Competitiveness of Bradyrhizobium japonicum inoculation strain for soybean nodule occupancy

The competitiveness of Bradyrhizobium japonicum inoculation strain against indigenous rhizobia was examined in a soil pot experiment. The effect of inoculation strain was evaluated under different soil conditions: with or without previously grown soybean and applied commercial inoculant. Molecular identification of inoculation strain and investigated rhizobial isolates, obtained from nodules representing inoculated treatments, was performed based on 16S rDNA and enterobacterial repetitive intergenic consensus (ERIC) sequencing. Inoculation strain showed a significant effect on the investigated parameters in both soils. Higher nodule occupancy (45% vs. 18%), nodule number (111% vs. 5%), nodule dry weight (49% vs. 9%), shoot length (15% vs. 7%), root length (31% vs. 13%), shoot dry weight (34% vs. 11%), shoot nitrogen content (27% vs. 2%), and nodule nitrogen content (9% vs. 5%) was detected in soil without previously grown soybean and applied commercial inoculant. Soil had a significant effect on the shoot, root and nodule nitrogen content, while interaction of experimental factors significantly altered dry weight and nitrogen content of shoots, roots and nodules, as well as number of nodules. Nodulation parameters were significantly related with shoot dry weight, shoot and nodule nitrogen content. Symbiotic performance of inoculation strains in the field could be improved through co-selection for their competitiveness and effectiveness.

American Foulbrood in the Czech Republic: ERIC II Genotype of Paenibacillus Larvae Is Prevalent

American foulbrood (AFB) is a dangerous disease of honeybees (Apis mellifera) caused by the spore-forming bacterium Paenibacillus larvae. According to the ERIC (enterobacterial repetitive intergenic consensus) classification, five genotypes are distinguished, i.e., I, II, III, IV, and V, which differ in their virulence and prevalence in colonies. In the Czech Republic, AFB prevalence is monitored by the State Veterinary Administration; however, the occurrence of specific P. larvae genotypes within the country remains unknown. In this study, our aim was to genotype field P. larvae strains collected in the Czech Republic according to the ERIC classification. In total, 102 field isolates from colonies with AFB clinical symptoms were collected from various locations in the Czech Republic, and the PCR genotypization was performed using ERIC primers. We confirmed the presence of both ERIC I and II genotypes, while ERIC III, IV, and V were not detected. The majority of samples (n = 82, 80.4%) were identified as ERIC II, while the ERIC I genotype was confirmed only in 20 samples (19.6%). In contrast to other European countries, the ERIC II genotype is predominant in Czech honeybee colonies. The ERIC I genotype was mostly detected in border regions close to Poland, Slovakia, and Austria.

Emergence of Colistin and Carbapenem Resistance in Extended-Spectrum β-Lactamase Producing Klebsiella pneumoniae Isolated from Chickens and Humans in Egypt

This study investigated the frequency of carbapenem and colistin resistance in ESBL-producing K. pneumoniae (ESBLK) isolates recovered from chickens and their environment, contact farm workers and hospitalized patients in Egypt. Further, the phenotypic and genotypic relationships between the community and hospital-acquired K. pneumoniae isolates in the same geographical area were investigated. From 272 total samples, 37 (13.6%) K. pneumoniae isolates were identified, of which 20 (54.1%) were hypervirulent. All isolates (100%) were multidrug-resistant (MDR) with multiple antibiotic resistance (MAR) indices ranging from 0.19 to 0.94. Colistin-resistant isolates (18.9%) displayed colistin MIC values >2 μg/mL, all harbored the mcr-1 gene. All isolates from patients (13/90, 14.4%), workers (5/22, 22.7%), chickens (9/100, 9%) and the environment (10/60, 16.7%) harbored a single or multiple β-lactamase genes, blaSHV, blaTEM, blaCTX-M1 and blaOXA-1, often in combination with carbapenemase genes (blaVIM, blaNDM-1 or blaIMP; 45.9%), the mcr-1 gene (18.9%) or both (13.5%). Enterobacterial repetitive intergenic consensus (ERIC)–PCR genotyping revealed 24 distinct ERIC types (ETs) with a discrimination index of 0.961. Six ETs showed clusters of identical isolates from chicken and human sources. The increased frequency and genetic relatedness of ESBLK and carbapenemase-producing K. pneumoniae (CPK) from chickens and humans pose a public health threat that urge more prudent use of antimicrobials in chicken farms to avoid the propagation and expansion of both ESBLK and CPK from the chicken sources to humans.

