High throughput application of ASTM D8332: Detailed prototype design and operating conditions for microplastic sampling of riverine systems

Microplastic sampling strategies for aquatic systems commonly employ small mesh nets to collect suspended microparticles. These methods work well for marine sampling campaigns; however, complex water systems such as freshwater rivers, effluent discharges, and stormwater ponds characterized by high total suspended solids and fast-moving water can cause the nets to clog, rip, or tear. Published in 2020, ASTM D8332 is an alternative approach to sampling complex water systems for microplastics involving pumping large volumes of water across a cascading stack of sieves to collect suspended particles. Here we show that ASTM D8332 can be applied to sample freshwater rivers for microplastic collection. A high throughput sampling prototype developed in this work is capable of pumping 1500 L of river water in 45 min to collect particles as small as 45 µm. The system is lightweight, modular, and easily transportable. It has a discrete power supply, allowing for the collection of microplastics anywhere along the river, including municipal discharges. The design minimizes the amount of plastic in the flow path and provides a practical way to measure field contamination. Finally, we outline lessons learned through extensive field trials and testing using this system sampling the North Saskatchewan River in Edmonton, Alberta. •Existing small mesh nets face limitations in freshwater rivers, encountering clogging and tearing issues from high suspended solids and fast moving water.•Using a standardized method, ASTM D8332 - a pumping-based approach is efficient for microplastic collection in freshwater rivers.•Lightweight, modular, plastic free prototype system pumps 1500 L of river water in 45 min, collecting particles as small as 45 µm. Successfully tested in the North Saskatchewan River.

Assessment of mould remediation in a healthcare setting following extensive flooding

BACKGROUND

A new hospital building was close to completion when a large pipe carrying clean water broke, causing extensive flooding.

AIM

To determine the flood-associated fungal risk to susceptible patients who would use that building.

METHODS

Though standard flood remediation by the builders was relatively straightforward, there was no model for specialist assessment of patient risk due to the flood-associated mould growth. As levels of background airborne fungal spores can be expected to vary significantly over time, we could not use absolute levels to indicate either an excess of airborne fungal spores or successful remediation. Therefore it was decided to use weekly settle plates, exposed at the same time in flooded (test) and equivalent non-flooded (control) areas to compensate for variations in background levels. Flood-related risk was estimated by the ratio between fungal colonies on the test and control sets of settle plates, rather than absolute number.

FINDINGS

Whereas the physical flood remediation, including the use of 'anti-fungal' treatments, was completed in three weeks post flooding, fungal contamination in flooded areas took 38 weeks to return to control levels and remained so for a further six weeks of observation.

CONCLUSION

By the use of this method, we were able to assure the absence of flood-associated fungal risk to susceptible patients who would use that building. We recommend that infection prevention and control teams consider using this approach should they be faced with similar situations.

Aggregative Soil Sampling Using Boot Covers Compared to Soil Grabs From Commercial Romaine Fields Shows Similar Indicator Organism and Microbial Community Recoveries

Aggregative boot cover sampling may be a more representative, practical, and powerful method for preharvest produce soil testing than grab sampling because boot covers aggregate soil from larger areas. Our study tests if boot cover sampling results reflect quality and safety indicator organisms and community diversity of grab sampling. We collected soil samples from commercial romaine lettuce fields spanning 5060 m2 using boot covers (n = 28, m = 1.1 ± 0.4 g; wearing boot covers and walking along the path), composite grabs (n = 28, m = 231 ± 24 g; consisting of 60 grabs of 3-5 g each), and high-resolution grabs (n = 72, m = 56 ± 4 g; taking one sample per stratum). Means and standard deviations of log-transformed aerobic plate counts (APCs) were 7.0 ± 0.3, 7.1 ± 0.2, and 7.3 ± 0.2 log(CFU/g) for boot covers, composite grabs, and high-resolution grabs, respectively. APCs did not show biologically meaningful differences between sample types. Boot covers recovered on average 0.6 log(CFU/g) more total coliforms than both grabs (p < 0.001) where means and standard deviations of log-transformed counts were 3.2 ± 1.0, 2.6 ± 0.6, and 2.6 ± 1.0 log(CFU/g) for boot covers, composite grabs, and high-resolution grabs, respectively. There were no generic E. coli detected in any sample by enumeration methods with LODs of 1.3-2.1 log(CFU/g) for boot covers and 0.5 log(CFU/g) for both grabs. By 16S rRNA sequencing, community species diversity (alpha diversity) was not significantly different within collection methods. While communities differed (p < 0.001) between soil sampling methods (beta diversity), variance in microbial communities was not significantly different. Of the 28 phyla and 297 genera detected, 25 phyla (89%) and 258 genera (87%) were found by all methods. Overall, aggregative boot cover sampling is similar to both grab methods for recovering quality and safety indicator organisms and representative microbiomes. This justifies future work testing aggregative soil sampling for foodborne pathogen detection.

Relative uncertainty-based Bayesian interlaboratory consensus building

An interlaboratory comparison is typically conducted among the laboratories for the purpose of providing quality assurance and control. To solve the interlaboratory agreement problem, a distinct type of metrological challenge, a new uncertainty-based Bayesian strategy was developed and tested among environmental laboratories. A holistic algorithm with the key phases of sampling, outlier analysis, recognition, and simulation-based structure identification was developed and is being addressed in place of conventional indices and plots. Computer simulations showed that the proposed hybrid approach has no discernible sensitivity to outliers and that the agreement structure is transparent and robust. Some meta-data is also generated by the analysis based on relative uncertainty. To measure the performance and capability of Bayesian consensus building algorithm, the uncertainty intervals were established and comparative evaluations have been carried out using the conventional techniques. As a result, the suggested algorithm can explore both the laboratory performances (harmony) and the conformity between two independent samples. The algorithmic procedure features a generalizable framework that may be adapted in other fields to obtain a consensus among the laboratories.

Measurement of SARS-CoV-2 in air and on surfaces in Scottish hospitals

BACKGROUND

There are still uncertainties in our knowledge of the amount of SARS-CoV-2 virus present in the environment - where it can be found, and potential exposure determinants - limiting our ability to effectively model and compare interventions for risk management.

AIM

This study measured SARS-CoV-2 in three hospitals in Scotland on surfaces and in air, alongside ventilation and patient care activities.

METHODS

Air sampling at 200 L/min for 20 min and surface sampling were performed in two wards designated to treat COVID-19-positive patients and two non-COVID-19 wards across three hospitals in November and December 2020.

FINDINGS

Detectable samples of SARS-CoV-2 were found in COVID-19 treatment wards but not in non-COVID-19 wards. Most samples were below assay detection limits, but maximum concentrations reached 1.7×10³ genomic copies/m³ in air and 1.9×10⁴ copies per surface swab (3.2×10² copies/cm² for surface loading). The estimated geometric mean air concentration (geometric standard deviation) across all hospitals was 0.41 (71) genomic copies/m³ and the corresponding values for surface contamination were 2.9 (29) copies/swab. SARS-CoV-2 RNA was found in non-patient areas (patient/visitor waiting rooms and personal protective equipment changing areas) associated with COVID-19 treatment wards.

CONCLUSION

Non-patient areas of the hospital may pose risks for infection transmission and further attention should be paid to these areas. Standardization of sampling methods will improve understanding of levels of environmental contamination. The pandemic has demonstrated a need to review and act upon the challenges of older hospital buildings meeting current ventilation guidance.

Optimizing sample collection methods for detection of respiratory viruses in poultry housing environments

Viral respiratory diseases, such as avian influenza, Newcastle disease, infectious bronchitis, and infectious laryngotracheitis, have considerable negative economic implications for poultry. Ensuring the virus-free status of a premises by environmental sampling after cleaning and disinfection is essential for lifting a quarantine and/or safely restocking the premises following an outbreak. The objectives of this study were to identify optimal sample collection devices and to determine the locations in poultry housing which are best for poultry respiratory virus sample collection. Chickens exposed to infectious bronchitis virus, which was used as a representative virus for enveloped poultry respiratory viruses, were housed in floor-pens in either a curtain-sided wood framed house or a cement block house. Foam swabs, cellulose sponges, polyester swabs, dry cotton gauze and pre-moistened cotton gauze were evaluated for comparative efficiency in recovering viral RNA. Cotton gauze pre-moistened with the viral transport media had the highest sensitivity among the devices (wood-framed house: 78% positive, geometric mean titer [GMT] of 2.6 log₁₀ 50% egg infectious doses [EID₅₀ ] equivalents/ml; cement-block houses: 55% positive, GMT of 1.7 log₁₀ EID₅₀ equivalents/ml). Targeting virus deposition sites is also crucial for efficient virus elimination procedures and subsequent testing, therefore 10 locations within the houses were compared for virus detection. In both housing types the highest viral RNA loads were recovered from the top of drinker lines within the pen. Places the chickens could contact directly (e.g., feeder rim) or were contacted by caretaker feet (hallway floor) also yielded higher levels of viral RNA more consistently. These results will facilitate the establishment of efficient environmental sampling procedures for respiratory viruses of poultry. This article is protected by copyright. All rights reserved.

