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https://www.readbyqxmd.com/read/28649236/the-validation-and-implications-of-using-whole-genome-sequencing-as-a-replacement-for-traditional-serotyping-for-a-national-salmonella-reference-laboratory
#1
Chris A Yachison, Catherine Yoshida, James Robertson, John H E Nash, Peter Kruczkiewicz, Eduardo N Taboada, Matthew Walker, Aleisha Reimer, Sara Christianson, Anil Nichani, Celine Nadon
Salmonella serotyping remains the gold-standard tool for the classification of Salmonella isolates and forms the basis of Canada's national surveillance program for this priority foodborne pathogen. Public health officials have been increasingly looking toward whole genome sequencing (WGS) to provide a large set of data from which all the relevant information about an isolate can be mined. However, rigorous validation and careful consideration of potential implications in the replacement of traditional surveillance methodologies with WGS data analysis tools is needed...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28646667/prevalence-and-characterization-of-extended-spectrum-%C3%AE-lactamase-esbl-and-ampc-%C3%AE-lactamase-producing-enterobacteriaceae-in-fresh-pork-meat-at-processing-level-in-germany
#2
Franziska Schill, Amir Abdulmawjood, Günter Klein, Felix Reich
ESBL or AmpC β-lactamase producing Enterobacteriaceae is an increasing concern in human medicine. A distribution via the food chain is discussed, but less is known about these bacteria on fresh pork meat. The aim of this study was to investigate the prevalence of ESBL/AmpC Enterobacteriaceae bacteria in fresh pork meat at processing level in Germany. The analysis comprised microbiological hygiene parameters and further pheno- and genotypical characterization of ESBL/AmpC isolates. The examination included three pools of meat and one corresponding meat juice sample from each of the tested pork meat batches (n=63)...
June 15, 2017: International Journal of Food Microbiology
https://www.readbyqxmd.com/read/28645183/in-defense-of-bacillus-thuringiensis-the-safest-and-most-successful-microbial-insecticide-available-to-humanity-a-response-to-efsa
#3
Ben Raymond, Brian A Federici
The Bacillus cereus group contains vertebrate pathogens such as Bacillus anthracis and Bacillus cereus and the invertebrate pathogen Bacillus thuringiensis. Microbial biopesticides based on B. thuringiensis (Bt) are widely recognized as being among the safest and least environmentally damaging insecticidal products available. Nevertheless, a recent food poisoning incident prompted a European Food Safety Authority review which argued that B. thuringiensis poses a health risk equivalent to B. cereus, a causative agent of diarrhoea...
June 22, 2017: FEMS Microbiology Ecology
https://www.readbyqxmd.com/read/28644413/clonal-diversity-of-esbl-producing-escherichia-coli-isolated-from-environmental-human-and-food-samples
#4
Elena Ojer-Usoz, David González, Ana Isabel Vitas
This study presents a comprehensive approach of a clonal diversity analysis of 448 Extended-spectrum β-lactamase (ESBL)-producing E. coli isolated from environmental, human and food samples in Spain. The phenotypic confirmation of ESBL production was performed by disc diffusion and microdilution methods, while Polymerase Chain Reaction (PCR) and sequencing were used for the molecular characterization of β-lactamase genes (blaCTX-M, blaSHV, blaTEM, blaOXA). Clonal relationship of isolates was determined by multi-locus sequence typing (MLST)...
June 23, 2017: International Journal of Environmental Research and Public Health
https://www.readbyqxmd.com/read/28643488/multidrug-resistance-mechanisms-of-carbapenem-resistant-klebsiella-pneumoniae-strains-isolated-in-chongqing-china
#5
Jinrong Yan, Shuli Pu, Xiaojiong Jia, Xiuyu Xu, Shuangshuang Yang, Jing Shi, Shan Sun, Liping Zhang
BACKGROUND: Carbapenem-resistant Klebsiella pneumoniae (CRKP) is considered a serious global threat. However, little is known regarding the multidrug resistance (MDR) mechanisms of CRKP. This study investigated the phenotypes and MDR mechanisms of CRKP and identified their clonal characteristics. METHODS: PCR and sequencing were utilized to identify antibiotic resistance determinants. Integron gene cassette arrays were determined by restriction fragment length polymorphism (RFLP) analysis...
