Microbiology

Biological synthesis of metal nanoparticles has caught the interest of scientists due to the environment friendly synthesis approach which yields metallic nanoparticles with antimicrobial potency. In the present study silver nanoparticles were produced using a green method with the assistance of Fusarium sp. fungal cell filtrate and their antimicrobial potency was explored. The silver nanoparticles depicted a surface plasma resonance of 434 nm when run in the Ultra Violet-Visible Spectrophotometer. The functional group present in the nanoparticles were investigated using an Attenuated Total Reflectance-Fourier Transform Infrared where -OH, C-H, amide I and amide II functional groups were notable. The morphology and crystallinity of the produced silver nanoparticles was investigated with the help of a Scanning Electron Microscope and X-ray Diffraction. The X-ray diffraction results revealed that the nanoparticles were crystalline in nature with a face centred cubic structure and a crystallite size of 38.5 nm. The Scanning Electron Microscope revealed that the nanoparticles were spherical with sizes ranging between 3 to 43 nm. Antimicrobial studies of the synthesised silver nanoparticles were conducted at different concentrations (1 mM, 10 mM, 20 mM and 100 mM) against disease causing microorganisms Bacillus subtilis, Staphylococcus aureus, Escherichia coli and Pseudomonas aeruginosa, the results showed that at a concentration of 1 mM there was no inhibition but as the concentration was increased to 20 mM and 100 mM, there was a notable inhibition with the maximum inhibition zone being 17 ± 0.6 mm. • The study involved synthesis, optimization and characterization of silver nanoparticles that were produced with the help of Fusarium sp. • Characterization of the silver nanoparticles revealed that the nanoparticles were crystalline and spherical in nature. • The antimicrobial results indicated that the nanoparticles had notable inhibition zones meaning they can be applied as antimicrobials.

Tylosin has been used as a livestock feed additive and antibiotic growth promoter for many years. However, the mode of action by which tylosin enhances animal growth is unclear. We used high throughput sequencing of 16S rRNA genes to investigate the effects of tylosin as a feed additive on swine gut microbiota. No significant difference in the rate of weight increase was observed between control and tylosin-treated pigs during a 10 week feeding trial. However, tylosin-treated pigs showed rapid increases in the relative abundance of the phylum Firmicutes. Increases in Firmicutes species are associated with (so-called) obese type gut microbiota. The abundance of species of four families of the phylum Firmicutes (Streptococcaceae, Peptococcaceae, Peptostreptococcaceae, and Clostridiaceae) correlated positively with host weight gain. The abundance of Streptococcaceae family bacteria was least affected by tylosin-treatment. Distribution analysis of operational taxonomic units (OTUs) show...

Streptomyces sp. TD-1 was identified as Streptomyces alboflavus based on its morphological characteristics, physiological properties, and 16S rDNA gene sequence analysis. The antifungal activity of the volatile-producing S. alboflavus TD-1 was investigated. Results showed that volatiles generated by S. alboflavus TD-1 inhibited storage fungi Fusarium moniliforme Sheldon, Aspergillus flavus, Aspergillus ochraceus, Aspergillus niger, and Penicillum citrinum in vitro. GC/MS analysis revealed that 27 kinds of volatile organic compounds were identified from the volatiles of S. alboflavus TD-1 mycelia, among which the most abundant compound was 2-methylisoborneol. Dimethyl disulfide was proved to have antifungal activity against F. moniliforme by fumigation in vitro.

Objetivos: O objetivo deste estudo in vitro consistiu em avaliar a eficácia da Terapia Fotodinâmica (TFD), utilizando Azul de Toluidina (AT) como fotosensibilizador e uma fonte de luz (LED) em biofilmes de Enterococcus faecalis e Candida albicans e comparar com o efeito do hipoclorito de sódio (NaOCl) aplicado isoladamente e em associação com a Terapia Fotodinâmica. Materiais e métodos: Biofilmes de mono-espécie de E. faecalis e C. albicans foram preparados e submetidos a 3 tratamentos: (1) TFD -60s, (2) NaOCl a 3% -10 min., (3) NaOCl TFD. O controlo positivo consistiu de um grupo não sujeito a tratamento e outro controlo foi feito com a aplicação isolada de LED. A determinação da massa celular bioativa remanescente foi realizada através de um método colorimétrico baseado na redução de 2,3-bis(2-methoxi-4-nitro-5-sulfophenil)-2Htetrazólio-5-carboxanilida (XTT). Resultados: O grupo da TFD apresentou uma redução significativa da massa celular bioativa com uma percentagem de sobrevivência de 24.76% para o E. faecalis e 17.14% para a C. albicans. A aplicação de NaOCl, como terapia isolada foi superior à da TFD no biofilme de E. faecalis e semelhante à TFD no biofilme de C. albicans. Não se verificaram diferenças estatisticamente significativas entre o grupo do NaOCl e a associação NaOCl e TFD. Conclusões: A terapia fotodinâmica (TFD) mostrou-se ativa sobre os biofilmes de C. albicans e E. faecalis, comparável ao NaOCl, na C. albicans.

Aims: Cross-contamination of feed with antibiotics causes pigs to become unintentionally exposed to low concentrations of antibiotics. This study investigates the effect of residues of doxycycline hyclate (DOX) in an ex vivo model of the intestinal tract of pigs, focusing on the microbial community, microbial activity, and the enrichment of resistant bacteria and resistance genes. Results: The effect of three concentrations DOX were tested; 1 and 4 mg/L correspond to the intestinal concentrations when pigs are fed a compound feed containing 3% of a therapeutic dose, and a reference concentration of 16 mg/L. These were continuously administered to a chemostat, simulating the microbial ecosystem of the pig cecum and inoculated with cecal content of organically grown pigs. The administration of even the lowest DOX concentration caused a significant decrease in bacterial activity, while the microbial community profile appeared to remain unaffected by any of the concentrations. A concentration of 1 mg/L DOX caused minor selection pressure for tetracycline-resistant Escherichia coli but no other groups enumerated with plate cultivation, while 4 mg/L induced major enrichment of tetracycline-resistant E. coli, Enterobacteriaceae and total anaerobes. High abundances of tet(Q), tet(M), tet(W), tet(O), and tet(B) were detected in the inoculum and also before antibiotic administration in the chemostat and did not significantly increase during administration of 1 and 4 mg/L DOX. Only 16 mg/L DOX caused minor enrichments. Conclusions: Cross-contamination concentrations of doxycycline, as a result of cross-contamination, cause a selection pressure for resistant bacteria and negatively affect microbial activity.

