Wastewater-based epidemiology has shown to be a promising and innovative approach to measure a wide variety of illicit drugs that are consumed in the communities. In the same way as for illicit ...drugs, wastewater-based epidemiology is a promising approach to understand the prevalence of viruses in a community-level.
The ongoing coronavirus disease 2019 (COVID-19) pandemic created an unprecedented burden on public health and diagnostic laboratories all over the world because of the need for massive laboratory testing. Many studies have shown the applicability of a centralized wastewater-based epidemiology (WBE) approach, where samples are collected at WWTPs. A more recent concept is a decentralized approach for WBE where samples are collected at different points of the sewer system and at polluted water bodies. The second being particularly important in countries where there are insufficient connections from houses to municipal sewage pipelines and thus untreated wastewater is discharged directly in environmental waters.
A decentralized approach can be used to focus the value of diagnostic tests in what we call targeted-WBE, by monitoring wastewater in parts of the population where an outbreak is likely to happen, such as student dorms, retirement homes and hospitals. A combination of centralized and decentralized WBE should be considered for an affordable, sustainable, and successful WBE implementation in high-, middle- and low-income countries.
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Whole-genome sequencing (WGS) has become an essential tool for public health surveillance and molecular epidemiology of infectious diseases and antimicrobial drug resistance. It provides precise ...geographical delineation of spread and enables incidence monitoring of pathogens at genotype level. Coupled with epidemiological and environmental investigations, it delivers ultimate resolution for tracing sources of epidemic infections. To ascertain the level of implementation of WGS-based typing for national public health surveillance and investigation of prioritized diseases in the European Union (EU)/European Economic Area (EEA), two surveys were conducted in 2015 and 2016. The surveys were designed to determine the national public health reference laboratories' access to WGS and operational WGS-based typing capacity for national surveillance of selected foodborne pathogens, antimicrobial-resistant pathogens, and vaccine-preventable diseases identified as priorities for European genomic surveillance. Twenty-eight and twenty-nine out of the 30 EU/EEA countries participated in the survey in 2015 and 2016, respectively. National public health reference laboratories in 22 and 25 countries had access to WGS-based typing for public health applications in 2015 and 2016, respectively. Reported reasons for limited or no access were lack of funding, staff, and expertise. Illumina technology was the most frequently used followed by Ion Torrent technology. The access to bioinformatics expertise and competence for routine WGS data analysis was limited. By mid-2016, half of the EU/EEA countries were using WGS analysis either as first- or second-line typing method for surveillance of the pathogens and antibiotic resistance issues identified as EU priorities. The sampling frame as well as bioinformatics analysis varied by pathogen/resistance issue and country. Core genome multilocus allelic profiling, also called cgMLST, was the most frequently used annotation approach for typing bacterial genomes suggesting potential bioinformatics pipeline compatibility. Further capacity development for WGS-based typing is ongoing in many countries and upon consolidation and harmonization of methods should enable pan-EU data exchange for genomic surveillance in the medium-term subject to the development of suitable data management systems and appropriate agreements for data sharing.
There is a lack of long-term studies that correlate different metrics of antibiotic consumption and resistance of invasive
The present study aims to investigate the correlation between national ...outpatients total antibiotic, penicillin and broad spectrum penicillins consumption expressed in daily doses per 1000 inhabitants per day (DID) with the ATC/DDDs, WHO version of 2019 (new version) and 2018 (old version), number of prescriptions per 1000 inhabitants per year (RxIDs) and number of packages per 1000 inhabitant per day (PIDs) with the resistance of invasive
in Slovenia in the period from 2000 to 2018. The prevalence of penicillin resistance of invasive
decreased by 47.13%, from 19.1% to 10.1%. Decline of resistance showed the highest correlation (R = 0.86) between RxIDs followed by PID (R = 0.85) and resistance of
. Higher correlation between total use of antibiotics expressed in DID WHO version 2019 (R = 0.80) than for WHO version 2018 (R = 0.78) was found. Very high (R = 0.84) correlation between use of β-lactams expressed in PID, and RxIDs (R = 0.82) and reasonable (R = 0.59) correlation expressed in DIDs version 2019 was shown as well. The consumption of broad -spectrum penicillins (J01CA and J01CR02) expressed in PID (R = 0.72) and RxIDs (0.57) correlated significantly with the resistance of
as well. A new finding of this study is that RxIDs correlated better with the resistance of
than total consumption of antibiotics expressed in DID and significant correlations exist between use of broad-spectrum penicillins expressed in PID and RxIDs.
The aim of this study was to present the epidemiology of invasive diseases caused by Neisseria meningitidis and Streptococcus pneumoniae in the pre-vaccine period, and Haemophilus influenzae in the ...post-vaccine period in a pediatric population from Serbia. Among the meningococci, serogroup B dominated (83%), followed by serogroup C (11.3%). High antigenic diversity was found, with fine type P1.5-1,10-4 being the most frequent. Moderate susceptibility to penicillin was common (55%). Within pneumococci, serotypes 19F, 14, 6B, 6A, 18C, 23F, 3, and 7F prevailed, while 19A was rare (3.6%). The coverages of PCV10 and PCV13 were 68% and 84%, respectively. Major sequence types were ST320, ST15, ST273, ST271, and ST81. Non-susceptibility to penicillin (66.7%), cefotaxime (37%), and macrolides (55%) was predominantly detected in vaccine-related serotypes. Among the 11 invasive H. influenzae isolates collected, there were six Hib, three non-type b, and two non-typeable strains (ntHi) that were antibiotic susceptible. These results imply a potential benefit of future Men-B vaccine implementations. For pneumococci, as PCV10 was recently introduced, a significant reduction of morbidity and antibiotic resistance might be expected. The efficiency of Hib vaccination is evident, but a shift towards non-type b and ntHi strains may be anticipated.
