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Molecular microbiology

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https://www.readbyqxmd.com/read/28334157/overview-of-freshwater-microbial-eukaryotes-diversity-a-first-analysis-of-publicly-available-metabarcoding-data
#1
Didier Debroas, Isabelle Domaizon, Jean-Francois Humbert, Ludwig Jardillier, Cécile Lepère, Anne Oudart, Najwa Taïb
Although they are widespread, diverse, and involved in biogeochemical cycles, microbial eukaryotes attract less attention than their prokaryotic counterparts in environmental microbiology. In this study, we used publicly available 18S barcoding data to define biases that may limit such analyses and to gain an overview of the planktonic microbial eukaryotic diversity in freshwater ecosystems. The richness of the microbial eukaryotes was estimated to 100,798 operational taxonomic units (OTUs) delineating 1267 clusters or phylogenetic units (PUs i...
March 1, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28334088/relapse-re-infection-and-mixed-infections-in-tuberculosis-disease
#2
Amanda McIvor, Hendrik Koornhof, Bavesh Davandra Kana
Tuberculosis (TB) disease can be characterized by genotypic and phenotypic complexity in Mycobacterium tuberculosis bacilli within a single patient. This microbiological heterogeneity has become an area of intense study due its perceived importance in drug tolerance, drug resistance and as a surrogate measure of transmission rates. This review presents a descriptive analysis of research describing the prevalence of mixed strain TB infections in geographically distinct locations. Despite significant variation in disease burden and a rampant HIV-TB co-epidemic, there was no difference in the prevalence range of mixed infections reported in African countries when compared to the rest of the world...
February 18, 2017: Pathogens and Disease
https://www.readbyqxmd.com/read/28327156/mycobacterium-goodii-endocarditis-following-mitral-valve-ring-annuloplasty
#3
Rohan B Parikh, Matthew Grant
BACKGROUND: Mycobacterium goodii is an infrequent human pathogen which has been implicated in prosthesis related infections and penetrating injuries. It is often initially misidentified as a gram-positive rod by clinical microbiologic laboratories and should be considered in the differential diagnosis. CASE PRESENTATION: We describe here the second reported case of M. goodii endocarditis. Species level identification was performed by 16S rDNA (ribosomal deoxyribonucleic acid) gene sequencing...
March 21, 2017: Annals of Clinical Microbiology and Antimicrobials
https://www.readbyqxmd.com/read/28323243/proteomics-of-facs-sorted-heterogeneous-corynebacterium-glutamicum-populations
#4
Andreas Harst, Stefan P Albaum, Tanja Bojarzyn, Christian Trötschel, Ansgar Poetsch
The metabolic status of individual cells in microbial cultures can differ, being relevant for biotechnology, environmental and medical microbiology. However, it is hardly understood in molecular detail due to limitations of current analytical tools. Here, we demonstrate that FACS in combination with proteomics can be used to sort and analyze cell populations based on their metabolic state. A previously established GFP reporter system was used to detect and sort single Corynebacterium glutamicum cells based on the concentration of branched chain amino acids (BCAA) using FACS...
March 17, 2017: Journal of Proteomics
https://www.readbyqxmd.com/read/28318535/organism-and-microbiome-analysis-techniques-and-implications-for-chronic-rhinosinusitis
#5
REVIEW
Ashleigh A Halderman, Andrew P Lane
Modern advances in DNA sequencing have allowed for the development of culture-independent techniques with application to infectious and inflammatory conditions, such as rhinosinusitis. Although paradigm-changing discoveries have resulted from molecular microbiologic methods for a number of diseases, insights provided into the role of bacteria in chronic rhinosinusitis have yet to be fully understood to the point of impacting clinical diagnosis and management. As culture-independent techniques continue to evolve and become more refined, it is likely that a better understanding will emerge of how the microbiome influences chronic rhinosinusitis pathogenesis and response to therapy...
