scholarly journals Acute Infectious Gastroenteritis: The Causative Agents, Omics-Based Detection of Antigens and Novel Biomarkers

Children ◽  
2021 ◽  
Vol 8 (12) ◽  
pp. 1112
Author(s):  
Haziqah Hasan ◽  
Nor Ashika Nasirudeen ◽  
Muhammad Alif Farhan Ruzlan ◽  
Muhammad Aiman Mohd Jamil ◽  
Noor Akmal Shareela Ismail ◽  
...  
Keyword(s):  
Drug Susceptibility ◽  
Outbreak Detection ◽  
Detection Methods ◽  
Clinical Workflow ◽  
Omics Technologies ◽  
Infectious Gastroenteritis ◽  
Causative Agents ◽  
Prediction Of Prognosis ◽  
Hospital Acquired ◽  
Or Genes

Acute infectious gastroenteritis (AGE) is among the leading causes of mortality in children less than 5 years of age worldwide. There are many causative agents that lead to this infection, with rotavirus being the commonest pathogen in the past decade. However, this trend is now being progressively replaced by another agent, which is the norovirus. Apart from the viruses, bacteria such as Salmonella and Escherichia coli and parasites such as Entamoeba histolytica also contribute to AGE. These agents can be recognised by their respective biological markers, which are mainly the specific antigens or genes to determine the causative pathogen. In conjunction to that, omics technologies are currently providing crucial insights into the diagnosis of acute infectious gastroenteritis at the molecular level. Recent advancement in omics technologies could be an important tool to further elucidate the potential causative agents for AGE. This review will explore the current available biomarkers and antigens available for the diagnosis and management of the different causative agents of AGE. Despite the high-priced multi-omics approaches, the idea for utilization of these technologies is to allow more robust discovery of novel antigens and biomarkers related to management AGE, which eventually can be developed using easier and cheaper detection methods for future clinical setting. Thus, prediction of prognosis, virulence and drug susceptibility for active infections can be obtained. Case management, risk prediction for hospital-acquired infections, outbreak detection, and antimicrobial accountability are aimed for further improvement by integrating these capabilities into a new clinical workflow.

scholarly journals Whole-Genome Sequencing for Bacterial Strain Typing Using the iSeq100 Platform

2020 ◽  
Vol 41 (S1) ◽  
pp. s434-s434
Author(s):  
Grant Vestal ◽  
Steven Bruzek ◽  
Amanda Lasher ◽  
Amorce Lima ◽  
Suzane Silbert
Keyword(s):  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Outbreak Detection ◽  
Epidemiological Surveillance ◽  
Whole Genome ◽  
Nucleotide Polymorphisms ◽  
Dna Libraries ◽  
Patient Health ◽  
Hospital Acquired ◽  
Reference Genomes

