Genetic Characterization of Fungi Isolated from the Environmental Swabs collected from a Compounding  Center Known to Cause Multistate Meningitis Outbreak  in United States Using ITS Sequencing

Sulaiman, Irshad M.; Jacobs, Emily; Simpson, Steven; Kerdahi, Khalil

doi:10.3390/pathogens3030732

Cited by 7 publications

(7 citation statements)

References 32 publications

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“…Compared to the 100s or 1000s of bacterial species identified, very few fungi or protist species (dozens) were identified at any point in the treatment scheme, despite the large amount of DNA and RNA sequence obtained, suggesting that they represent very little of the total microbial community. Two identified fungi, Enterocytozoon , detected in Q1, MFF, MF biofilm, and RO biofilm, and Onygenales , detected across all samples, are potential human pathogens infecting immunocompromised individuals ( Sulaiman et al, 2014 ). Despite the identification of these two fungi, overall the fungi represented less than 1 percent of the sequence reads identified in influent (Q1) water, and were otherwise plant pathogens such as Puccinia and Lentinus ( Fangkrathok et al, 2014 ; Gill et al, 2015 ).…”

Section: Discussionmentioning

confidence: 99%

Characterization of the Microbiome at the World’s Largest Potable Water Reuse Facility

et al. 2018

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Conventional water resources are not sufficient in many regions to meet the needs of growing populations. Due to cyclical weather cycles, drought, and climate change, water stress has increased worldwide including in Southern California, which serves as a model for regions that integrate reuse of wastewater for both potable and non-potable use. The Orange County Water District (OCWD) Advanced Water Purification Facility (AWPF) is a highly engineered system designed to treat and produce up to 100 million gallons per day (MGD) of purified water from a municipal wastewater source for potable reuse. Routine facility microbial water quality analysis is limited to standard indicators at this and similar facilities. Given recent advances in high throughput DNA sequencing techniques, complete microbial profiling of communities in water samples is now possible. By using 16S/18S rRNA gene sequencing, metagenomic and metatranscriptomic sequencing coupled to a highly accurate identification method along with 16S rRNA gene qPCR, we describe a detailed view of the total microbial community throughout the facility. The total bacterial load of the water at stages of the treatment train ranged from 3.02 × 106 copies in source, unchlorinated wastewater feed to 5.49 × 101 copies of 16S rRNA gene/mL after treatment (consisting of microfiltration, reverse osmosis, and ultraviolet/advanced oxidation). Microbial diversity and load decreased by several orders of magnitude after microfiltration and reverse osmosis treatment, falling to almost non-detectable levels that more closely resembled controls of molecular grade laboratory water than the biomass detected in the source water. The presence of antibiotic resistance genes and viruses was also greatly reduced. Overall, system design performance was achieved, and comprehensive microbial community analysis was found to enable a more complete characterization of the water/wastewater microbial signature.

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Section: Discussionmentioning

confidence: 99%

Characterization of the Microbiome at the World’s Largest Potable Water Reuse Facility

et al. 2018

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“…Molecular techniques have showed enormous potential for rapidly and accurately identifying the ecological agents of mucormycosis, which helps in conducting epidemiologic investigations. Molecular detection assays for the Mucorales are, however, not yet widely available ( 18 , 26 ).…”

Section: Discussionmentioning

confidence: 99%

“…These include the thermotolerant species M. racemosus , which either does not grow or else grows poorly at 37°C. The presence of fungal species has been considered to be an environmental microbiological indicator, and some of the fungi have been found to cause fungal infection ( 26 ).…”

Section: Discussionmentioning

confidence: 99%

Molecular Identification of Mucor and Lichtheimia Species in Pure Cultures of Zygomycetes

Ziaee

Zia

Bayat

et al. 2016

Jundishapur J Microbiol

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BackgroundThe Mucorales are an important opportunistic fungi that can cause mucormycosis in immunocompromised patients. The fast and precise diagnosis of mucormycosis is very important because, if the diagnosis is not made early enough, dissemination often occurs. It is now well established that molecular methods such as polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) are feasible and reliable tools for the early and accurate diagnosis of mucormycosis agents.ObjectivesThe present study was conducted to evaluate the validity of PCR-RFLP for the identification of Mucorales and some important Mucor and Lichtheimia species in pure cultures of Zygomycetes.Materials and MethodsSpecific sense and anti-sense primers were used to amplify the Mucorales, Mucor, and Lichtheimia DNA. The PCR products were digested by AfIII, XmnI, and AcII restriction enzymes, and the resultant restriction pattern was analyzed.ResultsOn the basis of the molecular and morphological data, we identified Mucor plumbeus (10.83%), M. circinelloides (9.17%), Lichtheimia corymbifera (9.17%), M. racemosus (5.83%), M. ramosissimus (3.33%), and L. blakesleeana (0.83%).ConclusionsIt seems that PCR-RFLP is a suitable technique for the identification of Mucorales at the species level.

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“…Thus far, DNA sequencing is considered the gold standard for rapid detection and species identification of human-pathogenic microorganisms of public health importance [ 13 , 14 , 15 ]. It has also been used to understand the population genetic structure, phylogenetic relationship, and taxonomic revision of various human-pathogenic bacteria causing foodborne illness.…”

Section: Introductionmentioning

confidence: 99%

“…It has also been used to understand the population genetic structure, phylogenetic relationship, and taxonomic revision of various human-pathogenic bacteria causing foodborne illness. More recently, nucleotide sequence characterization is routinely employed in effective epidemiologic studies to reveal transmission routes of emerging infectious diseases, and in the prevention and control of various foodborne and waterborne diseases [ 13 , 14 , 15 , 16 ]. Multilocus sequence typing has been successfully used in the species identification of Cronobacter spp.…”

Section: Introductionmentioning

confidence: 99%

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

Miranda

Banerjee

Simpson

et al. 2017

Foods

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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. In this study, we have examined 195 aliquots of enrichments from the nine major categories of foods (including baby and medical food, dairy products, dried food, frozen food, pet food, produce, ready-to-eat snacks, seafood, and spices) from 44 countries using conventional microbiological and molecular techniques. The typical colonies of Cronobacter were then identified by VITEK2 and real-time PCR. Subsequently, sequence typing was performed on the 51 recovered Cronobacter isolates at the 16S rRNA, rpoB and seven O-antigen loci for species identification in order to accomplish an effective surveillance program for the control and prevention of foodborne illnesses.

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Genetic Characterization of Fungi Isolated from the Environmental Swabs collected from a Compounding Center Known to Cause Multistate Meningitis Outbreak in United States Using ITS Sequencing

Cited by 7 publications

References 32 publications

Characterization of the Microbiome at the World’s Largest Potable Water Reuse Facility

Characterization of the Microbiome at the World’s Largest Potable Water Reuse Facility

Molecular Identification of Mucor and Lichtheimia Species in Pure Cultures of Zygomycetes

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

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