Latar belakang: Analisis polimorfisme suatu gen penting dilakukan untuk memperoleh informasi lebih awal dalam identifikasi penanda genetik yang berhubungan dengan sifat yang ingin dilihat. Metode RFLP menjadi salah satu metode yang dipilih karena dapat melihat polimorfisme urutan DNA yang dapat dideteksi melalui adanya perbedaan fragmen DNA setelah dipotong dengan menggunakan enzim endonuclease tertentu sehingga mampu menggambarkan polimorfisme dari suatu gen. Tujuan penelitian adalah untuk mengetahui adanya polimorfisme gen coagulase S. aureus resisten methicillin. Hasil: Amplifikasi menunjukkan produk PCR (amplicon) gen mecA dan coagulase dengan primer spesifik ke 25 isolate bakteri MRSA mempunyai positivitas sebesar 100%. Hasil dari PCR-RFLP menunjukkan empat pola RFLP dengan situs restriksi AluI pada 25 isolat. Proposi terbesar (64%) pada pola RFLP I (pola yang tidak terdigesti enzim restriksi AluI).

RSV, IAV, IBV, ADV, PIVs 1-3, and HMPV can be identified by direct fluorescent antibody and cell culture methods. In addition to these aforementioned viruses, HRV, HCoV, HBoV, PIV 4, and RSV serotype A and B can be detected by molecular methods. Recently, multiplex polymerase chain reaction (M-PCR) methods in which many respiratory

Respiratory tract infections (RTI) are among the most commonly seen infections in children across the world, with the highest rate of morbidity. Viruses are known to be the primary agent in these infections and mostly lead to upper RTIs. The most commonly seen viral agents of RTIs may be listed as rhinoviruses (HRV), influenza, parainfluenza (PIV), respiratory syncytial virus (RSV), adenovirus, and enteroviruses. In this study, prediagnosed children with acute RTI between January 2013 and May 2015 were included. Nasopharyngeal swab samples obtained from a total of 2,268 patients admitted to the

Background: mecA is a predefined gene causing methicillin resistance in Staphylococcus aureus (S. aureus) isolates; however, it has been shown that some methicillin-resistant S. aureus (MRSA) strains do not carry this gene. Recently, in isolates found to be MRSA-positive but mecA-negative, a new resistance gene called mecC, which is a homolog of mecA, has been reported. This study aimed to investigate the mecC and mecA genes in MRSA strains isolated from different geographic regions in Turkey. Methods: The sample of the study consisted of 494 MRSA strains isolated from seven geographical regions in Turkey between 2013 and 2016. The strains were obtained from 17 centers, comprising 13 university hospitals, three education and research hospitals, and one state hospital. Methicillin resistance in S. aureus strains was determined using the agar disk diffusion method with a cefoxitin disk and the agar dilution method with oxacillin. The mecC and mecA genes in MRSA strains was investigated by Polymerase Chain Reaction (PCR). Results: Of the MRSA strains investigated, 47.9% were isolated from intensive care units. Concerning sample type, 36.7% were detected in the respiratory tract (tracheal aspirate, sputum, etc.), 24.8% in blood, 18.7% in skin and soft tissues, 9.3% in nasal swabs, 5.4% in urine, 4.1% in ears, and 1% in sterile body fluid. Using PCR, mecC was not identified in any of the S. aureus strains isolated from different clinical microbiology laboratories. mecA gene positivity was found in 315 of the MRSA strains (63.8%). Staphylococcal Cassette Chromosome mec (SCCmec) type was identified in 232 strains (46.9%), of which 136 (58.7%) were type II, 75 (32.4%) were type IV, 12 (5.1%) were type IIIb, six (2.5%) were type I, and three (1.3%) were type III.

Son yıllarda geniş spektrumlu antibiyotiklerin yaygın kullanımı nedeniyle çoklu ilaca dirençli bakterilerde meydana gelen artışlar dünya çapında acil bir sorun haline gelmiştir. Bu çalışmada kan kültürü örneklerinden izole edilen Gram negatif bakterilerin antimikrobiyal direnç paternlerinin saptanarak ampirik tedavi ve antibiyotik kullanım politikalarına katkıda bulunulması amaçlanmıştır. Gereç ve Yöntemler: Laboratuvarımıza Haziran 2018-Haziran 2021 tarihleri arasında gönderilen kan kültüründen izole edilen 495 Gram negatif bakteri izolatı retrospektif olarak incelenmiştir. Bakterilerin identifikasyonu için konvansiyonel yöntemler ve tam otomatize cihaz (VITEK2, bioMerieux, Fransa) kullanılmıştır. Tiplendirme sonrasında izolatların antibiyotik duyarlılık testleri, VITEK2 sistemi ile yapılmış, EUCAST (European Committee on Antimicrobial Susceptibility Testing) kriterlerine göre yorumlanmıştır. Bulgular: Gram negatif izolatlar, sıklıkla yoğun bakım servislerinden izole edilmiştir (%39). Gram negatif bakteriyemilerde saptanan etkenler sıklık sırasına göre; Escherichia coli %33,9, Klebsiella pneumoniae %19,1, Acinetobacter spp. %18,5, Pseudomonas spp. %10,3 ve Enterobacter spp. %4,6 bulunmuştur. E.coli' de daha az direnç karbapenemlere (meropenem %0, imipenem %2,9 ve ertapenem %3,7) , tigesikline %1,8, ve amikasine karşı %2 saptanmıştır. Enterobacterales izolatlarında daha az direnç oranları sırasıyla karbapenemlere (%6,8-14,5) amikasine (%10,6) ve tigesikline (%15,9) karşı bulunmuştur. Pseudomonas spp.'de daha az direnç amikasine (%11,8) ve karbapenemlere (%13,7-22,7) karşı saptanmıştır. Sonuç: Karbapenemler, amikasin ve tigesiklin dışındaki bazı antibiyotiklere direnç oranlarının yüksek oranda saptanması, hastalara ampirik antibiyotik tedavinin dikkatli şekilde uygulanması gerektiğini göstermektedir. Bu sonuçların hastanemizde akılcı antibiyotik kullanımına ve ampirik tedavi seçimine katkı sağlayacağı kanaatindeyiz.

