Toward the Drug Factory Microbiome: Microbial Community Variations in Antibiotic-Producing Clean Rooms

A comprehensive technology strategy for microbial identification and contamination investigation in the sterile drug manufacturing facility-a case study

Objective

A comprehensive strategy for microbial identification and contamination investigation during sterile drug manufacturing was innovatively established in this study, mainly based on MALDI-TOF MS for the identification and complemented by sequencing technology on strain typing.

Methods

It was implemented to monitor the bacterial contamination of a sterile drug manufacturing facility, including its bacterial distribution features and patterns. In three months, two hundred ninety-two samples were collected covering multiple critical components of raw materials, personnel, environment, and production water.

Results

Based on our strategy, the bacterial profile across the production process was determined: 241/292 bacterial identities were obtained, and Staphylococcus spp. (40.25%), Micrococcus spp.(11.20%), Bacillus spp. (8.30%), Actinobacteria (5.81%), and Paenibacillus spp. (4.56%) are shown to be the most dominant microbial contaminants. With 75.8% species-level and 95.4% genus-level identification capability, MALDI-TOF MS was promising to be a first-line tool for environmental monitoring routine. Furthermore, to determine the source of the most frequently occurring Staphylococcus cohnii, which evidenced a widespread presence in the entire process, a more discriminating S. cohnii whole-genome SNP typing method was developed to track the transmission routes. Phylogenetic analysis based on SNP results indicated critical environment contamination is highly relevant to personnel flow in this case. The strain typing results provide robust and accurate information for the following risk assessment step and support effective preventive and corrective measures.

Conclusion

In general, the strategy presented in this research will facilitate the development of improved production and environmental control processes for the pharmaceutical industry, and give insights about how to provide more sound and reliable evidence for the optimization of its control program.

[Environmental Monitoring in a Pharmaceutical Manufacturing Facility Using a Culture Independent Approach]

Strict microbial control is required in manufacturing facilities to ensure the quality of pharmaceuticals and foods. Environmental microbial monitoring plays a fundamental role in reducing the risk of microbial contamination. Appropriate microbial control requires an understanding of abundance and community structures of microbes in the target environment. However, most of these microbes are not culturable using conventional methods. In this study, we determined the number of microbial particles and assessed the environmental microbiome in a pharmaceutical manufacturing facility, using high-throughput sequencing of rRNA gene fragments. Our results provide fundamental data for the evaluation and control of microbes in the pharmaceutical and food industries.

A review of the emergence of antibiotic resistance in bioaerosols and its monitoring methods

Despite significant public health concerns regarding infectious diseases in air environments, potentially harmful microbiological indicators, such as antibiotic resistance genes (ARGs) in bioaerosols, have not received significant attention. Traditionally, bioaerosol studies have focused on the characterization of microbial communities; however, a more serious problem has recently arisen due to the presence of ARGs in bioaerosols, leading to an increased prevalence of horizontal gene transfer (HGT). This constitutes a process by which bacteria transfer genes to other environmental media and consequently cause infectious disease. Antibiotic resistance in water and soil environments has been extensively investigated in the past few years by applying advanced molecular and biotechnological methods. However, ARGs in bioaerosols have not received much attention. In addition, ARG and HGT profiling in air environments is greatly limited in field studies due to the absence of suitable methodological approaches. Therefore, this study comprehensively describes recent findings from published studies and some of the appropriate molecular and biotechnological methods for monitoring antibiotic resistance in bioaerosols. In addition, this review discusses the main knowledge gaps regarding current methodological issues and future research directions.

