International Journal of Microbiology https://www.hindawi.com The latest articles from Hindawi © 2017 , Hindawi Limited . All rights reserved. Comparison of the Performance of Urinary Mycobacterium tuberculosis Antigens Cocktail (ESAT6, CFP10, and MPT64) with Culture and Microscopy in Pulmonary Tuberculosis Patients Wed, 18 Oct 2017 06:54:27 +0000 http://www.hindawi.com/journals/ijmicro/2017/3259329/ Pulmonary tuberculosis (TB) is a major global health problem and is one of the top 10 causes of death worldwide. Our study aimed to evaluate the performance of urinary Mycobacterium tuberculosis (Mtb) antigens cocktail (ESAT6, CFP10, and MPT64) compared with culture and microscopy. This descriptive cross-sectional study was conducted in Dr. Hasan Sadikin General Hospital, Bandung, from January 2014 to October 2016. A total of 141 pulmonary tuberculosis patients were included. Sputum samples were examined for acid-fast bacilli (ZN stain) and mycobacterial culture (LJ); the Mtb antigens cocktail was examined in the urine sample. The positivity rate of TB detection from the three methods was as follows: AFB 52/141 (36.9%), culture 50/141 (35.5%), and urinary Mtb antigens cocktail 95/141 (67.4%). Sensitivity, specificity, PPV, and NPV of urinary Mtb antigens cocktail were 68.2%, 33%, 31.6%, and 69.6%, respectively. Validity of combination of both methods with culture as a gold standard yielded sensitivity, specificity, PPV, and NPV of 90%, 28.6%, 40.9%, and 83.8%, respectively. Combination of urinary Mtb antigens cocktail with AFB as a screening test gives a good sensitivity, although the specificity is reduced. Urinary Mtb antigens cocktail can be used as screening test for pulmonary tuberculosis. Dewi Kartika Turbawaty, Adhi Kristianto Sugianli, Arto Yuwono Soeroto, Budi Setiabudiawan, and Ida Parwati Copyright © 2017 Dewi Kartika Turbawaty et al. All rights reserved. Isolation and Physiomorphological Characterization of Escherichia coli O157:H7-Infecting Bacteriophages Recovered from Beef Cattle Operations Mon, 16 Oct 2017 00:00:00 +0000 http://www.hindawi.com/journals/ijmicro/2017/7013236/ Bacteriophages, recovered from beef cattle environment and specifically targeting Escherichia coli O157:H7, were examined for their physiological and morphological characteristics. Degree of bacterial lysis and host range of isolated bacteriophages was determined against 55 isolates of E. coli O157:H7. Morphology of phages was examined under transmission electron microscope. Phage growth parameters, particularly rate of adsorption, rise period, latent period, and burst size were also determined. The stability of isolated phages was tested at acidic and alkaline pH, at high temperatures, and in cold storage. A total of 7 phages were isolated which showed lytic activity against 50 out of 55 isolates of E. coli O157:H7. Based on the morphology, phages were classified into Myoviridae or Siphoviridae family. Phages had a rise period between 19 and 40 min, a short latent period between 12 and 30 min, and a large burst size (89–631 virions per infected cell), indicating high lytic activity. Phages remained stable for 24 h at a wide pH (1–11) and temperature range (40–60°C) and for 90 d in cold storage. Characterization of bacteriophages, with a diverse host range of E. coli O157:H7, could aid in the development of effective biocontrol strategies for this pathogen in the food industry. Pushpinder Kaur Litt and Divya Jaroni Copyright © 2017 Pushpinder Kaur Litt and Divya Jaroni. All rights reserved. Isolation and Characterization of Thermophilic Bacteria from Jordanian Hot Springs: Bacillus licheniformis and Thermomonas hydrothermalis Isolates as Potential Producers of Thermostable Enzymes Sun, 15 Oct 2017 00:00:00 +0000 http://www.hindawi.com/journals/ijmicro/2017/6943952/ The aim of this study was the isolation and characterization of thermophilic bacteria from hot springs in Jordan. Ten isolates were characterized by morphological, microscopic, biochemical, molecular, and physiological characteristics. Sequencing of the 16S rDNA of the isolates followed by BLAST search revealed that nine strains could be identified as Bacillus licheniformis and one isolate as Thermomonas hydrothermalis. This is the first report on the isolation of Thermomonas species from Jordanian hot springs. The isolates showed an ability to produce some thermostable enzymes such as amylase, protease, cellulose, gelatins, and lecithin. Moreover, the UPGMA dendrogram of the enzymatic characteristics of the ten isolates was constructed; results indicated a high phenotypic diversity, which encourages future studies to explore further industrial and environmental applications. Balsam T. Mohammad, Hala I. Al Daghistani, Atef Jaouani, Saleh Abdel-Latif, and Christian Kennes Copyright © 2017 Balsam T. Mohammad et al. All rights reserved. Preinoculation of Soybean Seeds Treated with Agrichemicals up to 30 Days before Sowing: Technological Innovation for Large-Scale Agriculture Tue, 10 Oct 2017 00:00:00 +0000 http://www.hindawi.com/journals/ijmicro/2017/5914786/ The cultivation of soybean in Brazil experienced an expressive growth in the last decades. Soybean is highly demanding on nitrogen (N) that must come from fertilizers or from biological fixation. The N supply to the soybean crop in Brazil relies on the inoculation with elite strains of Bradyrhizobium japonicum, B. elkanii, and B. diazoefficiens, which are able to fulfill the crop’s N requirements and enrich the soil for the following crop. The effectiveness of the association between N2-fixing bacteria and soybean plants depends on the efficacy of the inoculation process. Seed treatment with pesticides, especially fungicides or micronutrients, may rapidly kill the inoculated bacteria, affecting the establishment and outcome of the symbiosis. The development of technologies that allow inoculation to become a successful component of industrial seed treatment represents a valuable tool for the seed industry, as well as for the soybean crop worldwide. In this article, we report the results of new technologies, developed by the company Total Biotecnologia Indústria e Comércio S/A of Brazil, for preinoculation of soybean seeds with bradyrhizobia, in the presence of agrichemicals. Our results demonstrate improved bacterial survival for up to 30 days after inoculation, without compromising nodulation, N2-fixation, and