Previous studies on SARS-CoV and MERS-CoV reported the detection of viral RNA in the stool of both symptomatic and asymptomatic individuals. These clinical observations suggest that municipal and ...hospital wastewater from affected communities may contain SARS-CoV-2 RNA. Recent studies have also reported the presence of SARS-CoV-2 RNA in human feces. Wastewater-based epidemiology (WBE) is a promising approach to understand the prevalence of viruses in a given catchment population, as wastewater contains viruses from symptomatic and asymptomatic individuals. The current study reports the first detection of SARS-CoV-2 RNA in untreated wastewater in Slovenia. Two sizes of centrifugal filters were tested: 30 kDa and 10 kDA AMICON® Ultra-15 Centrifugal Filters, where 10 kDA resulted in a higher concentration factor and higher recovery efficiency. The results in hospital wastewater show that WBE can be used for monitoring COVID −19 and could be applied in municipal wastewater treatment plants as a potential complementary tool for public health monitoring at population level.
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•The first study in Slovenia that reports the detection of SARS-CoV-2 in untreated wastewater.•66.7% (10/15) of untreated hospital wastewater samples tested positive for at least one SARS-CoV-2 RT-qPCR target.•SARS-CoV-2 RNA was detected in untreated hospital wastewater when only one COVID-19 patient was hospitalized.
In Slovenia, there is little data available on pneumococcal vaccination rates and no data on asymptomatic NPCR and serotypes in the population of nursing home residents in comparison to the elderly ...living in domestic environment, therefore the goal was to gain these data.
A cross sectional epidemiological study was performed. Nasopharyngeal swabs from 151 nursing home residents, 150 elderly living in domestic environment, and 38 adults less than 65 years old were collected twice (in two consecutive years). The swabs were analysed for pneumococcal identification and serotyping. Patient data were collected from medical files and medical history.
No statistically significant differences in NPCR were seen between compared groups in two consecutive years. An average NPCR in two consecutive years in nursing home residents was 1.45%, in the elderly living in domestic environment 0.85%, and in adults less than 65 years old 7.05%. Serotypes identified among nursing home residents were 6B and 9N, among the group of elderly living in domestic environment, 6A and among adults less than 65 years old, 35F, 18C and 3. Pneumococcal vaccination rates were low (3.3% in nursing home residents, 6% in the elderly from domestic environment and 0% in the group of adults less than 65 years old).
Our data suggests that NPCR and the proportion of people vaccinated with pneumococcal vaccine among the elderly are low. We identified different serotypes in all groups, only one person was a chronic carrier (serotype 35F).
COVID-19 is a persistent and ongoing global pandemic caused by the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). Non-anthropogenic factors, such as weather conditions and air quality ...are possible predictors of respiratory diseases, such as COVID-19. Weather conditions may also be a direct cause of biological interactions between SARS-CoV-2 and humans and vary widely between regions. The course of an epidemic is determined by several factors, including demographic and environmental parameters, many of which have an unknown correlation with COVID-19. The goal of this study is to access the influence of ground surface particulate matter and weather parameters on the dissemination of COVID-19 in Ljubljana, Slovenia.
Spearman rank correlation was used to investigate the association between new daily COVID-19 cases and weather data.
The current study has found correlations between weather variables and PM particles with new cases of COVID-19.
The correlations observed are highly dependent on the local policies that were in force during the period under study. The interaction between weather conditions and human behaviour may also be an important factor in understanding the relationship between weather and the spread of COVID -19.
Little is known about contaminated surfaces as a route of transmission for SARS-CoV- 2 and a systematic review is missing and urgently needed to provide guidelines for future research studies. As ...such, the aim of the present study was to review the current scientific knowledge and to summarize the existing studies in which SARS-CoV-2 has been detected in inanimate surfaces. This systematic review includes studies since the emergence of SARS-CoV-2, available in PubMed/MEDLINE and Scopus. Duplicate publications were removed, and exclusion criteria was applied to eliminate unrelated studies, resulting in 37 eligible publications. The present study provides the first overview of SARS-CoV-2 detection in surfaces. The highest detection rates occurred in hospitals and healthcare facilities with COVID-19 patients. Contamination with SARS-CoV-2 on surfaces was detected in a wide range of facilities and surfaces. There is a lack of studies performing viability testing for SARS-CoV-2 recovered from surfaces, and consequently it is not yet possible to assess the potential for transmission via surfaces.
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•SARS-CoV-2 RNA has been detected in a wide range of facilities and surfaces;•17.7% of samples in hospital settings and 10.1% in non-hospital settings were positive for SARS-CoV-2 RNA, using various molecular methods;•6 out of the 37 studies have evaluated the viability/infectivity of SARS-CoV-2 from 242 positive surface samples;•No viable virus could be isolated from the 242 samples with SARS-CoV-2 RNA detected by RT-qPCR;•COVID-19 fomite transmission has not been demonstrated.
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