Abundance and diversity of antibiotic resistance genes possibly released to ambient air by experiments in biology laboratories

Antibiotic resistance genes (ARG) have been considered as a global emerging threat to public health systems. As special locations where both antibiotics and ARGs are directly used, biology laboratories are poorly studied but potential important emission sources where not only the environmental stress is strong but also obtaining resistance is much easier comparing to other well studied hot spots including farms, hospitals, wastewater treatment plants and landfills where antibiotics but not ARGs are used or discharged. Therefore, in this study, 11 Swiss biology laboratories working on different fields and located in the city center, suburb and rural area were studied to reveal the abundance and diversity of airborne ARGs in them and their surrounding areas with Colony-forming units (CFU) cultivation and quantitative Polymerase Chain Reaction (qPCR). Most biology laboratories did not discharge significant amounts or varieties of ARGs and cultivable bacteria via air. No correlation was found between the number of CFUs and the abundance of 16S rRNA, but two clusters of correlated airborne ARGs, the animal husbandry related cluster, and city and hospital related cluster were identified in this study. Although most biology laboratories may not be the emission sources of a wide variety of airborne ARGs, the ARGs in the animal husbandry related cluster which are abundant in the animal laboratories and aadA1 which is abundant in the laboratories working on other eukaryocytes need to be furtherly studied to make sure if they are potential health risks for the researchers.

Patterns of antimicrobial resistance observed in the Middle East: Environmental and health care retrospectives

Antimicrobial resistance is one of the biggest worldwide challenging problems that associates with high morbidity and mortality rates. The resistance of bacteria to various antibiotic classes results in difficulties in the treatment of infectious diseases caused by those bacteria. This paper highlights and provides a critical overview of observational and experimental studies investigating the presence of antibiotic resistant bacteria in different environments in Middle East countries and the mechanisms by which bacteria acquire and spread resistance. The data of this research considered the published papers within the last ten years (2010-2020) and was carried out using PubMed. A total of 66 articles were selected in this review. This review covered studies done on antibiotic resistant bacteria found in a wide range of environments including foods, animals, groundwater, aquatic environments as well as industrial and hospital wastewater. They acquire and achieve their resistance through several mechanisms such as antibiotic resistant genes, efflux pumps and enzymatic reactions. However, the dissemination and spread of antibiotic resistant bacteria is affected by several factors like anthropogenic, domestic, inappropriate use of antibiotics and the expulsion of wastewater containing antibiotic residues to the environments. Therefore, it is important to increase the awareness regarding these activities and their effect on the environment and eventually on health.

The environmental risk assessment of cell-processing facilities for cell therapy in a Japanese academic institution

Cell therapy is a promising treatment. One of the key aspects of cell processing products is ensuring sterility of cell-processing facilities (CPFs). The objective of this study was to assess the environmental risk factors inside and outside CPFs. We monitored the temperature, humidity, particle number, colony number of microorganisms, bacteria, fungi, and harmful insects in and around our CPF monthly over one year. The temperature in the CPF was constant but the humidity fluctuated depending on the humidity outside. The particle number correlated with the number of entries to the room. Except for winter, colonies of microorganisms and harmful insects were detected depending on the cleanliness of the room. Seven bacterial and two fungal species were identified by PCR analyses. Psocoptera and Acari each accounted for 41% of the total trapped insects. These results provide useful data for taking the appropriate steps to keep entire CPFs clean.