yield in the field. Ricardo Silva Araujo, Sonia Purin da Cruz, Edson Luiz Souchie, Thomas Newton Martin, André Shigueyoshi Nakatani, Marco Antonio Nogueira, and Mariangela Hungria Copyright © 2017 Ricardo Silva Araujo et al. All rights reserved. Automated Flow Cytometry: An Alternative to Urine Culture in a Routine Clinical Microbiology Laboratory? Wed, 27 Sep 2017 09:14:51 +0000 http://www.hindawi.com/journals/ijmicro/2017/8532736/ The urine culture is the “gold standard” for the diagnosis of urinary tract infections (UTI) but constitutes a significant workload in the routine clinical laboratory. Due to the high percentage of negative results, there is a need for an efficient screening method, with a high negative predictive value (NPV) that could reduce the number of unnecessary culture tests. With the purpose of improving the efficiency of laboratory work, several methods for screening out the culture-negative samples have been developed, but none of them has shown adequate sensitivity (SE) and high NPV. Many authors show data about the efficacy of flow cytometry in the routine clinical laboratory. The aim of this article is to review and discuss the current literature on the feasibility of urine flow cytometry (UFC) and its utility as an alternative analytical technique in urinalysis. Patricia Mejuto, Mariam Luengo, and Julio Díaz-Gigante Copyright © 2017 Patricia Mejuto et al. All rights reserved. Corrigendum to “Spread of TEM, VIM, SHV, and CTX-M β-Lactamases in Imipenem-Resistant Gram-Negative Bacilli Isolated from Egyptian Hospitals” Mon, 25 Sep 2017 00:00:00 +0000 http://www.hindawi.com/journals/ijmicro/2017/5959128/ El sayed Hamdy Mohammed, Ahmed Elsadek Fakhr, Hanan Mohammed El sayed, Said abd Elmohsen Al Johery, Wesam Abdel Ghani Hassanein, and Ahmed Mansour Alzohairy Copyright © 2017 El sayed Hamdy Mohammed et al. All rights reserved. Antibiotic Resistant Bacterial Isolates from Captive Green Turtles and In Vitro Sensitivity to Bacteriophages Sun, 24 Sep 2017 00:00:00 +0000 http://www.hindawi.com/journals/ijmicro/2017/5798161/ This study aimed to test multidrug resistant isolates from hospitalised green turtles (Chelonia mydas) and their environment in North Queensland, Australia, for in vitro susceptibility to bacteriophages. Seventy-one Gram-negative bacteria were isolated from green turtle eye swabs and water samples. Broth microdilution tests were used to determine antibiotic susceptibility. All isolates were resistant to at least two antibiotics, with 24% being resistant to seven of the eight antibiotics. Highest resistance rates were detected to enrofloxacin (77%) and ampicillin (69.2%). More than 50% resistance was also found to amoxicillin/clavulanic acid (62.5%), ceftiofur (53.8%), and erythromycin (53.3%). All the enriched phage filtrate mixtures resulted in the lysis of one or more of the multidrug resistant bacteria, including Vibrio harveyi and V. parahaemolyticus. These results indicate that antibiotic resistance is common in Gram-negative bacteria isolated from hospitalised sea turtles and their marine environment in North Queensland, supporting global concern over the rapid evolution of multidrug resistant genes in the environment. Using virulent bacteriophages as antibiotic alternatives would not only be beneficial to turtle health but also prevent further addition of multidrug resistant genes to coastal waters. Alessandro Delli Paoli Carini, Ellen Ariel, Jacqueline Picard, and Lisa Elliott Copyright © 2017 Alessandro Delli Paoli Carini et al. All rights reserved. Predicted Cold Shock Proteins from the Extremophilic Bacterium Deinococcus maricopensis and Related Deinococcus Species Mon, 18 Sep 2017 08:43:46 +0000 http://www.hindawi.com/journals/ijmicro/2017/5231424/ While many studies have examined the mechanisms by which extremophilic Deinococci survive exposure to ionizing radiation, very few publications have characterized the cold shock adaptations of this group, despite many species being found in persistent cold environments and environments prone to significant daily temperature fluctuations. Bacterial cold shock proteins (Csps) are a family of conserved, RNA chaperone proteins that commonly play a role in cold temperature adaptation, including a downward shift in temperature (i.e., cold shock). The primary aim of this study was to test whether a representative, desert-dwelling Deinococcus, Deinococcus maricopensis, encodes Csps as part of its genome. Bioinformatic approaches were used to identify a Csp from D. maricopensis LB-34. The Csp, termed Dm-Csp1, contains sequence features of Csps including a conserved cold shock domain and nucleic acid binding motifs. A tertiary model of Dm-Csp1 revealed an anticipated Csp structure containing five anti-parallel beta-strands, and ligand prediction experiments identified N-terminally located residues capable of binding single-stranded nucleic acids. Putative Csps were identified from 100% of (27 of 27) Deinococci species for which genome information is available; and the Deinococci-encoded Csps identified contain a C-terminally located region that appears to be limited to members of the class Deinococci. Michael J. LaGier Copyright © 2017 Michael J. LaGier. All rights reserved. Clinical Characteristics and Laboratory Identification of Aerococcus Infections: An Australian Tertiary Centre Perspective Wed, 13 Sep 2017 07:18:02 +0000 http://www.hindawi.com/journals/ijmicro/2017/5684614/ Aerococci uncommonly cause urinary tract (UTI) and bloodstream infections (BSI). The clinical characteristics and laboratory identification rates of Aerococcus in the Australian context are unknown. A retrospective observational cohort study of patients with positive Aerococcus cultures between 2010 and 2015 was performed. Patients were analysed according to predefined “asymptomatic bacteriuria,” “UTI,” and “BSI” groups. Forty-seven [40 (85%) for urine and 7 (15%) for blood] isolates were identified [38% male, median age of 79 (IQR 62–85) years], with corresponding identification rates of 24.2/100,000/year for urine (0.02%) and 7.3/100,000/year for blood cultures (0.007%). Since the use of matrix-assisted laser desorption ionisation time-of-flight mass spectrometry (MALDI-TOF MS) identification rate in urine has increased from 14.7/100,000/year to 32/100,000/year (). For urine isolates, 14 (35%) met the definition for UTI whilst 