March 16, 2017: Otolaryngologic Clinics of North America
https://www.readbyqxmd.com/read/28317802/port-site-infections-by-nontuberculous-mycobacterium-a-retrospective-clinico-microbiological-study
#6
Roumi Ghosh, Soumen Das, Asmita De, Harish Kela, Makhan Lal Saha, Prasanta Kumar Maiti
BACKGROUND: Port-site infection (PSI) is a prevailing, chronic, nagging, treatment refractory complication of laparoscopic surgery (LS). It neutralizes the advantages of minimally invasive surgery and increases morbidity, treatment cost of patient, leading to loss of confidence on operating surgeon. PSIs are preventable with appropriate preoperative, intraoperative, and postoperative measures. Atypical mycobacterium is most commonly associated with nonhealing postlaparoscopic wound infections, causing outbreaks or sporadic cases worldwide...
January 2017: International Journal of Mycobacteriology
https://www.readbyqxmd.com/read/28316631/potential-impact-of-rapid-blood-culture-testing-for-gram-positive-bacteremia-in-japan-with-the-verigene-gram-positive-blood-culture-test
#7
Ken Kikuchi, Mari Matsuda, Shigekazu Iguchi, Tomonori Mizutani, Keiichi Hiramatsu, Michiru Tega-Ishii, Kaori Sansaka, Kenta Negishi, Kimie Shimada, Jun Umemura, Shigeyuki Notake, Hideji Yanagisawa, Hiroshi Takahashi, Reiko Yabusaki, Hideki Araoka, Akiko Yoneyama
Background. Early detection of Gram-positive bacteremia and timely appropriate antimicrobial therapy are required for decreasing patient mortality. The purpose of our study was to evaluate the performance of the Verigene Gram-positive blood culture assay (BC-GP) in two special healthcare settings and determine the potential impact of rapid blood culture testing for Gram-positive bacteremia within the Japanese healthcare delivery system. Furthermore, the study included simulated blood cultures, which included a library of well-characterized methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE) isolates reflecting different geographical regions in Japan...
2017: Canadian Journal of Infectious Diseases & Medical Microbiology
https://www.readbyqxmd.com/read/28303130/new-approaches-on-quantification-of-campylobacter-jejuni-in-poultry-samples-the-use-of-digital-pcr-and-real-time-pcr-against-the-iso-standard-plate-count-method
#8
Bojan Papić, Mateja Pate, Urška Henigman, Urška Zajc, Igor Gruntar, Majda Biasizzo, Matjaž Ocepek, Darja Kušar
Campylobacteriosis is the most frequently reported bacterial food-borne illness in the European Union and contaminated broiler meat is considered the most important source of infection in humans. The aim of the present study was to evaluate real-time PCR (qPCR) and digital PCR (dPCR) for quantification of Campylobacter jejuni in 75 broiler neck-skin samples collected from a poultry slaughterhouse, and to compare them with the ISO 10272-2 standard plate count method. For qPCR standard curve, C. jejuni-negative neck-skin samples were spiked with C...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28302076/uropathogenic-escherichia-coli-pathogenicity-islands-and-other-expec-virulence-genes-may-contribute-to-the-genome-variability-of-enteroinvasive-e-coli
#9
Laís Cristina da Silva, Ana Carolina de Mello Santos, Rosa Maria Silva
BACKGROUND: Enteroinvasive Escherichia coli (EIEC) may be the causative agent of part of those million cases of diarrhea illness reported worldwide every year and attributable to Shigella. That is because both enteropathogens have many common characteristics that difficult their identification either by traditional microbiological methods or by molecular tools used in the clinical laboratory settings. While Shigella has been extensively studied, EIEC remains barely characterized at the molecular level...
March 16, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28300642/distribution-and-phylogeny-of-brachyspira-spp-in-human-intestinal-spirochetosis-revealed-by-fish-and-16s-rrna-gene-analysis
#10
Pablo Rojas, Annett Petrich, Julia Schulze, Alexandra Wiessner, Christoph Loddenkemper, Hans-Jörg Epple, William Sterlacci, Michael Vieth, Judith Kikhney, Annette Moter
During six years as National Reference Laboratory for Spirochetes we investigated 149 intestinal biopsies from 91 patients, which were histopathologically diagnosed with human intestinal spirochetosis (HIS), using fluorescence in situ hybridization (FISH) combined with 16S rRNA gene PCR and sequencing. Aim of this study was to complement histopathological findings with FISH and PCR for definite diagnosis and species identification of the causative pathogens. HIS is characterized by colonization of the colonic mucosa of the human distal intestinal tract by Brachyspira spp...
