Clean your own house first: integrating sustainability into microbiology labs.

Microbiology laboratories are pivotal hubs for exploring the potential of microorganisms and addressing global challenges. Particularly, Environmental Microbiology facilities hold substantial influence in advancing knowledge and capabilities crucial for achieving the United Nations Sustainable Development Goals. This raises the imperative of integrating sustainable practices to mitigate the environmental impact of research activities and foster a culture of responsibility. Such an approach not only aligns with global sustainability objectives but also catalyses innovative, eco-conscious methodologies in scientific research aimed at tackling pressing environmental issues. Concerns regarding the environmental footprint of laboratory practices have stimulated innovative improvements within the scientific community, ranging from resource-efficient initiatives to the management of essential commodities like water and energy. This perspective discusses specific areas where microbiology laboratories can enhance their sustainability efforts, drawing on reports and case studies of pioneering groups. Additionally, it explores potential collaborators to support these endeavours and emphasises the pivotal role of early career researchers in driving this transition. By initiating discussions and sparking curiosity within the environmental microbial community, this commentary seeks to propel the microbial ecology field toward a greener future, starting from within the laboratory environment.

How to Evaluate If Microorganisms Isolated From Sterile Drug Production Environments Monitoring Are Undesirable.

This study addresses the identification of undesirable microorganisms (MOs) recovered during the environmental monitoring in manufacture of sterile medicinal products. We developed a methodology evaluation based on a decision tree; then, such approach was applied to hypothetical scenarios of uncommon MOs isolation in sterile drugs production settings. The scenarios were formulated on the basis of our field experience, in terms of both MOs selection and types of sampling site. The MOs were chosen in order to include emerging pathogens and MOs responsible for drug recall, and several sampling sites were considered for their detection (air, surfaces, and personnel). The classification of the unusual MOs revealed that most of them were undesirable, because they represented the loss of environmental control or a potential impact on the quality of the product. In some cases, the uncommon MOs were not considered as undesirable. Therefore, our results demonstrated the importance of a methodology, also in terms of recovery rate of unusual MOs and of the threshold probability for the unacceptability (e.g., 1% or 5%). The proposed methodology allowed an easy and documented evaluation for the undesirable MOs isolated from the environment of the analyzed settings for sterile drugs production.

Assessment of cleaning methods on bacterial burden of hospital privacy curtains: a pilot randomized controlled trial.

Healthcare-associated infections (HAIs) are an important global issue, leading to poor patient outcomes. A potential route of transmission of HAIs is through contact with hospital privacy curtains. The aim of this study is to evaluate cleaning on reduction of curtain bacterial burden. In this pilot cluster randomized controlled trial we compared the bacterial burden between three groups of 24 curtains on a regional burn/plastic surgery ward. A control group was not cleaned. Two groups were cleaned at 3-4 day intervals with either disinfectant spray or wipe. The primary outcome was the difference in mean CFU/cm2 between day 0 to day 21. The secondary outcome was the proportion of curtains contaminated with Methicillin-resistant Staphylococcus aureus (MRSA). By day 21, the control group was statistically higher (2.2 CFU/cm2) than spray (1.3 CFU/cm2) or wipe (1.5 CFU/cm2) (p < 0.05). After each cleaning at 3-4 day intervals, the bacterial burden on the curtains reduced to near day 0 levels; however, the level increased again over the intervening 3-4 days. By day 21, 64% of control curtains were contaminated with MRSA compared to 10% (spray) and 5% (wipe) (p < 0.05). This study show that curtains start clean and progressively become contaminated with bacteria. Regularly cleaning curtains with disinfectant spray or wipes reduces bacterial burden and MRSA contamination.

Assessment of the Presence of Resistance Genes Detected from the Environment and Selected Food Products in Benin.