Background: Hospital-acquired infections pose a significant threat to patient health. Laboratories are starting to consider whole-genome sequencing (WGS) as a molecular method for outbreak detection and epidemiological surveillance. The objective of this study was to assess the use of the iSeq100 platform (Illumina, San Diego, CA) for accurate sequencing and WGS-based outbreak detection using the bioMérieux EPISEQ CS, a novel cloud-based software for sequence assembly and data analysis. Methods: In total, 25 isolates, including 19 MRSA isolates and 6 ATCC strains were evaluated in this study: A. baumannii ATCC 19606, B. cepacia ATCC 25416, E. faecalis ATCC 29212, E. coli ATCC 25922, P. aeruginosa ATCC 27853 and S. aureus ATCC 25923. DNA extraction of all isolates was performed on the QIAcube (Qiagen, Hilden, Germany) using the DNEasy Ultra Clean Microbial kit extraction protocol. DNA libraries were prepared for WGS using the Nextera DNA Flex Library Prep Kit (Illumina) and sequenced at 2×150-bp on the iSeq100 according to the manufacturer’s instructions. The 19 MRSA isolates were previously characterized by the DiversiLab system (bioMérieux, France). Upon validation of the iSeq100 platform, a new outbreak analysis was performed using WGS analysis using EPISEQ CS. ATCC sequences were compared to assembled reference genomes from the NCBI GenBank to assess the accuracy of the iSeq100 platform. The FASTQ files were aligned via BowTie2 version 2.2.6 software, using default parameters, and FreeBayes version 1.1.0.46-0 was used to call homozygous single-nucleotide polymorphisms (SNPs) with a minimum coverage of 5 and an allele frequency of 0.87 using default parameters. ATCC sequences were analyzed using ResFinder version 3.2 and were compared in silico to the reference genome. Results: EPISEQ CS classified 8 MRSA isolates as unrelated and grouped 11 isolates into 2 separate clusters: cluster A (5 isolates) and cluster B (6 isolates) with similarity scores of ≥99.63% and ≥99.50%, respectively. This finding contrasted with the previous characterization by DiversiLab, which identified 3 clusters of 2, 8, and 11 isolates, respectively. The EPISEQ CS resistome data detected the mecA gene in 18 of 19 MRSA isolates. Comparative analysis of the ATCCsequences to the reference genomes showed 99.9986% concordance of SNPs and 100.00% concordance between the resistance genes present. Conclusions: The iSeq100 platform accurately sequenced the bacterial isolates and could be an affordable alternative in conjunction with EPISEQ CS for epidemiological surveillance analysis and infection prevention.Funding: NoneDisclosures: None

scholarly journals Comparison of Molecular Subtyping and Antimicrobial Resistance Detection Methods Used in a Large Multistate Outbreak of Extensively Drug-Resistant Campylobacter jejuni Infections Linked to Pet Store Puppies

2020 ◽  
Vol 58 (10) ◽  
Author(s):  
Lavin A. Joseph ◽  
Louise K. Francois Watkins ◽  
Jessica Chen ◽  
Kaitlin A. Tagg ◽  
Christy Bennett ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Campylobacter Jejuni ◽  
Multilocus Sequence Typing ◽  
The United States ◽  
Sequence Type ◽  
Outbreak Detection ◽  
Detection Methods ◽  
Drug Resistant ◽  
Molecular Subtyping ◽  
Content Type

ABSTRACT Campylobacter jejuni is a leading cause of enteric bacterial illness in the United States. Traditional molecular subtyping methods, such as pulsed-field gel electrophoresis (PFGE) and 7-gene multilocus sequence typing (MLST), provided limited resolution to adequately identify C. jejuni outbreaks and separate out sporadic isolates during outbreak investigations. Whole-genome sequencing (WGS) has emerged as a powerful tool for C. jejuni outbreak detection. In this investigation, 45 human and 11 puppy isolates obtained during a 2016–2018 outbreak linked to pet store puppies were sequenced. Core genome multilocus sequence typing (cgMLST) and high-quality single nucleotide polymorphism (hqSNP) analysis of the sequence data separated the isolates into the same two clades containing minor within-clade differences; however, cgMLST analysis does not require selection of an appropriate reference genome, making the method preferable to hqSNP analysis for Campylobacter surveillance and cluster detection. The isolates were classified as sequence type 2109 (ST2109)—a rarely seen MLST sequence type. PFGE was performed on 38 human and 10 puppy isolates; PFGE patterns did not reliably predict clustering by cgMLST analysis. Genetic detection of antimicrobial resistance determinants predicted that all outbreak-associated isolates would be resistant to six drug classes. Traditional antimicrobial susceptibility testing (AST) confirmed a high correlation between genotypic and phenotypic antimicrobial resistance determinations. WGS analysis linked C. jejuni isolates in humans and pet store puppies even when canine exposure information was unknown, aiding the epidemiological investigation during the outbreak. WGS data were also used to quickly identify the highly drug-resistant profile of these outbreak-associated C. jejuni isolates.