Evaluation of Antimicrobial activity and Genotoxic Potential of Capparis spinosa (L.) Plant Extracts

Objective: The aims of this study were to evaluate the antimicrobial activity and the genotoxic effect of both ethanolic and aqueous extracts of stem and leaf of Capparis spinosa (C. spinosa) plant on Escherichia coli (E. coli) ATCC 25922, Staphylococcus aureus (S. aureus) ATCC 6538P, clinical isolate of Methicillin-resistant S. aureus (MRSA) and Klebsiella pneumoniae (K. pneumoniae) and Candida albicans (C. albicans) ATCC 90028. Materials and Methods: The antimicrobial activity was determined using microbroth dilution method, while the genotoxic effect was investigated using randomly amplified polymorphic DNA (RAPD)-PCR and enterobacterial repetitive intergenic consensus (ERIC)-PCR. Results: The MIC values of both ethanolic and aqueous leaf and stem extracts of C. spinosa plant had a range 6.25 mg/ml to 100 mg/ml. In addition, it was found that ethanolic extract more effective than aqueous extract. The genotoxic activity of aqueous leaf extract, showed changes in both Random Amplified Polymorphic DNA (RAPD)-PCR and Enterobacterial Repetitive Intergenic Consensus (ERIC)-PCR profiles of E. coli strain treated with extract compared to untreated (negative) control. These changes included an alteration in the intensity, absence or appearance of new amplified fragments. Conclusions: Results of this study strongly show the genotoxic effect of aqueous leaf extract from C. spinosa plant on E. coli. The findings draw awareness to the possible toxic effect use of C. spinosa plant in traditional medicine and point out the capability of using C. spinosa to treat bacterial or fungal infections. More studies are needed to detect the exact ingredients of this plant as well as the mechanisms responsible for genotoxicity. Further in vivo genotoxicity studies are recommended to ensure and to evaluate the safety of using plants for therapeutic purposes. In addition, results of this study showed that molecular fingerprinting based on ERIC-PCR can be used to evaluate the genotoxic effect in the model bacterial species E. coli.

Genotyping of Acinetobacter baumannii that isolate from different cases by using ERIC

Determination of genetic relatedness typing between isolates has done for Acinetobacter baumannii isolates by using Enterobacterial Repetitive Intergenic Consensus-PCR (ERIC-PCR), the results of the current study showed the presence of a genetic relationship between bacterial isolates isolated from different clinical sources. The results of the study showed the presence of 18 patterns, the molecular weight of these bands ranged between (100-4000) bp. Dendogram analysis of the results showed that there was genetic relatedness between the isolates of Acinetobacter baumannii in only one clone while 37 isolated contain different genotyping.

Molecular Typing of Klebsiella pneumoniae Clinical Isolates by Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction

Aim. Klebsiella pneumoniae is one of the most important causes of nosocomial infections, including pneumonia, sepsis, and urinary tract infection. Enterobacterial repetitive intergenic consensus polymerase chain reaction (ERIC-PCR) technique is a quick, reliable, and cost-effective method for molecular typing of Enterobacteriaceae family members. This study aimed to detect genetic relatedness among K. pneumoniae isolates from hospitals in Hamadan city, using ERIC-PCR technique. Materials and Methods. A total of 72 K. pneumoniae isolates were collected from patients admitted to Besat and Sina hospitals. After detection and confirmation of K. pneumonia isolates by chemical and conventional microbiological methods, DNAs were extracted after 24 hours of incubation at 37°C, using the boiling method. ERIC-PCR technique was carried out, and the ERIC patterns were analyzed by online data analysis service (inslico.ehu.es). ERIC profiles were compared using Dice method and clustered by UPGMA (unweighted pair group method with arithmetic mean) program. Also, the samples were evaluated by PCR method for the detection of aerobactin gene within their genome. Finding. The genetic relatedness among K. pneumoniae isolates was studied, and results established the genetic diversity of the clinical isolates by detecting 25 different ERIC types, including 14 common types and 11 unique types. Also, none of the isolates had aerobactin gene. Discussion. The results of this study showed high genetic diversity among K. pneumoniae strains, indicating the polyclonal distribution of K. pneumoniae isolates in Hamadan hospitals. This diversity causes problems for the treatment of infections due to the circulation of diverse K. pneumoniae clones, which possibly have different antimicrobial susceptibility patterns.