Gram-negative bacilli can spread from the environment and through food products. This study aimed to characterize ESBL production and virulence genes from multidrug-resistant Gram-negative bacilli isolated from specimen collected from the environment, kitchen, and food products. A total of 130 samples were collected at local markets in seven different communities in Benin (Abomey-Calavi, Ouidah, Bohicon, Abomey, Parakou, Djougou, and Grand-Popo). Samples were cultured on McConkey and ChromID™ ESBL agar plates. The isolates were identified by the API 20E gallery. An antibiotic susceptibility test was carried out, and the detection of ESBL production and virulence-associated genes was carried out by Polymerase Chain Reaction (PCR). The data collected was coded and analyzed using GraphPad prism 7 software and Excel. The software R was used to calculate the correlation coefficient between the results of the detection of ESBL+ on agar and by the effect of the double synergy. The results showed that sixty-three (63) bacterial strains were isolated from the 130 samples, of which the dominant species was Chryseomonas luteola (10/63). The kitchen samples were the most contaminated with 36.50%. More than 40% of the isolates were resistant to at least three different classes of antibiotics. Also, blaSHV gene was detected in 33.33% (21/63) of the isolates and in all isolates of Pseudomonas aeruginosa (5/5%). 11.11% (7/63) of isolates were virulent with dominance of the fimH gene, especially with Escherichia coli (83.33%). The kitchen samples showed a high prevalence of ESBL-producing strains with fimH gene. This raises the problem of non-compliance with hygiene rules in community cooking and food handling.

COVID 19 mortality: Probable role of microbiome to explain disparity.

There is a significant difference between COVID 19 associated mortality between different countries. Generally the number of deaths per million population are higher in the developed countries despite better health care efficiency, drinking water quality and expected healthy life span (HALE) at the time of birth. Developing and underdeveloped countries on the other hand have lower mortality even with higher rural and slum populations along with incidence of diarrhea because of lack of sanitation. We analyzed data from 122 countries out of which 80 were high or upper middle income and 42 were low or low middle income countries. There was statistically significant positive correlation between COVID 19 deaths /million population and water current score, health efficiency, and HALE. Statistically significant negative correlation was observed with % rural population and fraction of diarrhea because of inadequate sanitation for all ages. Moreover analysis of 51 countries showed that there is significant negative correlation between COVID 19 deaths /million population and proportion of total population living in slums. We propose that high microbial exposure particularly gram negative bacteria can possibly induce interferon type I which might have a protective effect against COVID 19 since the countries with less mortality also tend to have lack of sanitation and high incidence of attendant diseases. So, far none of the predictive models have taken into account immune status of populations engendered by environmental microbial exposure or microbiome. There might be a need to look at dynamics of COVID 19 pandemic using immune perspective. The approach can potentially inform better policies including interventions.

Faecal contamination of the environment and child health: a systematic review and individual participant data meta-analysis.

BACKGROUND: Exposure to faecal contamination is believed to be associated with child diarrhoea and possibly stunting; however, few studies have explicitly measured the association between faecal contamination and health. We aimed to assess individual participant data (IPD) across multiple trials and observational studies to quantify the relationship for common faecal-oral transmission pathways. METHODS: We did a systematic review and meta-analysis of IPD from studies identified in an electronic search of PubMed, Web of Science, and Embase on May 21, 2018. The search was done in English, but full texts published in French, Portuguese, and Spanish were also reviewed. Eligible studies quantified (1) household-level faecal indicator bacteria concentrations along common faecal-oral transmission pathways of drinking water, soil, or food, on children's hands or fomites, or fly densities in food preparation areas; and (2) individual-level diarrhoea or linear growth measures for children younger than 5 years in low-income and middle-income countries. For the diarrhoea analysis, all definitions of diarrhoea were eligible but studies were excluded if they used a recall period longer than 7 days. For the linear growth analysis (using height-for-age Z scores [HAZ]), cross-sectional studies were excluded, because of the absence of longitudinal environmental contamination data measured before the growth outcomes. We used multilevel generalised mixed-effects models to estimate the odds ratio (OR) for diarrhoea and the difference in HAZ scores for individual studies associated with a 1-log10 higher measure of faecal contamination. Estimates from each study were combined under a random-effects meta-analysis framework. The study protocol was pre-registered with PROSPERO (CRD42018102114). FINDINGS: From 72 eligible studies, we included IPD for 20 studies in the meta-analyses, totalling 54 225 diarrhoea or linear growth observations matched to faecal indicator bacteria concentrations in drinking water, and a further 35 010 observations with faecal contamination data for the other transmission pathways. Child diarrhoea was associated with 1-log10 higher faecal indicator bacteria concentrations in drinking water (OR 1·09, 95% CI 1·04 to 1·13; p=0·0002, I2=34%, 95% CI 0 to 62) and on children's hands (1·11, 1·02 to 1·22; p=0·021, I2=0%, 0 to 71). Lower HAZ scores were associated with 1-log10 higher median faecal indicator bacteria concentrations in drinking water (HAZ -0·04, 95% CI -0·06 to -0·01; p=0·0054; I2=19%, 95% CI 0 to 63) and on fomites (-0·06, -0·12 to 0·00; p=0·044, I2=57%, 0 to 90). INTERPRETATION: Although summary measures from individual studies often report little or no effect of measured faecal contamination on child health, this multi-study IPD analysis indicates that household faecal indicator bacteria concentrations are associated with important adverse health outcomes in young children. Improved direct measures of exposure and enteric pathogens could help to better characterise the relationship and inform intervention design in future studies. FUNDING: None.