Clinical application of 222 nm wavelength ultraviolet C irradiation on SARS CoV-2 contaminated environments

This was a preliminary study on ultraviolet C (UVC) irradiation for SARS-CoV-2-contaminated hospital environments. Forty-eight locations were tested for SARS-CoV-2 using RT-PCR (33.3% contamination rate). After series dosages of 222-nm UVC irradiation, samples from the surfaces were negative at 15 s irradiation at 2 cm length (fluence: 81 mJ/cm²).

Characterizing the bioburden of ESBL-producing organisms in a neonatal unit using chromogenic culture media: a feasible and efficient environmental sampling method

INTRODUCTION

Infections due to extended spectrum beta-lactamase producing organisms (ESBL) have emerged as the leading cause of sepsis among hospitalized neonates in Botswana and much of sub-Saharan Africa and south Asia. Yet, ESBL reservoirs and transmission dynamics within the neonatal intensive care unit (NICU) environment are not well-understood. This study aimed to assess the efficiency and feasibility of a chromogenic-culture-media-based environmental sampling approach to characterize the ESBL bioburden within a NICU.

METHODS

A series of four point-prevalence surveys were conducted at a 36-bed NICU at a public tertiary referral hospital in Botswana from January-June 2021. Samples were collected on 4 occasions under semi-sterile technique using 1) flocked swabs & templates (flat surfaces); 2) sterile syringe & tubing (water aspiration); and 3) structured swabbing techniques (hands & equipment). Swabs were transported in physiological saline-containing tubes, vortexed, and 10 µL was inoculated onto chromogenic-agar that was selective and differential for ESBL (CHROMagar™ ESBL, Paris, France), and streaking plates to isolate individual colonies. Bacterial colonies were quantified and phenotypically characterized using biochemical identification tests.

RESULTS

In total, 567 samples were collected, 248 (44%) of which grew ESBL. Dense and consistent ESBL contamination was detected in and around sinks and certain high-touch surfaces, while transient contamination was demonstrated on medical equipment, caregivers/healthcare worker hands, insects, and feeding stations (including formula powder). Results were available within 24-72 h of collection. To collect, plate, and analyse 50 samples, we estimated a total expenditure of $269.40 USD for materials and 13.5 cumulative work hours among all personnel.

CONCLUSIONS

Using basic environmental sampling and laboratory techniques aided by chromogenic culture media, we identified ESBL reservoirs (sinks) and plausible transmission vehicles (medical equipment, infant formula, hands of caregivers/healthcare workers, & insects) in this NICU environment. This strategy was a simple and cost-efficient method to assess ESBL bioburden and may be feasible for use in other settings to support ongoing infection control assessments and outbreak investigations.

Bayesian accuracy estimates of environmental sampling for determining herd paratuberculosis infection status and its association with the within-herd individual fecal culture prevalence in Québec dairies

The objectives of this retrospective analysis were to: 1) estimate the diagnostic sensitivity (Se) and specificity (Sp) of bacterial culture of environmental samples for determining Mycobacterium avium subsp. paratuberculosis (MAP) infection status in Québec dairies, using a Bayesian Latent Class Model (BLCM); and 2) determine the association between the number of positive environmental samples and the individual fecal culture (IFC) apparent and true MAP within-herd prevalence. Environmental and individual fecal samples were collected from 87 commercial dairy herds participating in previous research projects. Environmental samples included two composite samples of 20 g collected from different locations within each of the following sites: an area where manure from the majority of adult cattle accumulates, a manure storage area and another site of manure accumulation chosen by the veterinarian. Samples were cultured using the MGIT Para TB culture liquid media and the BACTEC MGIT 960 system. The Se and Sp of environmental sampling were estimated using a one-test-one-population BLCM. Herds were considered positive for environmental sampling if at least one out of the six samples collected was positive. The apparent and true IFC within-herd MAP prevalence estimates for each herd were obtained using a two-stage cluster BLCM, then merged in a single dataset with the environmental sample results. The association between the within-herd MAP prevalence results (apparent and true), and the number of positive environmental samples was assessed using a zero-inflated negative binomial (ZINB) model. In all BLCMs, median posterior estimates and 95 % Bayesian credible intervals (BCI) were obtained with OpenBUGS statistical freeware. Se and Sp of environmental sampling were 43.7 % (95 % BCI: 32.5-55.5) and 96.2 % (95 % BCI: 84.2-99.8), respectively. Overall, the number of positive environmental samples increased with the apparent and true MAP within-herd prevalence. The true prevalence was higher than the apparent prevalence for a given number of positive environmental samples. The probability of not observing a positive environmental sample decreased with the prevalence. Despite its imperfect accuracy, environmental sampling is an inexpensive and non-invasive sampling method to determine MAP infection status in tie-stall herds that can be used as a proxy to estimate the true within-herd prevalence. The absence of positive environmental samples in a single sampling visit is likely an indicator of a very low within-herd prevalence rather than being MAP exempt.

Detection of Lassa virus in wild rodent feces: Implications for Lassa fever burden within households in the endemic region of Faranah, Guinea

Lassa arenavirus (LASV) is the cause of Lassa Fever in humans in West Africa. The multimammate mouse (Mastomys natalensis) is a reservoir host of LASV and the primary source of human infections. Humans are assumed to become infected due to contact with this animal or its excretions. Thus far, the available literature does not describe the sampling of feces as a means to detect LASV in M. natalensis populations. More evidence is needed to know if feces of naturally infected M. natalensis can be LASV-positive and an exposure risk to humans. This study sampled feces deposits in households from three villages in the LASV-endemic region of Faranah, Guinea. PCR analysis found 10 out of 88 samples to be positive for LASV, and sequencing showed clustering to previously identified Yarawelia and Dalafilani strains. We conclude that feces sampling is a viable, non-invasive method for the determination and sequencing of LASV strains.

Methods for interpolating missing data in aerobiological databases

Missing data is a common problem in scientific research. The availability of extensive environmental time series is usually laborious and difficult, and sometimes unexpected failures are not detected until samples are processed. Consequently, environmental databases frequently have some gaps with missing data in it. Applying an interpolation method before starting the data analysis can be a good solution in order to complete this missing information. Nevertheless, there are several different approaches whose accuracy should be considered and compared. In this study, data from 6 aerobiological sampling stations were used as an example of environmental data series to assess the accuracy of different interpolation methods. For that, observed daily pollen/spore concentration data series were randomly removed, interpolated by using different methods and then, compared with the observed data to measure the errors produced. Different periods, gap sizes, interpolation methods and bioaerosols were considered in order to check their influence in the interpolation accuracy. The moving mean interpolation method obtained the highest success rate as average. By using this method, a success rate of the 70% was obtained when the risk classes used in the alert systems of the pollen information platforms were taken into account. In general, errors were mostly greater when there were high oscillations in the concentrations of biotic particles during consecutive days. That is the reason why the pre-peak and peak periods showed the highest interpolation errors. The errors were also higher when gaps longer than 5 days were considered. So, for completing long periods of missing data, it would be advisable to test other methodological approaches. A new Variation Index based on the behaviour of the pollen/spore season (measurement of the variability of the concentrations every 2 consecutive days) was elaborated, which allows to estimate the potential error before the interpolation is applied.

Successful Isavuconazole Salvage Therapy for a Cryptococcus deuterogattii (AFLP6/VGII) Disseminated Infection in a European Immunocompetent Patient

Members of the Cryptococcus gattii species complex are notorious causes of cryptococcosis as they often cause severe, life-threatening infections. Here we describe a case of a severe disseminated C. deuterogattii infection in a previously healthy patient who was initially treated with amphotericin B, 5-fluorocytosine and fluconazole, which led to a good neurological response, but the infection in the lungs remained unaltered and was not completely resolved until switching the antifungal therapy to isavuconazole. The infection was likely acquired during a one-month stay at the Azores Islands, Portugal. Environmental sampling did not yield any cryptococcal isolate; therefore, the source of this apparent autochthonous case could not be determined. Molecular typing showed that the cultured C. deuterogattii isolates were closely related to the Vancouver Island outbreak-genotype.

SARS-CoV-2 in hospital indoor environments is predominantly non-infectious

Background

The ongoing SARS-CoV-2 pandemic has spread rapidly worldwide and disease prevention is more important than ever. In the absence of a vaccine, knowledge of the transmission routes and risk areas of infection remain the most important existing tools to prevent further spread.