The incidence of infectious diseases caused by the Enterobacteriaceae family of Uvurkhangai province in Mongolia is not decreasing and is recurring despite the implementation of preventive measures in the province. Nowadays, when the resistance of microorganisms negatively affects the health of humans and animals, food safety, the environment, and the economy, the lack of effective antibiotics for treatment is the reason for the research work on this topic. Based on the outbreak and surveillance of infectious diseases for the past 5 years, the pathological materials were received in the veterinary laboratory, two strains of Escherichia coli and also two strains Salmonella enterica subsp. abortus equi were isolated, and identified by conventional bacteriological and molecular methods. The antimicrobial susceptibility of the pathogen was determined using the disc diffusion method. The strains of E. coli were resistant to several antimicrobials, including vancomycin and neomycin, intermediate to colistin. The Salmonella enterica subsp. abortus equi showed resistance to ampicillin, vancomycin, gentamicin, and neomycin. Due to the presence of antimicrobial resistance, the results suggest a risk to public health as these pathogens. However, the four isolated bacteria in the family of Enterobacteriaceae showed susceptibility to groups of tetracycline and streptomycin. As a result of this study, it was determined that treatment with tetracycline and streptomycin is effective against bacterial infections caused by the Enterobacteriaceae group.

Antibiotic exposure leads to massive selective pressures that initiate the emergence and spread of antibiotic resistance in commensal and pathogenic bacteria. The slow process of developing new antibiotics makes this approach counterintuitive for combatting the rapid emergence of new antibiotic resistant pathogens. Therefore, alternative approaches such as, the development of nucleic acid-based anti-bacterial treatments, anti-bacterial peptides, bacteriocins, anti-virulence compounds and bacteriophage therapies should be exploited to cope infections caused by resistant superbugs. In this editorial, we discuss how the newly popular CRISPR-Cas system has been applied to combat antibiotic resistance.

High resistance to antimicrobials is associated with biofilm formation responsible for infectious microbes to withstand severe conditions. Therefore, new alternatives are necessary as biofilm inhibitors to control infections. In this study, the antimicrobial and antibiofilm activities of Fagonia indica extracts were evaluated against MDR clinical isolates. The extract exhibited its antibiofilm effect by altering adherence and disintegration of bacterial cell wall. Fagonia indica has antibacterial effect as minimum inhibitory concentration (MIC) values ranging from 125 to 500 µg mL-1 and minimum bactericidal concentration (MBC) value was 500-3000 µg mL-1 against multidrug resistant (MDR) clinical isolates. The extract exhibited its antibiofilm effect by altering adherence and disintegration of bacterial cell wall. Fagonia indica had antibacterial effect as minimum inhibitory concentration (MIC) values ranging from 125 to 500 µg mL-1 and minimum bactericidal concentration (MBC) value ...

Emergence of plasmid mediated colistin and extended spectrum β-lactamases (ESBL) resistant genes has been impacted the efficacy of colistin and β-lactams drugs like 3rd, 4th generation cephalosporin. Current study was aimed to investigate antimicrobial resistance genes (ARGs) among Escherichia coli isolates from meat producing commercial broilers in Pakistan. Two hundred (n=200) fecal samples were collected during January-2018 to August-2019. For isolation of E. coli, pink colonies on MacConkey agar were transferred to EMB agar. Metallic sheen color colonies were tested biochemically using API-20E kit. The molecular identification of E. coli (n=153) was targeted by amplification of uid gene through polymerase chain reaction (PCR) and different ARGs i.e. gentamicin, streptomycin, tetracycline, colistin, β-lactams drugs, quinolone and ampicillin followed by sequence analysis. Genotypically, followed by phenotypically of resistant ARGs of isolated PCR-confirmed E. coli (153) shoed resi...

Antibiotic exposure leads to massive selective pressures that initiate the emergence and spread of antibiotic resistance in commensal and pathogenic bacteria. The slow process of developing new antibiotics makes this approach counterintuitive for combatting the rapid emergence of new antibiotic resistant pathogens. Therefore, alternative approaches such as, the development of nucleic acid-based anti-bacterial treatments, anti-bacterial peptides, bacteriocins, anti-virulence compounds and bacteriophage therapies should be exploited to cope infections caused by resistant superbugs. In this editorial, we discuss how the newly popular CRISPR-Cas system has been applied to combat antibiotic resistance.

Background: Increasing antibiotic resistance warrants therapeutic alternatives to eradicate resistant bacteria. Combined phage-antibiotic therapy is a promising approach for eliminating bacterial infections and limiting the evolution of therapy-resistant diseases. Objectives: In the present study, we evaluated the effects of combinations of bacteriophages and antibiotics against multidrug-resistant (MDR) Klebsiella pneumoniae. Methods: Two MDR strains (GenBank no. MF953600 & MF953599) of K. pneumoniae were used. Bacteriophages were isolated from hospital sewage samples by employing a double agar overlay assay and identified by transmission electron microscopy. For further characterization of bacteriophages, the killing assay and host range test were performed. To assess therapeutic efficacy, phages (7.5 × 104 PFU/mL) were used in combination with various antibiotics. Results: The phage-cefepime and tetracycline combinations displayed promising therapeutic effects, restricting the gr...

Background. The term “persisters” refers to a small bacterial population that persists during treatment with high antibiotic concentration or dose in the absence of genetic resistance. The present study was designed to investigate the transcriptional response in indigenous Klebsiella pneumoniae under the ciprofloxacin stress. Methods. Isolation and identification of K. pneumoniae were carried out through standard microbiological protocols. The characterization of quinolone resistance was performed by estimating the quinolone susceptibility testing, MIC estimation, and detecting the QRDR and PMQR. Transcriptional response of the isolates to ciprofloxacin was determined using qPCR. Results. Among 34 isolates, 23 (67%) were resistant to ciprofloxacin. Both QRDR (gyrA and gyrB) and PMQR (qnrA, qnrB, and qnrS) were detected in the isolates, and all were found resistant to ciprofloxacin. The mRNA levels of both mutS and euTu under the influence of ciprofloxacin were significantly increase...