The archives are half-empty: an assessment of the availability of microbial community sequencing data.

As DNA sequencing has become more popular, the public genetic repositories where sequences are archived have experienced explosive growth. These repositories now hold invaluable collections of sequences, e.g., for microbial ecology, but whether these data are reusable has not been evaluated. We assessed the availability and state of 16S rRNA gene amplicon sequences archived in public genetic repositories (SRA, EBI, and DDJ). We screened 26,927 publications in 17 microbiology journals, identifying 2015 16S rRNA gene sequencing studies. Of these, 7.2% had not made their data public at the time of analysis. Among a subset of 635 studies sequencing the same gene region, 40.3% contained data which was not available or not reusable, and an additional 25.5% contained faults in data formatting or data labeling, creating obstacles for data reuse. Our study reveals gaps in data availability, identifies major contributors to data loss, and offers suggestions for improving data archiving practices.

The SaniPath Exposure Assessment Tool: A quantitative approach for assessing exposure to fecal contamination through multiple pathways in low resource urban settlements.

Inadequate sanitation can lead to exposure to fecal contamination through multiple environmental pathways and can result in adverse health outcomes. By understanding the relative importance of multiple exposure pathways, sanitation interventions can be tailored to those pathways with greatest potential public health impact. The SaniPath Exposure Assessment Tool allows users to identify and quantify human exposure to fecal contamination in low-resource urban settings through a systematic yet customizable process. The Tool includes: a project management platform; mobile data collection and a data repository; protocols for primary data collection; and automated exposure assessment analysis. The data collection protocols detail the process of conducting behavioral surveys with households, school children, and community groups to quantify contact with fecal exposure pathways and of collecting and analyzing environmental samples for E. coli as an indicator of fecal contamination. Bayesian analyses are used to estimate the percentage of the population exposed and the mean dose of fecal exposure from microbiological and behavioral data. Fecal exposure from nine pathways (drinking water, bathing water, surface water, ocean water, open drains, floodwater, raw produce, street food, and public or shared toilets) can be compared through a common metric-estimated ingestion of E. coli units (MPN or CFU) per month. The Tool generates data visualizations and recommendations for interventions designed for both scientific and lay audiences. When piloted in Accra, Ghana, the results of the Tool were comparable with that of an in-depth study conducted in the same neighborhoods and highlighted consumption of raw produce as a dominant exposure pathway. The Tool has been deployed in nine cities to date, and the results are being used by local authorities to design and prioritize programming and policy. The SaniPath Tool is a novel approach to support public-health evidence-based decision-making for urban sanitation policies and investments.

Detection of Lactate Dehydrogenase Elevating Virus in a Mouse Vivarium Using an Exhaust Air Dust Health Monitoring Program.

Lactate dehydrogenase elevating virus (LDV) continues to be one of the most common contaminants of cells and cell byproducts. As such, many institutions require that tumor cell lines, blood products, and products derived or passaged in rodent tissues are free of LDV as well as other pathogens that are on institutional exclusion lists prior to their use in rodents. LDV is difficult to detect by using a live-animal sentinel health monitoring program because the virus does not reliably pass to sentinel animals. After switching to an exhaust air dust health monitoring system, our animal resources center was able to detect a presumably long-standing LDV infection in a mouse colony. This health monitoring system uses IVC rack exhaust air dust collection media in conjunction with PCR analysis. Ultimately, the source of the contamination was identified as multiple LDV-positive patient-derived xenografts and multiple LDV-positive breeding animals. This case study is the first to demonstrate the use of environmental PCR testing as a method for detecting LDV infection in a mouse vivarium.