March 11, 2017: Anaerobe
https://www.readbyqxmd.com/read/28300153/brucella-spp-of-amphibians-comprise-genomically-diverse-motile-strains-competent-for-replication-in-macrophages-and-survival-in-mammalian-hosts
#11
Sascha Al Dahouk, Stephan Köhler, Alessandra Occhialini, María Pilar Jiménez de Bagüés, Jens Andre Hammerl, Tobias Eisenberg, Gilles Vergnaud, Axel Cloeckaert, Michel S Zygmunt, Adrian M Whatmore, Falk Melzer, Kevin P Drees, Jeffrey T Foster, Alice R Wattam, Holger C Scholz
Twenty-one small Gram-negative motile coccobacilli were isolated from 15 systemically diseased African bullfrogs (Pyxicephalus edulis), and were initially identified as Ochrobactrum anthropi by standard microbiological identification systems. Phylogenetic reconstructions using combined molecular analyses and comparative whole genome analysis of the most diverse of the bullfrog strains verified affiliation with the genus Brucella and placed the isolates in a cluster containing B. inopinata and the other non-classical Brucella species but also revealed significant genetic differences within the group...
March 16, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28287010/diagnosis-and-management-of-pneumocystis-jirovecii-infection
#12
P Lewis White, Matthijs Backx, Rosemary A Barnes
Pneumocystis jirovecii is a ubiquitous fungus, which causes pneumonia in humans. Diagnosis was hampered by the inability to culture the organism, and based on microscopic examination of respiratory samples or clinical presentation. New assays can assist in the diagnosis and even aid with the emergence of resistant infections. Areas Covered: This manuscript will provide background information on Pneumocystis pneumonia (PcP). Diagnosis, from radiological to non-microbiological (e.g. Lactate dehydrogenase) and microbiological investigations (Microscopy, PCR, β-D-Glucan) will be discussed...
March 13, 2017: Expert Review of Anti-infective Therapy
https://www.readbyqxmd.com/read/28285908/are-cdi-systems-multicolored-facultative-helping-greenbeards
#13
REVIEW
Elizabeth S Danka, Erin C Garcia, Peggy A Cotter
Competitive and cooperative interactions between organisms, including bacteria, can significantly impact the composition of a community and the fitness of its members, as well as the fitness of their hosts when communities are living on or within other organisms. Understanding the underlying mechanisms is critical to the development of strategies to control microbiological communities that impact animal and plant health and also for understanding the evolution of social behaviors, which has been challenging for evolutionary biologists...
March 9, 2017: Trends in Microbiology
https://www.readbyqxmd.com/read/28283525/molecular-viability-testing-of-uv-inactivated-bacteria
#14
Kris M Weigel, Felicia K Nguyen, Moira R Kearney, John S Meschke, Gerard A Cangelosi
The polymerase chain reaction (PCR) is effective at detecting bacterial DNA in samples, but it is unable to differentiate viable bacteria from inactivated cells or free DNA fragments. New PCR-based analytical strategies have been developed to address this limitation. Molecular viability testing (MVT) correlates bacterial viability with the ability to rapidly synthesize species-specific ribosomal RNA precursor (pre-rRNA) in response to brief nutritional stimulation. Previous studies demonstrated that MVT can assess bacterial inactivation by chlorine, serum, and low-temperature pasteurization...
March 10, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28283005/-comparison-of-maldi-tof-and-16s-rrna-methods-in-identification-of-viridans-group-streptococci
#15
Serap Süzük Yıldız, Banu Kaşkatepe, Salih Altınok, Mustafa Çetin, Alper Karagöz, Sümeyra Savaş
Accurate identification of viridans group streptococci (VGS) frequently encountered as a causative agent of infective endocarditis is always a challenge for the clinical microbiology laboratory. Clinical microbiology laboratories generally use semi automatic/full automatic systems, molecular methods and also conventional methods for the identification of these bacteria. There are recent published studies that have used MALDI-TOF (Matrix Assisted Laser Ionization Mass Spectrometry-Time of Flight) systems in the identification of VGS...