' Contributions AS, SM and SZH designed the study. AS, FR, SZH, MS and UW performed the sampling. AS, SZH and UW performed the experiments. MEB and MK supervised the study. BA and MAA analyzed the data statistically. AS, MAA, BA and MK wrote the article. FR, MS and MA reviewed the article.

Intense livestock farming practices enforcing the farmers to use antibiotics as food supplements on a routine basis. Aberrant use of antibiotics is associated with the emergence of antibiotics resistance and resistant superbugs. Keeping in view the current scenario, the present study was designed for the first time from Pakistan with a specific aim to estimate the prevalence of the carbapenem-resistant Klebsiella pneumoniae in veterinary settings and the waste in Pakistan. Methods: A total of 138 samples from various veterinary sources were collected by employing a nonprobability sampling technique. Isolation and phenotypic identification of carbapenem-resistant K. pneumoniae were performed according to the CLSI standard. Molecular detection of various antibiotic resistance genes (ARGs) was done through PCR by using specific primers against each ARG. According to the pasture scheme, the multilocus sequence typing (MLST) was performed to characterize the K. pneumoniae sequence types (STs). Results: According to the results of the study, overall 9.4% (13/138) isolates were confirmed carbapenem-resistant K. pneumoniae. Among various carbapenem ARGs particularly, the bla NDM-1 was found in 92.3% (12/13) isolates followed by bla OXA-48 84.6% (11/13). MLST results revealed that overall 3 STs were found in the study which includes ST29, ST11, and ST258. Taking together, this is the first study to our best knowledge which demonstrated the prevalence of carbapenem-resistant K. pneumoniae and its various STs prevalent in veterinary settings and the waste of Pakistan. Conclusion: Based on the above-mentioned facts, we suggested that veterinary settings and waste are the potential source and reservoir of carbapenem-resistant K. pneumoniae, which may be disseminated to the environment and ultimately can affect the public and companion livestock health.

Antibiotic therapy has a dual impact: wanted, in which it immediately inhibits the growth of bacteria and the unwanted, which is responsible for the evolution of antibiotic resistance. The dissociation of therapeutic effectiveness from the possible risk of the antibiotic resistance may be attained by taking the advantage of specific relations between these drugs, and the methods in which mutations associated with resistance against a specific antibiotic may modify these relations or it may increase the sensitivity of the bacterium to the other antibiotics. Although the practical implementation of this notion needs considerable advancement and confirmation that depends upon the improvements in the field of genomics and diagnostics, these interventions propose new paradigms, which may confine or inverse the evolution of antibiotic resistance.

Continuous occurrence of heavy metals is a major cause of environmental pollution due to its toxic effects. At minimum concentrations, these metals are highly reactive and can gather in the food chains and food web, causing major dangers to public health concerns. Soil samples were collected from Paharang drain, Faisalabad. Cadmium tolerant bacteria were isolated and evaluated for their MIC against Cd. The isolated bacterial strain GCFSD01 showed MIC value upto 30 mM/L. The bacterial strain with the highest resistance against Cd was selected for further study. Molecular characterization of bacterial isolate GCFSD01 was performed by 16S rRNA which confirmed it as Bacillus cereus. Optimum growth conditions of bacterial strain were also evaluated. Strain GCFSD01 showed optimum growth at pH 7 and 37 °C temperature. Our result revealed that B. cereus strain GCFSD01 reduced 61.3% Cd after 48 hrs. Multiple metal tolerance and Cd reduction by B. cereus indicate its potential for further use...

Antibiotic resistance against present antibiotics is rising at an alarming rate with need for discovery of advanced methods to treat infections caused by resistant pathogens. Silver nanoparticles are known to exhibit satisfactory antibacterial and antibiofilm activity against different pathogens. In the present study, the AgNPs were synthesized chemically and characterized by UV-Visible spectroscopy, scanning electron microscopy, and X-ray diffraction. Antibacterial activity against MDR K. pneumoniae strains was evaluated by agar diffusion and broth microdilution assay. Cellular protein leakage was determined by the Bradford assay. The effect of AgNPs on production on extracellular polymeric substances was evaluated. Biofilm formation was assessed by tube method qualitatively and quantitatively by the microtiter plate assay. The cytotoxic potential of AgNPs on HeLa cell lines was also determined. AgNPs exhibited an MIC of 62.5 and 125 μg/ml, while their MBC is 250 and 500 μg/ml. The...

The emergence of carbapenem-resistant bacterial pathogens is a significant and mounting health concern across the globe. At present, carbapenem resistance (CR) is considered as one of the most concerning resistance mechanisms and mainly found in gram-negative bacteria of the Enterobacteriaceae family. Although carbapenem resistance has been recognized in Enterobacteriaceae from last 20 years or so, recently it emerged as a global health issue as CR clonal dissemination of various Enterobacteriaceae members especially E. coli, and Klebsiella pneumoniae are reported from across the globe at an alarming rate. Phenotypically, carbapenems resistance is in due to the two key mechanisms, like structural mutation coupled with β-lactamase production and the ability of the pathogen to produce carbapenemases which ultimately hydrolyze the carbapenem. Additionally, penicillin-binding protein modification and efflux pumps are also responsible for the development of carbapenem resistance. Carbape...

Metallo-β-lactamases (MBLs) producing Pseudomonas aeruginosa are major threat for public health. They produce resistance against various antibiotics and remain low or no therapeutic options. A total of 200 clinical isolates of P. aeruginosa were collected from tertiary care hospital, Faisalabad. Isolates were sub-cultured on basic and selective media and confirmed by API 20NE. Phenotypic detection of carbapenamase, MBLs, antibiogram and MIC were determined as per CLSI guidelines. Molecular detection of blaVIM was performed using specific primers by PCR. Among 200 P. aeruginosa, majority (n=82) were isolated from pus samples followed by 28 from tracheal aspirates and 27 from sputum. Out of 110 (55%) MDR P. aeruginosa, 12 (11%) were positive for MHT and MBLs and blaVIM was identified in MBL positive isolates. Antibiogram revealed that all the isolates were resistant to β-lactam drugs including carbapenems followed by 95% to levofloxacin, 67% to doxycycline and more effective drugs wer...