scholarly journals Approaches to the evaluation of outbreak detection methods

2006 ◽  
Vol 6 (1) ◽  
Author(s):  
Rochelle E Watkins ◽  
Serryn Eagleson ◽  
Robert G Hall ◽  
Lynne Dailey ◽  
Aileen J Plant
Keyword(s):  
Outbreak Detection ◽  
Detection Methods

scholarly journals An experience with colistin applied in treatment of imunocompromised patients with peritonitis on peritoneal dialysis

2015 ◽  
Vol 72 (4) ◽  
pp. 379-382 ◽  
Author(s):  
Tatjana Djurdjevic-Mirkovic ◽  
Ljiljana Gvozdenovic ◽  
Gordana Majstorovic-Strazmester ◽  
Violeta Knezevic ◽  
Dejan Celic ◽  
...  
Keyword(s):  
Multiple Myeloma ◽  
Peritoneal Dialysis ◽  
Complete Recovery ◽  
First Episode ◽  
Exit Site ◽  
Causative Agents ◽  
Life Threatening ◽  
History Of ◽  
Acinetobacter Spp ◽  
Hospital Acquired

Introduction. Immunocompromised patients, such as those with multiple myeloma on peritoneal dialysis, are particularly susceptible to the occurrence of peritonitis. Case report. We presented a 56-year-old female patient with a 10-year history of multiple myeloma. The patient was on peritoneal dialysis since 2010. During 2012 the patient had the first episode of peritonitis that was successfully managed, but in 2013 the second episode of peritonitis occured. Analysis of dialysate culture and exit site swab revealed the presence of multiresistant Acinetobacter spp., which was susceptible only to colistin. Prompt colistin therapy was administered at the doses of 100,000 units/day during six days, which resulted in complete recovery of the patient, as well as improvement of local abdominal findings. Gram-negative bacteria (genus Acinetobacter) are common causative agents in hospital-acquired infections. Studies confirmed susceptibility of Acinetobacter to colistin, which was also the case with the presented patient. Intravenous administration of colistin resulted in a complete remission of this severe, life-threatening peritonitis. Conclusion. Patients with multiple myeloma and renal failure are highly prone to severe life-threatening infections.

scholarly journals Automated use of WHONET and SaTScan to detect outbreaks of Shigella spp. using antimicrobial resistance phenotypes

2009 ◽  
Vol 138 (6) ◽  
pp. 873-883 ◽  
Author(s):  
J. STELLING ◽  
W. K. YIH ◽  
M. GALAS ◽  
M. KULLDORFF ◽  
M. PICHEL ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Disease Surveillance ◽  
Laboratory Data ◽  
Disease Outbreak ◽  
Outbreak Detection ◽  
Detection Methods ◽  
Scan Statistic ◽  
National Network ◽  
Disease Outbreak Detection ◽  
Shigella Spp

SUMMARYAntimicrobial resistance is a priority emerging public health threat, and the ability to detect promptly outbreaks caused by resistant pathogens is critical for resistance containment and disease control efforts. We describe and evaluate the use of an electronic laboratory data system (WHONET) and a space–time permutation scan statistic for semi-automated disease outbreak detection. In collaboration with WHONET-Argentina, the national network for surveillance of antimicrobial resistance, we applied the system to the detection of local and regional outbreaks of Shigella spp. We searched for clusters on the basis of genus, species, and resistance phenotype and identified 19 statistical ‘events’ in a 12-month period. Of the six known outbreaks reported to the Ministry of Health, four had good or suggestive agreement with SaTScan-detected events. The most discriminating analyses were those involving resistance phenotypes. Electronic laboratory-based disease surveillance incorporating statistical cluster detection methods can enhance infectious disease outbreak detection and response.

scholarly journals Antibiotic resistance in Acinetobacter baumannii as agent of surgery infection and approaches to its overcoming by means of deca-methoxinum antiseptic

