Investigation of the human nasal microbiome in persons with long- and short-term exposure to methicillin-resistant Staphylococcus aureus and other bacteria from the pig farm environment

The Role of the Microbiome in Allergy, Asthma, and Occupational Lung Disease

PURPOSE OF REVIEW

The human commensal microbiota is now widely accepted as a key regulator of human health and disease. The composition of the mucosal associated microbiota has been shown to play a critical role in the lung health. The role of the mucosal microbiota in the development and severity of allergy, asthma, and occupational lung disease is only beginning to take shape. However, advances in our understanding of these links have tremendous potential to led to new clinical interventions to reduce allergy, asthma, and occupational lung disease morbidity.

RECENT FINDINGS

We review recent work describing the relationship and role of the commensal microbiota in the development of allergy, asthma, and occupational lung disease. Our review primarily focuses on occupational exposures and the effects of the microbiome, both in composition and function. Data generated from these studies may lead to the development of interventions targeted at establishing and maintaining a healthy microbiota. We also highlight the role of environmental exposures and the effects on the commensal microbial community and their potential association with occupational lung disease. This review explores the current research describing the role of the human microbiome in the regulation of pulmonary health and disease, with a specific focus on the role of the mucosal microbiota in the development of allergy, asthma, and occupational lung disease.

A review of the influence of environmental pollutants (microplastics, pesticides, antibiotics, air pollutants, viruses, bacteria) on animal viruses

Microorganisms, especially viruses, cause disease in both humans and animals. Environmental chemical pollutants including microplastics, pesticides, antibiotics sand air pollutants arisen from human activities affect both animal and human health. This review assesses the impact of chemical and biological contaminants (virus and bacteria) on viruses including its life cycle, survival, mutations, loads and titers, shedding, transmission, infection, re-assortment, interference, abundance, viral transfer between cells, and the susceptibility of the host to viruses. It summarizes the sources of environmental contaminants, interactions between contaminants and viruses, and methods used to mitigate such interactions. Overall, this review provides a perspective of environmentally co-occurring contaminants on animal viruses that would be useful for future research on virus-animal-human-ecosystem harmony studies to safeguard human and animal health.

A look at staphylococci from the one health perspective

Staphylococcus aureus and other staphylococcal species are resident and transient multihost colonizers as well as conditional pathogens. Especially S. aureus represents an excellent model bacterium for the "One Health" concept because of its dynamics at the human-animal interface and versatility with respect to host adaptation. The development of antimicrobial resistance plays another integral part. This overview will focus on studies at the human-animal interface with respect to livestock farming and to companion animals, as well as on staphylococci in wildlife. In this context transmissions of staphylococci and of antimicrobial resistance genes between animals and humans are of particular significance.

Commercial farmed swine harbour a variety of pathogenic bacteria and antimicrobial resistance genes

Introduction. The northern region of Thailand serves as a crucial area for swine production, contributing to the Thai community food supply. Previous studies have highlighted the presence of foodborne bacterial pathogens originating from swine farms in this region, posing a threat to both human and animal health.Gap statement. Multiple swine bacterial pathogens have been studied at a species level, but the distribution and co-occurrence of bacterial pathogens in agricultural swine has not been well established.Aim. Our study employed the intestinal scraping technique to directly examine the bacterial micro-organisms interacting with the swine host.Methodology. We used shotgun metagenomic sequencing to analyse the bacterial pathogens inhabiting the caecal microbiome of swine from five commercial farms in northern Thailand.Results. A variety of pathogenic and opportunistic bacteria were identified, including Escherichia coli, Clostridium botulinum, Staphylococcus aureus and the Corynebacterium genus. From a One Health perspective, these species are important foodborne and opportunistic pathogens in both humans and agricultural animals, making swine a critical pathogen reservoir that can cause illness in humans, especially farm workers. Additionally, the swine caecal microbiome contains commensal bacteria such as Bifidobacterium, Lactobacillus and Faecalibacterium, which are associated with normal physiology and feed utilization in healthy swine. Antimicrobial resistance genes were also detected in all samples, specifically conferring resistance to tetracycline and aminoglycosides, which have historically been used extensively in swine farming.Conclusion. The findings further support the need for improved sanitation standards in swine farms, and additional monitoring of agricultural animals and farm workers to reduce contamination and improved produce safety for human consumption.

Secretory IgA impacts the microbiota density in the human nose

BACKGROUND

Respiratory mucosal host defense relies on the production of secretory IgA (sIgA) antibodies, but we currently lack a fundamental understanding of how sIgA is induced by contact with microbes and how such immune responses may vary between humans. Defense of the nasal mucosal barrier through sIgA is critical to protect from infection and to maintain homeostasis of the microbiome, which influences respiratory disorders and hosts opportunistic pathogens.