26 (65%) were “asymptomatic bacteriuria.” Underlying urological abnormalities, catheterisation, and polymicrobial growth were common. Seventy percent of bacteriuria was treated regardless of colonisation or active infection status. Symptomatic patients were more likely to receive treatment (OR 7.2, 95% CI 1.4–35.3). In patients with BSI, 1 (14.2%) had endocarditis and 1 (14.2%) died. The majority of isolates were susceptible to penicillin (11/12 tested, 92%). Shanti Narayanasamy, Katherine King, Amanda Dennison, Denis W. Spelman, and Ar Kar Aung Copyright © 2017 Shanti Narayanasamy et al. All rights reserved. Environmentally Friendly Production of D(−) Lactic Acid by Sporolactobacillus nakayamae: Investigation of Fermentation Parameters and Fed-Batch Strategies Sun, 10 Sep 2017 00:00:00 +0000 http://www.hindawi.com/journals/ijmicro/2017/4851612/ The interest in the production of lactic acid has increased due to its wide range of applications. In the present study, the variables that affect fermentative D(−) lactic acid production were investigated: neutralizing agents, pH, temperature, inoculum percentage, agitation, and concentration of the medium components. An experimental design was applied to determine the optimal concentrations of the medium components and fermentation was studied using different feeding strategies. High production (122.41 g/L) and productivity (3.65 g/L·h) were efficiently achieved by Sporolactobacillus nakayamae in 54 h using a multipulse fed-batch technique with an initial medium containing 35 g/L of yeast extract (byproduct of alcohol production), 60 g/L of crystallized sugar, and 7.5 mL/L of salts. The fermentation process was conducted at 35°C and pH 6.0 controlled by NaOH with a 20% volume of inoculum and agitation at 125 rpm. The production of a high optically pure concentration of D(−) lactic acid combined with an environmentally friendly NaOH-based process demonstrates that S. nakayamae is a promising strain for D(−) lactic acid production. Susan Michelz Beitel, Luciana Fontes Coelho, Daiane Cristina Sass, and Jonas Contiero Copyright © 2017 Susan Michelz Beitel et al. All rights reserved. Multidrug Resistant Enteric Bacterial Pathogens in a Psychiatric Hospital in Ghana: Implications for Control of Nosocomial Infections Wed, 06 Sep 2017 00:00:00 +0000 http://www.hindawi.com/journals/ijmicro/2017/9509087/ Enteric bacteria are commonly implicated in hospital-acquired or nosocomial infections. In Ghana, these infections constitute an important public health problem but little is known about their contribution to antibiotic resistance. The aim of the study was to determine the extent and pattern of antibiotic resistance of enteric bacteria isolated from patients and environmental sources at the Accra Psychiatric Hospital. A total of 265 samples were collected from the study site including 142 stool and 82 urine samples from patients, 7 swab samples of door handle, and 3 samples of drinking water. Enteric bacteria were isolated using standard microbiological methods. Antibiograms of the isolates were determined using the disc diffusion method. Overall, 232 enteric bacteria were isolated. Escherichia coli was the most common (38.3%), followed by Proteus (19.8%), Klebsiella (17.7%), Citrobacter (14.7%), Morganella (8.2%), and Pseudomonas (1.3%). All isolates were resistant to ampicillin but sensitive to cefotaxime. The resistance ranged from 15.5% to 84.5%. Multidrug resistance was most prevalent (100%) among isolates of Proteus and Morganella and least prevalent among isolates of Pseudomonas (33.3%). Multidrug resistance among enteric bacteria at the study hospital is high and hence there is a need for screening before therapy to ensure prudent use of antibiotics. Kwabena O. Duedu, George Offei, Francis S. Codjoe, and Eric S. Donkor Copyright © 2017 Kwabena O. Duedu et al. All rights reserved. Baseline Antibody Titre against Salmonella enterica in Healthy Population of Mumbai, Maharashtra, India Thu, 31 Aug 2017 00:00:00 +0000 http://www.hindawi.com/journals/ijmicro/2017/9042125/ Objective. The aim of this study was to establish a baseline titre for the population of Mumbai, Maharashtra, India. Method. Four hundred healthy blood donors, attending blood donation camps, were screened using a survey questionnaire. Widal tube agglutination test was performed on the diluted sera (with 0.9% normal saline) of blood donors, with final dilution ranging from 1 : 40 to 1 : 320. Results. Out of 400 individuals providing samples, 78 (19.5%) individuals showed antibody titres ≥ 1 : 40 for at least one antigen and 322 (80.5%) showed no agglutination. The baseline antibody titres against O antigen and H antigen of Salmonella enterica serotype Typhi were found to be 1 : 40 and 1 : 80, respectively. Similarly, the baseline antibody titres for the H antigen of Salmonella enterica serotypes Paratyphi A and Paratyphi B were found to be 1 : 40 and 1 : 80, respectively. Conclusion. Thus, it was noted that the diagnostically significant cutoff of antibody titre from acute phase sample was ≥ 1 : 80 for S. Typhi O antigen and titre of ≥ 1 : 160 for both S. Typhi H antigen and S. Paratyphi BH antigen. Antibody titre of ≥ 1 : 80 can be considered significant for S. Paratyphi AH antigen. Rucha Patki, Sunil Lilani, and Dhaneshwar Lanjewar Copyright © 2017 Rucha Patki et al. All rights reserved. Feasibility of Metatranscriptome Analysis from Infant Gut Microbiota: Adaptation to Solid Foods Results in Increased Activity of Firmicutes at Six Months Thu, 24 Aug 2017 09:53:13 +0000 http://www.hindawi.com/journals/ijmicro/2017/9547063/ Newborns are rapidly colonized by microbes and their intestinal tracts contain highly dynamic and rapidly developing microbial communities in the first months of life. In this study, we describe the feasibility of isolating mRNA from rapidly processed faecal samples and applying deep RNA-Seq analysis to provide insight into the active contributors of the microbial community in early life. Specific attention is given to the impact of removing rRNA from the mRNA on the phylogenetic and transcriptional profiling and its analysis depth. A breastfed baby was followed in the first six months of life during adaptation to solid food, dairy products, and formula. It was found that, in the weaning period, the total transcriptional activity of Actinobacteria, mainly represented