September 2017: Annals of Laboratory Medicine
https://www.readbyqxmd.com/read/28642764/xylella-fastidiosa-host-range-and-advance-in-molecular-identification-techniques
#6
REVIEW
Paolo Baldi, Nicola La Porta
In the never ending struggle against plant pathogenic bacteria, a major goal is the early identification and classification of infecting microorganisms. Xylella fastidiosa, a Gram-negative bacterium belonging to the family Xanthmonadaceae, is no exception as this pathogen showed a broad range of vectors and host plants, many of which may carry the pathogen for a long time without showing any symptom. Till the last years, most of the diseases caused by X. fastidiosa have been reported from North and South America, but recently a widespread infection of olive quick decline syndrome caused by this fastidious pathogen appeared in Apulia (south-eastern Italy), and several cases of X...
2017: Frontiers in Plant Science
https://www.readbyqxmd.com/read/28642756/high-prevalence-of-macrolide-resistance-and-molecular-characterization-of-streptococcus-pyogenes-isolates-circulating-in-china-from-2009-to-2016
#7
Binghuai Lu, Yujie Fang, Yanyan Fan, Xingchun Chen, Junrui Wang, Ji Zeng, Yi Li, Zhijun Zhang, Lei Huang, Hongxia Li, Dong Li, Fengxia Zhu, Yanchao Cui, Duochun Wang
Streptococcus pyogenes, or group A Streptococcus, is a pathogen responsible for a wide range of clinical manifestations, from mild skin and soft tissue infections and pharyngitis to severe diseases. Its epidemiological characteristics should be comprehensively under surveillance for regulating the national prevention and treatment practice. Herein, a total of 140 S. pyogenes, including 38 invasive and 102 noninvasive isolates, were collected from infected patients in 10 tertiary general hospitals from 7 cities/provinces in China during the years 2009-2016...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28642752/a-comprehensive-epidemiological-research-for-clinical-vibrio-parahaemolyticus-in-shanghai
#8
Huan Li, Rong Tang, Yang Lou, Zelin Cui, Wenjing Chen, Qing Hong, Zhaohuan Zhang, Pradeep K Malakar, Yingjie Pan, Yong Zhao
Vibrio parahaemolyticus is one of the most important pathogen for seafood-borne gastroenteritis in Shanghai and the rest of the world. A total of 42 V. parahaemolyticus strains were isolated from 1900 fecal specimens collected from patients in Shanghai hospital presenting from January 2014 to December 2015. All isolates were evaluated for potential virulence factors [tdh, trh, and type three secretion system (T3SS) genes], typed using multilocus sequence typing (MLST) and screened for antimicrobial resistance phenotype and genotype...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28636666/molecular-and-microbiological-report-of-a-hospital-outbreak-of-ndm-1-carrying-enterobacteriaceae-in-mexico
#9
Paola Bocanegra-Ibarias, Elvira Garza-González, Rayo Morfín-Otero, Humberto Barrios, Licet Villarreal-Treviño, Eduardo Rodríguez-Noriega, Ulises Garza-Ramos, Santiago Petersen-Morfin, Jesus Silva-Sanchez
OBJECTIVES: To characterize the microbiological, molecular and epidemiological data of an outbreak of carbapenem-resistant Enterobacteriaceae (CRE) in a tertiary-care hospital in Mexico. METHODS: From September 2014 to July 2015, all CRE clinical isolates recovered during an outbreak in the Hospital Civil "Fray Antonio Alcalde" in Jalisco, Mexico were screened for antimicrobial susceptibility, carbapenemase production, carbapenemase-encoding genes, and plasmid profiles...
2017: PloS One
https://www.readbyqxmd.com/read/28633450/comparative-genomics-of-all-three-campylobacter-sputorum-biovars-and-a-novel-cattle-associated-c-sputorum-clade
#10
William G Miller, Emma Yee, Mary H Chapman, James L Bono
Campylobacter sputorum is a non-thermotolerant campylobacter that is primarily isolated from food animals such as cattle and sheep. C. sputorum is also infrequently associated with human illness. Based on catalase and urease activity, three biovars are currently recognized within C. sputorum: bv. sputorum (catalase negative, urease negative), bv. fecalis (catalase positive, urease negative), and bv. paraureolyticus (catalase negative, urease positive). A multi-locus sequence typing (MLST) method was recently constructed for C...