METHODS

We applied IgA-seq analysis to nasal microbiota samples from male and female healthy volunteers, to identify which bacterial genera and species are targeted by sIgA on the level of the individual host. Furthermore, we used nasal sIgA from the same individuals in sIgA deposition experiments to validate the IgA-seq outcomes.

CONCLUSIONS

We observed that the amount of sIgA secreted into the nasal mucosa by the host varied substantially and was negatively correlated with the bacterial density, suggesting that nasal sIgA limits the overall bacterial capacity to colonize. The interaction between mucosal sIgA antibodies and the nasal microbiota was highly individual with no obvious differences between potentially invasive and non-invasive bacterial species. Importantly, we could show that for the clinically relevant opportunistic pathogen and frequent nasal resident Staphylococcus aureus, sIgA reactivity was in part the result of epitope-independent interaction of sIgA with the antibody-binding protein SpA through binding of sIgA Fab regions. This study thereby offers a first comprehensive insight into the targeting of the nasal microbiota by sIgA antibodies. It thereby helps to better understand the shaping and homeostasis of the nasal microbiome by the host and may guide the development of effective mucosal vaccines against bacterial pathogens. Video Abstract.

Exposure to cooking fumes is associated with perturbations in nasal microbiota composition: A pilot study

Air pollution is one of the leading causes of overall mortality globally. Cooking emissions are a major source of fine particulate matter (PM2.5). However, studies on their potential perturbations on the nasal microbiota as well as their association with respiratory health are lacking. This pilot study aims to assess the environmental air quality among occupational cooks and its associations with nasal microbiota and respiratory symptoms. A total of 20 cooks (exposed) and 20 unexposed controls (mainly office workers), were recruited in Singapore from 2019 to 2021. Information on sociodemographic factors, cooking methods, and self-reported respiratory symptoms were collected using a questionnaire. Personal PM2.5 concentrations and reactive oxygen species (ROS) levels were measured using portable sensors and filter samplers. DNA was extracted from nasal swabs and sequenced using 16s sequencing. Alpha-diversity and beta-diversity were calculated, and between-group variation analysis of species was performed. Multivariable logistic regression was used to estimate odds ratios (ORs) and 95% confidence intervals (CIs) for associations between exposure groups and self-reported respiratory symptoms. Higher daily mean PM2.5 (P = 2 × 10-7) and environmental ROS exposure (P = 3.25 × 10-7) were observed in the exposed group. Alpha diversity of the nasal microbiota between the two groups was not significantly different. However, beta diversity was significantly different (unweighted UniFrac P = 1.11 × 10-5, weighted UniFrac P = 5.42 × 10-6) between the two exposure groups. In addition, certain taxa of bacteria were slightly more abundant in the exposed group compared to unexposed controls. There were no significant associations between the exposure groups and self-reported respiratory symptoms. In summary, the exposed group had higher PM2.5 and ROS exposure levels and altered nasal microbiotas as compared to unexposed controls, though further studies are required to replicate these findings in a larger population.

Lessons from Dairy Farmers for Occupational Allergy and Respiratory Disease

PURPOSE OF REVIEW

Exposure to bioaerosols at dairies has long been associated with allergy, respiratory disease, and decreases in lung function. Recent advancements in exposure assessments have aided our understanding on the size distribution and composition of these bioaerosols, but investigations focusing solely on exposures may overlook important intrinsic factors impacting worker's susceptibility to disease.

RECENT FINDINGS

In our review, we discuss the most recent studies examining the exposures and genetic factors that contribute to occupational disease in dairy work. We also review more recent concerns in livestock work associated with zoonotic pathogens, antimicrobial resistant genes, and the role of the human microbiome. The studies highlighted in this review demonstrate the need for further research to better understand bioaerosol exposure-response relationships in the context of extrinsic and intrinsic factors, antibiotic-resistant genes, viral pathogens, and the human microbiome to help inform effective interventions that improve respiratory health among dairy farmers.

