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https://www.readbyqxmd.com/read/28545050/prevalence-and-extent-of-heteroresistance-by-next-generation-sequencing-of-multidrug-resistant-tuberculosis
#1
Darwin J Operario, Alexander F Koeppel, Stephen D Turner, Yongde Bao, Suporn Pholwat, Sayera Banu, Suporn Foongladda, Stellah Mpagama, Jean Gratz, Oleg Ogarkov, Svetlana Zhadova, Scott K Heysell, Eric R Houpt
Amplicon-based Next Generation Sequencing (NGS) is an emerging method for Mycobacterium tuberculosis drug susceptibility testing (DST) but has not been well described. We examined 158 clinical multidrug-resistant M. tuberculosis isolates via NGS of 11 resistance-associated gene regions covering 3519 nucleotides. Across these gene regions, complete resistance or heteroresistance (defined as 1%-99% mutation) was present in at least one isolate in 6.3% of loci. The number of isolates with heteroresistance was highest for gyrA codon 94, rpoB codons 526 and 531, and embB codons 306, 372 and 406 (range 11-26% of isolates exhibited heteroresistance)...
2017: PloS One
https://www.readbyqxmd.com/read/28541836/description-of-candidatus-bartonella-fadhilae-n-sp-and-candidatus-bartonella-sanaae-n-sp-bartonellaceae-from-dipodillus-dasyurus-and-sekeetamys-calurus-gerbillinae-from-the-sinai-massif-egypt
#2
Mohammed Alsarraf, Eman M E Mohallal, Ewa J Mierzejewska, Jolanta Behnke-Borowczyk, Renata Welc-Falęciak, Małgorzata Bednarska, Lukasz Dziewit, Samy Zalat, Francis Gilbert, Jerzy M Behnke, Anna Bajer
Bartonella spp. are parasites of mammalian erythrocytes and endothelial cells, transmitted by blood-feeding arthropod ectoparasites. Different species of rodents may constitute the main hosts of Bartonella, including several zoonotic species of Bartonella. The aim of this study was to identify and compare Bartonella species and genotypes isolated from rodent hosts from the South Sinai, Egypt. Prevalence of Bartonella infection was assessed in rodents (837 Acomys dimidiatus, 73 Acomys russatus, 111 Dipodillus dasyurus, and 65 Sekeetamys calurus) trapped in 2000, 2004, 2008, and 2012 in four dry montane wadis around St...
May 25, 2017: Vector Borne and Zoonotic Diseases
https://www.readbyqxmd.com/read/28534230/trueperella-pyogenes-isolated-from-a-brain-abscess-of-an-adult-roebuck-capreolus-capreolus
#3
Jörn-Peter Wickhorst, Abdulwahed Ahmed Hassan, Omar Hashim Sheet, Tobias Eisenberg, Osama Sammra, Mazen Alssahen, Christoph Lämmler, Ellen Prenger-Berninghoff, Michael Zschöck, Markus Timke, Amir Abdulmawjood
The present study was designed to characterize phenotypically and genotypically a Trueperella pyogenes strain isolated from a brain abscess of an adult roebuck (Capreolus capreolus). The species identity could be confirmed by phenotypical investigations, by MALDI-TOF MS analysis, and by sequencing the 16S ribosomal RNA (rRNA) gene, the 16S-23S rRNA intergenic spacer region (ISR); by sequencing the target genes rpoB, gap, and tuf; and by detection of T. pyogenes chaperonin-encoding gene cpn60 with a previously developed loop-mediated isothermal amplification (LAMP) assay...