June 19, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28629366/molecular-characterization-of-clinical-imp-producing-klebsiella-pneumoniae-isolates-from-a-chinese-tertiary-hospital
#11
Kaisheng Lai, Yanning Ma, Ling Guo, Jingna An, Liyan Ye, Jiyong Yang
BACKGROUND: IMP-producing Klebsiella pneumoniae (IMPKpn) exhibits sporadic prevalence in China. The mechanisms related to the spread of IMPKpn remain unclear. METHODS: Carbapenem non-susceptible K. pneumoniae isolates were collected from our hospital. The genetic relatedness, antimicrobial susceptibility, as well as sequence types (ST) were analyzed by pulsed-field gel electrophoresis (PFGE), VITEK 2 AST test Kit, and multilocus sequence typing (MLST), respectively...
June 19, 2017: Annals of Clinical Microbiology and Antimicrobials
https://www.readbyqxmd.com/read/28627467/time-to-review-the-gold-standard-for-genotyping-vancomycin-resistant-enterococci-in-epidemiology-comparing-whole-genome-sequencing-with-pfge-and-mlst-in-three-suspected-outbreaks-in-sweden-during-2013-2015
#12
Birgitta Lytsy, Lars Engstrand, Åke Gustafsson, Rene Kaden
Vancomycin-resistant enterococci (VRE) are a challenge to the health-care system regarding transmission rate and treatment of infections. VRE outbreaks have to be controlled from the first cases which means that appropriate and sensitive genotyping methods are needed. The aim of this study was to investigate the applicability of whole genome sequencing based analysis compared to Pulsed-Field Gel Electrophoresis (PFGE) and Multi-Locus Sequence Typing (MLST) in epidemiological investigations as well as the development of a user friendly method for daily laboratory use...
June 15, 2017: Infection, Genetics and Evolution
https://www.readbyqxmd.com/read/28625989/rapid-high-throughput-identification-of-anthrax-causing-and-emetic-bacillus-cereus-group-genome-assemblies-using-btyper-a-computational-tool-for-virulence-based-classification-of-bacillus-cereus-group-isolates-using-nucleotide-sequencing-data
#13
Laura M Carroll, Jasna Kovac, Rachel A Miller, Martin Wiedmann
The Bacillus cereus group comprises nine species, several of which are pathogenic. Differentiating between isolates that may cause disease and those that do not is a matter of public health and economic importance, but can be particularly challenging due to the high genomic similarity of the group. To this end, we have developed BTyper, a computational tool that employs a combination of (i) virulence gene-based typing, (ii) multi-locus sequence typing (MLST), (iii) panC clade typing, and (iv) rpoB allelic typing to rapidly classify B...
June 16, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28622861/antimicrobial-susceptibility-and-genotyping-of-staphylococcus-aureus-isolates-collected-between-1986-and-2015-from-ovine-mastitis
#14
Elisa Azara, Maria Giovanna Piras, Antonio Parisi, Sebastiana Tola
In this research, 330 Staphylococcus aureus isolates, collected in Sardinia (Italy) in the period 1986-2015 from clinical ovine mastitis and used for the preparation of inactivated autogenous vaccines, were analyzed. Susceptibility to 12 antimicrobial agents was tested by disk diffusion, according to CLSI recommendations. Resistance genes were detected by PCR assays. The most of isolates (85.2%) were susceptible to all antimicrobials tested, suggesting that did not exist change of resistance over time. Two isolates were multidrug-resistant (MDR), one of them (isolate 1496) showed resistance to seven antibiotics including oxacillin and erythromycin...
June 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28619146/dynamics-of-cmy-2-producing-e-coli-in-a-broiler-parent-flock
#15
Anita Dame-Korevaar, Egil A J Fischer, Arjan Stegeman, Dik Mevius, Alieda van Essen-Zandbergen, Francisca Velkers, Jeanet van der Goot
Extended-spectrum β-lactamase and plasmid mediated AmpC β-lactamase (ESBL/pAmpC) producing bacteria are resistant to Extended Spectrum Cephalosporins (ESC), and are present in all levels of the broiler production chain. We determined the prevalence, concentration, and persistence of ESBL/pAmpC-Escherichia coli in a broiler parent flock during the rearing and laying period. One-day old chickens were housed in four separate pens. Until week 33 no antibiotics or coccidiostatics were used. During rearing 57 chickens in each pen (n=228), and in the laying period two groups of 33 chickens were individually sampled (n=66)...