Carbapenem-Resistant Enterobacteriaceae Outbreak in a Medical Ward in Spain: Epidemiology, Control Strategy, and Importance of Environmental Disinfection.

Introduction: Carbapenem-resistant Enterobacteriaceae (CRE) are a growing public health problem. We describe an outbreak by CRE and the measures to control it in a hospitalization unit in Spain. Methods: In June 2015, the system of prevention and control of CRE implemented in the hospital detected an increase in the incidence of patients with CRE in a mixed hospitalization facility (geriatrics, internal medicine, and pneumology), with the appearance of four related patients in 2 weeks, three of them being nosocomial cases. A multidisciplinary group was created and carried out: weekly screenings, general cleaning, four training sessions for personnel, two hand hygiene observation studies and environmental sampling. A higher incidence of new cases was detected in three adjoining rooms, in which environmental decontamination was performed with vaporized hydrogen peroxide. Results: In 5 months, a total of 18 cases were detected, 14 of them were nosocomial. Four different clones of Klebsiella pneumoniae OXA-48 were responsible for 83.3% of the cases. Adherence to hand hygiene increased from 36% to 85% after the training sessions. Seven percent of the environmental samples were positive for CRE in rooms with high incidence, moving to 0% after decontamination with hydrogen peroxide. Three patients died, one of them possibly associated with clinical infection due to CRE. Conclusions: Multidisciplinary information strategies, personnel training, and control of environmental reservoirs are effective to address outbreaks of CRE.

Life-Cycle Assessment (LCA) Analysis of Algal Fuels.

Life-cycle assessment (LCA) is one of the most attractive tools employed nowadays by environmental policy-makers as well as business decision-makers to ensure environmentally sustainable production/consumption of various goods/services. LCA is a systematic, rigorous, and standardized approach aimed at quantifying resources consumed/depleted, pollutants released, and the related environmental and health impacts through the course of consumption and production of goods/service. Algal fuels are no exception and their environmental sustainability could be well scrutinized using the LCA methodology. In line with that, this chapter is devoted to present guidelines on the technical aspects of LCA application in algal fuels while elaborating on major standards used, i.e., ISO 14040 and 14044 standards. Overall, LCA practitioners as well as technical experts dealing with algal fuels in both the public and private sectors could be the main target audience for these guidelines.

Impact of environmental biofilms: Industrial components and its remediation.

The growth of technology and requirements globally for various commodities has brought about new challenges. Biofilms are aggregations of microbial cells, which contaminate and spoil industrial components and environments. These microbial cells with extracellular polymeric substances colonize living and nonliving surfaces and pose a serious problem for all industries, affecting their processes, leading to a reduction of product quality and economic loss. Industries, such as medical, food, water, dairy, wine, marine, power plants are exposed to biofilm formation. Pipe blockages, waterlogging and reduction of the heat-transfer efficiency, hamper the operating system of plants. Many industries do not set up remedial measures to control biofilm formation as they are not aware of this threat. Various conventional methods to control these biofilms are adopted by industries in their regular workflow, but these are temporary solutions. This calls for further research into remediation of the biofilm and its control for industrial components. This review article addresses the problems of biofilms and proposes solutions for various industrial components. Nanotechnology promises several options, and bring about a new aspect into the industrial economy, by solving the problems of environmental biofilms.

Indirect assessment of porcine reproductive and respiratory syndrome virus status in pigs prior to weaning by sampling sows and the environment.

There is a need to develop cost effective approaches to sample large populations in particular to determine the disease status of pigs prior to weaning. In this study we assessed the presence of the porcine reproductive and respiratory syndrome virus (PRRSV) in the environment (surfaces and air) of farrowing rooms, and udder skin of lactating sows as an indirect measure of piglet PRRSV status. Samples were collected at processing and weaning every three weeks for 23 weeks after a PRRSV outbreak was diagnosed in a swine breeding herd. PRRSV was detected at processing in udder skin wipes, environmental wipes and airborne deposited particle samples up to 14 weeks post outbreak and at weaning in udder skin wipes up to 17 weeks post outbreak. Similar sensitivities were observed for udder skin wipes (43% [95% CI: 23%-66%]) and surface wipes (57% [95% CI: 34%-77%]) when compared to serum at the litter level from piglets at processing. PRRSV was detected in the environment and the udder skin of lactating sows, which indicates that aggregate samples of the environment or lactating sows may be used to evaluate the PRRSV status of the herd in pigs prior to weaning. However, the use of environmental samples to detect PRRSV by RT-PCR should not be used as the single method to assess the PRRSV status at the litter level. Furthermore, our findings also highlight potential sources of PRRSV infection for piglets in breeding herds.