Methods

Here we investigated the presence of the SARS-CoV-2 virus in the hospital environment at the Uppsala University Hospital Infectious Disease ward by RT-qPCR and determined the infectivity of the detected virus in vitro on Vero E6 cells.

Results

SARS-CoV-2 RNA was detected in several areas, although attempts to infect Vero E6 cells with positive samples were unsuccessful. However, RNase A treatment of positive samples prior to RNA extraction did not degrade viral RNA, indicating the presence of SARS-CoV-2 nucleocapsids or complete virus particles protecting the RNA as opposed to free viral RNA.

Conclusion

Our results show that even in places where a moderate concentration (Ct values between 30 and 38) of SARS-CoV-2 RNA was found; no infectious virus could be detected. This suggests that the SARS-CoV-2 virus in the hospital environment subsides in two states; as infectious and as non-infectious. Future work should investigate the reasons for the non-infectivity of SARS-CoV-2 virions.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12985-021-01556-6.

Environmental sampling of volatile organic compounds during the 2018 Camp Fire in Northern California

Trace analysis of volatile organic compounds (VOCs) during wildfires is imperative for environmental and health risk assessment. The use of gas sampling devices mounted on unmanned aerial vehicles (UAVs) to chemically sample air during wildfires is of great interest because these devices move freely about their environment, allowing for more representative air samples and the ability to sample areas dangerous or unreachable by humans. This work presents chemical data from air samples obtained in Davis, CA during the most destructive wildfire in California's history - the 2018 Camp Fire - as well as the deployment of our sampling device during a controlled experimental fire while fixed to a UAV. The sampling mechanism was an in-house manufactured micro-gas preconcentrator (µPC) embedded onto a compact battery-operated sampler that was returned to the laboratory for chemical analysis. Compounds commonly observed in wildfires were detected during the Camp Fire using gas chromatography mass spectrometry (GC-MS), including BTEX (benzene, toluene, ethylbenzene, m+p-xylene, and o-xylene), benzaldehyde, 1,4-dichlorobenzene, naphthalene, 1,2,3-trimethylbenzene and 1-ethyl-3-methylbenzene. Concentrations of BTEX were calculated and we observed that benzene and toluene were highest with average concentrations of 4.7 and 15.1 µg/m³, respectively. Numerous fire-related compounds including BTEX and aldehydes such as octanal and nonanal were detected upon experimental fire ignition, even at a much smaller sampling time compared to samples taken during the Camp Fire. Analysis of the air samples taken both stationary during the Camp Fire and mobile during an experimental fire show the successful operation of our sampler in a fire environment.

Evaluation of Methods of Enrichment and Compositing of Environmental Samples for Detection of Listeria monocytogenes

ABSTRACT

Various methods exist for the enrichment and detection of Listeria spp. and Listeria monocytogenes from environmental samples. Procedures for the compositing of environmental samples are not as well defined. In this study, different enrichment procedures involving buffered Listeria enrichment broth (BLEB), University of Vermont medium (UVM), and Fraser broth (FB) were evaluated to determine the limits of detection (LODs) for L. monocytogenes from culture and from swabs of stainless steel and to assess the efficacy of composite sampling by wet (pooling of primary enrichments) and dry (pooling of swabs) procedures. For detection of cells in pure culture, the computed values for the LOD at 95% probability (LOD95) using a single-step BLEB or two-step UVM-FB enrichment were 0.33 and 0.49 CFU/225 mL enrichment, respectively. No significant differences in detection were observed for procedures using either two-step BLEB-FB or UVM-FB enrichments for swabs of stainless steel when L. monocytogenes was inoculated at 2 to 6 log CFU; the LOD95 values were 3.82 and 3.62 log CFU per 4-in2 area, respectively. Wet compositing of L. monocytogenes from culture with and without romaine lettuce wash resident microbiota was conducted using BLEB-FB and UVM-FB enrichment methods; both allowed detection of the pathogen at ratios of 1:1, 1:2, 1:4, and 1:7 (1 positive sample to x negative samples) with no loss in sensitivity. From swabs of stainless steel, L. monocytogenes was detected similarly for both wet and dry composites of up to eight samples (1:7) with romaine lettuce wash. However, the BLEB-FB method allowed significantly faster detection (after 24 h of FB incubation) in composites of 1:4 and 1:7 samples compared with the UVM-FB method under the conditions tested. The results of this study provide data to evaluate the efficacies of the different enrichment procedures and aid in assessing the use of wet and dry compositing of environmental samples for use as part of a Listeria control plan in food production and processing facilities.

HIGHLIGHTS

Successful containment of two vancomycin-resistant Enterococcus faecium (VRE) outbreaks in a Dutch teaching hospital using environmental sampling and whole-genome sequencing

BACKGROUND

Vancomycin-resistant enterococci (VRE) may cause nosocomial outbreaks. This article describes all VRE carriers that were identified in 2018 at Elisabeth-Tweesteden Hospital, Tilburg, The Netherlands.

AIM

To investigate the genetic relatedness of VRE isolates and the possibility of a common environmental reservoir using environmental sampling and whole-genome sequencing (WGS).

METHODS

Infection control measures consisted of contact isolation, contact surveys, point prevalence screening, environmental sampling, cleaning and disinfection. VRE isolates were sequenced using a MiSeq sequencer (Illumina, San Diego, CA, USA), and assembled using SPAdes v.3.10.1. A minimal spanning tree and a neighbour joining tree based on allelic diversity of core-genome multi-locus sequence typing and accessory genes were created using Ridom SeqSphere+ software (Ridom GmbH, Münster, Germany).

FINDINGS

Over a 1-year period, 19 VRE carriers were identified; of these, 17 were part of two outbreaks. Before environmental cleaning and disinfection, 55 (14%) environmental samples were VRE-positive. Fifty-one isolates (23 patient samples and 28 environmental samples) were available for WGS analysis. Forty-four isolates were assigned to ST117-vanB, five were assigned to ST17-vanB, and two were assigned to ST80-vanB. Isolates from Outbreak 1 (N=22) and Outbreak 2 (N=22) belonged to ST117-vanB; however, WGS showed a different cluster type with 257 allelic differences.

CONCLUSION

WGS of two outbreak strains provided discriminatory information regarding genetic relatedness, and rejected the hypothesis of a common environmental reservoir. A high degree of environmental contamination was associated with higher VRE transmission. Quantification of environmental contamination may reflect the potential for VRE transmission and could therefore support the infection control measures.

Environmental detection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) from medical equipment in long-term care facilities undergoing COVID-19 outbreaks

Environmental sampling was conducted at long-term care facilities to determine the extent of surface contamination with severe acute respiratory syndrome coronavirus 2 virus. Medical equipment used throughout the facility was determined to be contaminated.

Multi-route transmission potential of SARS-CoV-2 in healthcare facilities

Understanding the transmission mechanism of SARS-CoV-2 is a prerequisite to effective control measures. To investigate the potential modes of SARS-CoV-2 transmission, 21 COVID-19 patients from 12-47 days after symptom onset were recruited. We monitored the release of SARS-CoV-2 from the patients' exhaled breath and systematically investigated environmental contamination of air, public surfaces, personal necessities, and the drainage system. SARS-CoV-2 RNA was detected in 0 of 9 exhaled breath samples, 2 of 8 exhaled breath condensate samples, 1 of 12 bedside air samples, 4 of 132 samples from private surfaces, 0 of 70 samples from frequently touched public surfaces in isolation rooms, and 7 of 23 feces-related air/surface/water samples. The maximum viral RNA concentrations were 1857 copies/m3 in the air, 38 copies/cm2 in sampled surfaces and 3092 copies/mL in sewage/wastewater samples. Our results suggest that nosocomial transmission of SARS-CoV-2 can occur via multiple routes. However, the low detection frequency and limited quantity of viral RNA from the breath and environmental specimens may be related to the reduced viral load of the COVID-19 patients on later days after symptom onset. These findings suggest that the transmission dynamics of SARS-CoV-2 differ from those of SARS-CoV in healthcare settings.

An outbreak of carbapenem-resistant Acinetobacter baumannii in a COVID-19 dedicated hospital

We describe an outbreak of carbapenem-resistant Acinetobacter baumannii (CRAB) in a COVID-19 dedicated hospital. The suspected mechanism of transfer was an environmental source that persisted despite evacuation and terminal cleaning of the entire hospital, and transmitted through healthcare workers' hands or equipment. This outbreak demonstrates that practices to prevent the spread of multidrug-resistant organisms must not be neglected during the COVID-19 pandemic.

