A case control study of environmental and occupational exposures associated with methicillin resistant Staphylococcus aureus nasal carriage in patients admitted to a rural tertiary care hospital in a high density swine region

Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) colonisation and infection among livestock workers and veterinarians: a systematic review and meta-analysis

OBJECTIVES

Methicillin-resistant Staphylococcus aureus (MRSA) is an increasing public health concern worldwide. The objective of this study was to calculate a summary odds ratio (OR) of livestock-associated MRSA colonisation and infection in humans, and to determine specific risk factors in livestock production contributing to MRSA colonisation.

METHODS

We screened PubMed and Embase for studies published from 2005 to 2019 inclusive, reporting livestock-associated (LA)-MRSA colonisation and infection among livestock workers/veterinarians, their families, and community members not regularly exposed to livestock. The primary outcome of interest was the OR of LA-MRSA colonisation comparing exposed and control groups. Quality was assessed according to the Newcastle-Ottawa quality assessment scale. A meta-analysis using a random-effects model was conducted to calculate a pooled OR. The heterogeneity in the meta-analysis was assessed using the I² method, and publication bias was evaluated using funnel plots.

RESULTS

A total of 3490 studies were identified by the search, with 37 studies including 53 matched exposed-control groups and 14 038 participants eligible for the meta-analysis. The pooled OR for LA-MRSA among livestock workers and veterinarians is 9.80 (95% CI 6.89 to 13.95; p=0.000; I2 =73.4), with no significant publication bias (Egger's p=0.66). The OR for swine workers was highest at 15.41 (95% CI 9.24 to 25.69), followed by cattle workers (11.62, 95% CI 4.60 to 29.36), veterinarians (7.63, 95% CI 3.10 to 18.74), horse workers (7.45, 95% CI 2.39 to 23.25), livestock workers (5.86, 95% CI 1.14 to 30.16), poultry workers (5.70, 95% CI 1.70 19.11), and industrial slaughterhouse workers (4.69, 95% CI 1.10 to 20.0).

CONCLUSIONS

Livestock workers, particularly swine farmers, are at significantly higher risk for LA-MRSA colonisation and subsequent infection. These results support the need for preventive practices to reduce LA-MRSA risk among those who handle and treat livestock.

TRIAL REGISTRATION NUMBER

CRD42019120403.

Acquisition Risk Factors of the SCCmec IX-Methicillin-Resistant Staphylococcus aureus in Swine Production Personnel in Chiang Mai and Lamphun Provinces, Thailand

Methicillin-resistant Staphylococcus aureus (MRSA) harboring the type-IX staphylococcal cassette chromosome mec (SCCmec) has been found in pigs and humans in Northern Thailand. However, knowledge of the prevalence and acquisition risk factors of this MRSA strain among swine production personnel (SPP) are needed. The nasal swab samples and data were collected from 202 voluntary SPP and 31 swine farms in Chiang Mai and Lamphun Provinces, Thailand in 2017. MRSA were screened and identified using mannitol salt agar, biochemical and antimicrobial susceptibility testing, multiplex PCR, and the SCCmec typing. The prevalence of MRSA was 7.9% (16/202) and 19.3% (6/31) among SPP and swine farms. All isolates were multidrug-resistant, and 55 of 59 isolates (93%) contained the type-IX SCCmec element. Data analysis indicated that education, working time, contact frequency, working solely with swine production, and personal hygiene were significantly related to MRSA acquisition (p < 0.05). The multivariate analysis revealed that pig farming experience, working days, and showering were good predictors for MRSA carriage among SPP (area under the curve (AUC) = 0.84). The biosecurity protocols and tetracycline use were significantly associated with MRSA detection in pig farms (p < 0.05). Hence, the active surveillance of MRSA and further development of local/national intervention for MRSA control are essential.

One Health in hospitals: how understanding the dynamics of people, animals, and the hospital built-environment can be used to better inform interventions for antimicrobial-resistant gram-positive infections

Despite improvements in hospital infection prevention and control, healthcare associated infections (HAIs) remain a challenge with significant patient morbidity, mortality, and cost for the healthcare system. In this review, we use a One Health framework (human, animal, and environmental health) to explain the epidemiology, demonstrate key knowledge gaps in infection prevention policy, and explore improvements to control Gram-positive pathogens in the healthcare environment. We discuss patient and healthcare worker interactions with the hospital environment that can lead to transmission of the most common Gram-positive hospital pathogens – methicillin-resistant Staphylococcus aureus, Clostridioides (Clostridium) difficile, and vancomycin-resistant Enterococcus – and detail interventions that target these two One Health domains. We discuss the role of animals in the healthcare settings, knowledge gaps regarding their role in pathogen transmission, and the absence of infection risk mitigation strategies targeting animals. We advocate for novel infection prevention and control programs, founded on the pillars of One Health, to reduce Gram-positive hospital-associated pathogen transmission.