by Bifidobacterium, decreased while that of Firmicutes increased over time. Moreover, Firmicutes and Actinobacteria, including the canonical Bifidobacteria as well as Collinsella, were found to be important contributors to carbohydrate fermentation and vitamin biosynthesis in the infant intestine. Finally, the expression of Lactobacillus rhamnosus-like genes was detected, likely following transfer from the mother who consumed L. rhamnosus GG. The study indicates that metatranscriptome analysis of the infant gut microbiota is feasible on infant stool samples and can be used to provide insight into the core activities of the developing community. Floor Hugenholtz, Jarmo Ritari, Lotta Nylund, Mark Davids, Reetta Satokari, and Willem M. de Vos Copyright © 2017 Floor Hugenholtz et al. All rights reserved. Prevalence of Bacterial Vaginosis and Associated Risk Factors among Women Complaining of Genital Tract Infection Wed, 02 Aug 2017 00:00:00 +0000 http://www.hindawi.com/journals/ijmicro/2017/4919404/ Background. Bacterial vaginosis is a global concern due to the increased risk of acquisition of sexually transmitted infections. Objectives. To determine the prevalence of bacterial vaginosis and bacteria causing aerobic vaginitis. Methods. A cross-sectional study was conducted among 210 patients between September 2015 and July 2016 at St. Paul’s Hospital. Gram-stained vaginal swabs were examined microscopically and graded as per Nugent’s procedure. Bacteria causing aerobic vaginitis were characterized, and their antimicrobial susceptibility pattern was determined. Results. The overall prevalence of bacterial vaginosis was 48.6%. Bacterial vaginosis was significantly associated with number of pants used per day () and frequency of vaginal bathing (). Of 151 bacterial isolates, 69.5% were Gram-negative and 30.5% were Gram-positive bacteria. The overall drug resistance level of Gram-positive bacteria was high against penicillin, tetracycline, and erythromycin. Cefoxitin and tobramycin were the most active drugs against Gram-positive bacteria. The overall drug resistance level of Gram-negative bacteria was high against tetracycline, ampicillin, and amoxicillin. Amikacin and tobramycin were the most active drugs against Gram-negative bacteria. Conclusions. The prevalence of bacterial vaginosis was high and was affected by individual hygiene. Routine culture of vaginal samples should be performed on patients with vaginitis and the drug susceptibility pattern of each isolate should be determined. Adane Bitew, Yeshiwork Abebaw, Delayehu Bekele, and Amete Mihret Copyright © 2017 Adane Bitew et al. All rights reserved. Characterization of Carbapenem-Resistant Acinetobacter baumannii Strains Isolated from Hospitalized Patients in Palestine Wed, 26 Jul 2017 00:00:00 +0000 http://www.hindawi.com/journals/ijmicro/2017/8012104/ The American Centers for Disease Control and Prevention (CDC) recognizes Acinetobacter baumannii as a source of global outbreaks and epidemics especially due to its increasing resistance to commercially available antibiotics. In this study, 69 single patient multidrug resistant isolates collected from all over Palestine, except Gaza, were studied. All the isolates were resistant to all the β–lactam antibiotics including the carbapenems. Of the 69 isolates, 82.6% were positive for , 14.5% were positive for , and 3% were positive for . None were positive for and . In addition, 5.8% and 0% were positive for and , respectively. Of the 69 isolates, none were positive for the aminoglycoside aphA6 gene while 93% were positive for the aphA1 gene. The acetyltransferases aacC1 and aacA4 genes tested positive in 22% and 13% of the isolates, respectively. The ompA biofilm-producing virulence gene was detected in all isolates. Finally, Multilocus Sequence Typing (MLST) of 13 isolates revealed that more than one strain of A. baumannii was circulating in Palestinian hospitals as results revealed that 7 isolates were of ST208, 2 isolates ST218, 1 isolate ST231, 1 isolate ST348, and 2 new Sequence Types. The detection of these drug resistant pathogens is a reminder of the importance of active surveillance for resistant bacteria in order to prevent their spread in hospital settings. Regeen Handal, Lulu Qunibi, Ibrahim Sahouri, Maha Juhari, Rula Dawodi, Hiyam Marzouqa, and Musa Hindiyeh Copyright © 2017 Regeen Handal et al. All rights reserved. Production, Characterization, and Antimicrobial Activity of Mycocin Produced by Debaryomyces hansenii DSMZ70238 Mon, 03 Jul 2017 07:50:42 +0000 http://www.hindawi.com/journals/ijmicro/2017/2605382/ The present study was conducted to estimate the antimicrobial activity and the potential biological control of the killer toxin produced by D. hansenii DSMZ70238 against several pathogenic microorganisms. In this study, the effects of NaCl, pH, and temperature, killer toxin production, and antimicrobial activity were studied. The results showed that the optimum inhibitory effect of killer toxin was at 8% NaCl, and the diameters of clear zones were 20, 22, 22, 21, 14, and 13 mm for Staphylococcus aureus, Escherichia coli, Klebsiella pneumoniae, Streptococcus pyogenes, Candida albicans, and Candida neoformans, respectively. The largest inhibition zones were observed at pH 4.5 with inhibition zone of 16, 18, 17, 18, 11, and 12 mm for the same microorganisms. The results also showed that 25°C is the optimal temperature for toxin killing activity against all targeted microorganisms. In addition, the activity of killer toxin significantly inhibited the growth of fungal mycelia for all target pathogenic fungi and the percentages of inhibition were 47.77, 48.88, 52.22, and 61.11% for Trichophyton rubrum, Alternaria alternata, Trichophyton concentricum, and Curvularia lunata, respectively. The results showed the highest growth rate of D. hansenii DSMZ70238 under condition of 8% NaCl concentration, pH 4.5, and 25°C for 72 h. Safaa A. S. Al-Qaysi, Halah Al-Haideri, Zaid Akram Thabit, Wijdan Hameed Abd Al-Razzaq Al-Kubaisy, and Jamal Abd Al-Rahman Ibrahim Copyright © 2017 Safaa A. S. Al-Qaysi et al. All rights reserved. Gene Expression and Molecular Characterization of a Xylanase from Chicken Cecum Metagenome Sun, 02 Jul 2017 08:37:28 +0000 http://www.hindawi.com/journals/ijmicro/2017/4018398/ A xylanase gene xynAMG1 with a 1,116-bp open reading frame, encoding an endo-β-1,4-xylanase, was