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Background Nosocomial infections and persistence of multidrug resistant biofilm forming Acinetobacter baumannii in hospitals has made it as a serious problem in healthcare settings worldwide. Methods A total of 100 A. baumannii clinical isolates from immunocompromised patients hospitalized in ICU were investigated for biofilm formation, the presence of biofilm related genes ( bap, ompA, csuE, fimH, epsA, bla PER-1 , bfmS, ptk, pgaB, csgA, kpsMII ), integron characterization and molecular typing based on REP-PCR. Results All isolates were resistant to three or more categories of antibiotics and considered as multidrug resistant (MDR). A total of 32 isolates were resistant to all tested antibiotics and 91% were extensively drug-resistance (XDR). All isolates were able to produce biofilm and 58% of isolates showed strong ability to biofilm formation. All strong biofilm forming A. baumannii isolates were XDR. All A. baumannii isolates carried at least one biofilm related gene. The most prevalent gene was csuE (100%), followed by pgaB (98%), epsA and ptk (95%), bfmS (92%) and ompA (81%). 98% of isolates carried more than 4 biofilm related genes, simultaneously. Class I integron (67%) was more frequent in comparison with class II (10%) ( P  < 0.05). The REP-PCR patterns were classified as 8 types (A-H) and 21 subtypes. The A1 (23%) and C1 (15%) clusters were the most prevalent among A. baumannii isolates ( P  < 0.05). According to the REP-PCR patterns, 23% of all isolates had a clonal relatedness. Conclusion Our study revealed the high frequency of biofilm forming XDR A. baumannii in ICU patients, with a high prevalence of biofilm related genes of csuE and pgaB. It seems that the appropriate surveillance and control measures are essential to prevent the emergence and transmission of XDR A. baumannii in our country.

Screening for various types of lactic acid bacteria (LAB) that form the biological agent γ-amino-butyric acid (GABA) is important to produce different kinds of GABA-containing fermented foods. So far, no GABA-producing LAB have been reported from Cambodian fermented foods. Most small-scale fermentations and even some industrial processes in this country still rely on indigenous LAB. The application of GABA-producing autochthonous starters would allow the production of Cambodian fermented foods with an additional nutritional value that meet the population’s dietary habits and that are also more attractive for the international food market. Matrix-assisted laser desorption/ionizing time-of-flight mass spectrometry (MALDI-TOF MS) and partial 16S rDNA sequencing were used to identify 68 LAB isolates from Cambodian fermented foods. These isolates were classified and grouped with (GTG)5 rep-PCR, resulting in 50 strains. Subsequently, all strains were investigated for their ability to produce GABA by thin layer chromatography. GABA-positive strains were further analyzed by the GABase assay. Of the six GABA-positive LAB strains—one Lactobacillus futsaii, two Lactobacillus namurensis, and three Lactobacillus plantarum strains—two Lactobacillus plantarum strains produced high amounts of GABA (20.34 mM, 16.47 mM). These strains should be further investigated for their potential application as GABA-producing starter cultures in the food applications.

Klebsiella pneumoniae is a multidrug-resistant (MDR) opportunistic pathogen that causes nosocomial infections. Virulence analysis and molecular typing as powerful approaches can provide relevant information on K. pneumoniae infection. In the current study, antibiotic resistance, virulence-associated genes analysis, as well as molecular typing of K. pneumoniae strains were investigated. Out of 505 clinical samples collected from hospitalized patients, 100 K. pneumoniae strains were isolated by standard microbiological methods and subjected to the phenotypic and genotyping analysis. The highest prevalence of resistance was observed against ciprofloxacin (75%), trimethoprim–sulfamethoxazole (73%) and nitrofurantoin (68%). Virulence associated genes including entB, traT, ybts, magA, iucC, htrA and rmpA were found in 80%, 62%, 75%, 5%, 30%, 72% and 48%, of the isolates, respectively. The prevalence of biofilm-associated genes including mrkA, fimH, and mrkD were equally 88% for all tested isolates. Moreover, the efflux pump genes including AcrAB, TolC and mdtK were observed in 41 (41%), 33 (33%) and 26 (26%) of the strains respectively. A significant statistical association was observed between MDR strains and high expression of efflux pump and biofilm genes. The K. pneumoniae strains were differentiated into 11 different genetic patterns using the repetitive element sequence-based PCR (rep-PCR) technique. High prevalence of resistance, presence of various virulence factors, high level of efflux pump, and biofilm gene expression in diverse clones of K. pneumoniae strains pose an important health issue in clinical settings.