Epidemiology of powdery mildew on cucurbits were studied in Rohilkhand region of Uttar Pradesh, India. Most of the cucurbits were found infected in one or the other localities of the study area which comprised eight districts of Rohilkhand region of Uttar Pradesh. The study area showed the occurrence of and . The knowledge regarding perpetuation of the pathogens and annual recurrence of the disease on cucurbits seems to remain evading in the near future.

Diarrhea, or as Indonesians usually refer it as mencret, is defined as defecation more than three times per day along with a change in the consistency of the stool to liquid with or without mucus and blood. There exist various causes of diarrhea in Indonesia, both viral and bacterial. The main pathogen causing diarrhea in our country is Rotavirus (40-60%), followed by Escherichia coli bacteria (20-30%), and the rest is dominated by other microorganisms (10-20%). Based upon previous research, probiotics and prebiotics have been shown to have potential in preventing and treating diarrhea caused by various pathogenic microorganisms. Probiotics are supplemented live bacteria that have a beneficial response on the health of human digestive organs by improving the balance of normal gut flora, whereas prebiotics are substrates that are not to be digested by the intestines, but instead bring benefits to the health of human digestive system that selectively stimulate the growth and activity of good bacteria in the gut. Bananas apparently contain a source of prebiotics that we are rarely aware of. The probiotic content of inulin and fructooligosaccharides (FOS) in bananas plays an important role in nourishing and stimulating the growth of probiotic bacteria. Accordingly, they are also considered "colonic foods" for the natural flora of the intestine. Fermented milk products, such as yogurt, have the benefir of inhibiting gastrointestinal infections. Aside from the aforementioned benefits, yogurt also contains anticancer effects, lowers blood cholesterol levels, and stimulates the immune system. The beverage innovation called "YOPI EN NUNO", which of this is a synbiotic banana yogurt with the addition of B. Lactis and L. rhamnosus GG bacterial starters has various advantageous potentials to prevent and treat acute diarrhea in children.

Urinary tract infections (UTIs) are the most common infections in pediatric patients characterized by the growth of bacteria in the urine in significant numbers. Antibiotics remain the primary treatment of UTI in children. However, there has been an increase in antibiotic resistance to uropathogens worldwide due to their inappropriate and extensive uses. There is considerable geographical variation in the distribution of bacteria and antibiotic resistance pattern. Thus, to prevent further resistance and provide empirical antibiotic options, this study aims to determine the profile of bacteria and antibiotics resistance pattern among UTI pediatric patients in Dr. Soetomo Hospital. This study was performed by collecting data from the urine culture logbook at the Clinical Microbiology Laboratory of Dr. Soetomo Hospital in July-October 2019. The sample was UTI patients aged one day – 18 years due to bacterial infection with a colony count of   ≥100,000 CFU/ml. In this study, 131 patient...

Escherichia coli is the main pathogen responsible for extraintestinal infections. A total of 196 clinical E. coli consecutively isolated during 2016 in Spain (100 from Lucus Augusti hospital in Lugo) and France (96 from Beaujon hospital in Clichy) were characterized. Phylogroups, clonotypes, sequence types (STs), O:H serotypes, virulence factor (VF)-encoding genes and antibiotic resistance were determined. Approximately 10% of the infections were caused by ST131 isolates in both hospitals and approximately 60% of these infections were caused by isolates belonging to only 10 STs (ST10, ST12, ST58, ST69, ST73, ST88, ST95, ST127, ST131, ST141). ST88 isolates were frequent especially in Spain while ST141 isolates significantly predominated in France. The 23 ST131 isolates displayed four clonotypes: CH40-30, CH40-41, CH40-22 and CH40-298. Only 13 (6.6%) isolates were carriers of ESBL enzymes. However, 37.2% of the isolates were multidrug-resistant (MDR). Approximately 40% of the MDR isol...

Antimicrobial agents are crucial for the treatment of many bacterial diseases in pigs, however, the massive use of critically important antibiotics such as colistin, fluoroquinolones and 3rd-4th-generation cephalosporins often selects for co-resistance. Based on a comprehensive characterization of 35 colistin-resistant Escherichia coli from swine enteric colibacillosis, belonging to prevalent Spanish lineages, the aims of the present study were to investigate the characteristics of E. coli clones successfully spread in swine and to assess the correlation of the in vitro results with in silico predictions from WGS data. The resistome analysis showed six different mcr variants: mcr-1.1; mcr-1.10; mcr-4.1; mcr-4.2; mcr-4.5; and mcr-5.1. Additionally, bla CTX-M-14 , bla CTX-M-32 and bla SHV-12 genes were present in seven genomes. PlasmidFinder revealed that mcr-1.1 genes located mainly on IncHI2 and IncX4 types, and mcr-4 on ColE10-like plasmids. Twenty-eight genomes showed a gyrA S83L substitution, and 12 of those 28 harbored double-serine mutations gyrA S83L and parC S80I, correlating with in vitro quinolone-resistances. Notably, 16 of the 35 mcrbearing genomes showed mutations in the PmrA (S39I) and PmrB (V161G) proteins. The summative presence of mechanisms, associated with high-level of resistance to quinolones/fluoroquinolones and colistin, could be conferring adaptive advantages to prevalent pig E. coli lineages, such as the ST10-A (CH11-24), as presumed for ST131. SerotypeFinder allowed the H-antigen identification of in vitro non-mobile (HNM) isolates, revealing that 15 of the 21 HNM E. coli analyzed were H39. Since the H39 is associated with the most prevalent O antigens worldwide within swine colibacillosis, such as O108 and O157, it would be probably playing a role in porcine colibacillosis to be considered as a valuable subunit antigen in the formulation of a broadly protective Enterotoxigenic E. coli (ETEC) vaccine. Our data show common features with other European countries in relation to a prevalent clonal group (CC10), serotypes (O108:H39, O138:H10, O139:H1, O141:H4), high plasmid content within the isolates and mcr location, which would support global alternatives to the use of antibiotics in pigs. Here, we report for first time a rare finding so far, which is the co-occurrence of double colistin-resistance mechanisms in a significant number of E. coli isolates.