cloned from a chicken cecum metagenome. The translated protein consisted of 372 amino acids including a putative signal peptide of 23 amino acids. The calculated molecular mass of the mature was 40,013 Da, with a theoretical pI value of 5.76. The amino acid sequence of showed 59% identity to endo-β-1,4-xylanase from Prevotella bryantii and Prevotella ruminicola and 58% identity to that from Prevotella copri. has two conserved motifs, DVVNE and TEXD, containing two active site glutamates and an invariant asparagine, characteristic of GH10 family xylanase. The xynAMG1 gene without signal peptide sequence was cloned and fused with thioredoxin protein (Trx.Tag) in pET-32a plasmid and overexpressed in Escherichia coli Tuner™(DE3)pLysS. The purified mature was highly salt-tolerant and stable and displayed higher than 96% of its catalytic activity in the reaction containing 1 to 4 M NaCl. It was only slightly affected by common organic solvents added in aqueous solution to up to 5 M. This chicken cecum metagenome-derived xylanase has potential applications in animal feed additives and industrial enzymatic processes requiring exposure to high concentrations of salt and organic solvents. Hind AL-Darkazali, Vithaya Meevootisom, Duangnate Isarangkul, and Suthep Wiyakrutta Copyright © 2017 Hind AL-Darkazali et al. All rights reserved. Prevalence of Virulence Genes Associated with Diarrheagenic Pathotypes of Escherichia coli Isolates from Water, Sediment, Fish, and Crab in Aby Lagoon, Côte d’Ivoire Tue, 06 Jun 2017 09:03:27 +0000 http://www.hindawi.com/journals/ijmicro/2017/9532170/ This study was conducted to characterize virulence genes of Escherichia coli isolates from water, sediment, fish, and crab in Aby Lagoon. Serogrouping was performed by EPEC antisera in 113 E. coli strains. The presence of diarrhea-associated genes (eae, stx, AggR, elt, and est) was assessed by multiplex PCR using specific primers. Based on the multiplex PCR, sixty-two isolates (42 from water, 19 from sediment, and 1 from crab) were positive for virulence genes, including 34 positive for elt (ETEC), 46 positive for est (ETEC), 24 positive for both elt and est, 6 positive for stx (EHEC), 1 positive for both stx + est, and 1 positive for both stx + elt. Genes eae (EPEC) and AggR (EAEC) were not detected. Nine serogroups (O114, O127, O55, O111, O86, O119, O126, O128, and O142) were identified. This study revealed the presence of diarrheagenic and nondiarrheagenic E. coli and potential public health risks if fishery products are not appropriately cooked. Ollo Kambire, Ama Antoinette Adingra, Konan Mathurin Yao, and Rose Koffi-Nevry Copyright © 2017 Ollo Kambire et al. All rights reserved. Isolation and Characterization of Yeasts Able to Assimilate Sugarcane Bagasse Hemicellulosic Hydrolysate and Produce Xylitol Associated with Veturius transversus (Passalidae, Coleoptera, and Insecta) Tue, 06 Jun 2017 00:00:00 +0000 http://www.hindawi.com/journals/ijmicro/2017/5346741/ Yeasts are an important component of insect gut microbial content, playing roles such as degradation of polymers and toxic compounds, biological control, and hormone, vitamin, and digestive enzyme production. The xylophagous beetle gut is a hyperdiverse habitat and a potential source of new species with industrial abilities such as enzyme production, pentose fermentation, and biodetoxification. In this work, samples of Veturius transversus (Passalidae, Coleoptera, and Insecta) were collected from the Central Amazon Rainforest. Their guts were dissected and a total of 20 microbial colonies were isolated using sugarcane bagasse hemicellulosic hydrolysate. They were identified as having 10 distinct biochemical profiles, and genetic analysis allowed identification as three clades in the genera Candida, Williopsis, and Geotrichum. All colonies were able to assimilate D-xylose and 18 were able to produce xylitol, especially a strain of Geotrichum, with a maximum yield of 0.502 g·g−1. These results agree with a previous prediction that the microbial community associated with xylophagous insects is a promising source of species of biotechnological interest. Italo Thiago Silveira Rocha Matos, Enedina Nogueira Assunção, Edson Junior do Carmo, Verena Makaren Soares, and Spartaco Astolfi-Filho Copyright © 2017 Italo Thiago Silveira Rocha Matos et al. All rights reserved. Molecular Identification of Aminoglycoside-Modifying Enzymes and Plasmid-Mediated Quinolone Resistance Genes among Klebsiella pneumoniae Clinical Isolates Recovered from Egyptian Patients Tue, 30 May 2017 08:33:03 +0000 http://www.hindawi.com/journals/ijmicro/2017/8050432/ Inappropriate use of antibiotics in clinical settings is thought to have led to the global emergence and spread of multidrug-resistant pathogens. The goal of this study was to investigate the prevalence of genes encoding aminoglycoside resistance and plasmid-mediated quinolone resistance among clinical isolates of Klebsiella pneumoniae. All K. pneumoniae isolates were phenotypically identified using API 20E and then confirmed genotypically through amplification of the specific K. pneumoniae phoE gene. All isolates were genotyped by the enterobacterial repetitive intergenic consensus polymerase chain reaction technique (ERIC-PCR). Antibiotic susceptibility testing was done by a modified Kirby-Bauer method and broth microdilution. All resistant or intermediate-resistant isolates to either gentamicin or amikacin were screened for 7 different genes encoding aminoglycoside-modifying enzymes (AMEs). In addition, all resistant or intermediate-resistant isolates to either ciprofloxacin or levofloxacin were screened for 5 genes encoding the quinolone resistance protein (Qnr), 1 gene encoding quinolone-modifying enzyme, and 3 genes encoding quinolone efflux pumps. Biotyping using API 20E revealed 13 different biotypes. Genotyping demonstrated that all isolates were related to 2 main phylogenetic groups. Susceptibility testing revealed that carbapenems and tigecycline were the most effective agents. Investigation of genes encoding AMEs revealed that acc(6′)-Ib was the most prevalent, followed by acc(3′)-II, aph(3′)-IV, and ant(3′′)-I. Examination of genes encoding Qnr proteins demonstrated that qnrB was the most prevalent, followed by qnrS, qnrD, and qnrC. It was found that 61%, 26%, and 12% of quinolone-resistant K. pneumoniae isolates harbored