BACKGROUND: Reliable species identification of cultured isolates is essential in clinical bacteriology. We established a new study algorithm named NOVA - Novel Organism Verification and Analysis to systematically analyze bacterial isolates that cannot be characterized by conventional identification procedures MALDI-TOF MS and partial 16 S rRNA gene sequencing using Whole Genome Sequencing (WGS).
RESULTS: We identified a total of 35 bacterial strains that represent potentially novel species. Corynebacterium sp. (n = 6) and Schaalia sp. (n = 5) were the predominant genera. Two strains each were identified within the genera Anaerococcus, Clostridium, Desulfovibrio, and Peptoniphilus, and one new species was detected within Citrobacter, Dermabacter, Helcococcus, Lancefieldella, Neisseria, Ochrobactrum (Brucella), Paenibacillus, Pantoea, Porphyromonas, Pseudoclavibacter, Pseudomonas, Psychrobacter, Pusillimonas, Rothia, Sneathia, and Tessaracoccus. Twenty-seven of 35 strains were isolated from deep tissue specimens or blood cultures. Seven out of 35 isolated strains identified were clinically relevant. In addition, 26 bacterial strains that could only be identified at the species level using WGS analysis, were mainly organisms that have been identified/classified very recently.
CONCLUSIONS: Our new algorithm proved to be a powerful tool for detection and identification of novel bacterial organisms. Publicly available clinical and genomic data may help to better understand their clinical and ecological role. Our identification of 35 novel strains, 7 of which appear to be clinically relevant, shows the wide range of undescribed pathogens yet to define.

In the Pseudomonas aeruginosa type strain PA14, 40 genes are known to encode for diguanylate cyclases (DGCs) and/or phosphodiesterases (PDEs), which modulate the intracellular pool of the nucleotide second messenger c-di-GMP. While in general, high levels of c-di-GMP drive the switch from highly motile phenotypes towards a sessile lifestyle, the different c-di-GMP modulating enzymes are responsible for smaller and in parts nonoverlapping phenotypes. In this study, we sought to utilize previously recorded P. aeruginosa gene expression datasets on 414 clinical isolates to uncover transcriptional changes as a result of a high expression of genes encoding DGCs. This approach might provide a unique opportunity to bypass the problem that for many c-di-GMP modulating enzymes it is not known under which conditions their expression is activated. However, while we demonstrate that the selection of subgroups of clinical isolates with high versus low expression of sigma factor encoding genes served the identification of their downstream regulons, we were unable to confirm the predicted DGC regulons, because the high c-di-GMP associated phenotypes were rapidly lost in the clinical isolates,. Further studies are needed to determine the specific mechanisms underlying the loss of cyclase activity upon prolonged cultivation of clinical P. aeruginosa isolates.

In a multicenter study, we determined a prevalence rate of 4% for azole-resistant Aspergillus fumigatus in Taiwan. Resistance emerged mainly from the environment (TR34/L98H, TR34/L98H/S297T/F495I, and TR46/Y121F/T289A mutations) but occasionally during azole treatment. A high mortality rate observed for azole-resistant aspergillosis necessitates diagnostic stewardship in healthcare and antifungal stewardship in the environment.

UNASSIGNED: Multidrug resistant Staphylococcus aureus in clinical and environmental samples is a global problem. Data comparing antibiogram of bacteria from these two sources in Nigeria is scarce. Therefore, this study compares antibiogram of isolates from both sources from Dutsin-Ma, Katsina State, Nigeria.
UNASSIGNED: A total of 120 and 150 clinical and aquatic samples respectively were collected for a five months period. Samples were analyzed for isolation of S. aureus using mannitol salt agar. Bacteria identification were carried out using standard biochemical characterization. Antibiogram of the isolates were determined using disc diffusion methods and comparison with Clinical Laboratory Standard Institute (CLSI)\'s Standard.
UNASSIGNED: A total of 120 and 45 S. aureus were isolated from both clinical and aquatic samples respectively. Highest (100.0%) resistance to cloxacillin was observed among isolates from each source. Clinical and aquatic isolates showed least resistance of 20.0% and 48.0% respectively to gentamicin. All isolated S. aureus (165) from this studies were multidrug resistant with different antibiotic resistant pattern.
UNASSIGNED: This study revealed that multidrug resistance strains of S. aureus can be isolated from both clinical and drinking water sources, hence, a public health significance that calls for urgent attention by clinicians and public health workers.

During a Phase 2b study with SYN-004 (ribaxamase) for prevention of Clostridium difficile infection (CDI) conducted in North America and Eastern Europe, 45 C. difficile isolates from subjects with laboratory-confirmed CDI and or colonized with C. difficile were collected and characterized. Several C. difficile PCR ribotypes, including 027 and 198, were identified.

