Pulsed Field Gel Electrophoresis: Past, present, and future

López‐Canovas, Lilia; Benitez, Máximo B. Martínez; Isidrón, José Alfredo Herrera; Soto, Eduardo Flores

doi:10.1016/j.ab.2019.02.020

Cited by 36 publications

(25 citation statements)

References 157 publications

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“…On the other hand, larger DNA molecules take a longer time to re-orient. The larger DNA molecules that migrate slower than the set pulse time tend to migrate as one band through the gel matrix (Le Tang et al, 2017 ; Lopez-Canovas et al, 2019 ).…”

Section: Detection Methods Of Viruses In Wastewatermentioning

confidence: 99%

Viruses in wastewater: occurrence, abundance and detection methods

Corpuz

Buonerba

Vigliottá

et al. 2020

Science of The Total Environment

228

178

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This paper presents an updated and comprehensive review on the different methods used for detection and quantification of viruses in wastewater treatment systems. The analysis of viability of viruses in wastewater and sludge is another thrust of this review. Recent studies have mostly focused on determining the abundance and diversity of viruses in wastewater influents, in samples from primary, secondary, and tertiary treatment stages, and in final effluents. A few studies have also examined the occurrence and diversity of viruses in raw and digested sludge samples. Recent efforts to improve efficiency of virus detection and quantification methods in the complex wastewater and sludge matrices are highlighted in this review. A summary and a detailed comparison of the pre-treatment methods that have been utilized for wastewater and sludge samples are also presented. The role of metagenomics or sequencing analysis in monitoring wastewater systems to predict disease outbreaks, to conduct public health surveillance, to assess the efficiency of existing treatment systems in virus removal, and to re-evaluate current regulations regarding pathogenic viruses in wastewater is discussed in this paper. Challenges and future perspectives in the detection of viruses, including emerging and newly emerged viruses such as the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2), in wastewater systems are discussed in this review.

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Section: Detection Methods Of Viruses In Wastewatermentioning

confidence: 99%

Viruses in wastewater: occurrence, abundance and detection methods

Corpuz

Buonerba

Vigliottá

et al. 2020

Science of The Total Environment

228

178

View full text Add to dashboard Cite

show abstract

“…The isolation and identification of pathobiontic bacteria was attempted from clinical samples, that is, bronchoalveolar lavage fluid (BLF), endotracheal aspirates (ES), sputum, and blood [16]. The genetic relatedness of the resulting isolates was analysed using pulse-field gel electrophoresis (PFGE) [17][18][19][20][21][22], whole genome sequencing, and sequence comparisons (Supplemental Methods).…”

Section: Pathobiontic Bacterial Species Isolation and Genetic-relatedmentioning

confidence: 99%

Super-dominant pathobiontic bacteria in the nasopharyngeal microbiota as causative agents of secondary bacterial infection in influenza patients

Qin

Geng

Zhou

et al. 2020

Emerging Microbes & Infections

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The source of secondary lower respiratory tract bacterial infections in influenza patients is not fully understood. A casecontrol study was conducted during the 2017-2018 influenza epidemic period in Beijing, China. Nasopharyngeal swabs were collected from 52 virologically confirmed influenza patients and 24 healthy medical staff. The nasopharyngeal microbiota taxonomic composition was analysed using high-throughput sequencing of the 16S rRNA gene V3-V4 regions. The super-dominant pathobiontic bacterial genus (SDPG) was defined as that accounting for >50% of sequences in a nasopharyngeal swab. We attempted to isolate bacteria of this genus from both nasopharyngeal swabs and lower-respiratory tract samples and analyse their genetic similarities. We observed a significantly lower taxonomy richness in influenza cases compared with healthy controls. A SDPG was detected in 61% of severe cases but in only 24% of mild cases and 29% of healthy controls. In 10 cases, the species isolated from lower-respiratory tract infection sites were identified as belonging to the nasopharyngeal microbiota SDPG. Genetically identical strains were isolated from both nasopharyngeal swabs and lower-respiratory tract infection sites, including 23 Acinetobacter baumannii strains from six severe cases, six Klebsiella pneumoniae strains from two severe cases, five Pseudomonas aeruginosa strains from one severe and one mild case, and four Corynebacterium striatum strains from two severe cases. The SDPG in the nasopharyngeal microbiota are the likely cause of subsequent infection in influenza patients.

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“…Typing of bacterial strains can aid in outbreak investigation by revealing clonality and possible routes of transmission and by linking clinical isolates to environmental reservoirs (4). Typing methods include those that rely on genomic fingerprinting methods using DNA amplification, such as REP-PCR, BOX-PCR, and ERIC-PCR (5, 6), DNA-based methods that do not require amplification, such as pulsed-field gel electrophoresis (PFGE) (7), whole-genome sequencing (WGS) (8,9), and methods that are not DNA based, such as matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS) (10,11). Typeability, ease of use, ease of interpretation, rapidity, reproducibility, discriminatory power, cost, and available expertise are important considerations when choosing a typing method (4,12).…”

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confidence: 99%

Fourier Transform Infrared Spectroscopy Is a New Option for Outbreak Investigation: a Retrospective Analysis of an Extended-Spectrum-Beta-Lactamase-Producing Klebsiella pneumoniae Outbreak in a Neonatal Intensive Care Unit

et al. 2020

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The IR Biotyper is a new automated typing system based on Fourier-transform infrared (FT-IR) spectroscopy that gives results within 4 h. We aimed (i) to use the IR Biotyper to retrospectively analyze an outbreak of extended-spectrum beta-lactamase-producing Klebsiella pneumoniae (ESBL-KP) in a neonatal intensive care unit and to compare results to BOX-PCR and whole-genome sequencing (WGS) results as the gold standard and (ii) to assess how the cutoff values used to define clusters affect the discriminatory power of the IR Biotyper. The sample consisted of 18 isolates from 14 patients. Specimens were analyzed in the IR Biotyper using the default analysis settings, and spectra were analyzed using OPUS 7.5 software. The software contains a feature that automatically proposes a cutoff value to define clusters; the cutoff value defines up to which distance the spectra are considered to be in the same cluster. Based on FT-IR, the outbreak represented 1 dominant clone, 1 secondary clone, and several unrelated clones. FT-IR results, using the cutoff value generated by the accompanying software after 4 replicates, were concordant with WGS for all but 1 isolate. BOX-PCR was underdiscriminatory compared to the other two methods. Using the cutoff value generated after 12 replicates, the results of FT-IR and WGS were completely concordant. The IR Biotyper can achieve the same typeability and discriminatory power as genome-based methods. However, to attain this high performance requires either previous, strain-dependent knowledge about the optimal technical parameters to be used or validation by a second method.

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Pulsed Field Gel Electrophoresis: Past, present, and future

Cited by 36 publications

References 157 publications

Viruses in wastewater: occurrence, abundance and detection methods

Viruses in wastewater: occurrence, abundance and detection methods

Super-dominant pathobiontic bacteria in the nasopharyngeal microbiota as causative agents of secondary bacterial infection in influenza patients

Fourier Transform Infrared Spectroscopy Is a New Option for Outbreak Investigation: a Retrospective Analysis of an Extended-Spectrum-Beta-Lactamase-Producing Klebsiella pneumoniae Outbreak in a Neonatal Intensive Care Unit

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