acc(6′)-Ib-cr, oqxAB, and qebA, respectively. The current study demonstrated a high prevalence of aminoglycoside and quinolone resistance genes among clinical isolates of K. pneumoniae. Mohamed F. El-Badawy, Wael M. Tawakol, Shaymaa W. El-Far, Ibrahim A. Maghrabi, Saleh A. Al-Ghamdi, Moselhy S. Mansy, Mohammed S. Ashour, and Mohamed M. Shohayeb Copyright © 2017 Mohamed F. El-Badawy et al. All rights reserved. Staphylococcus saprophyticus Recovered from Humans, Food, and Recreational Waters in Rio de Janeiro, Brazil Wed, 24 May 2017 00:00:00 +0000 http://www.hindawi.com/journals/ijmicro/2017/4287547/ Staphylococcus saprophyticus is an important agent of urinary tract infection (UTI) in young women, but information about this pathogen in human microbiota and in common environment is lacking. The aim of this study was to characterize S. saprophyticus isolates from genitoanal microbiota of 621 pregnant women, 10 minas cheese packs, and five beaches in Rio de Janeiro city and compare PFGE profiles of these isolates with five UTI PFGE clusters described in this city. We investigated 65 S. saprophyticus isolates from microbiota, 13 from minas cheese, and 30 from beaches and 32 UTI isolates. Antimicrobial resistance was determined by disk diffusion, MIC by agar dilution, and PCR. Erythromycin-resistance genes erm(C), msr(A), msr(B), mph(C), and lin(A) were found in 93% of isolates. Trimethoprim-sulfamethoxazole resistance correlated with dfrG or dfrA genes. Three cefoxitin-resistant isolates carried the mecA gene. All isolates obtained from cheese were susceptible to all antimicrobial agents. Six of 10 pregnant women with >1 isolate had monoclonal colonization. Isolates from pregnant women shared 100% similarity with UTI PFGE cluster types A and E obtained almost 10 years previously, suggesting temporal persistence of S. saprophyticus. Antimicrobial resistance of beach isolates reflected the profiles of human isolates. Taken together, results indicate a shared source for human and environmental isolates. Viviane Santos de Sousa, Ana Paula de Souza da-Silva, Leif Sorenson, Raphael Paiva Paschoal, Renata Fernandes Rabello, Eloiza Helena Campana, Márcia Soares Pinheiro, Lyssa Oliveira Ferreira dos Santos, Natacha Martins, Ana Carolina Nunes Botelho, Renata Cristina Picão, Sérgio Eduardo Longo Fracalanzza, Lee Woodland Riley, George Sensabaugh, and Beatriz Meurer Moreira Copyright © 2017 Viviane Santos de Sousa et al. All rights reserved. High Doses of Halotolerant Gut-Indigenous Lactobacillus plantarum Reduce Cultivable Lactobacilli in Newborn Calves without Increasing Its Species Abundance Wed, 17 May 2017 00:00:00 +0000 http://www.hindawi.com/journals/ijmicro/2017/2439025/ To elucidate the ecological effect of high oral doses of halotolerant (resistant to table salt) indigenous-gut bacteria on other commensals early in life, we conducted a culture-based study to quantify the effect of intestinal Lactobacillus plantarum strain of bovine origin (with remarkable aerobic growth capabilities and inhibitory activity against Escherichia coli O157:H7 and F5) on clinical health and gut lactobacilli/coliforms in newborn calves. In a double-blind placebo-randomized trial twelve colostrum-fed calves, consecutively born at a farm, were fed L. plantarum within 12 hours from birth at low ( CFU/day) or high concentrations () or placebo (q24 h, 5 d; 10 d follow-up). We developed a 2.5% NaCl-selective culture strategy to facilitate the enumeration of L. plantarum-strain-B80, and tested 384 samples (>1,152 cultures). L. plantarum-B80-like colonies were detected in a large proportion of calves (58%) even before their first 24 hours of life indicating endemic presence of the strain in the farm. In contrast to studies where human-derived Lactobacillus LGG or rhamnosus had notoriously high, but short-lived, colonization, we found that L. plantarum colonized stably with fecal shedding of  log10·g−1 (irrespective of dose, ). High doses significantly reduced other fecal lactic acid bacteria (e.g., lactobacilli, ) and slightly reduced body weight gain in calves after treatment. For the first time, a halotolerant strain of L. plantarum with inhibitory activity against a human pathogen has the ability to inhibit other lactobacilli in vivo without changing its species abundance, causing transintestinal translocation, or inducing clinical disease. The future selection of probiotics based on halotolerance may expand therapeutic product applicability. Alexander Rodriguez-Palacios, Henry R. Staempfli, and J. Scott Weese Copyright © 2017 Alexander Rodriguez-Palacios et al. All rights reserved. Pigeon Pea and Cowpea-Based Cropping Systems Improve Vesicular Arbuscular Mycorrhizal Fungal Colonisation of Subsequent Maize on the Alfisols in Central Malawi Thu, 11 May 2017 00:00:00 +0000 http://www.hindawi.com/journals/ijmicro/2017/2096314/ Mycorrhizal associations contribute to the sustainability of crop production systems through their roles in nutrient cycling and other benefits in the soil-plant ecosystems. A two-year study was conducted on the Alfisols of Lilongwe and Dowa districts, Central Malawi, to assess the vesicular-arbuscular mycorrhizal (VAM) fungal colonisation levels in pigeon pea, cowpea, and maize grown in sole cropping, legume-cereal, and legume-legume intercropping systems and in the maize grown in short rotation (year 2) as influenced by the previous cropping systems and N fertilizer application. The gridline intersect method was used to assess the VAM fungal colonisation levels. Results showed that all treatments that included legumes whether grown as sole crop, in legume-cereal or in legume-legume cropping systems in the previous year, had significantly higher (P < 0.05) VAM fungal colonisation of the rotational maize crop roots by a range 39% to 50% and 19% to 47% than those in maize supplied and not supplied with N fertilizer, respectively, in a maize-maize short rotation, at the Lilongwe site. A similar trend was reported for the Dowa site. Furthermore, there were positive correlations between VAM fungal colonisation and the plant P content, dry matter yield, and nodule numbers. Further studies may help to assess the diversity of VAM fungal species in Malawi soils and identify more adaptive ones for inoculation studies. Keston O. W. Njira, Ernest Semu, Jerome P. Mrema, and Patson C. Nalivata Copyright © 2017 Keston O. W. Njira et