Prevalence of Salmonella enterica Isolated from Food Contact and Nonfood Contact Surfaces in Cambodian Informal Markets

ABSTRACT

The lack of hygiene and sanitation practices and insufficient infrastructure in Cambodian informal markets may increase the risk of food contamination, specifically raw vegetables, which in turn may increase the chances of contracting a foodborne disease. The aims of this study in informal markets in Cambodia were (i) to quantify the prevalence of Salmonella enterica based upon differences in season of the year (rainy versus dry), surface types (food contact surfaces versus nonfood contact surfaces), and location of vendors within the market (inside versus outside) and (ii) to characterize S. enterica serotype prevalence. A total of 310 samples were screened for S. enterica prevalence following the U.S. Department of Agriculture guidelines, and results were confirmed by PCR assay. Whole genome sequencing was used to determine the serotype for each isolate in silico using SeqSero 1.0 on draft genomes. A total of 78 samples were confirmed positive for S. enterica. During the dry season, S. enterica was more prevalent on food contact surfaces than on nonfood contact surfaces (estimated probability of detection [confidence interval]: 0.41 [0.25, 0.59] and 0.17 [0.08, 0.32], respectively; P = 0.002), but no differences were apparent in the rainy season. No differences in S. enterica prevalence were found based on location within the market (P = 0.61). Sixteen S. enterica serotypes were detected across multiple surfaces. The most common S. enterica serotypes were Rissen (18 isolates), Hvittingfoss (11), Corvallis (10), Krefeld (8), Weltevreden (6), and Altona (6). Accurate data on the prevalence of S. enterica in informal markets are crucial for the development of effective surveillance and implementation of suitable intervention strategies at the domestic level, thus preventing foodborne illness.

HIGHLIGHTS

Environmental and air sampling are efficient methods for the detection and quantification of foot-and-mouth disease virus

Foot-and-mouth disease virus (FMDV) can be found in all secretions and excretions and the breath of acutely infected animals. FMDV can survive in the environment, providing an opportunity for surveillance. The objective of this study was to assess the efficiency of sampling methods for the recovery and quantification of FMDV from a range of environmental surfaces and in aerosols. Selected surfaces, based on those likely to be found on farms, were spiked with a range of concentrations of FMDV, left to dry and then the surface was swabbed with an electrostatic dust cloth. For aerosol sampling, FMDV was nebulised at different concentrations and distances from the sampler. Recovery of viral RNA and infectious virus was measured by RT-qPCR and virus isolation respectively. FMDV RNA was detected from all surfaces at all concentrations except from glass. Infectious virus was recovered from all surfaces but only at higher concentrations. The higher the starting concentration of virus the more efficient the recovery was from surfaces and recovery was more consistent from non-porous surfaces than porous surfaces. FMDV was detected in aerosol samples and the amount of virus recovered decreased as the distance between the nebuliser and sampler increased. The higher the starting concentration of virus the more efficient the recovery was from sampled aerosols. The information provided in this study could be used to direct environmental and aerosol sampling approaches in the field and improve the detection efficiency of FMDV from an environment, thus extending the toolbox available for diagnosis and surveillance of this pathogen.

Prevalence of Cronobacter spp. and Salmonella in Milk Powder Manufacturing Facilities in the United States

ABSTRACT

The U.S. Food and Drug Administration (FDA) conducted a sampling assignment in 2014 to ascertain the prevalence of Cronobacter spp. and Salmonella in the processing environment of facilities manufacturing milk powder. Cronobacter was detected in the environment of 38 (69%) of 55 facilities. The average prevalence of Cronobacter in 5,671 subsamples (i.e., swabs and sponges from different facility locations) was 4.4%. In the 38 facilities where Cronobacter was detected, the average prevalence of positive environmental subsamples was 6.25%. In 20 facilities where zone information of the sampling location was complete, Cronobacter was most frequently detected in zone 4, followed by zone 3, then zone 2, with zone 1 yielding the lowest percentage of positive samples. The prevalence of Cronobacter across the zones was statistically different (P < 0.05). There was no significant association between product type (i.e., lactose, whey products, buttermilk powder, and nonfat dried milk) and prevalence of Cronobacter in the facility. Salmonella was detected in the environment of three (5.5%) of the 55 facilities; all three facilities produced dried whey product. The overall prevalence of Salmonella in 5,714 subsamples was 0.16%. In facilities in which Salmonella was detected, the average prevalence was 2.5%. Salmonella was most frequently detected in zone 4, followed by zone 3. Salmonella was not detected in zone 1 or zone 2. The disparity between Salmonella and Cronobacter prevalence indicates that additional measures may be required to reduce or eliminate Cronobacter from the processing environment.

HIGHLIGHTS

Identifying the Risk of SARS-CoV-2 Infection and Environmental Monitoring in Airborne Infectious Isolation Rooms (AIIRs)

Healthcare workers (HCWs) are at high risk of occupational exposure to the new pandemic human coronavirus, SARS-CoV-2, and are a source of nosocomial transmission in airborne infectious isolation rooms (AIIRs). Here, we performed comprehensive environmental contamination surveillance to evaluate the risk of viral transmission in AIIRs with 115 rooms in three buildings at the Shanghai Public Health Clinical Center, Shanghai, during the treatment of 334 patients infected with SARS-CoV-2. The results showed that the risk of airborne transmission of SARS-CoV-2 in AIIRs was low (1.62%, 25/1544) due to the directional airflow and strong environmental hygiene procedures. However, we detected viral RNA on the surface of foot-operated openers and bathroom sinks in AIIRs (viral load: 55.00–3154.50 copies/mL). This might be a source of contamination to connecting corridors and object surfaces through the footwear and gloves used by HCWs. The risk of infection was eliminated by the use of disposable footwear covers and the application of more effective environmental and personal hygiene measures. With the help of effective infection control procedures, none of 290 HCWs was infected when working in the AIIRs at this hospital. This study has provided information pertinent for infection control in AIIRs during the treatment of COVID-19 patients.

Viral indicators for tracking domestic wastewater contamination in the aquatic environment

Waterborne enteric viruses are an emerging cause of disease outbreaks and represent a major threat to global public health. Enteric viruses may originate from human wastewater and can undergo rapid transport through aquatic environments with minimal decay. Surveillance and source apportionment of enteric viruses in environmental waters is therefore essential for accurate risk management. However, individual monitoring of the >100 enteric viral strains that have been identified as aquatic contaminants is unfeasible. Instead, viral indicators are often used for quantitative assessments of wastewater contamination, viral decay and transport in water. An ideal indicator for tracking wastewater contamination should be (i) easy to detect and quantify, (ii) source-specific, (iii) resistant to wastewater treatment processes, and (iv) persistent in the aquatic environment, with similar behaviour to viral pathogens. Here, we conducted a comprehensive review of 127 peer-reviewed publications, to critically evaluate the effectiveness of several viral indicators of wastewater pollution, including common enteric viruses (mastadenoviruses, polyomaviruses, and Aichi viruses), the pepper mild mottle virus (PMMoV), and gut-associated bacteriophages (Type II/III FRNA phages and phages infecting human Bacteroides species, including crAssphage). Our analysis suggests that overall, human mastadenoviruses have the greatest potential to indicate contamination by domestic wastewater due to their easy detection, culturability, and high prevalence in wastewater and in the polluted environment. Aichi virus, crAssphage and PMMoV are also widely detected in wastewater and in the environment, and may be used as molecular markers for human-derived contamination. We conclude that viral indicators are suitable for the long-term monitoring of viral contamination in freshwater and marine environments and that these should be implemented within monitoring programmes to provide a holistic assessment of microbiological water quality and wastewater-based epidemiology, improve current risk management strategies and protect global human health.

Masks and closed-loop ventilators prevent environmental contamination by COVID-19 patients in negative-pressure environments

Herein, we report that nosocomial infection of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) may be mitigated by using surgical masks and closed looped ventilation for both non-critical and critical patients. These preventive measures resulted in no viral contamination of surfaces in negative pressure environments.

Environmental sampling to assess the bioburden of Mycobacterium avium subspecies paratuberculosis in drylot pens on California dairies

Mycobacterium avium subspecies paratuberculosis (MAP) is a bacterium that can cause substantial economic losses in infected dairy herds due to reduced milk production and increased cow-replacement costs. In order to control MAP in dairies with drylot pens, a standardized environmental sampling protocol to quantify MAP in fecal slurry was developed based on an existing protocol for freestall pens. Specifically, following a 24 h hold of the flush, a grab sample of approximately 10 ml of fecal slurry was collected every 1 m along the flush lane of the drylot pens, avoiding individual cow fecal pats. To determine the reliability and repatability of the new environmental sampling protocol for estimation of MAP bioburden at the pen level, two collectors simultaneously collected fecal slurry samples every day for 3 days from six drylot cow pens on two Central California dairies. During the study period no cow movement between pens was allowed with the exception of sick cows. The study herds had MAP seroprevalence of 5.8% and 3.2%, respectively, based on whole pen serum ELISA results. Variance components models for quantitative real-time PCR (qPCR) results showed samples collected from different pens on different dairies accounted for greater variablitiy in MAP concentration (65%), while samples collected by different collectors had the least variability (0.1%). In contrast, variability in MAP concentration in environmental samples collected on different days had 25% variability. The intraclass correlation coefficient showed high reliability (93%) of environmental sampling simultaneously by different collectors. In contrast, the reliability of environmental sampling at different days was 65%, which was similar to the reliability for sampling by different collectors on different days. Investigators can expect high reliability when employing the new environmental sampling protocol along with qPCR testing of environmental samples from drylot pens.