May 23, 2017: Folia Microbiologica
https://www.readbyqxmd.com/read/28533767/characterization-of-mycobacterium-chelonae-like-strains-by-comparative-genomics
#4
Christiane L Nogueira, Luiz G P de Almeida, Maria C Menendez, Maria J Garcia, Luciano A Digiampietri, Erica Chimara, Margo Cnockaert, Juan C Palomino, Françoise Portaels, Anandi Martin, Peter Vandamme, Sylvia C Leão
Isolates of the Mycobacterium chelonae-M. abscessus complex are subdivided into four clusters (CHI to CHIV) in the INNO-LiPA® Mycobacterium spp DNA strip assay. A considerable phenotypic variability was observed among isolates of the CHII cluster. In this study, we examined the diversity of 26 CHII cluster isolates by phenotypic analysis, drug susceptibility testing, whole genome sequencing and single-gene analysis. Pairwise genome comparisons were performed using several approaches, including average nucleotide identity (ANI) and genome-to-genome distance (GGD) among others...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28533241/arr-cb-a-rifampin-resistance-determinant-found-active-or-cryptic-in-clostridium-bolteae
#5
Jean-Christophe Marvaud, Thierry Lambert
Clostridium bolteae, which belongs to the Clostridium clostridioforme complex is a member of the human gut microbiota. Recent analysis of seven genomes of C. bolteae revealed the presence of an arr-like gene. Among these strains only 90A7 was found to be resistant to rifampin in the absence of alteration in RpoB. Cloning of arr-cb from 90A7 in Escherichia coli combined with directed mutagenesis demonstrated that Arr-cb is functional but that a Q127→R variant present in 90A9 and 90B3 was inactive. qRT-PCR analysis indicated that arr-cb was silent in the four remaining strains due to a defective transcription...
May 22, 2017: Antimicrobial Agents and Chemotherapy
https://www.readbyqxmd.com/read/28533186/delayed-identification-of-acinetobacter-baumannii-during-an-outbreak-owing-to-disrupted-blaoxa-51-like-by-isaba19
#6
Amjad Ahmadi, Himen Salimizand
Early detection of Acinetobacter baumannii, an emerging pathogen in hospital settings, is of interest. The blaOXA-51-like family had been used as a marker to detect A. baumannii. During an infection outbreak, 14 isolates produced a 1.7-kb PCR band instead of 353 bp for this marker. This work sought the reasons behind the increased marker size. Characterisation of isolates was done by API-20NE, gyrB multiplex PCR and 16S-23S rRNA ITS sequencing. The 1.7-kb band generated and the complete blaOXA-51-like variant were sequenced to find the probable integrated element...
May 19, 2017: International Journal of Antimicrobial Agents
https://www.readbyqxmd.com/read/28533123/molecular-characterization-of-caulobacter-crescentus-mutator-strains
#7
Marinalva Martins-Pinheiro, Alice R Oliveira, Alexy O Valencia, Frank S Fernandez-Silva, Larissa G Silva, Carina O Lopes-Kulishev, Valeria C S Italiani, Marilis V Marques, Carlos F Menck, Rodrigo S Galhardo
Mutator strains were identified by screening random Tn5 insertion clones of Caulobacter crescentus. We identified clones with robust increases in mutation rates with Tn5 insertions in the mutY, mutS, mutL and uvrD genes, known to act in mutation-preventing pathways in Escherichia coli. Analysis of mutations in the rpoB gene revealed that in both the parental strain and mismatch repair-deficient mutants, A:T→G:C transitions predominate by a large margin over C:G→T:A. We have also investigated the role of the error-prone polymerase encoded by imuC (dnaE2) in spontaneous mutagenesis, and found that a imuC mutant strain shows mutation rates and sequences comparable to the parental strain...
May 19, 2017: Gene
https://www.readbyqxmd.com/read/28532975/emission-of-extensively-drug-resistant-acinetobacter-baumannii-from-hospital-settings-to-the-natural-environment
#8
M Seruga Music, J Hrenovic, I Goic-Barisic, B Hunjak, D Skoric, T Ivankovic
BACKGROUND: Acinetobacter baumannii is a leading emerging pathogen that is frequently recovered from patients during hospital outbreaks. The role of environmental A. baumannii reservoirs is therefore of great concern worldwide. AIM: To investigate the connection between A. baumannii causing hospital outbreaks and environmental isolates from hospital wastewater, urban sewage and river water as the final natural recipient of wastewaters. METHODS: Clinical isolates from patients with hospital-acquired pneumonia and environmental isolates from water were collected during a two-month monitoring period...
