Enhancing Bioinformatics and Genomics Courses: Building Capacity and Skills via Lab Meeting Activities: Fostering a Culture of Critical Capacities to Read, Write, Communicate and Engage in Rigorous Scientific Exchanges.

Reading, writing, publishing, and publicly presenting scientific works are vital for a young researcher's profile building and career development. Generally, the traditional educational curricula do not offer training possibilities to learn and practice how to prepare, write, and present scientific works. These are rather a part of lab meeting activities in research groups. The lack of such training is more critical in some developing countries because this adds to the rare opportunities to discuss and become involved in the exchanges on state of the art scientific literature. Here the authors relate their experience in introducing a weekly 1-day lab meeting in the framework of two previously organized 3-month courses on "Bioinformatics and Genome Analyses". The main activities which are developed during these lab meetings include scientific literature follow up as well as preparing and presenting oral and written scientific reviews. These activities prove to be useful for a student's self-confidence building, for enhancing their active participation during the lectures and practical sessions, as well as for the positive impact on running the whole course program. Incorporation of such lab meeting activities in the course program significantly improves the capacity building of the participants, their analytical and critical reading of scientific literature, as well as communication skills. In this work it is shown how to proceed with the different steps involved in the implementation of lab meeting activities, and to recommend their regular institution in similar courses.

Distribution, Diversity and Antibiotic Resistance of Pseudomonas spp. Isolated from the Water Dams in the North of Tunisia.

Natural environment is one of the important reservoirs to disseminate antibiotic resistance, most of the antibiotics resistance researches were focused on clinical isolates. Thus, this work aimed to analyze surface water samples collected from dams and rivers in the north of Tunisia. Pseudomonas species were confirmed using biochemical and molecular identifications. Resistance was studied by testing their susceptibility against 19 antibiotics using the disc diffusion method moreover the virulence factors were studied by PCR targeting 13 genes. 104 isolates were confirmed as Pseudomonas genera distributed into 21 species. The most abundant species is P. aeruginosa (22.11%), followed by P. protegens (12.5%). No resistance phenotypes were observed towards imipenem, meropenem, ceftazidime, colistin, ciprofloxacin and amikacin. A high resistance level was observed against cefoxitin (94.23%), amoxicillin-clavulanic acid (67.31%), nalidixic acid (62.5%), streptomycin (57.69%), ticarcillin (43.27%), fosfomycin (64.42%) and tetracycline (23.08%). A low rate of resistance was observed against cefotaxime (16.35%) and gentamicin (7.69%). The majority (70.19%) of isolates were Multidrug-resistant (MDR). 12 of virulence genes were found in all P. aeruginosa isolates. Our results showed that Pseudomonas isolates could be an important reservoir of antibiotic resistance from environment sites.

Aridity modulates belowground bacterial community dynamics in olive tree.

Aridity negatively affects the diversity and abundance of edaphic microbial communities and their multiple ecosystem services, ultimately impacting vegetation productivity and biotic interactions. Investigation about how plant-associated microbial communities respond to increasing aridity is of particular importance, especially in light of the global climate change predictions. To assess the effect of aridity on plant associated bacterial communities, we investigated the diversity and co-occurrence of bacteria associated with the bulk soil and the root system of olive trees cultivated in orchards located in higher, middle and lower arid regions of Tunisia. The results indicated that the selective process mediated by the plant root system is amplified with the increment of aridity, defining distinct bacterial communities, dominated by aridity-winner and aridity-loser bacteria negatively and positively correlated with increasing annual rainfall, respectively. Aridity regulated also the co-occurrence interactions among bacteria by determining specific modules enriched with one of the two categories (aridity-winners or aridity-losers), which included bacteria with multiple PGP functions against aridity. Our findings provide new insights into the process of bacterial assembly and interactions with the host plant in response to aridity, contributing to understand how the increasing aridity predicted by climate changes may affect the resilience of the plant holobiont.

Designing and running an advanced Bioinformatics and genome analyses course in Tunisia.