Environmental investigation of respiratory pathogens during the Hajj 2016 and 2018

BACKGROUND

Respiratory tract infections are common in the context of the Hajj pilgrimage and respiratory pathogens can be transmitted via contact with contaminated surfaces. We sampled surfaces during the Hajj to detect the presence of respiratory bacteria and viruses.

METHODS

Frequently touched surfaces at Mecca, Mina, Arafat and Medina were sampled. The common respiratory pathogens were tested by qPCR.

RESULTS

70/142 (49.3%) environmental samples collected were positive for at least one respiratory pathogen. Among the positive samples, Klebsiella pneumoniae was the bacterium most frequently tested positive (57.1%), followed by Streptococcus pneumoniae (12.9%), Staphylococcus aureus (10.0%) and Haemophilus influenzae (7.1%). 32.9% positive samples tested positive for rhinovirus and 1.4% for coronavirus. Surfaces with the highest rates of positive samples were kitchen tables (100%), water fountain faucet (73.3%) and edge of water coolers lid (84.6%). Samples collected in Mina were the most frequently contaminated with 68.8% being positive for at least one pathogen and 18.8% positive for a combination of multiple pathogens.

CONCLUSION

These preliminary results indicate that respiratory pathogens are common in environmental surfaces from areas frequented by Hajj pilgrims. Further larger-scale studies are needed to better assess the possible role of environmental respiratory pathogens in respiratory infections in Hajj pilgrims.

Development of a rapid-viability PCR method for detection of Clostridioides difficile spores from environmental samples

Clostridioides difficile is a common pathogen that is well known to survive for extended periods of time on environmental healthcare surfaces from fecal contamination. During epidemiological investigations of healthcare-associated infections, it is important to be able to detect whether or not there are viable spores of C. difficile on surfaces. Current methods to detect C. difficile can take up to 7 days for culture and in the case of detection by PCR, viability of the spores cannot be ascertained. Prevention of C. difficile infection in healthcare settings includes adequate cleaning and disinfection of environmental surfaces which increases the likelihood of detecting dead organisms from an environmental sample during an investigation. In this study, we were able to adapt a rapid-viability PCR (RV-PCR) method, first developed for detection of viable Bacillus anthracis spores, for the detection of viable C. difficile spores. RV-PCR uses the change in cycle threshold after incubation to confirm the presence of live organisms. Using this modified method we were able to detect viable C. difficile after 22 h of anaerobic incubation in Cycloserine Cefoxitin Fructose Broth (CCFB). This method also used bead beating combined with the Maxwell 16 Casework kit for DNA extraction and purification and a real-time duplex PCR assay for toxin B and cdd3 genes to confirm the identity of the C. difficile spores. Spiked environmental sponge-wipes with and without added organic load were tested to determine the limit of detection (LOD). The LOD from spiked environmental sponge-wipe samples was 10⁴ spores/mL but after incubation initial spore levels of 10¹ spores/mL were detected. Use of this method would greatly decrease the amount of time required to detect viable C. difficile spores; incubation of samples is only required for germination (22 h or less) instead of colony formation, which can take up to 7 days. In addition, PCR can then quickly confirm or deny the identity of the organism at the same time it would confirm viability. The presence of viable C. difficile spores could be detected at very low levels within 28 h total compared to the 2 to 10-day process that would be needed for culture, identification and toxin detection.

paratuberculosis infection in dairy herds in Northern Antioquia (Colombia) and associated risk factors using environmental sampling

This cross-sectional study aimed to determine Mycobacterium avium subsp. paratuberculosis (MAP) herd-level prevalence using a quantitative real-time PCR method (qPCR), performed on environmental samples. Secondly, the study aimed to explore herd-level risk factors associated with the presence of MAP in dairy herds with in-paddock milking facilities of the Northern region of the Province of Antioquia (Colombia). Study herds (n = 292) located in 61 different districts from six municipalities were randomly selected amongst 7794 dairies registered in the foot-and-mouth disease vaccination records from 2015. The sampling strategy considered a proportional allocation, both at municipality and district level. Participant herds were visited once between June and October 2016 to collect one composite environmental sample and to complete a risk assessment questionnaire. Each composite environmental sample contained material from six different sites of concentration of adult cattle and/or high traffic areas (e.g. areas surrounding waterers and feeders, areas surrounding the current mobile milking-unit places). Identification of MAP was achieved using a duplex qPCR (Bactotype MAP PCR Kit^®, Qiagen). A herd was considered as MAP infected if the environmental sample was positive in the qPCR. Information about the general characteristics of the herd, management practices, and knowledge about the disease was collected using the risk-assessment questionnaire. The information on risk factors was analyzed using a multivariable logistic regression model. The apparent herd-level prevalence was 4.1% (12/292; 95% CI: 1.8-6.4). Herds with a history of mixed farming of cattle with other ruminants had higher odds of being MAP infected than herds without (OR = 3.9; 95% CI: 1.2-13.2). Our study demonstrates the MAP prevalence in dairy herds from Antioquia, Colombia and the possible relationship between MAP environmental positivity with the history of mixed farming of cattle with other susceptible ruminants.

Association between meteorological factors, spatiotemporal effects, and prevalence of influenza A subtype H7 in environmental samples in Zhejiang province, China

BACKGROUND

Human infection with the H7N9 virus has been reported recurrently since spring 2013. Given low pathogenicity of the virus in poultry, the outbreak cannot be noticed easily until a case of human infection is reported. Studies showed that the prevalence of influenza A subtype H7 in environmental samples is associated with the number of human H7N9 infection, with the latter associated with meteorological factors. Understanding the association between meteorological factors and the prevalence of H7 subtype in the environmental samples can shed light on how the virus propagates in the environment for disease control.

METHOD

Environmental samples and meteorological data (precipitation, temperature, relative humidity, sunshine duration, and wind speed) collected in Zhejiang province, China, during 2013-2017 were used. A Bayesian hierarchical binomial logistic spatiotemporal model which captures spatiotemporal effects was adopted to model the prevalence of H7 subtype with the meteorological factors.

RESULTS

The monthly overall prevalence of H7 subtype in the environmental samples was usually <30%. Compared with the odds at median, moderately low precipitation (49.19-115.60 mm), moderately long sunshine duration (4.22-9.25 h) and low temperature (<9.33 °C) were statistically significantly associated with a higher adjusted odds of detecting an H7-positive sample, whereas moderately high precipitation (119.51-146.85 mm), short and moderately short sunshine duration (<1.77 h; 4.00-4.17 h), and high temperature (>23.09 °C) were statistically significantly associated with a lower adjusted odds. The adjusted odds increased multiplicatively by 1.11 per 1% increase in relative humidity.

CONCLUSION

Since the prevalence of H7 subtype in environmental samples was associated with meteorological conditions and the number of human H7N9 infection, an environmental surveillance program which incorporates meteorological conditions in planning allows for early detection of the spread of the virus in the environment and better preparation for the outbreak in the human population.

Poly(amine) modified kaolinite clay for VOC capture

Polyethylenimine (PEI) functionalized kaolinite clay was successfully prepared, characterized, and assessed for the remediation of volatile organic compounds (VOCs) comprising the aldehyde, carboxylic acid, and disulfide functional group classes. A gas chromatographic vapor capture assay evaluated the capability of unmodified and modified clay material to capture representative aldehyde, carboxylic acid, and disulfide VOCs in a laboratory setting. Unmodified kaolinite (Kao) clay was moderately or poorly effective at remediating these VOCs, while the poly(amine) functionalized Kao was capable of capturing VOCs in the vapor phase with reductions up to 100%. Sample cartridge tubes were packed with PEI-functionalized clay in order to assess their ability to reduce the detectable volatile fatty acid load at an open-air rendering plant in a relevant field test for applying these materials in a packed-bed scrubber application. The PEI-Kao packed cartridges were capable of significantly reducing the detectable concentration of volatile fatty acid effluent from the rendering operation. These volatile fatty acids are major contributors to nuisance odors associated with rendering.

Molecular epidemiology of environmental Cryptococcus species isolates based on amplified fragment length polymorphism

OBJECTIVE

Cryptococcosis is a major opportunistic fungal infection caused by members of the genus Cryptococcus, mainly those belonging to the Cryptococcus neoformans/Cryptococcus gattii species complexes. Here, we report a comprehensive molecular epidemiological study of the environmental distribution of Cryptococcus isolates in Shiraz, Iran with review of litreature.