April 11, 2017: Journal of Hospital Infection
https://www.readbyqxmd.com/read/28527793/prevalence-of-non-aureus-staphylococcus-species-causing-intramammary-infections-in-canadian-dairy-herds
#9
Larissa A Z Condas, Jeroen De Buck, Diego B Nobrega, Domonique A Carson, Sohail Naushad, Sarne De Vliegher, Ruth N Zadoks, John R Middleton, Simon Dufour, John P Kastelic, Herman W Barkema
Non-aureus staphylococci (NAS), the microorganisms most frequently isolated from bovine milk worldwide, are a heterogeneous group of numerous species. To establish their importance as a group, the distribution of individual species needs to be determined. In the present study, NAS intramammary infection (IMI) was defined as a milk sample containing ≥1,000 cfu/mL in pure or mixed culture that was obtained from a cohort of cows assembled by the Canadian Bovine Mastitis Research Network. Overall, 6,213 (6.3%) of 98,233 quarter-milk samples from 5,149 cows and 20,305 udder quarters were associated with an NAS IMI...
May 17, 2017: Journal of Dairy Science
https://www.readbyqxmd.com/read/28515453/validation-of-reference-genes-for-the-normalization-of-the-rt-qpcr-gene-expression-of-virulence-genes-of-erwinia-amylovora-in-apple-shoots
#10
Monika Kałużna, Anita Kuras, Joanna Puławska
To study the expression of pathogenicity-related genes in Erwinia amylovora, seven candidate reference genes (ffh, glyA, gyrA, proC, pykA, recA, rpoB) were selected and validated with the following five different mathematic algorithms: geNorm, NormFinder, BestKeeper, the delta CT method and the RefFinder web-based tool. An overall comprehensive ranking output from each of the selected software programs revealed that proC and recA, followed by ffh and pykA, were the most stably expressed genes and can be recommended for the normalization of RT-qPCR data...
May 17, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28514600/evaluating-five-different-loci-rbcl-rpob-rpoc1-matk-and-its-for-dna-barcoding-of-indian-orchids
#11
Iffat Parveen, Hemant Kumar Singh, Saloni Malik, Saurabh Raghuvanshi, Shashi Bhushan Babbar
Orchidaceae, one of the largest families of angiosperms, is represented in India by 1600 species distributed in diverse habitats. Orchids are in high demand due to their beautiful flowers and therapeutic properties. Overexploitation and habitat destruction have made many orchid species endangered. In the absence of effective identification methods, illicit trade of orchids continues unabated. Considering DNA barcoding as a potential identification tool, species discrimination capability of five loci, ITS matK, rbcL, rpoB and rpoC1, was tested in 393 accessions of 94 Indian orchid species belonging to 47 genera, including one listed in Appendix I of CITES and 26 medicinal species...
May 17, 2017: Genome Génome / Conseil National de Recherches Canada
https://www.readbyqxmd.com/read/28513421/clinical-and-bacteriological-characteristics-associated-with-clustering-of-multidrug-resistant-tuberculosis
#12
J-Y J-Y Feng, L G Jarlsberg, K Salcedo, J Rose, M Janes, S-Y G Lin, D H Osmond, K C Jost, M K Soehnlen, J Flood, E A Graviss, E Desmond, P K Moonan, P Nahid, P C Hopewell, M Kato-Maeda
<h2>SETTING:</h2><p>The impact of the genetic characteristics of Mycobacterium tuberculosis on the clustering of multidrug-resistant tuberculosis (MDR-TB) has not been analyzed together with clinical and demographic characteristics.</p><h2>OBJECTIVE:</h2><p>To determine factors associated with genotypic clustering of MDR-TB in a community-basedstudy.</p><h2>DESIGN:</h2><p>We measured the proportion of clustered cases among MDR-TB patients and determined the impact of clinical and demographic characteristics and that of three M...