May 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28619013/mlst-genotypes-of-campylobacter-jejuni-isolated-from-broiler-products-dairy-cattle-and-human-campylobacteriosis-cases-in-lithuania
#16
Sigita Ramonaite, Egle Tamuleviciene, Thomas Alter, Neringa Kasnauskyte, Mindaugas Malakauskas
BACKGROUND: Campylobacter (C.) jejuni is the leading cause of human campylobacteriosis worldwide. We performed a molecular epidemiological study to investigate the genetic relationship among C. jejuni strains isolated from human diarrhoeal patients, broiler products and dairy cattle in Lithuania. METHODS: The C. jejuni isolates from human clinical cases, dairy cattle and broiler products were genotyped using multilocus sequence typing (MLST). Allele numbers for each housekeeping gene, sequence type (ST), and clonal complex (CC) were assigned by submitting the DNA sequences to the C...
June 15, 2017: BMC Infectious Diseases
https://www.readbyqxmd.com/read/28619007/whole-genome-sequencing-analyses-of-listeria-monocytogenes-that-persisted-in-a-milkshake-machine-for-a-year-and-caused-illnesses-in-washington-state
#17
Zhen Li, Ailyn Pérez-Osorio, Yu Wang, Kaye Eckmann, William A Glover, Marc W Allard, Eric W Brown, Yi Chen
BACKGROUND: In 2015, in addition to a United States multistate outbreak linked to contaminated ice cream, another outbreak linked to ice cream was reported in the Pacific Northwest of the United States. It was a hospital-acquired outbreak linked to milkshakes, made from contaminated ice cream mixes and milkshake maker, served to patients. Here we performed multiple analyses on isolates associated with this outbreak: pulsed-field gel electrophoresis (PFGE), whole genome single nucleotide polymorphism (SNP) analysis, species-specific core genome multilocus sequence typing (cgMLST), lineage-specific cgMLST and whole genome-specific MLST (wgsMLST)/outbreak-specific cgMLST...
June 15, 2017: BMC Microbiology
https://www.readbyqxmd.com/read/28614360/comparative-genomics-of-cryptococcus-neoformans-var-grubii-associated-with-meningitis-in-hiv-infected-and-uninfected-patients-in-vietnam
#18
Jeremy N Day, Seet Qihui, Lam Tuan Thanh, Phan Hai Trieu, Anh Duong Van, Nha Hoang Thu, Tran Thi Hong Chau, Nguyen P H Lan, Nguyen Van Vinh Chau, Philip M Ashton, Guy E Thwaites, Maciej F Boni, Marcel Wolbers, Niranjan Nagarajan, Patrick B O Tan, Stephen Baker
The vast burden of cryptococcal meningitis occurs in immunosuppressed patients, driven by HIV, and is caused by Cryptococcus neoformans var. grubii. We previously reported cryptococcal meningitis in Vietnam arising atypically in HIV uninfected, apparently immunocompetent patients, caused by a single amplified fragment length polymorphism (AFLP) cluster of C. neoformans var. grubii (VNIγ). This variant was less common in HIV infected individuals; it remains unclear why this lineage is associated with apparently immunocompetent patients...
June 2017: PLoS Neglected Tropical Diseases
https://www.readbyqxmd.com/read/28604829/phylogenetic-analysis-of-mycobacterium-massiliense-strains-having-recombinant-rpob-gene-laterally-transferred-from-mycobacterium-abscessus
#19
Byoung-Jun Kim, Ga-Na Kim, Bo-Ram Kim, Tae-Sun Shim, Yoon-Hoh Kook, Bum-Joon Kim
Recent multi locus sequence typing (MLST) and genome based studies indicate that lateral gene transfer (LGT) events in the rpoB gene are prevalent between Mycobacterium abscessus complex strains. To check the prevalence of the M. massiliense strains subject to rpoB LGT (Rec-mas), we applied rpoB typing (711 bp) to 106 Korean strains of M. massiliense infection that had already been identified by hsp65 sequence analysis (603 bp). The analysis indicated 6 smooth strains in M. massiliense Type I (10.0%, 6/60) genotypes but no strains in M...
2017: PloS One
https://www.readbyqxmd.com/read/28600774/multilocus-sequence-typing-mlst-for-cronobacter-spp
#20
Susan Joseph, Stephen Forsythe
MLST is a molecular typing technique that involves the identification and clustering of bacterial isolates based on the partial sequence analysis of multiple housekeeping genes (generally seven) which are distributed across the length of the genome of the organism. The Cronobacter whole genus MLST scheme can be successfully used for an accurate species level identification and classification of this complex genus.
2017: Methods in Molecular Biology
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