scholarly journals COVID-19 Community Transmission and Super Spreaders in Rural Villages from Manabi Province in the Coastal Region of Ecuador Assessed by Massive Testing of Community-Dwelling Population

2021 ◽  
Author(s):  
Maria Belén Rodriguez-Paredes ◽  
Paolo Alexander Vallejo-Janeta ◽  
Diana Morales-Jadan ◽  
Byron Freire-Paspuel ◽  
Esteban Ortiz-Prado ◽  
...  
Keyword(s):  
Rural Communities ◽  
Quantitative Polymerase Chain Reaction ◽  
Coastal Region ◽  
Community Dwelling ◽  
First Semester ◽  
Rural Villages ◽  
Viral Loads ◽  
High Prevalence ◽  
Community Transmission ◽  
Polymerase Chain

Neglected rural communities in Latin America are highly vulnerable to COVID-19 due to a poor health infrastructure and limited access to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) diagnosis. Manabí is a province of the Coastal Region of Ecuador characterized by a high prevalence of rural population living under poverty conditions. In the current study, we present the retrospective analysis of the results of a massive SARS-CoV-2 testing operation in nonhospitalized populations from Manabí carried out from August to September 2020. A total of 4,003 people from 15 cantons were tested for SARS-CoV-2 by reverse-transcriptase quantitative polymerase chain reaction, resulting in an overall infection rate of 16.13% for SARS-CoV-2, with several communities > 30%. Moreover, 29 SARS-CoV-2 super-spreader community-dwelling individuals with viral loads above 108 copies/mL were found. These results support that uncontrolled COVID-19 community transmission was happening in Manabí during the first semester of COVID-19 pandemic. This report endorses the utility of massive SARS-CoV-2 testing among asymptomatic population for control and surveillance of COVID-19.

scholarly journals Estimating epidemiologic dynamics from cross-sectional viral load distributions

Science ◽  
2021 ◽  
pp. eabh0635
Author(s):  
James A. Hay ◽  
Lee Kennedy-Shaffer ◽  
Sanjat Kanjilal ◽  
Niall J. Lennon ◽  
Stacey B. Gabriel ◽  
...  
Keyword(s):  
Population Distribution ◽  
Quantitative Polymerase Chain Reaction ◽  
Cross Sectional ◽  
Outbreak Management ◽  
Viral Loads ◽  
Time Estimates ◽  
Load Distributions ◽  
Random Samples ◽  
Combining Data ◽  
Polymerase Chain

Estimating an epidemic’s trajectory is crucial for developing public health responses to infectious diseases, but case data used for such estimation are confounded by variable testing practices. We show that the population distribution of viral loads observed under random or symptom-based surveillance, in the form of cycle threshold (Ct) values obtained from reverse-transcription quantitative polymerase chain reaction testing, changes during an epidemic. Thus, Ct values from even limited numbers of random samples can provide improved estimates of an epidemic’s trajectory. Combining data from multiple such samples improves the precision and robustness of such estimation. We apply our methods to Ct values from surveillance conducted during the SARS-CoV-2 pandemic in a variety of settings and offer alternative approaches for real-time estimates of epidemic trajectories for outbreak management and response.

scholarly journals Effect of Screening for Methicillin-Resistant Staphylococcus aureus Carriage by Polymerase Chain Reaction on the Duration of Unnecessary Preemptive Contact Isolation

2008 ◽  
Vol 29 (11) ◽  
pp. 1077-1079 ◽  
Author(s):  
Ilker Uçkay ◽  
Hugo Sax ◽  
Anne Iten ◽  
Véronique Camus ◽  
Gesuele Renzi ◽  
...  
Keyword(s):  
Staphylococcus Aureus ◽  
Polymerase Chain Reaction ◽  
Hospital Readmission ◽  
Quantitative Polymerase Chain Reaction ◽  
Chain Reaction ◽  
Methicillin Resistant ◽  
Contact Isolation ◽  
High Prevalence ◽  
Chromogenic Agar ◽  
Polymerase Chain

A high prevalence of methicillin-resistant Staphylococcus aureus (MRSA) carriage at hospital readmission among previous MRSA carriers warrants screening and preemptive isolation precautions. The replacement of culture on chromogenic agar with rapid quantitative polymerase chain reaction for readmission screening reduces the number of unnecessary preemptive isolation-days by 54% (from 6.88 to 3.14 isolation-days) and related costs by 45% (from US$113.2 to US$62.1) for patients who test negative for MRSA.

scholarly journals Controlled Human Infection With Bordetella pertussis Induces Asymptomatic, Immunizing Colonization