Genome data, with underlying new knowledge, are accumulating at exponential rate thanks to ever-improving sequencing technologies and the parallel development of dedicated efficient Bioinformatics methods and tools. Advanced Education in Bioinformatics and Genome Analyses is to a large extent not accessible to students in developing countries where endeavors to set up Bioinformatics courses concern most often only basic levels. Here, we report a pioneering pilot experience concerning the design and implementation, from scratch, of a three-months advanced and extensive course in Bioinformatics and Genome Analyses in the Institut Pasteur de Tunis. Most significantly the outcome of the course was upgrading the participants' skills in Bioinformatics and Genome Analyses to recognized international standards. Here we detail the different steps involved in the implementation of this course as well as the topics covered in the program. The description of this pilot experience might be helpful for the implementation of other similar educational projects, notably in developing countries, aiming to go beyond basics and providing young researchers with high-level skills.

Highly divergent Mollicutes symbionts coexist in the scorpion Androctonus australis.

Androctonus australis is one of the most ubiquitous and common scorpion species in desert and arid lands from North Africa to India and it has an important ecological role and social impact. The bacterial community associated to this arachnid is unknown and we aimed to dissect its species composition in the gut, gonads, and venom gland. A 16S rRNA gene culture-independent diversity analysis revealed, among six other taxonomic groups (Firmicutes, Betaproteobacteria, Gammaproteobacteria, Flavobacteria, Actinobacteria, and Cyanobacteria), a dominance of Mollicutes phylotypes recorded both in the digestive tract and the gonads. These related Mollicutes include two Spiroplasma phylotypes (12.5% of DGGE bands and 15% of clones), and a new Mycoplasma cluster (80% of clones) showing 16S rRNA sequence identities of 95 and 93% with Mollicutes detected in the Mexican scorpions Centruroides limpidus and Vaejovis smithi, respectively. Such scorpion-associated Mollicutes form a new lineage that share a distant ancestor with Mycoplasma hominis. The observed host specificity with the apparent phylogenetic divergence suggests a relatively long co-evolution of these symbionts with the scorpion hosts. From the ecological point of view, such association may play a beneficial role for the host fitness, especially during dormancy or molt periods.

Association between sHLA-G and HLA-G 14-bp deletion/insertion polymorphism in Crohn's disease.

The aim of this study was to evaluate the association between the HLA-G 14-bp deletion/insertion (Del/Ins) polymorphism and soluble (s) HLA-G production in patients with Crohn's disease (CD). We analyzed also the sHLA-G molecules by ELISA and western blot in plasma samples. Among unselected patients, the 14-bp Del/Ins polymorphism was not significantly associated with increased CD risk neither for alleles (P = 0.371) nor for genotypes (P = 0.625). However, a significant association was reported between the 14-bp Del/Ins polymorphism and CD, in particular in young-onset CD patients for alleles [P = 0.020, odds ratio (OR) = 2.438, 95% confidence interval (CI): 1.13-5.25] but not with adult-onset CD patients. A significant association was reported concerning the genotype Ins/Ins for young-onset CD patients (P = 0.029, OR = 3.257, 95% CI: 1.08-9.77). We observed also a significant increase in sHLA-G measured by ELISA in CD patients compared to controls (P = 0.002). The 14-bp Del/Del and 14-bp Del/Ins genotypes are the high HLA-G producers. Among sHLA-G(positive) patients, 43% of subjects present dimers of HLA-G. The presence of dimers seems to be related to the advanced stages of the disease. The 14-bp Del/Ins polymorphism is associated with an increased risk of CD particularly in young-onset CD patients and controls sHLA-G plasma levels. Dimers of sHLA-G are frequent in advanced disease stages. The above findings indicate that the genetic 14-bp Del/Ins polymorphism in exon 8 of the HLA-G gene is associated with the risk of CD and suggest a role for sHLA-G as a prognostic marker for progressive disease.

Prevalence, antimicrobial resistance and genetic lineages of Enterococcus spp. from vegetable food, soil and irrigation water in farm environments in Tunisia.