2019 ◽  
Vol 1 (2) ◽  
pp. 18-22
Author(s):  
O A Nazarchuk ◽  
V I Nahaichuk
Keyword(s):  
Antibiotic Resistance ◽  
Antibiotic Sensitivity ◽  
Antibiotic Resistant ◽  
Clinical Strains ◽  
Minimal Inhibitory Concentrations ◽  
Hospital Acquired Infections ◽  
Causative Agents ◽  
Resistant Strains ◽  
Burn Disease ◽  
Hospital Acquired

Introduction. Non-fermenting Gram-negative bacilli are known as one of the most frequent causative agents of hospital-acquired infections. Acinetobacter baumannii, as causative agent of infection complications of different localization, has obtained recently high resistance to anti-biotics and has belonged to ESKAPE group of pathogens. Antimicrobials, recommended for the prophylaxis and therapy of hospital-acquired infections, have been failing in their effectiveness and lead to selection of antibiotic resistant strains of A. baumannii. The aim of this research was to substantiate the way of overcoming of resistance in clinical strains of A. baumannii, by means of synergic antimicrobial activity of antibiotics and antiseptic decamethoxinum®. Material and methods. The research was carried out on 190 clinical strains of A. baumannii, isolated from patients with burn disease during the period 2011–2015. The sensitivity of clinical strains of A. baumannii was determined to such antibiotics as ampicillin/sulbactam, cefoperazone, cefoperazone/sulbactam, meropenem, imipenem, amikacin, ciprofloxacin, gatifloxacin and antiseptic decamethoxinum® (DCM; Registration certificate No UA/14444/01/01 since 24.06.2015. Order of the Ministry of Health of Ukraine No 373). The sensitivity of A. baumannii to antibiotics and DCM was determined by means of disk diffusion test and serial dilution (Order of the Ministry of Health of Ukraine No167 since 05.04.2007; EUCAST expert rules).The study of the influence of antiseptic DCM on the sensitivity of acinetobacteria to antibiotics was studied on 35 clinical strains of A. baumannii, drafted from the general number of isolates enrolled in the research. For this, the sensitivity of A. baumannii to antibiotics in the presence of sub-minimal inhibitory concentrations (subMIC) of DCM was identified. The received experimental data were analyzed by “Statistica 6.0”. Results and discussion. The changes of antibiotic sensitivity profile of A. baumannii for five years were shown. It was found that the sensitivity of A. baumannii to majority of antibiotics, selected for study, decreased significantly. But the only ampicillin/sulbactam was found to have vice versa tendency. We found the rising quantity of antibiotic resistant strains of A. baumannii. At the same time, high resistance of acinetobacteria to fluoroquinolones (ciprofloxacin– 96,1%; gatifloxacin– 95,8%) was found in 2015. The in vitro research of combined activity of DCM antiseptic remedy and early mentioned antibiotics against clinical strains of A. baumannii demonstrated the reveal antibiotic effectiveness. As follows, minimal inhibitory concentrations of antibiotics decreased in 1.5–4 times in the mediums which contained subMIC of DCM. Especially this tendency was found in resistant clinical strains. Conclusion. Under selective influence of antibiotics protected by β-lactamase inhibitors, carbapenems, fluoroquinolones aminoglycosides increase the antibiotic resistance in A. baumannii, causative agents of infectious complications in patients with burn disease. The antiseptic remedy decamethoxinum® helps to improve antibiotic sensitivity in resistant A. baumannii.

scholarly journals The importance of age-specific data in routine syndromic surveillance

2017 ◽  
Vol 9 (1) ◽  
Author(s):  
Roger Morbey ◽  
Alex J. Elliot ◽  
Gillian E. Smith
Keyword(s):  
Public Health ◽  
Hospital Admissions ◽  
Age Distribution ◽  
Age Groups ◽  
Health Indicators ◽  
Older Age ◽  
Outbreak Detection ◽  
Detection Methods ◽  
Surveillance Systems ◽  
Wide Range