Background: Escherichia coli biofilm formation has mostly been assessed in specific pathogenic E. coli groups. Here, we assessed the early biofilm formation (EBF), i.e., adhesion stage, using the BioFilm Ring Test R on 394 E. coli clinical isolates (EC) [196 consecutively isolated (CEC) in 2016 and 198 ESBL-producing E. coli (ESBLEC) isolated in 2015]. Then, biofilm-forming ability was contrasted with phylogroups, clonotypes (fumC-fimH), and sequence types (STs), all being used to define clones, virulence factors (VF), and FimB. Result: According to both biofilm production levels at 2, 3, and 5 h, and EBF kinetics over 5 h, CEC and ESBLEC isolates segregated into three EBF groups: strong (G1), moderate (G2), and weak (G3) producers. At 2 h, strong producers were more frequent among CEC (n = 28; 14.3%) than among ESBLEC (n = 8; 4%) (P = 0.0004). As CEC and ESBLEC isolates showed similar individual EBF kinetics in each group, a comparison of isolate features between each group was applied to gathered CEC and ESBLEC isolates after 2 h of incubation, 2 h being the most representative time point of the CEC and ESBLEC isolate segregation into the three groups. Phylogroup B2 displayed by 51.3% of the 394 isolates was more frequent in G1 (77.8%) than in G3 (47.6%) (P = 0.0006). The 394 isolates displayed 153 clones, of which 31 included at least three isolates. B2-CH14-2-ST127, B2-CH40-22-ST131, B2-CH52-5/14-ST141, and E-CH100-96-ST362 clones were associated with G1 (P < 0.03) and accounted for 41.7% of G1 isolates. B2-CH40-30-ST131 clone was associated with G3 (P < 0.0001) and accounted for 25.5% of G3 isolates. VF mean was higher among G1 than among G3 isolates (P < 0.001). FimB-P2 variant was associated with G1 (P = 0.0011) and FimB-P1 variant was associated with G3 (P = 0.0023). Clone, some VF, and FimB were associated with EBF, with clonal lineage being able to explain 72% of the variability of EBF. Conclusion: Among our 394 isolates, <10% are able to quickly and persistently produce high biofilm levels over 5 h. These isolates belong to a few clones previously

Molecular Epidemiology of Bacteraemic ESBL-Producing E. coli operon FM955459, sat, and kpsMII-K2). Although the 96 ESBL-EC isolates showed 21 O serogroups and 17 H flagellar antigens, 39 belonged to serotype O25b:H4 (ST131 isolates). The second most prevalent serotype (O15:H1) was found to be associated with another important high-risk clone (ST393). In conclusion, the ST131 was the most frequent sequence type, being the H30Rx subclone responsible for the significant increase of ESBL-EC isolates since 2006. Here, we report two new virotypes (E and F) of the H30Rx subclone emerged in 2011. Future molecular studies are needed to understand the dynamics of expansion of this successful high-risk subclone in order to prevent its spread and establish the importance of the two new virotypes.

Porcine Escherichia coli ST131 isolates are scarcely documented. Here, whole genome sequencing and core genome (CG) and plasmidome analysis of seven isolates collected from diarrheic piglets and four from pork meat were performed. All of the 11 ST131 isolates belonged to serotype O25b:H4 and clade B and showed fimH22 allele or mutational derivatives. The 11 porcine isolates possessed virulence traits that classified the isolates as avian pathogenic, uropathogenic, and extraintestinal pathogenic E. colilike (APEC-, UPEC-, and ExPEC-like) and constituted virotype D. The CG was performed for all porcine isolates in addition to 73 ST131 reference isolates from different origins. Within clade B, the CG showed nine subclusters, allowing us to describe five new subclades (B6, B6-like, B7, B8, and B9). There was an association between subclade B6, PST43, virotype D2, and food origin, whereas subclade B7 included PST9 isolates with virotype D5 from diarrheic piglets (p = 0.007). The distance between human and porcine isolates from subclades B6 and B7 had an average of 20 and 15 SNP/Mb, respectively. [F2:A-:B1]-IncF, ColE1-like, and IncX plasmids were the most prevalent. Besides, IncF plasmids harbored a ColV region frequent among APEC isolates. Antimicrobial resistance genes conferring resistance to penicillin, tetracycline, quinolones, and colistin were the most common. The mcr-1.1 gene was detected in 5 of 11 porcine isolates, integrated into the chromosome of one isolate and into plasmids in the remainder isolates (two MOB H11 /IncHI2-ST4, one MOB P3 /IncX4, and one MOB F 12 /IncF [F2:A-:B1] supposedly cointegrated with an IncHI2). The surrounding environments of the mcr-1 cassette showed variability. However, there were conserved structures within the same plasmid family. In conclusion, CG analysis defined five new subclades. The ST131 porcine isolates belonged to new subclades B6 and B7. Moreover, porcine and clinical human isolates were strongly related. The 11 porcine ST131 isolates harbored a wide variety of plasmids, virulence, and resistance genes.

Fırsatçı mantarlar, nozokomiyal enfeksiyonların önemli nedenlerinden biri olup, başta Candida türleri olmak üzere birçok farklı maya mantarı, immün sistemi baskılanmış hastalardan artan sıklıkta izole edilmektedir. Bunlardan bir kısmı yaygın kullanılan antifungallere dirençli olduğundan, uygun tedaviye başlamak için hızlı ve doğru tanımlama gereklidir. Bu çalışmada, Candida türlerinin tanımlanmasında API ® ID 32C (bioMerieux, Fransa) ve Phoenix™ Yeast ID Panel (Becton Dickinson Diagnostics, ABD) ticari tanımlama sistemlerinin karşılaştırılması ve morfolojik özelliklerin tanımlamaya etkisinin değerlendirilmesi amaçlanmıştır. Çalışmaya, Ekim 2013-Ocak 2014 tarihleri arasında Uludağ Üniversitesi Sağlık Uygulama ve Araştırma Merkezinde yatan 137 hastanın klinik örneklerinden izole edilen toplam 211 (111 idrar, 34 kan/vasküler kateter, 27 üst/alt solunum yolu örneği, 16 apse/püy, 13 boğaz/vajen sürüntüsü ve 10 steril vücut sıvısı) maya suşu alınmıştır. Örnekler kanlı agar, kromojenik agar (CHROMagar Candida, BD, ABD) ve Sabouraud dekstroz agara (SDA) ekilmiş ve izole edilen maya kolonileri çimlenme borusu ve mısır unu/ Tween-80 agardaki mikroskobik morfolojileri açısından değerlendirilmiştir. Tüm suşlar aynı zamanda her iki ticari sistemle de üretici firmaların önerileri doğrultusunda tanımlanmıştır. Sistemler arasındaki uyumsuz sonuçlar, izolatların morfolojik özellikleri dikkate alınarak çözümlenmeye çalışılmıştır. Çalışmamızda, izolatların 159'u her iki sistemle de aynı şekilde tanımlanmış ve sistemler arasındaki uyum %75.4 olarak saptanmıştır. Uyumlu tanımlama bulgularına göre en sık izole edilen tür C.albicans (%44.1) olmuş, bunu

infections, diagnostic and therapeutic dilemmas, and high morbidity and mortality in patients with haematological malignancies. Both B. cereus and B. licheniformis may be among the 'new' Gram-positive pathogens to cause serious infection in patients with neutropenia.