BACKGROUND: The objective of this study was to determine the species, clonal diversity, antibiotic resistance and virulence of enterococci in different environments. Seventy-one samples of farm origin (34 of food vegetables, 27 of soil and ten of irrigation water) and 19 samples of vegetables from five markets, were inoculated in Slanetz-Bartley agar plates supplemented or not with gentamicin (SB-Gen and SB plates, respectively) for enterococci recovery. RESULTS: Enterococci were obtained from 72.2% of tested samples in SB media (food vegetables from farms, 88.2%; soil and irrigation water, 51%; food vegetables from markets, 84.2%), and 65 enterococcal isolates were obtained. Enterococcus faecium was the most prevalent species (52.3%), followed by E. hirae (35.4%), E. faecalis (6.15%), and E. casseliflavus (6.15%). Antibiotic resistance detected among these enterococci was as follows (percentage/detected gene): ciprofloxacin (60%), erythromycin (18.4%/erm(B)), tetracycline (15.4%/tet(M)-tet(L)), kanamycin (15.4%/aph(3')-III), chloramphenicol (7.7%), streptomycin (3%/ant(6)), vancomycin (6.15%/vanC2)), teicoplanin (0%) and ampicillin (0%). High-level gentamicin-resistant (HLR-G) enterococci were detected in SB-Gen plates in 14 of 90 tested samples (15.5%), and 15 isolates were characterized: ten E. faecalis, four E. faecium and one E. hirae. All HLR-G enterococci carried the aac(6')-aph(2″), erm(B) and tet(M) genes, among other resistance genes. The HLR-G isolates showed high genetic diversity (ten different PFGE profiles), and were ascribed to the sequence types ST2, ST16, ST28 and new ST528 (in E. faecalis), and ST56, new ST885 and new ST886 (in E. faecium). CONCLUSION: Food vegetables in the farm or market settings are frequently contaminated by HLR-G enterococci, and these microorganisms could reach the human intestine through the food chain, if hygienic conditions are not followed. © 2015 Society of Chemical Industry.

Characterization of Staphylococcus aureus from Raw Meat Samples in Tunisia: Detection of Clonal Lineage ST398 from the African Continent.

Livestock-associated Staphylococcus aureus isolates, and especially those belonging to ST398, have been increasingly described in colonized and infected animals and humans, and also in food samples in several countries. The purpose of this study was to determine the frequency of S. aureus and methicillin-resistant S. aureus (MRSA) isolates in raw meat samples destined for food consumption in Tunisia, and to characterize the recovered isolates. One hundred sixty-nine food samples of animal origin were collected. Samples were inoculated onto selective mediums for S. aureus and MRSA recovery. Different molecular typing methods were implemented (pulsed-field gel electrophoresis [PFGE], multilocus sequence typing, spa-, agr-, and SCCmec typing). MRSA was detected in 2 of these 169 samples (1.2%), both of which were of chicken origin. The two MRSA isolates (one/sample) were typed as ST30-CC30-t012-agrIII-SCCmecV and ST398-CC398-t4358-agrI-SCCmecIVa. The MRSA ST398 strain presented resistance, in addition to ß-lactams, to tetracycline (tet[M]) and erythromycin (erm[C]) and harbored the sen, hla, hlg, and hlgv virulence genes. Methicillin-susceptible S. aureus (MSSA) isolates were recovered from 42 of the 169 tested samples (24.8%). A high diversity of spa types (n=21) and SmaI-PFGE patterns (27 different profiles; 4 nontypeable) were detected among MSSA isolates. Four MSSA isolates were typed as ST398/CC398. The percentage of antimicrobial resistance and detected genes in MSSA isolates were as follows: tetracycline (28.6% tet[K] and tet[L]), kanamycin (9.5%, aph[3']-IIIa), tobramycin (2.4%, ant[4']-Ia), erythromycin (14.3%, erm[A], erm[C], msr[A]), and penicillin (95%). The genes lukS-lukF were detected in two MSSA isolates (4.5%), the gene tst in one isolate, and the gene eta in five isolates. To our knowledge, this is the first detection of MRSA and MSSA ST398 in food in an African country. The risk of transmission of S. aureus and MRSA carrying different antimicrobial resistance and virulence genes through the food chain cannot be ignored.

Halanaerobium sehlinense sp. nov., an extremely halophilic, fermentative, strictly anaerobic bacterium from sediments of the hypersaline lake Sehline Sebkha.