May 16, 2017: International Journal of Tuberculosis and Lung Disease
https://www.readbyqxmd.com/read/28511895/diagnostic-performance-of-anyplex-ii-mtb-mdr-xdr-for-detection-of-resistance-to-first-and-second-line-drugs-in-mycobacterium-tuberculosis
#13
F Pérez-García, M J Ruiz-Serrano, P López Roa, Fermín Acosta, Laura Pérez-Lago, D García-De-Viedma, E Bouza
PURPOSE: Genotypic methods have considerably improved the diagnosis of multidrug-resistant (MDR) tuberculosis. One of these tests is Anyplex II MTB/MDR/XDR (Anyplex). Our aim was to evaluate the diagnostic performance of this multiplex PCR. METHODS: We conducted our study on 47 MDR tuberculosis and 14 pan-susceptible strains. We evaluated the ability of Anyplex to detect resistance mutations in rpoB (rifampin [RIF]), katG and inhA (isoniazid [INH]), gyrA (fluoroquinolones [FLQ]), and rrs and eis (aminoglycosides [AMG])...
May 13, 2017: Journal of Microbiological Methods
https://www.readbyqxmd.com/read/28507065/mutants-in-the-%C3%AE-subunit-of-the-rna-polymerase-impairing-the-surface-associated-motility-and-virulence-of-acinetobacter-baumannii
#14
María Pérez-Varela, Jordi Corral, Juan Andrés Vallejo, Soraya Rumbo-Feal, Germán Bou, Jesús Aranda, Jordi Barbé
Acinetobacter baumannii is a major cause of antibiotic-resistant nosocomial infections worldwide. In this study, several rifampin-resistant spontaneous mutants obtained from the A. baumannii ATCC 17978 strain were isolated that differed in their point mutations in the rpoB gene, encoding the β-subunit of the RNA polymerase. All mutants harboring amino acid substitutions in positions 522 or 540 of the RpoB protein were impaired in surface-associated motility and had attenuated virulence in the fertility model of Caenorhabditis elegans The transcriptional profile of these mutants included six down-regulated genes encoding proteins homologous to transporters and metabolic enzymes widespread among A...
May 15, 2017: Infection and Immunity
https://www.readbyqxmd.com/read/28502279/evidence-and-molecular-characterization-of-bartonella-spp-and-hemoplasmas-in-neotropical-bats-in-brazil
#15
P Ikeda, M C Seki, A O T Carrasco, L V Rudiak, J M D Miranda, S M M Gonçalves, E G L Hoppe, A C A Albuquerque, M M G Teixeira, C E Passos, K Werther, R Z Machado, M R André
The order Chiroptera is considered the second largest group of mammals in the world, hosting important zoonotic virus and bacteria. Bartonella and hemotropic mycoplasmas are bacteria that parasite different mammals' species, including humans, causing different clinical manifestations. The present work aimed investigating the occurrence and assessing the phylogenetic positioning of Bartonella spp. and Mycoplasma spp. in neotropical bats sampled from Brazil. Between December 2015 and April 2016, 325 blood and/or tissues samples were collected from 162 bats comprising 19 different species sampled in five states of Brazil...
May 15, 2017: Epidemiology and Infection
https://www.readbyqxmd.com/read/28501582/molecular-detection-of-rifampicin-resistance-by-genexpert-%C3%A2-assay-among-treated-and-untreated-pulmonary-tuberculosis-patients-from-khyber-pakhtunkhwa-pakistan
#16
Hazir Rahman, Shakir Ullah Khan, Muhamamd Amjad Khan, Muhammad Qasim, Abdul Jabbar, Sadiq Noor, Zakir Khan, Taj Ali Khan, Mubbashir Hussain, Noor Muhammad, Nawab Ali
OBJECTIVES: Drug-resistant tuberculosis (TB) is an emerging health problem. Rifampicin (RIF) is the major first-line drug against TB. RIF resistance can be used as a marker for the detection of multidrug-resistant TB (MDR-TB). The purpose of this study was to determine the RIF resistance pattern of Mycobacterium tuberculosis complex isolates among treated and untreated patients in Khyber Pakhtunkhwa, Pakistan. METHODS: A total of 349 drug-treated and untreated TB-diagnosed patients were enrolled in this study...