al. All rights reserved. Molecular Study of Acinetobacter baumannii Isolates for Metallo-β-Lactamases and Extended-Spectrum-β-Lactamases Genes in Intensive Care Unit, Mansoura University Hospital, Egypt Mon, 08 May 2017 00:00:00 +0000 http://www.hindawi.com/journals/ijmicro/2017/3925868/ Acinetobacter baumannii (A. baumannii) has been known as a causative pathogen of hospital acquired infections. The aim of this study is to examine the presence of A. baumannii among clinical isolates from intensive care unit (ICU) in Mansoura University Hospital (MUH), its antibiotic resistance pattern, and prevalence of antibiotic resistance genes metallo-β-lactamases (MBLs) and extended-spectrum-β-lactamases (ESBLs) among A. baumannii isolates. A. baumannii was identified by colony morphology, API 20E, and confirmed by detecting the bla OXA-51-like carbapenemase gene by PCR. Phenotypic expression of MBLs resistance was demonstrated by Combined Disk Test (CDT) in 273 isolates (97.5%) and of ESBLs was demonstrated by double disc synergy method (DDST) in 6 isolates (2.1%). MBLs genes were positive in 266 isolates (95%) and ESBLs genes were positive in 8 isolates (2.9%). The most frequent genes of MBLs studied genes were IMP (95.7%) followed by SIM and GIM (47.1% and 42.9%; resp.). For ESBL genes, the most frequent gene was TEM (2.9%). From this study, we conclude that multidrug resistant (MDR) A. baumannii with MBLs activity was the most common isolate. Careful monitoring for the presence of MDR A. baumannii among hospitalized patients is recommended to avoid wide dissemination of antibiotic resistance. Nashwa M. Alkasaby and Maysaa El Sayed Zaki Copyright © 2017 Nashwa M. Alkasaby and Maysaa El Sayed Zaki. All rights reserved. Antimicrobial Activity of a Cationic Guanidine Compound against Two Pathogenic Oral Bacteria Thu, 04 May 2017 00:00:00 +0000 http://www.hindawi.com/journals/ijmicro/2017/5924717/ This study evaluated the potential antimicrobial properties of a polyguanidine (CatDex) on two oral bacteria. Chlorhexidine gluconate 1340 μmoL L−1 (CHX 0.12%) was used as control. Streptococcus mutans (S. mutans) and Porphyromonas gingivalis (P. gingivalis) were grown in BHI media. Bacterial sensitivity and antimicrobial activity were determined by the minimum inhibitory concentration (MIC) and Kirby-Bauer methods. To study side effects, that is, toxicity, dental pulp stem cells (DPSCs) were used. Fluorometric cytotoxicity and confocal microscopy assays were used in order to test cell viability. CatDex inhibited growth of S. mutans at all concentrations and growth of P. gingivalis at all concentrations except 25 μmoL L−1. The MIC of CatDex was 50 μmoL L−1 for both S. mutans and P. gingivalis. The inhibition of bacteria exposed for 8 h at 50 μmoL L−1 of CatDex exhibited increased antimicrobial activity over time, with 91% inhibition in both bacteria. The antimicrobial activities of CatDex and CHX were similar when tested on two common bacteria. CatDex was significantly less toxic to DPSCs. CatDex toxicity depended on time and not on concentration. With regard to clinical relevance, CatDex may have potential as a novel antimicrobial agent. Further studies are in progress. E. Escamilla-García, A. G. Alcázar-Pizaña, J. C. Segoviano-Ramírez, C. Del Angel-Mosqueda, A. P. López-Lozano, E. Cárdenas-Estrada, M. A. De La Garza-Ramos, C. E. Medina-De La Garza, and M. Márquez Copyright © 2017 E. Escamilla-García et al. All rights reserved. Effects of Medicinal Plant Extracts and Photosensitization on Aflatoxin Producing Aspergillus flavus (Raper and Fennell) Tue, 02 May 2017 08:51:04 +0000 http://www.hindawi.com/journals/ijmicro/2017/5273893/ This study was undertaken with an aim of exploring the effectiveness of medicinal plant extracts in the control of aflatoxin production. Antifungal properties, photosensitization, and phytochemical composition of aqueous and organic extracts of fruits from Solanum aculeastrum, bark from Syzygium cordatum, and leaves from Prunus africana, Ocimum lamiifolium, Lippia kituiensis, and Spinacia oleracea were tested. Spores from four-day-old cultures of previously identified toxigenic fungi, UONV017 and UONV003, were used. Disc diffusion and broth dilution methods were used to test the antifungal activity. The spores were suspended in 2 ml of each extract separately and treated with visible light (420 nm) for varying periods. Organic extracts displayed species and concentration dependent antifungal activity. Solanum aculeastrum had the highest zones of inhibition diameters in both strains: UONV017 (mean =  mm) and UONV003 (mean =  mm) at 600 mg/ml. Aqueous extracts had no antifungal activity because all diameters were below 8 mm. Solanum aculeastrum had the lowest minimum inhibitory concentration at 25 mg/ml against A. flavus UONV017. All the plant extracts in combination with light reduced the viability of fungal conidia compared with the controls without light, without extracts, and without both extracts and light. Six bioactive compounds were analyzed in the plant extracts. Medicinal plant extracts in this study can control conidia viability and hence with further development can control toxigenic fungal spread. Loise M. Njoki, Sheila A. Okoth, and Peter M. Wachira Copyright © 2017 Loise M. Njoki et al. All rights reserved. Antimicrobial Resistance of Salmonella enterica Serovars Typhi and Paratyphi Isolates from a General Hospital in Karawaci, Tangerang, Indonesia: A Five-Year Review Thu, 06 Apr 2017 00:00:00 +0000 http://www.hindawi.com/journals/ijmicro/2017/6215136/ Typhoid and paratyphoid fever known as enteric fever pose important global public health problem, with 21.6 million cases and approximately 250,000 deaths annually. It is a prevalent disease in Indonesia, but data on the antimicrobial resistance pattern is limited. This study aim was to provide data on the antimicrobial resistance pattern of S. Typhi and S. Paratyphi bloodstream isolates in a general hospital in Karawaci, Tangerang, Banten, Indonesia, during the period of January 2011 to December 2015. Susceptibility against antimicrobials was detected according to the guidelines of the Clinical and Laboratory Standards Institute (CLSI). Out of a total of 168 isolates 55.4% were S. Typhi and 44.6% S. Paratyphi A. Most of the isolates, 92.9%, were from children aged 6–18 years and adult population. There was low resistance of