Tracking Pseudomonas aeruginosa transmissions due to environmental contamination after discharge in ICUs using mathematical models.

Pseudomonas aeruginosa (P. aeruginosa) is an important cause of healthcare-associated infections, particularly in immunocompromised patients. Understanding how this multi-drug resistant pathogen is transmitted within intensive care units (ICUs) is crucial for devising and evaluating successful control strategies. While it is known that moist environments serve as natural reservoirs for P. aeruginosa, there is little quantitative evidence regarding the contribution of environmental contamination to its transmission within ICUs. Previous studies on other nosocomial pathogens rely on deploying specific values for environmental parameters derived from costly and laborious genotyping. Using solely longitudinal surveillance data, we estimated the relative importance of P. aeruginosa transmission routes by exploiting the fact that different routes cause different pattern of fluctuations in the prevalence. We developed a mathematical model including background transmission, cross-transmission and environmental contamination. Patients contribute to a pool of pathogens by shedding bacteria to the environment. Natural decay and cleaning of the environment lead to a reduction of that pool. By assigning the bacterial load shed during an ICU stay to cross-transmission, we were able to disentangle environmental contamination during and after a patient's stay. Based on a data-augmented Markov Chain Monte Carlo method the relative importance of the considered acquisition routes is determined for two ICUs of the University hospital in Besançon (France). We used information about the admission and discharge days, screening days and screening results of the ICU patients. Both background and cross-transmission play a significant role in the transmission process in both ICUs. In contrast, only about 1% of the total transmissions were due to environmental contamination after discharge. Based on longitudinal surveillance data, we conclude that cleaning improvement of the environment after discharge might have only a limited impact regarding the prevention of P.A. infections in the two considered ICUs of the University hospital in Besançon. Our model was developed for P. aeruginosa but can be easily applied to other pathogens as well.

Clostridioides difficile on Ohio swine farms (2015): A comparison of swine and human environments and assessment of on-farm risk factors.

Swine are known reservoirs for Clostridioides difficile, formerly known as Clostridium difficile, and transmission from swine to human farm workers is strongly suggested by previous studies. This cross-sectional study evaluated the potential role of farm environmental surfaces, including those in worker breakrooms and swine housing areas, in the possible transmission of C. difficile from swine to farm workers. Environmental surfaces and piglet faeces at 13 Ohio swine farms were sampled in 2015. Typical culturing techniques were performed to isolate C. difficile from samples, and amplification of toxin genes (tcdA, tcdB and cdtB) and PCR-ribotyping were used to genetically characterize recovered isolates. In addition, sequencing of toxin regulatory gene, tcdC, was done to identify the length of identified deletions in some isolates. A survey collected farm-level management risk factor information. Clostridioides difficile was recovered from all farms, with 42% (188/445) of samples testing positive for C. difficile. Samples collected from all on-farm locations recovered C. difficile, including farrowing rooms (60%, 107/178), breakrooms (50%, 69/138) and nursery rooms (9%, 12/129). Three ribotypes recovered from both swine and human environments (078, 412 and 005) have been previously implicated in human disease. Samples taken from farrowing rooms and breakrooms were found to have greater odds of C. difficile recovery than those taken from nursery rooms (OR = 40.5, OR = 35.6, p < .001 respectively). Farms that weaned ≥23,500 pigs per year had lower odds of C. difficile recovery as compared to farms that weaned fewer pigs (OR = 0.4, p = .01) and weekly or more frequent cleaning of breakroom counters was associated with higher odds of C. difficile recovery (OR = 11.7, p < .001). This study provides important insights into the presence and characterization of C. difficile found in human environments on swine farms and highlights how these areas may be involved in transmission of C. difficile to swine farm workers and throughout the facility.

Aspergillus spp. prevalence in Primary Health Care Centres: Assessment by a novel multi-approach sampling protocol.