Bacterial blight (causal agent Pseudomonas syringae complex, Psc) is an endemic and economically important disease of northern highbush blueberry production in Canada and the Pacific Northwest of the USA. To date, there is no comprehensive survey of the disease in the region and detailed characterization of associated pathogens from Pacific western Canada. Therefore, we did comprehensive disease survey and characterization of associated pseudomonads population using pathogen morphology, biochemical tests, and molecular characterization. We isolated 380 strains of pseudomonads from symptomatic plants from 32 research and commercial fields in 10 diverse geographic locations in British Columbia. We used P . syringae specific (Psy) primers and identified 197 Psy-PCR positive isolates out of 380. We further sequenced Psy-PCR positive isolates of pseudomonads using four housekeeping genes and identified four phylogenomic species: P. syringae (40%), Pseudomonas avellanae (29%), Pseudomonas viridiflava (20%), and phylogenomic species A (7%). P . avellanae and P. viridiflava are new phylogenomic species of Psc causing bacterial blight in highbush blueberry. We found some patterns among geographical locations and highbush blueberry varieties in the frequency distribution of isolates of these phylogenomic species. Genetic fingerprinting with rep-PCR assays identified a very high genetic diversity of pseudomonads populations among geographical locations, varieties, and phylogenomic species. Biochemical characterization (LOPAT- levan, oxidase, pectolytic activity, arginine dihydrolase, and tobacco hypersensitivity) revealed that the vast majority of isolates were Pseudomonas Group Ia. Findings of this study provide insight into the population biology of pseudomonads infecting highbush blueberry, provide information for disease diagnosis, and exploit disease management options, including identifying sources of disease resistance. Key points • High prevalence of bacterial blight caused by P. syringae complex (Psc) in highbush blueberry in Pacific western Canada • We report two new phylogenomic species of Psc, P. viridiflava and P. avellanae, that cause bacterial blight and canker disease in highbush blueberry • The genetic diversity of the population of Psc was very high

Acetic acid bacteria are involved in many food and beverage fermentation processes. They play an important role in cocoa bean fermentation through their acetic acid production. They initiate the development of some of the flavor precursors that are necessary for the organoleptic quality of cocoa, and for the beans’ color. The development of starter cultures with local strains would enable the preservation of the microbial biodiversity of each country in cocoa-producing areas, and would also control the fermentation. This approach could avoid the standardization of cocoa bean fermentation in the producing countries. One hundred and thirty acetic acid bacteria were isolated from three different cocoa-producing countries, and were identified based on their 16S rRNA gene sequence. The predominate strains were grown in a cocoa pulp simulation medium (CPSM-AAB) in order to compare their physiological traits regarding their specific growth rate, ethanol and lactic acid consumption, acetic acid production, and relative preferences of carbon sources. Finally, the intraspecific diversity of the strains was then assessed through the analysis of their genomic polymorphism by (GTG)5-PCR fingerprinting. Our results showed that Acetobacter pasteurianus was the most recovered species in all of the origins, with 86 isolates out of 130 cultures. A great similarity was observed between the strains according to their physiological characterization and genomic polymorphisms. However, the multi-parametric clustering results in the different groups highlighted some differences in their basic metabolism, such as their efficiency in converting carbon substrates to acetate, and their relative affinity to lactic acid and ethanol. The A. pasteurianus strains showed different behaviors regarding their ability to oxidize ethanol and lactic acid into acetic acid, and in their relative preference for each substrate. The impact of these behaviors on the cocoa quality should be investigated, and should be considered as a criterion for the selection of acetic acid bacteria starters.

This is the primary study at Matrouh Governorate to unveil antibiotic resistance, biofilm formation, silver nanoparticles (Ag-NPs) effect using electron microscopy, and REP-PCR analysis of Staphylococcus aureus strains isolated from COVID-19 patients, contaminated food, and Morel’s diseased sheep and goats. A total of 15 S. aureus strains were isolated; five from each of the COVID-19 patients, Morel's diseased sheep and goats, and contaminated food. All strains were considered multidrug-resistant (MDR). All strains showed the presence of biofilm. Morphological changes in the cell surface of the bacterium were evidenced, and penetration with the rupture of some bacterial cells. Based on REP-PCR analysis, 4 clusters (C1-C4) with dissimilarity between clusters C1 and C2 8% and between C3 and C4 15%. Cluster I included 3 strains from contaminated food with a similarity of 97%, and Cluster II included 2 strains from contaminated food and 2 from COVID-19-infected patients with a similarity of 96% (confirming the zoonotic nature of this pathogen). Cluster III contained 4 strains isolated from Morel's diseased sheep & goats with a similarity ratio of 99% in comparison the 4th cluster contained 3 strains isolated from COVID-patients and one from Morel's diseased sheep & goats with a similarity ratio of 92%.