UNASSIGNED: Acinetobacterb aumannii (A. baumannii) is an important pathogen in health care associated infections. Quinolone resistance has emerged in this pathogen.
UNASSIGNED: The aim of the present study was to determine the presence of mutations of gyrA gene and parC genes by Restriction Fragment Length Polymorphism Polymerase Chain Reaction (RFLP-PCR) among clinical isolates of A. baumanii.
UNASSIGNED: The study was carried out on 140 clinical isolates of A. baumannii. The isolates were subjected to molecular study of mutations of gyrA gene and parC genes by RFLP-PCR beside determination of Minimal Inhibitory Concentration (MIC) by macro dilution tube method.
UNASSIGNED: The isolates of A. baumannii were resistant to ciprofloxacine and levofloxacin at MIC >4 µg/ml. The most isolates had MIC >128 µg/ml (42.3%). All resistant strains to ciprofloxacin of A. baumannii had mutations in gyrA and parC. The most frequent mutations were combined mutations in both genes (85.5%) and 5% had single mutation either in gyrA or parC. The most frequently combined mutations were associated with MIC >128 µg/ml (42.3%).
UNASSIGNED: From this study we can conclude that resistance to ciprofloxacin was common in clinical isolates of A. baumannii. The most frequent mutations were present in gyrA and parC. However, mutations in parC alone were not uncommon. Further large scale studies are required to elucidate the resistance pattern of A. baumannii and its molecular mechanisms.

OBJECTIVE: Typhoid and paratyphoid fever continue to be important causes of illness and death in parts of Asia, being associated with poor sanitation and consumption of unsafe food and water. Antimicrobial resistance has emerged to traditional first-line drugs, namely, the fluoroquinolones, as well as to third-generation cephalosporins, posing challenges to treatment. Azithromycin has proven to be an effective alternative for treatment of uncomplicated typhoid fever. The purpose of this study was to determine the antimicrobial susceptibility, clinical outcome and serotype distribution pattern of clinical isolates belonging to Salmonella enterica subspecies enterica.
METHODS: All clinical isolates of S. enterica obtained from blood, sterile body fluids, as well as stool and urine samples at Amrita Institute of Medical Sciences and Research Centre, Kerala, India, between August 2011 and July 2013 were included in the study and processed based on standard microbiology protocols.
RESULTS: A total of 118 isolates of Salmonella were obtained during the study period. Out of these, 79 were of S. Typhi (66.95%), followed by isolates of S. Paratyphi A (22; 18.64%) and S. Typhimurium 12 (10.17%). Five isolates could not be identified further. There was 100% susceptibility to ceftriaxone in all S. enterica subspecies. Ciprofloxacin susceptibility was 32.91% for S. Typhi and 40.90% for S. Paratyphi A as determined by the disk diffusion method. The susceptibility profile of S. Typhi isolates to different antimicrobials was as follows: chloramphenicol (94.93%), ampicillin (77.21%), cotrimoxazole (75.94%) and azithromycin (78.48%). For S. Typhi, the minimum inhibitory concentration (MIC) of ciprofloxacin required to inhibit the growth of 50% of organisms was 0.5 μg/mL (intermediate) and MIC required to inhibit the growth of 90% of organisms was 1 μg/mL (resistant). S. Typhimurium was 100% susceptible to cotrimoxazole, ampicillin, ceftriaxone, chloramphenicol, ofloxacin and azithromycin. Susceptibility to ciprofloxacin was 66.66%. Patients from whom S. Typhimurium was isolated had comorbidities with documented risk. Of the 118 patients, 3 expired. Two had typhoid fever and were in sepsis at admission. One had S. Typhimurium and was suffering from multiple myeloma.
CONCLUSIONS: S. Typhi was the predominant isolate. All isolates were susceptible to ceftriaxone. Chloramphenicol susceptibility was >90%. No multidrug-resistant Salmonella strains were isolated. Susceptibility to ciprofloxacin for S. Typhi was 33%. Recovery rate was 97%.

The present study reports a simple and robust method for synthesis of silver and gold nanoparticles using Coleus forskohlii root extract as reducing and stabilizing agent. Stable silver nanoparticles (AgNPs) and gold nanopoarticles (AuNPs) were formed on treatment of an aqueous silver nitrate (AgNO3) and chloroauric acid (HAuCl4) solutions with the root extract. The nanoparticles obtained were characterized by UV-Visible spectroscopy, Transmission electron microscopy (TEM), X-ray diffraction (XRD) and Fourier-transform infrared spectroscopy (FT-IR). UV-Vis and TEM analysis indicate that with higher quantities of root extract, the interaction is enhanced leading to size reduction of spherical metal nanoparticles. XRD confirms face-centered cubic phase and the diffraction peaks can be attributed to (111), (200), (222) and (311) planes for these nanoparticles. These synthesized Ag and Au nanoparticles were found to exhibit excellent bactericidal activity against clinically isolated selected pathogens such as Escherichia coli (E. coli), Pseudomonas aeruginosa (P. aeruginosa) and Staphylococcus aureus (S. aureus). The synthesized AgNPs were also found to function as an efficient green catalyst in the reduction of anthropogenic pollutant 4-nitrophenol (4-NP) to 4-aminophenol (4-AP) by sodium borohydride, which was apparent from the periodical color change from bright yellow to colorless, after the addition of AgNPs.