S. Typhi against ampicillin, trimethoprim-sulfamethoxazole, ceftriaxone, ciprofloxacin, and levofloxacin, similar to previous studies in Indonesia. In the 2011–2015 period, resistance rates against most antimicrobials and MDR rate of S. Typhi and S. Paratyphi were low, emphasizing that there is a distinct epidemiological dynamic of the enteric fever in Indonesia. Nata Pratama Hardjo Lugito and Cucunawangsih Copyright © 2017 Nata Pratama Hardjo Lugito and Cucunawangsih. All rights reserved. Control of Passion Fruit Fungal Diseases Using Essential Oils Extracted from Rosemary (Rosmarinus officinalis) and Eucalyptus (Eucalyptus agglomerata) in Egerton University Main Campus Njoro, Kenya Tue, 28 Mar 2017 08:54:33 +0000 http://www.hindawi.com/journals/ijmicro/2017/2814581/ Growth of fruits which form an important part of human diet has been jeopardized by the many fungal diseases that are present today. This study was conceived to isolate the most common fungal pathogens in passion fruits. Fungi were isolated using potato dextrose agar in addition to characterization using morphological, cultural, and biochemical means. Extraction of essential oils from rosemary (Rosmarinus officinalis) and eucalyptus (Eucalyptus agglomerata) was done. Before carrying the sensitivity test of essential oils to the fungal isolates, constituents of the essential oils were determined. The most common fungal pathogens isolated from passion fruits were Alternaria spp. (45%), Fusarium spp. (22%), Colletotrichum spp. (17%), and Penicillium spp. (16%). There was a relationship between heating time and yield of essential oils in rosemary () and eucalyptus (). Conversely, there was no significant difference in the amount of essential oils produced by rosemary and eucalyptus (). Furthermore, there was a significant difference in growth inhibition of the fungal pathogens between essential oils from rosemary and eucalyptus (). Fungal pathogens isolated from passion fruits can be controlled using essential oils from rosemary and eucalyptus. The oils need to be produced in large scale. Paul Njenga Waithaka, Eliud Mugu Gathuru, Benson Muriuki Githaiga, and Salome Nduta Kimani Copyright © 2017 Paul Njenga Waithaka et al. All rights reserved. Bacterial Isolates and Their Antimicrobial Susceptibility Patterns of Wound Infections among Inpatients and Outpatients Attending the University of Gondar Referral Hospital, Northwest Ethiopia Sun, 12 Mar 2017 00:00:00 +0000 http://www.hindawi.com/journals/ijmicro/2017/8953829/ Background. The widespread uses of antibiotics, together with the length of time over which they have been available, have led to the emergence of resistant bacterial pathogens contributing to morbidity and mortality. This study was aimed to assess bacterial isolates and their drug susceptibility patterns from inpatients and outpatients with pus and/or wound discharge. Methods. A cross-sectional study was conducted at the University of Gondar Referral Hospital from March to May, 2014. Wound swab samples were collected from each study participant and inoculated into appropriate media. The bacterial pathogens were identified using standard microbiological methods. Antimicrobial susceptibility tests were performed using disk diffusion technique following Kirby-Bauer method. Results. A total of 137 study subjects were included in the study with bacterial isolation rate of 115 (83.9%). Of all, 81 (59.1%) were males. Seventy-seven (57%) of the isolates were Gram-negative and 59 (43%) were Gram-positive. From the total isolates, Staphylococcus aureus was the most predominant isolate 39/115 (34%) followed by Klebsiella species (13%), coagulase negative staphylococci spp. (12%) and Pseudomonas aeruginosa. Gram-positive isolates were resistant to ampicillin (86.4%), amoxicillin (83%), penicillin (81.3%), oxacillin (74.6%), and tetracycline (59.4%), while Gram-negative isolates were resistant to amoxicillin (97.4%), ampicillin (94.8%), tetracycline (72.7%), trimethoprim/sulfamethoxazole (66%), and chloramphenicol (54.5%). Conclusion. High prevalence of bacterial isolates was found, Staphylococcus aureus being the most dominant. High rates of multiple drug resistance pathogens to the commonly used antimicrobial agents were isolated. Therefore, concerned bodies should properly monitor the choice of antibiotics to be used as prophylaxis and empiric treatment in the study area. Aynalem Mohammed, Mengistu Endris Seid, Teklay Gebrecherkos, Moges Tiruneh, and Feleke Moges Copyright © 2017 Aynalem Mohammed et al. All rights reserved. Bacteriological Profile and Antimicrobial Susceptibility Patterns of Bacteria Isolated from Pus/Wound Swab Samples from Children Attending a Tertiary Care Hospital in Kathmandu, Nepal Mon, 06 Mar 2017 00:00:00 +0000 http://www.hindawi.com/journals/ijmicro/2017/2529085/ In Nepal, little is known about the microbiological profile of wound infections in children and their antimicrobial susceptibility patterns. Total of 450 pus/wound swab samples collected were cultured using standard microbiological techniques and the colonies grown were identified with the help of biochemical tests. The antimicrobial susceptibility testing was performed by Kirby-Bauer disc diffusion technique. Methicillin-resistant Staphylococcus aureus isolates were detected by using cefoxitin disc and confirmed by determining minimum inhibitory concentrations (MIC) of oxacillin. 264 (59%) samples were culture positive. The highest incidence of bacterial infections was noted in the age group of less than 1 year (76%). Out of 264 growth positive samples, Gram-positive bacteria were isolated from 162 (61%) samples and Gram-negative bacteria were found in 102 (39%) samples. Staphylococcus aureus (99%) was the predominant Gram-positive bacteria isolated and Pseudomonas aeruginosa (44%) was predominant Gram-negative bacteria. About 19% of S. aureus isolates were found to be methicillin-resistant MIC of oxacillin ranging from 4 μg/mL to 128 μg/mL. Among the children of Nepal, those of age less than 1 year were at higher risk of wound infections by bacteria. Staphylococcus aureus followed by Pseudomonas aeruginosa were the most common bacteria causing wound infections in children. Salu Rai, Uday Narayan Yadav, Narayan Dutt Pant, Jaya Krishna Yakha, Prem Prasad Tripathi, Asia Poudel, and Binod Lekhak Copyright © 2017 Salu Rai et al. All rights reserved.