ObjectiveTo investigate whether aberration detection methods for syndromicsurveillance would be more useful if data were stratified by age band.IntroductionWhen monitoring public health incidents using syndromicsurveillance systems, Public Health England (PHE) uses the ageof the presenting patient as a key indicator to further assess theseverity, impact of the incident, and to provide intelligence on thelikely cause. However the age distribution of cases is usually notconsidered until after unusual activity has been identified in the all-ages population data. We assessed whether monitoring specific agegroups contemporaneously could improve the timeliness, specificityand sensitivity of public health surveillance.MethodsFirst, we examined a wide range of health indicators from the PHEsyndromic surveillance systems to identify for further study thosewith the greatest seasonal variation in the age distribution of cases.Secondly, we examined the identified indicators to ascertain whetherany age bands consistently lagged behind other age bands. Finally,we applied outbreak detection methods retrospectively to age specificdata, identifying periods of increased activity that were only detectedor detected earlier when age-specific surveillance was used.ResultsSeasonal increases in respiratory indicators occurred first inyounger age groups, with increases in children under 5 providingearly warning of subsequent increases occurring in older age groups.Also, we found age specific indicators improved the specificity ofsurveillance using indicators relating to respiratory and eye problems;identifying unusual activity that was less apparent in the all-agespopulation.ConclusionsRoutine surveillance of respiratory indicators in young childrenwould have provided early warning of increases in older age groups,where the burden on health care usage, e.g. hospital admissions, isgreatest. Furthermore this cross-correlation between ages occurredconsistently even though the age distribution of the burden ofrespiratory cases varied between seasons. Age specific surveillancecan improve sensitivity of outbreak detection although all-agesurveillance remains more powerful when case numbers are low.

scholarly journals Group B Streptococcus detection in pregnant women: comparison of real-time PCR assay, culture, and the Xpert GBS rapid test

2019 ◽  
Author(s):  
Laura Vieira ◽  
Amanda Vilaverde Perez ◽  
Monique M Machado ◽  
Michele L Kayser ◽  
Daniela V Vettori ◽  
...  
Keyword(s):  
Antenatal Care ◽  
Pregnant Women ◽  
Real Time ◽  
Group B Streptococcus ◽  
Prophylactic Antibiotic ◽  
Rapid Test ◽  
Turnaround Time ◽  
Detection Methods ◽  
Causative Agents ◽  
Group B

Abstract Background: Group B Streptococcus (GBS) is one of the most important causative agents of neonatal sepsis. As administration of prophylactic antibiotics during labor can prevent GBS infection, routine screening for this bacterium in prenatal care before the onset of labor is recommended. However, many women present in labor without having undergone such testing during antenatal care, and the turnaround time of detection methods is insufficient for results to be obtained before delivery. Methods: Vaginal and anorectal specimens were collected from 270 pregnant women. Each sample was tested by Xpert GBS, qPCR, and culture for GBS detection. Results: The overall prevalence of maternal GBS colonization was 30.7% according to Xpert GBS, 51.1% according to qPCR, and 14.3% according to cultures. Considering the qPCR method as the reference, the Xpert GBS had a sensitivity of 53% and specificity of 93%. Positive Xpert GBS results were correlated to marital status (married or cohabitating) and with prematurity as a cause of neonatal hospitalization. Positive cultures were related with ischemic–hypoxic encephalopathy requiring therapeutic hypothermia. Conclusions: Combined enrichment/qPCR and the Xpert GBS rapid test found a high prevalence of GBS colonization. The Xpert GBS technique gives faster results and could be useful for evaluating mothers who present without antenatal GBS screening results and are at risk of preterm labor, thus allowing institution of prophylactic antibiotic therapy. Keywords: Group B Streptococcus ; Streptococcus agalactiae ; Xpert GBS; real-time polymerase chain reaction; antenatal care

scholarly journals Group B Streptococcus detection in pregnant women: comparison of real-time PCR assay, culture, and the Xpert GBS rapid test