2019 ◽  
Vol 71 (2) ◽  
pp. 403-411 ◽  
Author(s):  
Hans de Graaf ◽  
Muktar Ibrahim ◽  
Alison R Hill ◽  
Diane Gbesemete ◽  
Andrew T Vaughan ◽  
...  
Keyword(s):  
Bordetella Pertussis ◽  
Quantitative Polymerase Chain Reaction ◽  
Human Infection ◽  
Wild Type ◽  
Immunological Responses ◽  
Inoculum Dose ◽  
Colony Forming Units ◽  
Community Transmission ◽  
Polymerase Chain ◽  
Immunoglobin G

Abstract Background Bordetella pertussis is among the leading causes of vaccine-preventable deaths and morbidity globally. Human asymptomatic carriage as a reservoir for community transmission of infections might be a target of future vaccine strategies, but has not been demonstrated. Our objective was to demonstrate that asymptomatic nasopharyngeal carriage of Bordetella pertussis is inducible in humans and to define the microbiological and immunological features of presymptomatic infection. Methods Healthy subjects aged 18–45 years with an antipertussis toxin immunoglobin G (IgG) concentration of <20 international units/ml were inoculated intranasally with nonattenuated, wild-type Bordetella pertussis strain B1917. Safety, colonization, and shedding were monitored over 17 days in an inpatient facility. Colonization was assessed by culture and quantitative polymerase chain reaction. Azithromycin was administered from Day 14. The inoculum dose was escalated, aiming to colonize at least 70% of participants. Immunological responses were measured. Results There were 34 participants challenged, in groups of 4 or 5. The dose was gradually escalated from 103 colony-forming units (0% colonized) to 105 colony-forming units (80% colonized). Minor symptoms were reported in a minority of participants. Azithromycin eradicated colonization in 48 hours in 88% of colonized individuals. Antipertussis toxin IgG seroconversion occurred in 9 out of 19 colonized participants and in none of the participants who were not colonized. Nasal wash was a more sensitive method to detect colonization than pernasal swabs. No shedding of Bordetella pertussis was detected in systematically collected environmental samples. Conclusions Bordetella pertussis colonization can be deliberately induced and leads to a systemic immune response without causing pertussis symptoms. Clinical Trials Registration NCT03751514.

Midturbinate Swabs Are Comparable to Nasopharyngeal Swabs for Quantitative Detection of Respiratory Syncytial Virus in Infants

2018 ◽  
Vol 8 (6) ◽  
pp. 554-558 ◽  
Author(s):  
Anne J Blaschke ◽  
Matt McKevitt ◽  
Krow Ampofo ◽  
Tammi Lewis ◽  
Hao Chai ◽  
...  
Keyword(s):  
Polymerase Chain Reaction ◽  
Respiratory Syncytial Virus ◽  
Real Time ◽  
Reverse Transcription ◽  
Quantitative Polymerase Chain Reaction ◽  
Quantitative Detection ◽  
Chain Reaction ◽  
Viral Loads ◽  
Polymerase Chain ◽  
Syncytial Virus

Abstract Nasopharyngeal (NP) swabs are generally used to detect respiratory syncytial virus (RSV) in infants. However, midturbinate (MT) swabs may provide comparable results. In this study, we enrolled hospitalized infants aged <24 months with RSV and collected NP and MT swabs. The resulting viral loads measured by real-time reverse-transcription quantitative polymerase chain reaction were similar. Most parents preferred MT swabs over NP swabs.

scholarly journals High prevalence ofLegionellain non-passenger merchant vessels

2016 ◽  
Vol 145 (4) ◽  
pp. 647-655 ◽  
Author(s):  
S. L. COLLINS ◽  
D. STEVENSON ◽  
M. MENTASTI ◽  
A. SHAW ◽  
A. JOHNSON ◽  
...  
Keyword(s):  
Legionella Pneumophila ◽  
Potable Water ◽  
Quantitative Polymerase Chain Reaction ◽  
Indicator Bacteria ◽  
Chain Reaction ◽  
Three Samples ◽  
High Prevalence ◽  
Polymerase Chain ◽  
The Uk ◽  
Sequence Types