METHOD

A total of 406 samples were obtained from Eucalyptus trees and 139 samples from pigeon droppings. Cryptococcus species identification and genotyping were performed by amplified fragment length polymorphism (AFLP) fingerprinting sequencing and sequencing of the ITS rDNA region.

RESULTS

Majority of the isolates belonged to the Naganishia taxon (n=69) including N. albida (formerly C. albidus, n=62), N. globosa (formerly C. saitoi, n=4), N. adeliensis (formerly C. adeliensis, n=2), N. diffluens (formerly C. diffluens, n=1), and the identified C. neoformans isolates (n=25) belonged to genotype AFLP1/VNI (n=22) and AFLP1B/VNII (n=3).

CONCLUSION

More research efforts should be employed to isolate C. gattii species complex from environmental niches in Iran and provide additional evidence related to novel molecular types.

Rate of contamination of hospital privacy curtains in a burns/plastic ward: A longitudinal study

BACKGROUND

Since hospital patient privacy curtains can harbor bacteria, are high-touch surfaces, and are cleaned infrequently, they may be involved in pathogen transmission. The aim of this longitudinal prospective study was to understand curtain contamination to inform curtain hygiene protocols, thereby minimizing the role of curtains in pathogen transmission.

METHODS

Over 21 days, cultures of 10 freshly laundered curtains (8 test curtains surrounding patient beds and 2 controls in an unoccupied staff room) were taken in the Regional Burns/Plastics Unit. Contact plates were used to sample the curtains near the edge hem where they are most frequently touched. Microbial contamination and the presence of methicillin-resistant Staphylococcus aureus (MRSA) were determined.

RESULTS

By day 3, test curtains showed increased microbial contamination (mean colony-forming units [CFU]/cm² = 1.17) compared to control curtains (mean CFU/cm² = 0.19). Test curtains became increasingly contaminated over time, with mean CFU/cm² for days 17 and 21 of 1.86 and 5.11, respectively. By day 10, 1/8 test curtains tested positive for MRSA, and 5/8 were positive by day 14.

CONCLUSIONS

Patient privacy curtains became progressively contaminated with bacteria, including MRSA. Between days 10 and 14 after being hung, curtains showed increased MRSA positivity. This may represent an opportune time to intervene, either by cleaning or replacing the curtains.

Highlighting the complexities of a groundwater pilot study during an avian influenza outbreak: Methods, lessons learned, and select contaminant results

The highly pathogenic avian influenza (H5N2) outbreak in the Midwestern United States (US) in 2015 was historic due to the number of birds and poultry operations impacted and the corresponding economic loss to the poultry industry and was the largest animal health emergency in US history. The U.S. Geological Survey (USGS), with the assistance of several state and federal agencies, aided the response to the outbreak by developing a study to determine the extent of virus transport in the environment. The study goals were to: develop the appropriate sampling methods and protocols for measuring avian influenza virus (AIV) in groundwater, provide the first baseline data on AIV and outbreak- and poultry-related contaminant occurrence and movement into groundwater, and document climatological factors that may have affected both survival and transport of AIV to groundwater during the months of the 2015 outbreak. While site selection was expedient, there were often delays in sample response times due to both relationship building between agencies, groups, and producers and logistical time constraints. This study's design and sampling process highlights the unpredictable nature of disease outbreaks and the corresponding difficulty in environmental sampling of such events. The lessons learned, including field protocols and approaches, can be used to improve future research on AIV in the environment.

The Presence of Norovirus and Adenovirus on Environmental Surfaces in Relation to the Hygienic Level in Food Service Operations Associated with a Suspected Gastroenteritis Outbreak

Norovirus (NoV) gastroenteritis outbreaks appear frequently in food service operations (FSOs), such as in restaurants and canteens. In this study the presence of NoV and adenovirus (AdV) genomes was investigated on the surfaces of premises, especially in kitchens, of 30 FSOs where foodborne gastroenteritis outbreaks were suspected. The objective was to establish a possible association between the presence of virus genomes on surfaces and a visual hygienic status of the FSOs. NoV genome was found in 11 and AdV genome in 8 out of 30 FSOs. In total, 291 swabs were taken, of which 8.9% contained NoV and 5.8% AdV genome. The presence of NoV genomes on the surfaces was not found to associate with lower hygiene level of the premises when based on visual inspection; most (7/9) of the FSOs with NoV contamination on surfaces and a completed evaluation form had a good hygiene level (the best category). Restaurants had a significantly lower proportion of NoV-positive swabs compared to other FSOs (canteens, cafeteria, schools etc.) taken together (p = 0.00014). The presence of a designated break room for the workers was found to be significantly more common in AdV-negative kitchens (p = 0.046). Our findings suggest that swabbing is necessary for revealing viral contamination of surfaces and emphasis of hygiene inspections should be on the food handling procedures, and the education of food workers on virus transmission.

Valuation of ecosystem services of commercial shrub willow (Salix spp.) woody biomass crops

The development of shrub willow as a bioenergy feedstock contributes to renewable energy portfolios in many countries with temperate climates and marginal croplands due to excessive moisture. However, to fully understand the potential of shrub willow as an alternative crop on marginal cropland, more research is needed to understand the potential of shrub willow for providing a variety of ecosystem services. At the same time, there is much need for research developing strategies to value ecosystem services beyond conventional valuation systems (e.g., monetary, intrinsic). In this context, this project investigates the ecosystem services of shrub willow woody biomass from an environmental science perspective, and proposes a new avenue to assess ecosystem services for management purposes based on the relative value of key ecosystem services under various land management strategies (i.e., willow vs. corn vs. hay). On marginal cropland in the US Northeast, shrub willow may be used to replace crops like corn or hay. Transitioning from conventional corn or hay to willow tends to reduce nutrient loss and erosion, improve biodiversity and adaptability to climate change, and increase access to recreational activities. However, it is unlikely to change soil carbon pools or greenhouse gas emissions at the soil-atmosphere interface. By encouraging decision makers to weigh the pros and cons of each management decision (i.e., willow vs. corn vs. hay) based on the situation, the ecosystems services valuation method used here provides a clear framework for decision making in a watershed management context.

Rate of contamination of hospital privacy curtains on a burns and plastic surgery ward: a cross-sectional study

BACKGROUND

Surfaces in the patient environment may play a role in microbial transmission if they become colonized by bacteria. Patient privacy curtains are one such surface that may pose a high risk for transmission because they are high-contact surfaces, are infrequently cleaned, and healthcare workers are less likely to wash their hands after contacting inanimate objects such as curtains.

AIM

To determine the amount and type of bacterial colonization of patient privacy curtains at a regional burns/plastic surgery unit.

METHODS

Privacy curtain contamination on the burns/plastic surgery ward was determined for two separate occasions six months apart: 23 curtains on August 2015 and 26 curtains on January 2016. Dey-Engley neutralizing agar (DENA) replicate organism detection and counting (RODAC) contact plates were used daily to sample curtains near the edge hem where they are most frequently touched. Microbial contamination was reported as cfu/cm² and the presence of meticillin-resistant Staphylococcus aureus (MRSA) was determined. Swabs were also taken of any open wounds and from tracheostomy sites on the ward.

FINDINGS

Curtain contamination in August 2015 was 0.7-4.7 cfu/cm² with 22% testing positive for MRSA, whereas contamination on January 2016 was 0.6-13.3 cfu/cm² with 31% of curtains testing positive for MRSA.

CONCLUSION

Curtains on the burns/plastic surgery ward become colonized with significant quantities of bacteria. Future studies will need to address the rate of colonization and the clinical impact of this colonization to better inform cleaning protocols.

Isolation of Cryptococcus gattii from a Castanopsis argyrophylla tree hollow (Mai-Kaw), Chiang Mai, Thailand

The pathogenic yeast Cryptococcus gattii was isolated from a tree hollow of a Castanopsis argyrophylla King ex Hook.f. (Fagaceae) in Chiang Mai, Thailand. Molecular characterization with amplified fragment length polymorphism analysis and multi-locus sequence typing showed that this isolate belonged to genotype AFLP4/VGI representing C. gattii sensu stricto. Subsequent comparison of the environmental isolate with those from clinical samples from Thailand showed that they grouped closely together in a single cluster.