Exposure to Aspergillus conidia may cause adverse effects on human health; however, no specific recommendations for routine assessments of Aspergillus in the clinical environment have been suggested so far. This study intended to determine the prevalence of Aspergillus in the clinical environment, focusing on ten Primary Health Care Centres (PHCC) through a novel multi-approach sampling protocol. Air and passive sampling, culture-based methods and a probe-based real-time assay for the detection of four clinically relevant Aspergillus sections were performed. Aspergillus spp. was observed in all PHCC, with highest prevalence on floor surface swabs (n=81) (18% on MEA; 6.94% on DG18). Regarding air samples (n=81), highest Aspergillus counts were found in the waiting room (94% MEA; 18% DG18), where Nigri was the most prevalent Aspergillus section. The use of a multi-approach sampling protocol to assess Aspergillus burden in the analysed PHCC has greatly contributed to risk characterization, highlighting the need to implement corrective measures in order to avoid fungal presence in those settings.

Risk Assessment After a Severe Hospital-Acquired Infection Associated With Carbapenemase-Producing Pseudomonas aeruginosa.

Importance: Resistance of gram-negative bacilli to carbapenems is rapidly emerging worldwide. In 2016, the World Health Organization defined the hospital-built environment as a core component of infection prevention and control programs. The hospital-built environment has recently been reported as a source for outbreaks and sporadic transmission events of carbapenemase-producing gram-negative bacilli from the environment to patients. Objective: To assess risk after the identification of an unexpected, severe, and lethal hospital-acquired infection caused by carbapenemase-producing Pseudomonas aeruginosa in a carbapenemase-low endemic setting. Design, Settings, and Participants: A case series study in which a risk assessment was performed on all 11 patients admitted to the combined cardiothoracic surgery and pulmonary diseases ward and the hospital-built environment in the Radboud University Medical Center, the Netherlands, in February 2018. Exposures: Water and aerosols containing carbapenemase-producing (Verona integron-mediated metallo-ß-lactamase [VIM]) P aeruginosa. Main Outcomes and Measures: Colonization and/or infection of patients and/or contamination of the environment after the detection of 1 patient infected with carbapenemase-producing (VIM) P aeruginosa. Results: A total of 5 men (age range, 60-84 years) and 6 women (age range, 55-74 years) were admitted to the combined cardiothoracic surgery and pulmonary diseases ward. The risk assessment was performed after carbapenemase-producing (VIM) P aeruginosa was unexpectedly detected in a man in his early 60s, who had undergone a left-sided pneumonectomy and adjuvant radiotherapy. No additional cases (colonization or infection) of carbapenemase-producing (VIM) P aeruginosa were detected. Plausible transmission of carbapenemase-producing P aeruginosa from the hospital environment to the patient via the air was confirmed by whole-genome sequencing, which proved the relation of Pseudomonas strains from the patient, the shower drains in 8 patient rooms, 1 sink, and an air sample. Conclusions and Relevance: This study suggests that rethinking the hospital-built environment, including shower drains and the sewage system, will be crucial for the prevention of severe and potential lethal hospital-acquired infections.

Bacterial Contamination on Latrine Surfaces in Community and Household Latrines in Kathmandu, Nepal.

A lack of sanitation infrastructure is a major contributor to the global burden of diarrheal disease, particularly in low-income countries. Access to basic sanitation was identified as part of the 2015 United Nations Sustainable Development Goals. However, current definitions of "basic" sanitation infrastructure exclude community or shared sanitation, due to concerns around safety, equity, and cleanliness. The purpose of this study was to measure and compare bacterial contamination on community and household latrine surfaces in Kathmandu, Nepal. One hundred and nineteen swab samples were collected from two community and five household latrines sites. Community latrine samples were taken before and after daily cleaning, while household samples were collected at midday, to reflect normal conditions. Concentrations of total coliforms and Escherichia coli were measured using membrane filtration methods. Results found almost no differences between bacterial contamination on latrine surfaces in community and household latrines, with the exception of latrine slabs/seats that were more contaminated in the community latrines under dirty conditions. The study also identified surfaces with higher levels of contamination. Findings demonstrated that well-maintained community latrines may be as clean, or cleaner, than household latrines and support the use of community latrines for improving access to sanitation infrastructure in a low-income country setting.