May 10, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/28501448/pseudomonas-versuta-sp-nov-isolated-from-antarctic-soil
#17
Wah Seng See-Too, Sergio Salazar, Robson Ee, Peter Convey, Kok-Gan Chan, Álvaro Peix
In this study we analysed three bacterial strains coded L10.10(T), A4R1.5 and A4R1.12, isolated in the course of a study of quorum-quenching bacteria occurring in Antarctic soil. The 16S rRNA gene sequence was identical in the three strains and showed 99.7% pairwise similarity with respect to the closest related species Pseudomonas weihenstephanensis WS4993(T). Therefore, the three strains were classified within the genus Pseudomonas. Analysis of housekeeping genes (rpoB, rpoD and gyrB) sequences showed similarities of 84-95% with respect to the closest related species of Pseudomonas, confirming its phylogenetic affiliation...
April 18, 2017: Systematic and Applied Microbiology
https://www.readbyqxmd.com/read/28492472/molecular-surveillance-of-cronobacter-spp-isolated-from-a-wide-variety-of-foods-from-44-different-countries-by-sequence-typing-of-16s-rrna-rpob-and-o-antigen-genes
#18
Nancy Miranda, Pratik Banerjee, Steven Simpson, Khalil Kerdahi, Irshad M Sulaiman
Cronobacter spp. are emerging infectious bacteria that can cause acute meningitis and necrotizing enterocolitis in neonatal and immunocompromised individuals. Although this opportunistic human-pathogenic microorganism has been isolated from a wide variety of food and environmental samples, it has been primarily linked to foodborne outbreaks associated with powdered infant formula. The U.S. Food and Drug Administration use the presence of these microbes as one of the criteria to assess food adulteration and to implement regulatory actions...
May 11, 2017: Foods (Basel, Switzerland)
https://www.readbyqxmd.com/read/28487209/molecular-characterisation-of-carbapenemases-in-urban-pigeon-droppings-in-france-and-algeria
#19
Houda Morakchi, Lotfi Loucif, Djamila Gacemi-Kirane, Jean-Marc Rolain
OBJECTIVES: The main objective of this study was to detect the presence of carbapenemase-encoding genes in stool samples of urban pigeons. METHODS: Stool samples were collected from 73 pigeons in two Mediterranean cities, namely Marseille (France) and Annaba (Algeria). Faecal samples were screened by real-time PCR and standard PCR for the presence of carbapenemase-encoding genes. RESULTS: Carbapenem resistance genes were detected in 16 (21...
May 6, 2017: Journal of Global Antimicrobial Resistance
https://www.readbyqxmd.com/read/28485632/mycobacterium-tuberculosis-infection-in-a-domesticated-korean-wild-boar-sus-scrofa-coreanus
#20
Min-Goo Seo, In-Ohk Ouh, Munki Kim, Jienny Lee, Young-Hoan Kim, Jae-Cheul Do, Dongmi Kwak
Tuberculosis, a chronic progressive disease, has been reported in bovine, swine, and primate species. Here, we report the first case of Mycobacterium tuberculosis infection in a Korean wild boar ( Sus scrofa coreanus). The owners this domesticated boar brought it to the Gyeongbuk Veterinary Service Laboratory in Korea after it was found dead and severely emaciated. Demarcated yellowish white nodules were found around the larynx and retropharyngeal lymph node during necropsy. The lungs had diffuse fibrinous pleuritis, severe congestion, and scattered nodules...
May 9, 2017: Journal of Food Protection
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