SUMMARYThere is a paucity of information on the risk from potable water in non-passenger merchant vessels (NPMVs) particularly with regard toLegionellaand other bacteria. This retrospective study examined water samples from 550 NPMVs docked in eight UK ports. A total of 1027 samples from 412 NPMVs were examined for total aerobic colony counts (ACC), coliforms,Escherichia coliand enterococci; 41% of samples yielded ACC above the action level (>1 × 103c.f.u./ml) and 4·5% contained actionable levels (>1 c.f.u./100 ml) of faecal indicator bacteria. Eight hundred and three samples from 360 NPMVs were cultured specifically forLegionellaand 58% of vessels proved positive for these organisms with 27% of samples showing levels greater than the UK upper action limit of 1 × 103c.f.u./l. Cabin showers (49%) and hospital shower (45%) were frequently positive. A subset of 106 samples was analysed by quantitative polymerase chain reaction forLegionellaand identified a further 11Legionella-positive NPMVs, returning a negative predictive value of 100%. There was no correlation between NPMV age or size and any microbial parameters (P> 0·05).Legionella pneumophilaserogroup 1 was isolated from 46% of NPMVs and sequence-based typing of 17 isolates revealed four sequence types (STs) previously associated with human disease. These data raise significant concerns regarding the management of microbial andLegionellarisks on board NPMVs and suggest that better guidance and compliance are required to improve control.

scholarly journals Evaluation of GBV-C / HVG viremia in HIV-infected women

2012 ◽  
Vol 54 (1) ◽  
pp. 31-35 ◽  
Author(s):  
Synara Araújo Silva ◽  
Célia Lima Rodrigues ◽  
Aléia Faustino Campos ◽  
José Eduardo Levi
Keyword(s):  
Polymerase Chain Reaction ◽  
Real Time ◽  
Quantitative Polymerase Chain Reaction ◽  
Polymerase Chain Reaction Method ◽  
Taqman Assay ◽  
Chain Reaction ◽  
Viral Loads ◽  
Additional Information ◽  
Factors Influencing ◽  
Polymerase Chain

The present study aimed at standardizing a real-time quantitative polymerase chain reaction assay to evaluate the presence of GBV-C/HGV RNA. A "TaqMan" assay using primers and probe derived from the 5¢ NCR region was developed and validated. Two hundred and fifty-three plasma samples from HIV-infected women were tested for GBV-C viremia and antibody against the envelope protein 2. GBV-C RNA was detected in 22.5% of the patients whereas the antibody was identified in 25.3% of the cohort. Detection of viral RNA and of antibodies was mutually exclusive. Viral loads showed a mean of 1,777 arbitrary units / mL, being 1.1 and 13,625 arbitrary units / mL respectively the lowest and highest values measured. We conclude that the real-time quantitative polymerase chain reaction method developed is appropriate for the investigation of GBV-C RNA since it was shown to be highly specific and sensitive, as well as requiring few steps, preventing contamination and providing additional information as to the relative viremia of carriers, a parameter that must be included in studies evaluating the co-factors influencing the clinical outcome of HIV/AIDS.

scholarly journals Torque teno sus virus 1 and 2 viral loads in faeces of porcine circovirus 2-positive pigs

2015 ◽  
Vol 84 (2) ◽  
pp. 91-95 ◽  
Author(s):  
Alessandra M. M. G. de Castro ◽  
Cintia M. Baldin ◽  
Cintia M. Favero ◽  
Priscilla F. Gerber ◽  
Rafael I. Cipullo ◽  
...  
Keyword(s):  
Quantitative Polymerase Chain Reaction ◽  
Porcine Circovirus ◽  
Age Group ◽  
Nursery Pigs ◽  
Viral Loads ◽  
Faecal Samples ◽  
Disease Condition ◽  
Porcine Circovirus 2 ◽  
Polymerase Chain ◽  
Torque Teno Sus Virus

Recently, studies have suggested an association between the Torque teno sus virus (TTSuV) and the Porcine circovirus-2 (PCV2) in PCV2-associated disease cases. The aim of this study was to verify TTSuVs loads in pig faeces from PCV2-positive animals with and without diarrhea from PCVAD-affected and PCV2-unvaccinated herds. A total of 80 faecal samples were collected individually from nursery and grow-finish pigs with (n = 40) or without (n = 40) diarrhea. The samples were tested for PCV2 and TTSuVs by using DNA binding dye SYBR Green quantitative polymerase chain reaction (qPCR). Torque teno sus virus k2 (TTSuVk2) load in the faeces was significantly higher in the nursery pigs with diarrhea, and these pigs also exhibited significantly higher PCV2 (P < 0.01) faecal matter loads compared to the non-diarrheic animals from the same age group. Torque teno sus virus 1 (TTSuV1) viral loads were the same regardless of age group and disease condition. There were no correlations between PCV2 and TTSuV1 or TTSuVk2 and TTSuV1 viral loads; however, a weak correlation (r = 0.23, P = 0.03) was found between TTSuVk2 and PCV2 viral loads. In conclusion, TTSuVk2 viral loads were significantly higher in the diarrheic faeces from the nursery pigs. Additionally, the higher loads of PCV2 and TTSuVk2 in the nursery-diarrheic animals revealed that diarrhea might have an important role in the spread of both viruses in herds.