A strictly anaerobic, extremely halophilic, Gram-positive, rod-shaped bacterium was isolated from the hypersaline (>20% NaCl) surface sediments of Sehline Sebkha in Tunisia. The strain, designated 1Sehel(T), was strictly halophilic and proliferated at NaCl concentrations of between 5% and 30% (saturation), with optimal growth at 20% NaCl. Strain 1Sehel(T) was non-spore-forming, non-motile, appearing singly or in pairs, or occasionally as long chains and measured 0.5-0.8 µm by 3-10 µm. Strain 1Sehel(T) grew optimally at pH values of 7.4 but had a very broad pH range for growth (pH 5.2-9.4). It grew at temperatures between 20 and 50 °C with an optimum at 43 °C. Strain 1Sehel(T) required yeast extract for growth. The isolate fermented glucose, galactose, fructose, glycerol, mannose, maltose, ribose, pyruvate and sucrose. The fermentation products from glucose utilization were lactate, acetate, formate, ethanol, CO2 and H2. The G+C ratio of the DNA was 32.7 mol%. The major fatty acids were C15:1ω6c/7c, C16:1ω7c, C16:0 and C15:0. On the basis of phylogenetic and physiological properties, strain 1Sehel(T) (=DSM 25582(T)=JCM 18213(T)) is proposed as the type strain of Halanaerobium sehlinense sp. nov., within the family Halanaerobiaceae.

Antimicrobial resistance, virulence genes, and genetic lineages of Staphylococcus pseudintermedius in healthy dogs in tunisia.

Nasal swabs of 100 healthy dogs were obtained in 2011 in Tunisia and tested for Staphylococcus pseudintermedius recovery. Antimicrobial resistance profile and virulence gene content were determined. Multilocus-sequence-typing (MLST) and SmaI-pulsed-field gel electrophoresis (PFGE) were investigated. S. pseudintermedius was recovered in 55 of the 100 tested samples (55 %), and one isolate per sample was further studied. All 55 S. pseudintermedius isolates were susceptible to methicillin (MSSP) but showed resistance to the following antimicrobials (% resistant isolates/resistance gene): penicillin (56.4/blaZ), tetracycline (40/tetM), trimethoprim-sulfamethoxazole (23.7), fusidic acid (9), kanamycin (3.7/aph(3´)-Ia), erythromycin-clindamycin (1.8/erm(B)), streptomycin (1.8/ant(6)-Ia), chloramphenicol (1.8) and ciprofloxacin (1.8). The following toxin genes were identified (% of isolates): lukS/F-I (98.2), expA (5.5), se-int (98.2), sec canine (1.8), siet (100), sea (5.5), seb (3.6), sec (10.9), sed (54.5), sei (5.5), sej (29.1), sek (3.6), ser (9.1), and hlg v (38.2). Ten different sequence-types were detected among 11 representative MSSP isolates: ST20, ST44, ST69, ST70, ST78, ST100, ST108, ST160, ST161, and ST162, the last three ones revealing novel alleles or allele combinations. Eleven different PFGE-patterns were identified in these isolates. The nares of healthy dogs could be a reservoir of antimicrobial resistant and virulent MSSP, highlighting the presence of the recently described exfoliating gene expA and several enterotoxin genes.

Uneven distribution of Halobacillus trueperi species in arid natural saline systems of Southern Tunisian Sahara.

The genetic diversity of a collection of 336 spore-forming isolates recovered from five salt-saturated brines and soils (Chott and Sebkhas) mainly located in the hyper-arid regions of the southern Tunisian Sahara has been assessed. Requirements and abilities for growth at a wide range of salinities\ showed that 44.3 % of the isolates were extremely halotolerant, 23 % were moderate halotolerant, and 32.7 % were strict halophiles, indicating that they are adapted to thrive in these saline ecosystems. A wide genetic diversity was documented based on 16S-23S rRNA internal transcribed spacer fingerprinting profiles (ITS) and 16S rRNA gene sequences that clustered the strains into seven genera: Bacillus, Gracilibacillus, Halobacillus, Oceanobacillus, Paenibacillus, Pontibacillus, and Virgibacillus. Halobacillus trueperi was the most encountered species in all the sites and presented a large intraspecific diversity with a multiplicity of ITS types. The most frequent ITS type included 42 isolates that were chosen for assessing of the intraspecific diversity by BOX-PCR fingerprinting. A high intraspecific microdiversity was documented by 14 BOX-PCR genotypes whose distribution correlated with the strain geographic origin. Interestingly, H. trueperi isolates presented an uneven geographic distribution among sites with the highest frequency of isolation from the coastal sites, suggesting a marine rather than terrestrial origin of the strains. The high frequency and diversity of H. trueperi suggest that it is a major ecosystem-adapted microbial component of the Tunisian Sahara harsh saline systems of marine origin.

Antimicrobial Activities and Mode of Flavonoid Actions.