Innovating Governance for Planetary Health with Three Critically Informed Frames

In May 2019, the Intergovernmental Science-Policy Platform on Biodiversity and Ecosystem Services warned that "around one million animal and plant species are now threatened with extinction." In September 2019, Naomi Klein, an astute writer on environmental change, described the interconnected social and ecological breakdowns on the planet in a new book. Ecological crises noted by these and other scholars speak well to the rise of planetary health as a new scholarship. Loss of biodiversity has manifold negative impacts on health, for example, rise of zoonotic infections and changes in healthy microbiome. But reducing our ecological footprints is not enough. We ought to change mindsets, the narrow science, and technology governance regimes that value nature and other life forms instrumentally by their usefulness to us. I describe three new, broader and critically informed, frames on governance for planetary health. First, I explain why we ought to acknowledge animal sentience, for example, as recognized in Article 13 of the Lisbon Treaty in 2009. I describe how political determinants of health, power, and agency operate at multiple sociological and planetary loci, not only among human beings but also at human and nonhuman animal interfaces. Second, planetary health calls for a shift toward ecological and political determinants beyond a narrow anthropocentric view, while resisting the entrenched dogma of exponential growth with finite planetary natural resources. Third, for critically informed governance of emerging technologies in planetary health (e.g., glycomics, artificial intelligence, health care robots), I refer to a question highlighted recently (Frodeman, 2019): "When Plato (more exactly, Juvenal) asked who guards the guardians, he was questioning whether any group can be trusted to look past its own interests for the common good." Hence, it is time we broaden the question "Who will guard the guardians?" beyond the scientific community, to actors in science policy as well. Policy questions cannot be limited to "which social issues emerge from a new technology?" but ought to include, "who should be framing science and technology policy, and why?" Youth leaders of the global climate movement such as Greta Thunberg and others are now rightly asking these epistemological questions that might contribute toward a new social contract on health for all sentient beings on planet Earth. While ecological changes accelerate and a new space industry is emerging, governance for planetary health will continue to be at the epicenter of systems thinking, responsible innovation and science policy in the 21st century.

Hospital Microbiome Variations As Analyzed by High-Throughput Sequencing

Hospital-acquired infections remain a serious threat to human life and are becoming a top public health issue. As the latest advances in sequencing technologies have allowed the unbiased identification of bacterial communities, we aimed to implement emerging omics technologies to characterize a hospital's microbiome at the center of Cairo, Egypt. To this end, we screened surfaces and inanimate objects in the hospital, focusing on bed sheets and door knobs, with additional screening for resistant microbes and resistance genes. While bacterial load and community composition were not dramatically different between door knobs of hospital units with different hygiene levels, the bacterial communities on door knob samples were richer and more diverse than those detected on bed sheets. Bacteria detected on door knobs were a mix of those associated with dust/particulate matter/debris (e.g., Bacillus, Geobacillus, Aeribacillus) and skin-associated bacteria (e.g., Staphylococcus, Corynebacterium). The latter were among the core genera shared by all analyzed samples. Conversely, bacteria that were more abundant in bed sheets were not associated with a particular source (e.g., Pseudomonas and Nitrobacter). Resistance screening indicated an expansion of a mobile beta-lactamase-encoding gene (bla_TEM), reflecting its current global spread. This study is a first step toward more comprehensive screening of hospital surfaces and correlating their microbiome with hospital outbreaks or chronic infections. We conclude that, as hospitals are unique built environments, these findings can inform future infection control strategies in hospitals and health care-related built environments, and attest to the importance of the emerging hospital microbiome research field.

Air and waterborne microbiome of a pharmaceutical plant provide insights on spatiotemporal variations and community resilience after disturbance

Background

The presence of microrganisms in pharmaceutical production plant environments is typically monitored by cultural methods, however these cannot detect the unculturable fraction of the microbial community. To get more accurate information on the composition of these indoor microbial communities, both water and air microbiome from a pharmaceutical production plant were profiled by 16S amplicon sequencing.

Results

In the water system, we found taxa which typically characterize surface freshwater, groundwater and oligotrophic environments. The airborne microbiome resulted dominated by taxa usually found in outdoor air in combination with human-associated taxa. The alpha- and beta- diversity values showed that the heat-based sanitization process of the water plant affects the composition of the water microbiome by transiently increasing both diversity and evenness. Taxonomic compositional shifts were also detected in response to sanitization, consisting in an increase of Firmicutes and α-Proteobacteria. On the other hand, seasonality seems to be the main driver of bacterial community composition in air of this work environment.

Conclusions

This approach resulted useful to describe the taxonomy of these indoor microbiomes and could be further applied to other built environments, in which the knowledge of the microbiome composition is of relevance. In addition, this study could assist in the design of new guidelines to improve microbiological quality control in indoor work environments.

Electronic supplementary material

The online version of this article (10.1186/s12866-018-1267-8) contains supplementary material, which is available to authorized users.