Diversity Analysis of Genus Vibrio in Enterocytozoon Hepatopenaei (EHP) Infected Shrimp with Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC PCR) Method

Udang merupakan salah satu komoditas unggulan nasional dan memiliki nilai ekonomi yang tinggi. Produksi udang budidaya di Indonesia tahun 2012-2017 mengalami kenaikan secara signifikan. Meski mengalami kenaikan, masih terdapat masalah yang harus diatasi, salah satunya adalah penyakit yang disebabkan oleh parasit Enterocytozoon Hepatopenaei (EHP). Infeksi EHP mengganggu sel tubulus hepatopankreas. Lesi yang disebabkan oleh EHP dapat menjadi tempat pertumbuhan koloni Vibrio sehingga meningkatkan kemungkinan munculnya penyakit lain. Penelitian ini bertujuan untuk mengetahui keanekaragaman Vibrio pada udang terinfeksi EHP yang dianalisis dengan Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC PCR). ERIC PCR dapat membedakan strain bakteri yang berkerabat dekat, prosedur kerja yang sederhana, cepat dan murah. Bakteri Vibrio diisolasi dari hepatopankreas, feses dan air udang terinfeksi EHP dan udang sehat (kontrol), dilanjutkan dengan ekstraksi DNA, ERIC PCR, elektroforesis dan konstruksi pohon filogenetik. Hasil penelitian menunjukkan bahwa jumlah bakteri Vibrio pada hepatopankreas, air dan feses udang terinfeksi EHP lebih tinggi dibandingkan dengan udang sehat. Udang terinfeksi EHP memiliki keanekaragaman Vibrio yang lebih rendah dari pada udang sehat. Hal ini menunjukkan adanya spesies Vibrio spesifik yang mendominasi pada udang terinfeksi EHP.

Enterobacterial Repetitive Intergenic Consensus (ERIC) as a tool for genetic characterisation of bacterial isolates in Nigeria

Genetic characterisation as a tool for identification of bacterial isolates in Nigeria has been on the increase in recent years, and the 16s rRNA typing has been a preferred method. Due to cost limitations, there is a need to explore other genetic options. Enterobacterial Repetitive Intergenic Consensus (ERIC) polymerase chain reaction (PCR) analysis is a PCR- only based system which offers the advantage of reduced cost. This study set out to explore the use of ERIC-PCR in genetic characterisation of some selected bacterial isolates from Nigeria and compare it with genetic characterisation using 16s rRNA sequence typing. ERIC-PCR and 16s rRNA typing were carried out on 15 isolates following previously described protocols. Using 16s rRNA typing, thirteen different bacterial species were identified of which majority (85.7%) were Gram negative, with 57.1% belonging to the Enterobacteriaceae family. Using ERIC-PCR, only 13 of the 15 isolates (86.7%) could be typed, resulting in the identification of the 13 different types. ERIC-PCR was able to accurately differentiate between two members of the Proteus species, as well as identify the organisms as similar based on the banding pattern. The results show that ERIC-PCR may play a role as a bacterial identification tool but this role might be more suited to differentiating closely related members of a genus or typing within species rather than general bacterial identification. Keywords: Genetic characterisation, 16s rRNA, ERIC-PCR, Nigeria

Genetic Characterization Among Carbapenem-resistant Escherichia coli Strains Using Enterobacterial Repetitive Intergenic Consensus Polymerase Chain Reaction (ERIC-PCR) Fingerprinting in South Africa

Background Carbapenems belong to beta-lactam class of antibiotics usually considered as the last line of defense because they can be effective against severe infections caused by prevalent multidrug-resistant (MDR) pathogens. However, carbapenems can be deactivated by bacteria that produce carbapenemase (beta-lactamase). This study was conducted to screen for carbapenem-resistance genes (CRGs) harbored by pathogenic strains of Escherichia coli recovered from different environmental samples. We also assessed the genetic relatedness among selected E. coli pathotypes using enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR).Method: Molecular identification and characterization of the presumptive isolates were performed using PCR and isolates that exhibited antimicrobial resistance (AMR) phenotypically were further screened for some relevant CRGs (blaNDM−1, blaKPC and blaOXA−48−like). Furthermore, ERIC-PCR was used to determine the similarity and diversity of 31 E. coli strains which were randomly selected from the different sources analyzed in this study.Result Our findings revealed a total of 238 presumptive E. coli isolates, out of which 192 were confirmed positive for uidA gene. Further screening revealed 77 (40%) isolates belong to six key E. coli pathotypes and 70 of them exhibited phenotypic AMR. Additionally, twenty-nine (41%) of the 70 MDR pathogenic E. coli strains harbored CRGs; with 24 strains harboring blaNDM−1, 8 harboring blaKPC and 2 harboring blaOXA−48−like genes.Conclusion Findings also suggest that the selected E. coli pathotypes belonged to different genomic clusters, while the cluster analysis showed a possible genetic diversity among aquatic and farm isolates. Proper treatment of final effluents before discharge as well as the development of more effective strategies to control and manage the use of antimicrobial agents were strongly recommended.