The emergence of antibiotics-resistant bacteria has been a serious concern for medical professionals over the last decade. Therefore, developing new and effective antimicrobials with modified or different modes of action is a continuing imperative. In this context, our study focuses on evaluating the antimicrobial activity of different chemically synthesized flavonoids (FLAV) to guide the chemical synthesis of effective antimicrobial molecules. A set of 12 synthesized molecules (4 chalcones, 4 flavones and 4 flavanones), bearing substitutions with chlorine and bromine groups at the C6' position and methoxy group at the C4' position of the B-ring were evaluated for antimicrobial activity toward 9 strains of Gram-positive and Gram-negative bacteria and 3 fungal strains. Our findings showed that most tested FLAV exhibited moderate to high antibacterial activity, particularly against Staphylococcus aureus with minimum inhibitory concentrations (MIC) between the range of 31.25 and 125 µg/mL and that chalcones were more efficient than flavones and flavanones. The examined compounds were also active against the tested fungi with a strong structure-activity relationship (SAR). Interestingly, leakage measurements of the absorbent material at 260 nm and scanning electron microscopy (SEM) demonstrated that the brominated chalcone induced a significant membrane permeabilization of S. aureus.

High diversity of genetic lineages and virulence genes in nasal Staphylococcus aureus isolates from donkeys destined to food consumption in Tunisia with predominance of the ruminant associated CC133 lineage.

BACKGROUND: The objective of this study was to determine the genetic lineages and the incidence of antibiotic resistance and virulence determinants of nasal Staphylococcus aureus isolates of healthy donkeys destined to food consumption in Tunisia. RESULTS: Nasal swabs of 100 donkeys obtained in a large slaughterhouse in 2010 were inoculated in specific media for S. aureus and methicillin-resistant S. aureus (MRSA) recovery. S. aureus was obtained in 50% of the samples, being all of isolates methicillin-susceptible (MSSA). Genetic lineages, toxin gene profile, and antibiotic resistance mechanisms were determined in recovered isolates. Twenty-five different spa-types were detected among the 50 MSSA with 9 novel spa-types. S. aureus isolates were ascribed to agr type I (37 isolates), III (7), II (4), and IV (2). Sixteen different sequence-types (STs) were revealed by MLST, with seven new ones. STs belonging to clonal clomplex CC133 were majority. The gene tst was detected in 6 isolates and the gene etb in one isolate. Different combinations of enterotoxin, leukocidin and haemolysin genes were identified among S. aureus isolates. The egc-cluster-like and an incomplete egc-cluster-like were detected. Isolates resistant to penicillin, erythromycin, fusidic acid, streptomycin, ciprofloxacin, clindamycin, tetracycline, or chloramphenicol were found and the genes blaZ, erm(A), erm(C), tet(M), fusC were identified. CONCLUSIONS: The nares of donkeys frequently harbor MSSA. They could be reservoirs of the ruminant-associated CC133 lineage and of toxin genes encoding TSST-1 and other virulence traits with potential implications in public health. CC133 seems to have a broader host distribution than expected.

Prevalence and characterization of extended-spectrum beta-lactamase (ESBL)- and CMY-2-producing Escherichia coli isolates from healthy food-producing animals in Tunisia.

The prevalence of extended-spectrum beta-lactamase (ESBL)- and plasmidic AmpC-beta-lactamase (pAmpC-BL)-producing Escherichia coli isolates has been studied in food-producing animals at the farm level in Tunisia, and recovered isolates were characterized for the presence of other resistance genes and integrons. Eighty fecal samples of food-producing animals (23 sheep, 22 chickens, 22 cattle, six horses, five rabbits, and two dromedaries) were obtained from 35 different farms in Tunisia in 2011. Samples were inoculated onto MacConkey agar plates supplemented with cefotaxime (2 mg/L) for cefotaxime-resistant (CTX(R)) E. coli recovery. CTX(R) E. coli isolates were detected in 11 out of 80 samples (13.8%), and one isolate per sample was further characterized (10 from chickens and one from a dromedary). The 11 CTX(R) isolates were distributed into phylogroups: B1 (five isolates), A (two isolates), D (three isolates), and B2 (one isolate). The following beta-lactamase genes were detected: bla(CTX-M-1) (seven isolates), bla(CTX-M-1)+bla(TEM-135) (one isolate), bla(CTX-M-1)+bla(TEM-1b) (one isolate), and bla(CMY-2) (two isolates). All ESBL- and pAmpC-BL-producing E. coli strains showed unrelated pulsed-field gel electrophoresis patterns. Seven isolates contained class 1 integrons with four gene cassette arrangements: dfrA17-aadA5 (three isolates), dfrA1-aadA1 (two isolates), dfrA15-aadA1 (one isolate), and aadA1 (one isolate). All isolates showed tetracycline resistance and contained the tet(A) +/- tet(B) genes. Virulence genes detected were as follows (number of isolates in parentheses): fimA (10); aer (eight); papC (two); and papGIII, hly, cnf, and bfp (none). Chicken farms constitute a reservoir of ESBL- and pAmpC-BL-producing E. coli isolates of the CTX-M-1 and CMY-2 types that potentially could be transmitted to humans via the food chain or by direct contact.