African swine fever outbreak on a medium-sized farm in Uganda: biosecurity breaches and within-farm virus contamination

In Uganda, a low-income country in east Africa, African swine fever (ASF) is endemic with yearly outbreaks. In the prevailing smallholder subsistence farming systems, farm biosecurity is largely non-existent. Outbreaks of ASF, particularly in smallholder farms, often go unreported, creating significant epidemiological knowledge gaps. The continuous circulation of ASF in smallholder settings also creates biosecurity challenges for larger farms. In this study, an on-going outbreak of ASF in an endemic area was investigated on farm level, including analyses of on-farm environmental virus contamination. The study was carried out on a medium-sized pig farm with 35 adult pigs and 103 piglets or growers at the onset of the outbreak. Within 3 months, all pigs had died or were slaughtered. The study included interviews with farm representatives as well as biological and environmental sampling. ASF was confirmed by the presence of ASF virus (ASFV) genomic material in biological (blood, serum) and environmental (soil, water, feed, manure) samples by real-time PCR. The ASFV-positive biological samples confirmed the clinical assessment and were consistent with known virus characteristics. Most environmental samples were found to be positive. Assessment of farm biosecurity, interviews, and the results from the biological and environmental samples revealed that breaches and non-compliance with biosecurity protocols most likely led to the introduction and within-farm spread of the virus. The information derived from this study provides valuable insight regarding the implementation of biosecurity measures, particularly in endemic areas.

Is airborne transmission of Acinetobacter baumannii possible: A prospective molecular epidemiologic study in a tertiary care hospital

BACKGROUND

Understanding the dynamics of aerial spread of Acinetobacter may provide useful information for production of effective control measurements. We investigated genetic relationships between air and clinical isolates of Acinetobacter baumannii in an intensive care unit (ICU) setting.

METHODS

We conducted a prospective surveillance study in a tertiary care hospital for 8 months. A total of 186 air samples were taken from 2 ICUs. Clonal characteristics of air isolates were compared with the prospective clinical strains and the previously isolated strains of ICU patients over a 23-month period.

RESULTS

Twenty-six (11.4%) air samples yielded A baumannii, of which 24 (92.3%) isolates were carbapenem-resistant. The Acinetobacter concentration was the highest in bedside sampling areas of infected patients (0.39 CFU/m³). Air isolates were clustered in 13 genotypes, and 7 genotypes (including 18 air strains) were clonally related to the clinical strains of 9 ICU patients. One clone continued to be cultured over 27 days in ICU air, and air isolates could be clonally related to 7-week retrospective and approximately 15-week prospective clinical strains.

CONCLUSIONS

The results of this study suggest that infected patients could spread significant amounts of Acinetobacter to ICU air. These strains could survive in air for some weeks and could likely still infect new patients after some months. Special control measurements may be required against the airborne spread of Acinetobacter in ICUs.

Understanding the rates of nonpolar organic chemical accumulation into passive samplers deployed in the environment: Guidance for passive sampler deployments

Polymeric passive samplers have become a common method for estimating freely dissolved concentrations in environmental media. However, this approach has not yet been adopted by investigators conducting remedial investigations of contaminated environmental sites. Successful adoption of this sampling methodology relies on an understanding of how passive samplers accumulate chemical mass as well as developing guidance for the design and deployment of passive samplers. Herein, we outline the development of a simple mathematical relationship of the environmental, polymer, and chemical properties that control the uptake rate. This relationship, called a timescale, is then used to illustrate how each property controls the rate of equilibration in samplers deployed in the water or in the sediment. Guidance is also given on how to use the timescales to select an appropriate polymer, deployment time, and suite of performance reference compounds. Integr Environ Assess Manag 2016;12:486-492. © 2015 SETAC.

Snapshot fecal survey of domestic animals in rural Ghana for Mycobacterium ulcerans

Identifying the source reservoirs of Mycobacterium ulcerans is key to understanding the mode of transmission of this pathogen and controlling the spread of Buruli ulcer (BU). In Australia, the native possum can harbor M. ulcerans in its gastrointestinal tract and shed high concentrations of the bacteria in its feces. To date, an analogous animal reservoir in Africa has not been identified. Here we tested the hypothesis that common domestic animals in BU endemic villages of Ghana are reservoir species analogous to the Australian possum. Using linear-transects at 10-meter intervals, we performed systematic fecal surveys across four BU endemic villages and one non-endemic village in the Asante Akim North District of Ghana. One hundred and eighty fecal specimens from a single survey event were collected and analyzed by qPCR for the M. ulcerans diagnostic DNA targets IS2404 and KR-B. Positive and negative controls performed as expected but all 180 test samples were negative. This structured snapshot survey suggests that common domestic animals living in and around humans do not shed M. ulcerans in their feces. We conclude that, unlike the Australian native possum, domestic animals in rural Ghana are unlikely to be major reservoirs of M. ulcerans.

Sex differences in jaw muscle duty factors during exercise in two environments: A pilot study

It is unknown if females and males use jaw muscles similarly during exercise. This pilot study assessed jaw elevator muscle duty factors (DFs=time of muscle activity/total recording time) at repeated sessions to test if DFs are reliable and different between sexes during exercises in two environments. Ten female and seven male subjects recruited from university soccer teams provided informed consent. Surface electromyography was recorded from masseter and temporalis muscles during biting and leg-extension laboratory exercises. Average activities to produce 20N bite-forces for each muscle and subject determined thresholds (5-80%·T20N) for subject-specific DF calculations during exercises performed in laboratory and natural environments. Subjects self-recorded via portable electromyography equipment during in-field leg-extension and weight-lifting exercises. Effects of variables on DFs were assessed via ANOVA (α=0.05) and simple effects testing (Bonferroni-adjusted p⩽0.012). All subjects used jaw muscles during exercises in both environments. DFs between laboratory sessions were reliable (R=0.84). During laboratory exercises, male temporalis DFs were significantly higher than female DFs from both muscles (p⩽0.001). During in-field exercises females had higher DFs during weight-lifting while males had higher DFs during leg-extensions. In-field sex differences were significant at most thresholds and showed larger effect sizes for leg-extension compared to weight-lifting exercises.

Use of RODAC plates to measure containment of Mycobacterium tuberculosis in a Class IIB biosafety cabinet during routine operations

OBJECTIVE/BACKGROUND

Guidelines for the manipulation of Mycobacterium tuberculosis (MTB) cultures require a Biosafety Level 3 (BSL-3) infrastructure and accompanying code of conduct. In this study, we aimed to validate and apply detection methods for viable mycobacteria from surfaces in a BSL-3 MTB laboratory.

METHODS

We evaluated phenotypic (Replicate Organism Detection and Counting [RODAC] plates) and molecular (propidium monoazide [PMA]-based polymerase chain reaction [PCR]) approaches for the detection of viable mycobacteria, as well as the effect of 70% ethanol applied for 5min for disinfection against mycobacteria. For validation of the method, recovery of serial dilutions of Mycobacterium bovis bacillus Calmette-Guérin from glass slides was measured. Subsequently, we stamped surfaces in and around the biosafety cabinet (BSC) after different technicians had manipulated high bacterial load suspensions for routine drug-susceptibility testing in a Class II BSC.

RESULTS

RODAC stamping could detect as few as three bacteria on slides stamped either 5min or 60min after inoculation. PMA-based PCR, tested in parallel, did not pass validation. Mycobacteria were still detected after 5-min disinfection with ethanol 70%. In the BSL-3, from 201 RODAC-stamped surfaces, MTB was detected in four: three inside a BSC-on a tube cap and on an operator's gloves-and one outside, on an operator's gown.

CONCLUSION

RODAC plates detect mycobacteria at low numbers of microorganisms. In addition, this method allowed us to show that 70% ethanol does not reliably kill mycobacteria when applied for 5min to a dried surface, and that MTB bacilli may arrive outside a Class II BSC during routine practice, although the route could not be documented.

Detection and termination of an extended low-frequency hospital outbreak of GIM-1-producing Pseudomonas aeruginosa ST111 in Germany

BACKGROUND

Metallo-β-lactamase German imipenemase-1 (GIM-1)-mediated carbapenem resistance is emerging in Germany but has not spread beyond a very localized region. The aim of this study was to describe the first outbreak of an extensively drug-resistant GIM-1-carrying Pseudomonas aeruginosa strain affecting 29 patients in a tertiary care hospital from 2002-2013.

METHODS

The outbreak was studied retrospectively and prospectively by a combination of molecular methods (carbapenemase polymerase chain reaction [PCR]), genotyping (DiversiLab, pulsed field gel electrophoresis and multi-locus sequence typing, bioMérieux, Marcy l'Etoile, France), descriptive epidemiology, and extensive environmental investigations using swabs with liquid transport medium, blaGIM-1 PCR, directly from the medium and culture.

RESULTS

Of the 29 affected patients, 24 had been admitted to a surgical intensive care unit at some point, where environmental sampling revealed a high burden of blaGIM-1 in the wastewater system. The outbreak strain was found in several sinks and on a reusable hair washbasin. Initially, general infection control measures were applied; thereafter, specific measures were implemented, including the restriction of washbasin use. Continued surveillance over a period of 2 years has revealed no further case of GIM-1-carrying Pseudomonas aeruginosa.