2019 ◽  
Author(s):  
Laura Vieira ◽  
Amanda Vilaverde Perez ◽  
Monique M Machado ◽  
Michele L Kayser ◽  
Daniela V Vettori ◽  
...  
Keyword(s):  
Pregnant Women ◽  
Group B Streptococcus ◽  
Prophylactic Antibiotic ◽  
Rapid Test ◽  
Turnaround Time ◽  
Detection Methods ◽  
Institutional Research ◽  
Delivery Methods ◽  
Causative Agents ◽  
Group B

Abstract Background Group B Streptococcus (GBS) is one of the most important causative agents of neonatal sepsis. As administration of prophylactic antibiotics during labor can prevent GBS infection, routine screening for this bacterium in prenatal care before the onset of labor is recommended. However, many women present in labor without having undergone such testing during antenatal care, and the turnaround time of detection methods is insufficient for results to be obtained before delivery. Methods Vaginal and anorectal specimens were collected from 270 pregnant women. Each sample was tested by Xpert GBS, PCR, and culture for GBS detection. Results The overall prevalence of maternal GBS colonization was 30.7% according to Xpert GBS, 51.1% according to PCR, and 14.3% according to cultures. Considering the PCR method as the reference, the Xpert GBS had a sensitivity of 53% and specificity of 93%. Positive Xpert GBS results were associated with marital status (married or cohabitating) and with prematurity as a cause of neonatal hospitalization. Positive cultures were associated with ischemic–hypoxic encephalopathy requiring therapeutic hypothermia. Conclusions Combined enrichment/PCR and the Xpert GBS rapid test found a high prevalence of GBS colonization. The Xpert GBS technique gives faster results and could be useful for evaluating mothers who present without antenatal GBS screening results and are at risk of preterm labor, thus allowing institution of prophylactic antibiotic therapy. Trial Registration: The study was approved by the institutional Research Ethics Committee (CAAE: 59688316.0.0000.5327)

scholarly journals Klebsiella pneumoniae yfiRNB operon affects biofilm formation, polysaccharide production and drug susceptibility

Microbiology ◽  
2014 ◽  
Vol 160 (12) ◽  
pp. 2595-2606 ◽  
Author(s):  
Mónica G. Huertas ◽  
Lina Zárate ◽  
Iván C. Acosta ◽  
Leonardo Posada ◽  
Diana P. Cruz ◽  
...  
Keyword(s):  
Klebsiella Pneumoniae ◽  
Biofilm Formation ◽  
Surface Characteristics ◽  
Opportunistic Pathogen ◽  
Drug Susceptibility ◽  
Cellulose Production ◽  
Resistant Strains ◽  
Drug Resistant Strains ◽  
Type 3 ◽  
Hospital Acquired

Klebsiella pneumoniae is an opportunistic pathogen important in hospital-acquired infections, which are complicated by the rise of drug-resistant strains and the capacity of cells to adhere to surfaces and form biofilms. In this work, we carried out an analysis of the genes in the K. pneumoniae yfiRNB operon, previously implicated in biofilm formation. The results indicated that in addition to the previously reported effect on type 3 fimbriae expression, this operon also affected biofilm formation due to changes in cellulose as part of the extracellular matrix. Deletion of yfiR resulted in enhanced biofilm formation and an altered colony phenotype indicative of cellulose overproduction when grown on solid indicator media. Extraction of polysaccharides and treatment with cellulase were consistent with the presence of cellulose in biofilms. The enhanced cellulose production did not, however, correlate with virulence as assessed using a Caenorhabditis elegans assay. In addition, cells bearing mutations in genes of the yfiRNB operon varied with respect to the WT control in terms of susceptibility to the antibiotics amikacin, ciprofloxacin, imipenem and meropenem. These results indicated that the yfiRNB operon is implicated in the production of exopolysaccharides that alter cell surface characteristics and the capacity to form biofilms – a phenotype that does not necessarily correlate with properties related with survival, such as resistance to antibiotics.

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