January 2017: Mikrobiyoloji Bülteni
https://www.readbyqxmd.com/read/28275072/strategies-for-optimizing-the-diagnostic-predictive-value-of-clostridium-difficile-molecular-diagnostics
#16
Larry K Kociolek
Because nucleic acid amplification tests (NAATs) do not distinguish Clostridium difficile infection (CDI) and asymptomatic C. difficile carriage, the diagnostic predictive value of NAATs is limited when used in patients with low probability of CDI. In this issue of the Journal of Clinical Microbiology, Truong et al. report significant reductions in hospital-onset CDI and oral vancomycin utilization at their institution following implementation of a novel intervention that leveraged their clinical bioinformatics resources to prevent C...
March 8, 2017: Journal of Clinical Microbiology
https://www.readbyqxmd.com/read/28268197/microbial-invasion-of-the-amniotic-cavity-in-mid-trimester-pregnancies-using-molecular-microbiology
#17
Shelley Rowlands, Jennifer A Danielewski, Sepehr N Tabrizi, Susan P Walker, Suzanne M Garland
OBJECTIVE: To determine the frequency of microbial invasion of the amniotic cavity in the midtrimester of pregnancy in patients undergoing amniocentesis for clinical indications. STUDY DESIGN: Prospective investigation of the amniotic fluid of 344 asymptomatic women recruited in mid pregnancy for the presence of microbial DNA. Amniotic samples obtained at time of amniocentesis for genetic testing on women between 15-22 weeks gestation were tested specifically for the presence of Ureaplasma urealyticum, Ureaplasma parvum, Mycoplasma hominis and Mycoplasma genitalium, as well as for other bacteria and fungi using broad-range PCR only...
March 4, 2017: American Journal of Obstetrics and Gynecology
https://www.readbyqxmd.com/read/28261050/membrane-active-antimicrobial-peptides-translating-mechanistic-insights-to-design
#18
REVIEW
Jianguo Li, Jun-Jie Koh, Shouping Liu, Rajamani Lakshminarayanan, Chandra S Verma, Roger W Beuerman
Antimicrobial peptides (AMPs) are promising next generation antibiotics that hold great potential for combating bacterial resistance. AMPs can be both bacteriostatic and bactericidal, induce rapid killing and display a lower propensity to develop resistance than do conventional antibiotics. Despite significant progress in the past 30 years, no peptide antibiotic has reached the clinic yet. Poor understanding of the action mechanisms and lack of rational design principles have been the two major obstacles that have slowed progress...
2017: Frontiers in Neuroscience
https://www.readbyqxmd.com/read/28260753/molecular-characterization-of-methicillin-resistance-staphylococcus-aureus-mrsa-from-different-tertiary-care-hospitals-in-bangladesh
#19
S Roy, T K Barman, M A Hossain, S K Paul, N Haque, S Ahmed, S A Nasreen, M S Hossain, S R Sarkar, N Kubayashi, N Laskar
Infections caused by Staphylococcus aureus were treated by methicillin, but about 95% of S. aureus has been resistance to methicillin, both in the community and hospitals and are increasing day by day. MRSA produces altered penicillin binding protein, PBP2a, due to the expression of mecA gene. Some strains of both the MRSA and MSSA carry PVL gene. This cross sectional observational study was conducted to detect the molecular-characterization of methicillin resistant Staphylococcus aureus (MRSA) and carried out in the Department of Microbiology, Mymensingh Medical College from July 2014 to December 2015...
January 2017: Mymensingh Medical Journal: MMJ
https://www.readbyqxmd.com/read/28260537/characterisation-of-invasive-clinical-haemophilus-influenzae-isolates-in-queensland-australia-using-whole-genome-sequencing
#20
M Staples, R M A Graham, A V Jennison
Haemophilus influenzae is an important aetiological organism of both adult and child respiratory disease. The number of non-typeable (NTHi) invasive H. influenzae isolates referred to the Queensland (QLD) Public Health Microbiology laboratory has increased notably year-by-year. In this study we used whole-genome sequencing to molecularly characterise 100 referred invasive H. influenzae, including 74 NTHi isolates over a 15-year period, observing the carriage of capsular and putative virulence genes, including the major adhesins, antimicrobial resistance genes and population diversity...
March 6, 2017: Epidemiology and Infection
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