Background Accurate identification of larval habitats of Ae. aegypti is considered an essential step in targeted control; of this important vector of several arboviruses including dengue and chikungunya viruses. This study determined Ae. aegyptiproductivity in selected larval habitats in Msambweni, Kwale County, Kenya. Methods A total of 664 potential larval habitats were identified and classified based on their use and material into seven habitat types including: buckets, drums, jerrycans, pots, small domestic containers (SDC), tires and others during the habitat census survey. All Ae. aegypti immatures in 83 representative larval habitats were counted daily for 30 consecutive days during a wet and a dry season. All pupae were removed and allowed to emerge in the laboratory. Results Of 664 larval habitats examined at baseline, 144 larval habitats (21.7%) were found to be infested with Aedes aegypti larvae. 71% of the pupae were collected from tires and pots combined, which together...

Bacterial leaf blight (BLB) disease of rice caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most destructive diseases worldwide in rice-growing regions. The Ineffectiveness of chemicals in disease management has increased the interest in phage therapy. In this study, we isolated 19 bacteriophages, infecting Xoo, from a rice field, which belonged to phage families Siphoviridae, Myoviridae, and Podoviridae on the basis of electron microscopy. Among 19 phages, Phage vB_XooS_NR08, a member of the Siphoviridae family, expressed antibacterial activity against all Xoo strains tested and did not lyse X. campestris and other unrelated bacterial hosts. Phage NR08 showed more than 80% viability at a temperature range of 4°C–40°C, pH range of 5–9, and direct exposure to sunlight for 2 h, whereas UV light and chemical agents were highly detrimental. In a one-step growth curve, NR08 has a 40-min latent period, followed by a 30-min burst period with a burst size of 250 particle/bacteri...

Background: To cope with the increasing number of patients on long-term hemodialysis (HD), especially those with diabetic nephropathy, we designed a fully automated HD system to decrease staff workload and hence human errors related to HD treatment. In this study, we evaluated this new system as a clinical trial. Methods: Based on a dialysis machine combined with a central dialysate delivery system (CDDS), the new system is characterized by the use of back ultrafiltrated dialysate (BUD) as a substitute fluid for priming, bonus shot and blood return, and the attachment of double endotoxin retentive filters (ETRFs). Results: The subjects comprised 61 patients from five HD facilities enrolled in a randomized, open-labeled crossover study after giving written informed consent. A total of 348 HD treatments for 58 of the 61 patients were studied under a protocol designed in accordance with good clinical practice (GCP) guidelines and approved by the respective institutional review boards. No severe adverse effects were observed with either the test or control systems. The incidence of clinical events, including blood pressure decline, residual blood, and error in fluid removal, was not statistically significant in either group. Neither endotoxins nor bacteria were detected in the dialysate passing through the double filters. Conclusions: This study confirmed the safety and effectiveness of an automated HD system based on CDDS.

In this article, we describe the 6 HCV Genotyping 9G test and its evaluation by using clinical samples and plasmid DNA standards. In tests with 981 plasmid DNA standards, the 6 HCV Genotyping 9G test showed higher than 92.5% sensitivity and 99.4% specificity. The 6 HCV Genotyping 9G test was compared with the VERSANT HCV Genotype 2.0 assay (LiPA 2.0) for detection and discrimination of HCV genotypes in clinical samples. The results of both tests were verified by genomic sequencing. The 6 HCV Genotyping 9G test demonstrated a 100% agreement with the sequencing results, which was higher than LiPA 2.0. These results indicate that the 6 HCV Genotyping 9G test can be a reliable, sensitive, and accurate diagnostic tool for the correct identification of HCV genotypes in clinical specimens. 6 HCV Genotyping 9G test can genotype six HCV types in 1 PCR in 30 min after PCR amplification. The 6 HCV Genotyping 9G test, thus provide critical information to physicians and assist them to apply accurate drug regimen for the effective hepatitis C treatment.

Diferentes literaturas sugieren que el consumo de cannabis es un importante problema para la salud pública. El cannabis, por su naturaleza ilegal, llega a sus usuarios sin cumplimiento de normas adecuadas de cultivo, almacenamiento, procesamiento y tráfico; lo que puede generar diversos contaminantes, que pueden ser químicos, físicos o microbianos. La presencia de contaminantes microbianos es un riesgo para la salud de los usuarios, sobre todo en pacientes con el sistema inmune comprometido. Costa Rica no cuenta con estudios sobre la presencia de contaminantes microbianos en el cannabis comercializado, por lo que este estudio pretendía establecer si los hay en las muestras incautadas en seis regiones del territorio costarricense y relacionar este hecho con riesgos para la salud de sus consumidores. En dichas muestras se realizaron pruebas de conteo total de bacterias aeróbicas, levaduras y hongos según los procedimientos establecidos por la Farmacopea de los Estados Unidos de América (USP). Para la identificación de microorganismos potencialmente patógenos, se realizaron los procedimientos descritos por la USP, el uso del sistema API y metodología de identificación morfológica de hongos. Los conteos totales de bacterias, de levaduras y hongos superan los límites establecidos por USP en la mayoría de las muestras. Se hallaron cuatro tipos de hongos: Aspergillus sp., Scopulariopsis sp, Fusarium sp y Penicillum sp y cinco especies bacterianas: Staphylococcus aureus, S. xylosus, S. lentus, Enterobacter cloacae y E. sakazakki. La contaminación hallada requiere de un debate para el establecimiento de una verdadera política de regulación, tanto para fin terapéutico como para fines recreativos.