Diversity of the desert truffle Terfezia boudieri Chatin. in southern Tunisia.

This study reports the genetic diversity of Terfezia boudieri collected from southern Tunisia. The study was carried out using 135 truffle fruiting bodies harvested from seven different locations. Twenty-eight Terfezia claveryi fruiting bodies were also sampled from one of the seven locations. A PCR-based technique was used to amplify the internal transcribed spacer (ITS) region of the rDNA, including the ITS1-5.8S-ITS2. The PCR products were digested with the four restriction enzymes RsaI, HhaI, AluI, and HinfI. Based on the HinfI patterns, T. boudieri specimens were separated into two different haplotypes (I and II). Nucleotide sequences of some representative amplicons were also obtained. Based on the phylogenetic results, three T. boudieri genotypes could be differentiated. One sequence, SKtb1, retrieved from PCR-RFLP of haplotype I, was obtained from a low pH soil in association with Helianthemum kahiricum . Based on the results presented in the current study, this isolate may represent a novel taxa within the Terfezia genus.

Diversity of genetic lineages among CTX-M-15 and CTX-M-14 producing Escherichia coli strains in a Tunisian hospital.

Fourteen broad-spectrum-cephalosporin-resistant Escherichia coli isolates were recovered between June and December 2007 in a Tunisian hospital. Genes encoding extended-spectrum-beta-lactamases (ESBL) and other resistance genes were characterized by PCR and sequencing. The following ESBL genes were identified: bla (CTX-M-15) (12 isolates), bla (CTX-M-14a) (one isolate), and bla (CTX-M-14b) (one isolate). The bla (OXA-1) gene was detected in 13 bla (CTX-M)-producing strains and a bla (TEM-1) gene in 6 of them. The ISEcp1 sequence was found upstream of bla (CTX-M) genes in 8 of 14 strains, and orf477 or IS903 downstream of this gene in 13 strains. Nine of the strains carried class 1 integrons and five different gene cassette arrangements were detected, dfrA17-aadA5 being the most common. One of the strains (bla (CTX-M-14a)-positive) harbored three class 1 integrons, and one of them was non-previously described containing as gene cassettes new variants of aac(6')-Ib and cmlA1 genes and it was linked to the bla (CTX-M-14a) gene flanked by a truncated ISEcp1 sequence (included in GenBank with accession number JF701188). CTX-M-15-producing strains were ascribed to phylogroup B2 (six isolates) and D (six isolates). Multilocus-sequence-typing revealed ten different sequence-types (STs) among ESBL-positive E. coli strains with prevalence of ST405 (four strains of phylogroup D) and ST131 types (two strains of phylogroup B2 and serogroup O25b). A high clonal diversity was also observed among studied strains by pulsed-field-gel-electrophoresis (11 unrelated profiles). CTX-M-15 is an emergent mechanism of resistance in the studied hospital and the world-disseminated 0:25b-ST131-B2 and ST405-D clones have been identified among CTX-M-15-producing isolates.

Robusta coffee beans post-harvest microflora: Lactobacillus plantarum sp. as potential antagonist of Aspergillus carbonarius.

Coffee contamination by ochratoxigenic fungi affects both coffee quality as well as coffee price with harmful consequences on the economy of the coffee exporting countries for whom which is their main source of income. Fungal strains were isolated from coffee beans and identified as black Aspergilli. Ochratoxigenic moulds like Aspergillus carbonarius were screened and selected for detailed studies. Also lactic acid bacteria (LAB) were isolated from silage coffee pulp and their antifungal activity was tested on dual-culture agar plate. Ten of the isolated LAB demonstrated antifungal effect against A. carbonarius. API 50 CH and APIZYM were used to perform phenotypic identification. 16S rDNA sequencing was made to confirm the results.

