteria of APEC targets 8 virulence associated genes; enteroaggregative toxin (astA), Type 1 fimbria adhesion (fimH), iron-repressible protein (irp2), P fimbriae (papC), aerobactin (iucD), temperature-sensitive hemagglutinin (tsh), vacuolating autotransporter toxin (vat), and colicin V plasmid operon (cva/cvi) genes. The number of detected genes could be used as a reliable index of their virulence. E. coli strains already typed as an APEC always harbor 5 to 8 genes, but non-APEC strains harbor less than 4 genes. Assuming the criteria of an APEC is possession of 5 or more virulence associated genes; we found that all 50 E. coli strains were classified as APEC strains. The RAPD analysis showed that the E. coli strains could be grouped into 35 of RAPD types by using these two different RAPD primer sets, RAPD analysis primer 4 5'AAGAGCCCGT5', and RAPD analysis primer 6 5'CCCGTCAGCA3'. The current study confirmed the endemic nature of APEC in broiler flocks in Jordan. It is essential that the biosecurity on poultry farms should be improved to prevent the introduction and dissemination of APEC and other agents. Furthermore, farmers need to be educated about the signs, lesions, and the importance of this agent.

Imported and Intensive Care Unit-BornAcinetobacter baumanniiClonal Complexes: One-Year Prospective Cohort Study in Intensive Care Patients

The main objective of this study was to assess the frequency and possible sources of colonization and infection by Acinetobacter in the intensive care unit (ICU) of a university hospital in Rio de Janeiro, Brazil, and characterize the isolates for relatedness to internationally and locally disseminated lineages. Patients consecutively admitted to the ICU from April 2007 to April 2008 were screened for colonization and infection. Species were identified by rpoB sequencing. The presence of acquired and intrinsic carbapenemase genes was assessed by polymerase chain reaction (PCR). Strains were typed by random amplification of polymorphic DNA (RAPD)-PCR, pulsed-field gel electrophoresis, and multilocus sequence typing (MLST) using the schemes hosted at the University of Oxford (UO) and Institut Pasteur (IP). Of 234 patients, 98 (42%) had at least one specimen positive for the Acinetobacter isolate, and 24 (10%) had infection. A total of 22 (92%) infections were caused by Acinetobacter baumannii and one each (4%) by Acinetobacter nosocomialis and Acinetobacter berezinae. A. baumannii isolates from 60 patients belonged to RAPD types that corresponded to MLST clonal complexes (CCs) 109/1 (UO/IP scheme, known as International Clone I), CC 110/110 (UO/IP), CC 113/79 (UO/IP), and CC 104/15 (UO/IP). Most CCs were carbapenem resistant and carried the bla(OXA-23)-like gene. Strains were introduced by patients transferred from other wards of the same hospital (11 patients, 18%) or acquired from cross-transmission within the ICU (49 patients, 82%). A. nosocomialis lineage sequence type 260 colonized 10% of the whole study population. A. baumannii have become established in this hospital as a part of a global epidemic of successful clones. Once introduced into the hospital, such clones have become entrenched among patients in the ICU.