An Assessment of the In Vitro Models and Clinical Trials Related to the Antimicrobial Activities of Phytochemicals

An increased number antibiotic-resistant bacteria have emerged with the rise in antibiotic use worldwide. As such, there has been a growing interest in investigating novel antibiotics against antibiotic-resistant bacteria. Due to the extensive history of using plants for medicinal purposes, scientists and medical professionals have turned to plants as potential alternatives to common antibiotic treatments. Unlike other antibiotics in use, plant-based antibiotics have the innate ability to eliminate a broad spectrum of microorganisms through phytochemical defenses, including compounds such as alkaloids, organosulfur compounds, phenols, coumarins, and terpenes. In recent years, these antimicrobial compounds have been refined through extraction methods and tested against antibiotic-resistant strains of Gram-negative and Gram-positive bacteria. The results of the experiments demonstrated that plant extracts successfully inhibited bacteria independently or in combination with other antimicrobial products. In this review, we examine the use of plant-based antibiotics for their utilization against antibiotic-resistant bacterial infections. In addition, we examine recent clinical trials utilizing phytochemicals for the treatment of several microbial infections.

Across-Shift Changes in Viable Nasal Bacteria among Waste-Incineration Plant Workers-A Pilot Study

The aim of this pilot study was to assess the time-related changes in viable nasal bacteria concentrations among waste-incineration plant (WIP) workers compared to a group of office building (OB) workers outside the plant. In total, 20 volunteers participated in the study, including 14 WIP and 6 OB workers. WIP workers were divided into two sub-groups: supervisory staff (SVS) and maintenance and repair workers (MRW). Nasal swabs were collected before and after the morning work shift. Airborne bacteria were sampled with a six-stage impactor to assess the bioaerosol size distribution. The analysis showed that a significant, almost three-fold increase in nasal bacterial concentration was found only among WIP workers, and this referred mainly to anaerobic species. The load of anaerobic bacteria at the beginning of work was 12,988 CFU/mL, and after work shift 36,979 CFU/mL (p < 0.01). Significant increases in microbial concentrations was found only in the MRW subgroup, among non-smoking workers only. The results showed increased bacterial concentration in WIP nasal samples for as many as 12 bacterial species, including, e.g., Streptococcus constellatus, Peptostreptococcus spp., E. coli, and P. mirabilis. These preliminary data confirmed that the nasal swab method was helpful for assessment of the workers’ real-time exposure to airborne bacteria.

WORKbiota: A Systematic Review about the Effects of Occupational Exposure on Microbiota and Workers' Health

The characterization of human microbiota and the impact of its modifications on the health of individuals represent a current topic of great interest for the world scientific community. Scientific evidence is emerging regarding the role that microbiota has in the onset of important chronic illnesses. Since individuals spend most of their life at work, occupational exposures may have an impact on the organism’s microbiota. The purpose of this review is to explore the influence that different occupational exposures have on human microbiota in order to set a new basis for workers’ health protection and disease prevention. The literature search was performed in PubMed, Cochrane, and Scopus. A total of 5818 references emerged from the online search, and 31 articles were included in the systematic review (26 original articles and 5 reviews). Exposure to biological agents (in particular direct contact with animals) was the most occupational risk factor studied, and it was found involved in modifications of the microbiota of workers. Changes in microbiota were also found in workers exposed to chemical agents or subjected to work-related stress and altered dietary habits caused by specific microclimate characteristics or long trips. Two studies evaluated the role of microbiota changes on the development of occupational lung diseases. Occupational factors can interface with the biological rhythms of the bacteria of the microbiota and can contribute to its modifications and to the possible development of diseases. Future studies are needed to better understand the role of the microbiota and its connection with occupational exposure to promote projects for the prevention and protection of global health.

Dynamics of the Human Nasal Microbiota and Staphylococcus aureus CC398 Carriage in Pig Truck Drivers across One Workweek

Drivers of pig trucks constitute a potential route of human transmission of livestock-associated methicillin-resistant Staphylococcus aureus clonal complex 398 (LA-MRSA CC398). In this study, we determined MRSA prevalence in pig truck drivers (n = 47) and monitored the nasal microbiota of 9 drivers 3 times daily throughout 1 workweek (n = 113 samples) and compared it to that of their spouses (n = 25 samples from 6 spouses) and 89 nonexposed subjects. S. aureus isolates (n = 232) derived from a subset of nasal and truck samples were whole-genome sequenced. The nasal alpha diversity of drivers in the beginning of the workday was lower than that of nonexposed subjects. During the workday, it increased significantly. Similarly, the drivers’ nasal composition shifted during the workday, becoming increasingly different from that of their spouses and nonexposed individuals. Clustering into community state types (CSTs) revealed frequent switches from either S. aureus- or Corynebacterium-dominated CSTs in the mornings to a Psychrobacter-dominated CST during the workday. Six intermittent MRSA carriers were mostly MRSA negative in the mornings, and their nasal microbiota resembled that of nonexposed subjects. When acquiring MRSA during the workday, they switched to the Psychrobacter-dominated CST. In contrast, the nasal microbiota of two persistent MRSA carriers was dominated by staphylococci. In conclusion, we show that the nasal microbiota of pig truck drivers is very dynamic, undergoes drastic changes during workdays, and differs from that of nonexposed subjects even before pig contact. MRSA-carrying drivers may eventually introduce MRSA into the community and health care facilities. Carriage dynamics, however, showed that for most drivers, CC398 MRSA is rapidly lost and only rarely causes transmission to spouses.