CONCLUSION

This long-term outbreak highlights the potential of molecular methods in surveillance for multidrug-resistant pathogens and in environmental sampling and the successful containment by application of specific control measures targeting biofilms within sink drains as potential environmental reservoirs for P aeruginosa.

Environmental sampling of Ceratonia siliqua (carob) trees in Spain reveals the presence of the rare Cryptococcus gattii genotype AFLP7/VGIV

BACKGROUND

Cryptococcus gattii is a pathogenic basidiomycetous yeast that is emerging in temperate climate zones worldwide. C. gattii has repetitively been isolated from numerous tree species. Ongoing environmental sampling and molecular characterization is essential to understand the presence of this primary pathogenic microorganism in the Mediterranean environment.

AIMS

To report the first isolation of the rare C. gattii genotype AFLP7/VGIV from the environment in Europe.

METHODS

Samples were collected from woody debris of carob trees (Ceratonia siliqua) and olive trees (Olea europaea) in El Perelló, Tarragona, Spain. Cryptococcus species were further characterized by using URA5-RFLP, MALDI-TOF, AFLP and MLST. The antifungal susceptibility profile to amphotericin B, 5-fluorocytosine, fluconazole, itraconazole, posaconazole and voriconazole was determined using Sensititre Yeast One and E-test.

RESULTS

Cultures from one carob tree revealed the presence of ten Cryptococcus-like colonies. One colony was identified as C. gattii, and subsequent molecular characterization showed that it was an α mating-type that belonged to the rare genotype AFLP7/VGIV. Antifungal susceptibility testing showed values within the range of sensitivity described for other isolates of the same genotype and within the epidemiological cutoff values for this species.

CONCLUSIONS

The isolation of the rare C. gattii genotype AFLP7/VGIV in Spain is the first report in the European environment, implying the possible presence in other regions of the Mediterranean area, and underlines that clinicians must be aware for C. gattii infections in healthy individuals.

Environmental sampling for respiratory pathogens in Jeddah airport during the 2013 Hajj season

BACKGROUND

Respiratory tract infections (RTIs) are common during the Hajj season and are caused by a variety of organisms, which can be transmitted via the air or contaminated surfaces. We conducted a study aimed at sampling the environment in the King Abdul Aziz International (KAAI) Airport, Pilgrims City, Jeddah, during Hajj season to detect respiratory pathogens.

METHODS

Active air sampling was conducted using air biosamplers, and swabs were used to sample frequently touched surfaces. A respiratory multiplex array was used to detect bacterial and viral respiratory pathogens.

RESULTS

Of the 58 environmental samples, 8 were positive for at least 1 pathogen. One air sample (1 of 18 samples, 5.5%) tested positive for influenza B virus. Of the 40 surface samples, 7 (17.5%) were positive for pathogens. These were human adenovirus (3 out of 7, 42.8%), human coronavirus OC43/HKU1 (3 out of 7, 42.8%), Haemophilus influenzae (1 out of 7, 14.2%), and Moraxella catarrhalis (1 out of 7, 14.2%). Chair handles were the most commonly contaminated surfaces. The handles of 1 chair were cocontaminated with coronavirus OC43/HKU1 and H influenzae.

CONCLUSION

Respiratory pathogens were detected in the air and on surfaces in the KAAI Airport in Pilgrims City. Larger-scale studies based on our study are warranted to determine the role of the environment in transmission of respiratory pathogens during mass gathering events (eg, Hajj) such that public health preventative measures might be better targeted.

Microbiological analysis of environmental samples collected from child care facilities in North and South Carolina

BACKGROUND

Children cared for outside the home are at an increased risk of enteric disease. Microbiological analyses were performed on environmental samples collected from child care facilities in North and South Carolina.

METHODS

There were 326 samples collected from 40 facilities corresponding to common surfaces (77% of samples) and the hands of care providers (23% of samples). Samples were analyzed for total aerobic plate counts (APCs), total coliforms, biotype I Escherichia coli, and pathogens Shigella spp, Salmonella enterica, E coli O157, Campylobacter jejuni, and human norovirus.

RESULTS

Median APCs and coliform counts for hands were 4.6 and 1.0 log10 colony-forming units (CFU) per hand, respectively. Median APCs for surfaces were 2.0 and 2.6 log10 CFU for flat and irregular surfaces, respectively. Coliforms were detected in 16% of samples, with counts ranging from 1.0 log10 to > 4.3 log10 CFU, with higher counts most often observed for hand rinse samples. Biotype I E coli counts were below assay detection limits (< 1 log10 CFU) for all but 1 sample. No samples were positive for any of the 4 bacterial pathogens, whereas 4 samples showed evidence of human norovirus RNA.

CONCLUSION

The relative absence of pathogens and biotype I E coli in environmental samples suggests the child care facilities sampled in this study managed fecal contamination well.

Air and surface contamination patterns of meticillin-resistant Staphylococcus aureus on eight acute hospital wards

BACKGROUND

Meticillin-resistant Staphylococcus aureus (MRSA) can be recovered from hospital air and from environmental surfaces. This poses a potential risk of transmission to patients.

AIM

To investigate associations between MRSA isolates recovered from air and environmental surfaces with those from patients when undertaking extensive patient and environmental sampling.

METHODS

This was a prospective observational study of patients and their environment in eight wards of a 700-bed tertiary care hospital during 2010 and 2011. Sampling of patients, air and surfaces was carried out on all ward bays, with more extended environmental sampling in ward high-dependency bays and at particular times of the day. The genetic relatedness of isolates was determined by DNA microarray profiling and spa typing.

FINDINGS

MRSA was recovered from 30/706 (4.3%) patients and from 19/132 (14.4%) air samples. On 9/132 (6.8%) occasions both patient and air samples yielded MRSA. In 32 high-dependency bays, MRSA was recovered from 12/161 (7.4%) patients, 8/32 (25%) air samples, and 21/644 (3.3%) environmental surface samples. On 10/132 (7.6%) occasions, MRSA was isolated from air in the absence of MRSA-positive patients. Patient demographic data combined with spa typing and DNA microarray profiling revealed four likely transmission clusters, where patient and environmental isolates were deemed to be very closely related.

CONCLUSION

Air sampling yielded MRSA on frequent occasions, especially in high-dependency bays. Environmental and air sampling combined with patient demographic data, spa typing and DNA microarray profiling indicated the presence of clusters that were not otherwise apparent.

NUSIMEP-7: uranium isotope amount ratios in uranium particles

The Institute for Reference Materials and Measurements (IRMM) has extensive experience in the development of isotopic reference materials and the organization of interlaboratory comparisons (ILC) for nuclear measurements in compliance with the respective international guidelines (ISO Guide 34:2009 and ISO/IEC 17043:2010). The IRMM Nuclear Signatures Interlaboratory Measurement Evaluation Program (NUSIMEP) is an external quality control program with the objective of providing materials for measurements of trace amounts of nuclear materials in environmental matrices. Measurements of the isotopic ratios of the elements uranium and plutonium in small amounts, typical of those found in environmental samples, are required for nuclear safeguards and security, for the control of environmental contamination and for the detection of nuclear proliferation. The measurement results of participants in NUSIMEP are evaluated according to international guidelines in comparison to independent external certified reference values with demonstrated metrological traceability and uncertainty. NUSIMEP-7 focused on measurements of uranium isotope amount ratios in uranium particles aiming to support European Safeguards Directorate General for Energy (DG ENER), the International Atomic Energy Agency's (IAEA) network of analytical laboratories for environmental sampling (NWAL) and laboratories in the field of particle analysis. Each participant was provided two certified test samples: one with single and one with double isotopic enrichment. These NUSIMEP test samples were prepared by controlled hydrolysis of certified uranium hexafluoride in a specially designed aerosol deposition chamber at IRMM. Laboratories participating in NUSIMEP-7 received the test samples of uranium particles on two graphite disks with undisclosed isotopic ratio values n((234)U)/n((238)U), n((235)U)/n((238)U) and n((236)U)/n((238)U). The uranium isotope ratios had to be measured using their routine analytical procedures. Measurement of the major ratio n((235)U)/n((238)U) was obligatory; measurement of the minor ratios n((234)U)/n((238)U) and n((236)U)/n((238)U) was optional. Of the twenty-four institutes that registered for NUSIMEP-7, 17 have reported their results achieved by different analytical methods. The results of NUSIMEP-7 confirm the capability of laboratories in measuring n((234)U)/n((238)U), n((235)U)/n((238)U) and n((236)U)/n((238)U) in uranium particles of the size below 1 μm diameter. Furthermore, they underpin the recent advances in instrumental techniques in the field of particle analysis. In addition, feedback from the measurement communities from nuclear safeguards, nuclear security and earth sciences was collected in view of identifying future needs for NUSIMEP interlaboratory comparisons.