scholarly journals High prevalence of carriage of mcr-1-positive enteric bacteria among healthy children from rural communities in the Chaco region, Bolivia, September to October 2016

2018 ◽  
Vol 23 (45) ◽  
Author(s):  
Tommaso Giani ◽  
Samanta Sennati ◽  
Alberto Antonelli ◽  
Vincenzo Di Pilato ◽  
Tiziana di Maggio ◽  
...  
Keyword(s):  
Rural Communities ◽  
National Level ◽  
Enteric Bacteria ◽  
Resistant Bacteria ◽  
Healthy Children ◽  
Antibiotic Resistant ◽  
Rural Villages ◽  
Professional Exposure ◽  
High Prevalence ◽  
Chaco Region

Background The mcr-1 gene is a transferable resistance determinant against colistin, a last-resort antimicrobial for infections caused by multi-resistant Gram-negatives. Aim To study carriage of antibiotic-resistant bacteria in healthy school children as part of a helminth control and antimicrobial resistance survey in the Bolivian Chaco region. Methods From September to October 2016 we collected faecal samples from healthy children in eight rural villages. Samples were screened for mcr-1- and mcr-2 genes. Antimicrobial susceptibility testing was performed, and a subset of 18 isolates representative of individuals from different villages was analysed by whole genome sequencing (WGS). Results We included 337 children (mean age: 9.2 years, range: 7–11; 53% females). The proportion of mcr-1 carriers was high (38.3%) and present in all villages; only four children had previous antibiotic exposure. One or more mcr-1-positive isolates were recovered from 129 positive samples, yielding a total of 173 isolates (171 Escherichia coli, 1 Citrobacter europaeus, 1 Enterobacter hormaechei). No mcr-2 was detected. Co-resistance to other antimicrobials varied in mcr-positive E. coli. All 171 isolates were susceptible to carbapenems and tigecycline; 41 (24.0%) were extended-spectrum β-lactamase producers and most of them (37/41) carried bla CTX-M-type genes. WGS revealed heterogeneity of clonal lineages and mcr-genetic supports. Conclusion This high prevalence of mcr-1-like carriage, in absence of professional exposure, is unexpected. Its extent at the national level should be investigated with priority. Possible causes should be studied; they may include unrestricted use of colistin in veterinary medicine and animal breeding, and importation of mcr-1-positive bacteria via food and animals.

scholarly journals Polyester Nasal Swabs Collected in a Dry Tube are a Robust and Inexpensive, Minimal Self-Collection Kit for SARS-CoV-2 Testing

2020 ◽  
Author(s):  
Leah R. Padgett ◽  
Lauren A. Kennington ◽  
Charlotte L. Ahls ◽  
Delini K. Samarasinghe ◽  
Yuan-Po Tu ◽  
...  
Keyword(s):  
Elevated Temperatures ◽  
Quantitative Polymerase Chain Reaction ◽  
High Capacity ◽  
Cold Chain ◽  
Load Testing ◽  
Clinical Specimens ◽  
Viral Loads ◽  
Nasal Swabs ◽  
Polymerase Chain ◽  
Phosphate Buffered Saline

AbstractBackgroundPolyester nasal swabs stored in saline or in a dry tube were evaluated as an alternative to foam nasal swabs for SARS-CoV-2 testing by reverse transcription quantitative polymerase chain reaction (RT-qPCR) since they may be inexpensively manufactured at high capacity.MethodsSurrogate clinical specimens were prepared by inoculating foam and polyester nasal swabs with residual SARS-CoV-2 positive clinical specimens diluted in porcine or human matrix. Dry swab elution with phosphate buffered saline (PBS) was evaluated by vortex, swab swirling, and passive methodologies. Surrogate and clinical nasal specimen stability were evaluated at refrigerated (4°C) and elevated temperatures (40°C for 12 hours, 32°C hold) through 72 hours.ResultsPolyester swabs demonstrated equivalent performance to foam swabs for detection of low and high SARS-CoV-2 viral loads. Dry swab elution performed with PBS and mechanical disruption by vortex resulted in nearly complete quantitative recovery of virus. Dry polyester and foam surrogate specimens were stable through 72 hours both when refrigerated and after high temperature excursion, which simulated specimen transport without cold chain. Similarly, clinical specimens collected with polyester swabs and stored dry were stable through 72 hours in the presence and absence of cold chain. Polyester surrogate specimens stored in saline were stable through 72 hours refrigerated but only through 48 hours at elevated temperatures.ConclusionsPolyester nasal swabs stored in dry collection tubes comprise a robust and inexpensive self-collection method for SARS-CoV-2 viral load testing, which is stable under conditions required for home collection and shipment to the laboratory.

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