Nitrification is a key process for N-removal in engineered and natural environments, but recent findings of novel nitrifying microorganisms with surprising features revealed that our knowledge of this functional guild is still incomplete. Especially nitrite oxidationthe second step of nitrification -is catalyzed by a phylogenetically diverse bacterial group, and only recently bacteria of the phylum Chloroflexi have been identified as thermophilic nitrite-oxidizing bacteria (NOB). Among these, Nitrolancea hollandica was isolated from a laboratory-scale nitrifying bioreactor operated at 35 • C with a high load of ammonium bicarbonate. However, its distribution remains cryptic as very few closely related environmental 16S rRNA gene sequences have been retrieved so far. In this study, we demonstrate how such thermophilic NOB can be enriched using modified mineral media inoculated with samples from a wastewater side-stream reactor operated at 39.5 • C. Distinct cultivation conditions resulted in quick and reproducible high enrichment of two different strains of Nitrolancea, closely related to Nl. hollandica. The same cultivation approach was applied to a complex nitrite-oxidizing pre-enrichment at 42 • C inoculated with biomass from a geothermal spring in the Copahue volcano area in Neuquen, Argentina. Here, an additional distinct representative of the genus Nitrolancea was obtained. This novel species had 16S rRNA and nitrite oxidoreductase alpha subunit (nxrA) gene sequence identities to Nl. hollandica of 98.5% and 97.2%, respectively. A genomic average nucleotide identity between the Argentinian strain and Nl. hollandica of 91.9% indicates that it indeed represents a distinct species. All Nitrolancea cultures formed lancet-shaped cells identical to Nl. hollandica and revealed similar physiological features, including the capability to grow at high nitrite concentrations. Growth was optimal at temperatures of 35-37 • C and was strongly enhanced by ammonium supplementation. Genomic comparisons revealed that the four Nitrolancea strains share 2399 out of 3387 orthologous gene clusters and encode similar key functions. Our results define general growth conditions that enable the selective enrichment of Nitrolancea from artificial and natural environments. In most natural habitats these NOB apparently are of low abundance and their proliferation depends on the balanced presence of nitrite and ammonium, with an optimal incubation temperature of 37 • C.

Nitrification is a key process for N-removal in engineered and natural environments, but recent findings of novel nitrifying microorganisms with surprising features revealed that our knowledge of this functional guild is still incomplete. Especially nitrite oxidationthe second step of nitrification -is catalyzed by a phylogenetically diverse bacterial group, and only recently bacteria of the phylum Chloroflexi have been identified as thermophilic nitrite-oxidizing bacteria (NOB). Among these, Nitrolancea hollandica was isolated from a laboratory-scale nitrifying bioreactor operated at 35 • C with a high load of ammonium bicarbonate. However, its distribution remains cryptic as very few closely related environmental 16S rRNA gene sequences have been retrieved so far. In this study, we demonstrate how such thermophilic NOB can be enriched using modified mineral media inoculated with samples from a wastewater side-stream reactor operated at 39.5 • C. Distinct cultivation conditions resulted in quick and reproducible high enrichment of two different strains of Nitrolancea, closely related to Nl. hollandica. The same cultivation approach was applied to a complex nitrite-oxidizing pre-enrichment at 42 • C inoculated with biomass from a geothermal spring in the Copahue volcano area in Neuquen, Argentina. Here, an additional distinct representative of the genus Nitrolancea was obtained. This novel species had 16S rRNA and nitrite oxidoreductase alpha subunit (nxrA) gene sequence identities to Nl. hollandica of 98.5% and 97.2%, respectively. A genomic average nucleotide identity between the Argentinian strain and Nl. hollandica of 91.9% indicates that it indeed represents a distinct species. All Nitrolancea cultures formed lancet-shaped cells identical to Nl. hollandica and revealed similar physiological features, including the capability to grow at high nitrite concentrations. Growth was optimal at temperatures of 35-37 • C and was strongly enhanced by ammonium supplementation. Genomic comparisons revealed that the four Nitrolancea strains share 2399 out of 3387 orthologous gene clusters and encode similar key functions. Our results define general growth conditions that enable the selective enrichment of Nitrolancea from artificial and natural environments. In most natural habitats these NOB apparently are of low abundance and their proliferation depends on the balanced presence of nitrite and ammonium, with an optimal incubation temperature of 37 • C.

The phylogenetic relationships of Pyricularia species and species from related genera were established from sequences of the internal transcribed spacer ribosomal RNA gene. Phylogenetic analysis disclosed a consistent correlation with spore morphology. Most Pyricularia species studied, and two species of Dactylaria that have obpyriform conidia, fell within the Magnaporthaceae cluster with high bootstrap support. Pyricularia variabilis was more related to Dactylaria, Tumularia or Ochroconis species than to the Magnaporthaceae. Dactylaria and species of Nakataea, Ochroconis, Pyriculariopsis and Tumularia were distinct from the Magnaporthaceae, and the genus Dactylaria is polyphyletic. The combination of morphological and molecular characters, such as spore morphology and ITS ribosomal DNA sequences data, suggested that conidial shape could be a primary character to distinguish Pyricularia from related genera.

Copahue is an acidic geothermal volcanic region in the northwest corner of Neuquén Province, Argentina. In the area, there are various ponds, pools and hot springs with different temperatures, pH values and levels of anthropogenic influence. In this study, the prokaryotic biodiversity of five representative ponds was studied by using two complementary molecular ecology techniques: phylogenetic analysis of 16S rRNA bacterial and archaeal genes and FISH (or CARD-FISH) for quantitative estimation of biodiversity. The results, supported by multivariate statistical analysis, showed that the biodiversity in Copahue ponds seemed to be determined by temperature. High temperature ponds were dominated by archaea, mainly apparently novel representatives from the orders Sulfolobales and Thermoplasmatales that had no close cultivated relatives. By contrast, moderate temperature ponds were colonised by well-characterised sulphur-oxidising bacteria related to acidic environments, such as other geothermal sites or acid mine drainage, and archaea were absent. By combining the biodiversity results from this study and the reported physicochemical features of Copahue, a preliminary model of the possible biogeochemical interaction was outlined for moderate and high temperature ponds.