The absence of new antibiotics is guiding more and more researchers to specific ecosystems. One hundred sixty-three Actinobacteria isolates were isolated from Merzouga sand and screened for their antibacterial and antifungal activities. To test the antimicrobial effect of isolates, four microorganisms known as human potential pathogens were used. The electrophoretic profiles of isolates obtained by repetitive element PCR fingerprinting (rep-PCR) were compared by clustering. Results showed that among the tested isolates, 59% were active against one or more of testing Gram positive, Gram negative and the yeast Candida albicans. The importance of culture media for the activity expression was revealed. Comparative analysis of antimicrobial activity divided isolates into fifteen groups. The comparison of the average diameters of inhibition zones using Minitab V.17 allowed subdividing the 15 groups into 20 subgroups. Dendrogram derived from the BOXA1R-PCR fingerprints showed that 36 isolates were grouped in 16 clusters containing from two to four isolates while 127 isolates were not grouped. The tested antimicrobial activities showed a high biological diversity with important inhibition of pathogens tested. The rep-PCR revealed a high taxonomic diversity of isolates. The combination of antimicrobial activity and repetitive element PCR results revealed the diverse pattern of Merzouga sand dune Actinobacteria.

This study was conducted for identifying phylogenetic relationships between 15 scab-causing Streptomyces species including S. bottropensis, S. europaeiscabiei , S. scabiei , S. stelliscabiei and, other 11 Streptomyces sp. All of the strains were originally isolated from symptomatic potatoes in Erzurum Province, The Eastern Anatolia Region of Turkey. Some morphological and biochemical properties of the strains were defined in our former research. Then, 16 s rRNA regions of them were sequenced. After the sequence data assembly, phylogenetic analyzes were performed. The phylogenetic analyses revealed that the strains are involved in the same major group and, substantially similar to reference strains. Additionally, some subgroup formations were also recorded. Moreover, Repetitive element-based PCR (Rep-PCR), Enterobacterial repetitive intergenic consensus (ERIC-PCR), and BOX-PCR fingerprinting molecular typing methods were used for as molecular typing methods. According to our knowledge, this is the first report on phylogenetic relationships of scab-causing Streptomyces species from Turkey. However, the identification of most pathogenic strains remained at the species level.

Seventy-five pectinolytic strains collected from vegetables grown in the counties of Santarém, Belterra, and Mojuí dos Campos, located in the western region of the Pará State, Brazil, were studied according to their pathological and genetic variability. The strains were grouped in 5 clusters according to pathogenicity in potato, pepper, carrot, and onion, and 38 strains were selected for genetic analysis using rep-PCR. These strains were divided into 35 genetic groups according to rep-PCR at 70% similarity. These results indicated high pathological and genetic variability of the strains causing soft rot in vegetables in the western region of the Pará State, which will be used in etiological research and for the development and assessment of management techniques for the soft rot in vegetables in this region. RESUMO: Setenta e cinco isolados de bactérias pectinolíticas coletados de hortaliças cultivadas nos municípios de Santarém, Belterra e Mojuí dos Campos, região oeste do Estado do Pará, Brasil, foram estudadas de acordo com sua variabilidade patológica e genética. Os isolados foram agrupados em cinco grupos de acordo com a patogenicidade em batata, pimenta, cenoura e cebola, e 38 isolados foram selecionados para análise genética por rep-PCR. Esses isolados foram divididos em 35 grupos genéticos de acordo com rep-PCR a 70% de similaridade. Esses resultados indicaram alta variabilidade patológica e genética dos isolados causadores da podridão mole em hortaliças da região oeste do Pará, os quais serão utilizados em pesquisas etiológicas e para o desenvolvimento e avaliação de técnicas de manejo da podridão mole em hortaliças nesta região.