16S-23S rRNA intergenic spacer region variability in the genus Frankia.

16S-23S rRNA internally transcribed spacer (ITS) sequences from 53 Frankia strains were sequenced and sized from polymerase chain reaction amplification products and compiled with 14 selected 16S-23S ITS sequences from public database. Frankia genomes included two to three ITS copies lacking length polymorphism except for nine strains. No tRNA gene was encountered in this region. Frankia strains exhibited various lengths (369 to 452 nt) and a wide range of sequence similarity (35-100%) in the ITS region. The average pairwise distance varied from 0.368 (clusters 1 and 2) to 0.964 (clusters 3 and 4) and was 0.397, 0.138, 0.129, and 0.016, respectively, for cluster 4 (saprophytic non-infective/non-effective), clusters 1 and 3 (facultative symbiotic), and cluster 2 (obligate symbiotic). This suggests a gradual erosion of Frankia diversity concomitantly with a shift from saprophytic non-infective/non-effective to facultative and symbiotic lifestyle. Comparative sequence analyses of the 16S-23S rRNA intergenic spacer region of Frankia strains are not useful to assign them to their respective cluster or host infection group. Accurate assignment required the inclusion of the adjacent 16S and 23S rRNA gene fragments.

Phylogenetic affiliation of the desert truffles Picoa juniperi and Picoa lefebvrei.

The molecular phylogeny and comparative morphological studies reported here provide evidence for the recognition of the genus Picoa, an hypogeous desert truffle, in the family Pyronemataceae (Ascomycota, Pezizales). Picoa juniperi and Picoa lefebvrei were reassigned to the genus Picoa based on large subunit (LSU) sequence (28S) rDNA and internal transcribed spacer (ITS) rDNA (including the partial 18S, ITS1, ITS2, 5.8S gene, and partial 28S of the nuclear rDNA) data. Morphological studies of spores, asci, perida, and gleba revealed high similarities between P. lefebvrei and P. juniperi, thereby confirming the membership of both species in the genus Picoa. These two species were primarily distinguishable based on ascospore ornamentation.

First report of VIM metallo-ß-lactamase production in Escherichia coli and Klebsiella pneumoniae clinical isolates from Gaza Strip, Palestine.

INTRODUCTION: Even though the increasing incidence of VIM-producing E. coli and K. pneumoniae has been reported worldwide, studies are still lacking in Palestine. The aim of this study was to screen carbapenem-resistant E. coli and K. pneumoniae bacteria in the Gaza Strip, Palestine and further to characterize carbapenemase-producing isolates. METHODS: A total of 69 E. coli and 27 K. pneumoniae isolates were obtained from three Gaza hospitals and recovered from urine, wound swabs, blood and ear discharge. The screening for metallo-ß-lactamases (MBLs) was performed by using the imipenem-EDTA disc synergy test. The detection of ß-lactamases genes, detection of non-ß-lactam genes and the characterization of integrons were performed by PCR and sequencing. The clonal relationship among the isolates was determined by pulsed-field gel electrophoresis (PFGE). RESULTS: Our study showed that 4 E. coli (5.8%) and 5 K. pneumoniae (18.5%) were positive by the imipenem-EDTA disc synergy test. Bla VIM-4 was detected in six isolates and bla VIM-28 was identified in three isolates. The ß-lactamases genes in the VIM-producing K. pneumoniae isolates were bla CTX-M-15 (n=3), bla CTX-M-14 (n=1), bla SHV-1 (n=3), bla SHV-12 (n=1), bla TEM-1 (n=1) and bla OXA-1 (n=1). Aac(6')-Ib-cr gene was confirmed in four E. coli and in two K. pneumoniae isolates. QnrS1 was identified in two K. pneumoniae isolates. The class 1 integron was identified with the different gene cassette; dfrA17-aadA5, dfrA5, dfrA12-orf-aadA2 and dfrA17-aadA5 were identified. CONCLUSIONS: Our study indicated for the first time the emergence of multidrug-resistant VIM-containing K. pneumoniae and E. coli isolates of clinical origin in Gaza Strip hospitals.