IMPORTANCE In Denmark, the number of human methicillin-resistant Staphylococcus aureus (MRSA) cases has increased dramatically since the early 2000s, starting from imported cases and spreading in the community. However, today, approximately one-third of all new cases are attributed to livestock-associated MRSA clonal complex 398 (LA-MRSA CC398). This mirrors the increase in pig farms, of which 95% are now positive for LA-MRSA, and this has been caused mainly by three dominant lineages enriched for a number of key antimicrobial resistance genes. Although most human LA-MRSA CC398 infections in Denmark are linked to livestock contact, still up to one-third are not. Pig truck drivers constitute a previously understudied occupation group which may transmit LA-MRSA CC398 to household members, the community, and hospitals. In this study, we demonstrate dramatic work-related changes in the nasal microbiota of pig truck drivers, as well as in their carriage of LA-MRSA CC398. However, they likely do not constitute an important reservoir for LA-MRSA CC398 dissemination.

Genetic diversity of healthcare-associated methicillin-resistant Staphylococcus aureus isolates from Southern Iran

Staphylococcus aureus is a common pathogen causing hospital infections. The increasing rate of healthcare-associated infections caused by methicillin-resistant Staphylococcus aureus (MRSA) in developing countries has led to many public health problems. This study aimed to investigate the molecular epidemiology as well as the antibiotic resistance pattern of clinical isolates of MRSA from Southern Iran. A total of 135 S. aureus isolates were collected from the patients referred to three hospitals in South Iran. The phenotypic and genotypic diagnosis of MRSA isolates was performed by disk diffusion and PCR methods, respectively. The antibiotic resistance pattern for MRSA isolates was performed using Kirby-Bauer method. The molecular epidemiology of isolates was performed by MLST, Spa typing and SCCmec typing. From 135 S. aureus isolates, 50 (37%) MRSA strains were detected from which two different sequence types including ST239 and ST605 were identified. SCCmec type III was the most common profile (50%) and t030 was the predominant spa type (48%) among the strains. The MRSA isolates had the highest resistance to penicillin (100%), tetracycline (88%), levofloxacin (86%), ciprofloxacin (84%), erythromycin (82%), gentamicin (80%), and clindamycin (78%). The results of this study show that the most common genetic type among the MRSA isolates was ST239-SCCmec III/t030. The rapid and timely detection of MRSA and the administration of appropriate antibiotics according to the published antibiotic resistance patterns are essential. Furthermore, the continuous and nationwide MRSA surveillance studies are necessary to investigate clonal distribution and spreading of MRSA from community to hospitals.

A Clinical Trial to Evaluate the Efficacy of α-Viniferin in Staphylococcus aureus - Specific Decolonization without Depleting the Normal Microbiota of Nares

Staphylococcus aureus is currently a significant multidrug-resistant bacterium, causing severe healthcare-associated and community-acquired infections worldwide. The current antibiotic regimen against this pathogen is becoming ineffective due to resistance, in addition, they disrupt the normal microbiota. It highlights the urgent need for a pathogen-specific drug with high antibacterial efficacy against S. aureus. α-Viniferin, a bioactive phytochemical compound, has been reported to have excellent anti-Staphylococcus efficacy as a topical agent. However, so far, there were no clinical trials that have been conducted to elucidate its efficacy. The present study aimed to investigate the antibacterial efficacy of α-viniferin against S. aureus in a ten-day clinical trial. Based on the results, α-viniferin showed 50% minimum inhibitory concentrations (MIC₅₀ values) of 7.8 μg/ml in culture broth medium. α-Viniferin was administered in the nares three times a day for ten days using a sterile cotton swab stick. Nasal swab specimens were collected before (0 days) and after finishing the trial (10^th day), and then analyzed. In the culture and RT-PCR-based analysis, S. ureus was reduced significantly: 0.01. In addition, 16S ribosomal RNA-based amplicon sequencing analysis showed that S. aureus reduced from 51.03% to 23.99% at the genus level. RNA-seq analysis was also done to gain insights into molecular mechanisms of α-viniferin against S. aureus, which revealed that some gene groups were reduced in 5-fold FC cutoff at two times MIC conditions. The study results demonstrate α-viniferin as a potential S. aureus-specific drug candidate.