Impact of occupational exposure on human microbiota

PURPOSE OF REVIEW

Recent evidence suggests that environmental exposures change the adult human microbiome. Here, we review recent evidence on the impact of the work microbiome and work-related chemical, metal and particulate exposures on the human microbiome.

RECENT FINDINGS

Prior literature on occupational microbial exposures has focused mainly on the respiratory effects of endotoxin, but a recent study suggests that not all endotoxin is the same; endotoxin from some species is proinflammatory, whereas endotoxin from other species is anti-inflammatory. Work with animals can change the adult human microbiome, likely through colonization. Early studies in military personnel and animal models of gulf war illness show that military exposures change the gut microbiome and increase gut permeability. Heavy metal and particulate matter exposure, which are often elevated in occupational settings, also change the gut microbiome.

SUMMARY

An emerging body of literature shows that work-related exposures can change the human microbiome. The health effects of these changes are currently not well studied. If work exposures lead to disease through alterations in the human microbiome, exposure cessation without addressing changes to the human microbiome may be ineffective for disease prevention and treatment.

Chicken Meat-Associated Enterococci: Influence of Agricultural Antibiotic Use and Connection to the Clinic

Industrial farms are unique, human-created ecosystems that provide the perfect setting for the development and dissemination of antibiotic resistance. Agricultural antibiotic use amplifies naturally occurring resistance mechanisms from soil ecologies, promoting their spread and sharing with other bacteria, including those poised to become endemic within hospital environments. To better understand the role of enterococci in the movement of antibiotic resistance from farm to table to clinic, we characterized over 300 isolates of Enterococcus cultured from raw chicken meat purchased at U.S. supermarkets by the Consumers Union in 2013. Enterococcus faecalis and Enterococcus faecium were the predominant species found, and antimicrobial susceptibility testing uncovered striking levels of resistance to medically important antibiotic classes, particularly from classes approved by the FDA for use in animal production. While nearly all isolates were resistant to at least one drug, bacteria from meat labeled as raised without antibiotics had fewer resistances, particularly for E. faecium Whole-genome sequencing of 92 isolates revealed that both commensal- and clinical-isolate-like enterococcal strains were associated with chicken meat, including isolates bearing important resistance-conferring elements and virulence factors. The ability of enterococci to persist in the food system positions them as vehicles to move resistance genes from the industrial farm ecosystem into more human-proximal ecologies.IMPORTANCE Bacteria that contaminate food can serve as a conduit for moving drug resistance genes from farm to table to clinic. Our results show that chicken meat-associated isolates of Enterococcus are often multidrug resistant, closely related to pathogenic lineages, and harbor worrisome virulence factors. These drug-resistant agricultural isolates could thus represent important stepping stones in the evolution of enterococci into drug-resistant human pathogens. Although significant efforts have been made over the past few years to reduce the agricultural use of antibiotics, continued assessment of agricultural practices, including the roles of processing plants, shared breeding flocks, and probiotics as sources for resistance spread, is needed in order to slow the evolution of antibiotic resistance. Because antibiotic resistance is a global problem, global policies are needed to address this threat. Additional measures must be taken to mitigate the development and spread of antibiotic resistance elements from farms to clinics throughout the world.

Evaluation of Methicillin-Resistant Staphylococcus aureus Carriage and High Livestock Production Areas in North Carolina through Active Case Finding at a Tertiary Care Hospital

Recent reports from the Netherlands document the emergence of novel multilocus sequence typing (MLST) types (e.g., ST-398) of methicillin-resistant Staphylococcus aureus (MRSA) in livestock, particularly swine. In Eastern North Carolina (NC), one of the densest pig farming areas in the United States, as many as 14% of MRSA isolates from active case finding in our medical center have no matches in a repetitive sequence-based polymerase chain reaction (rep-PCR) library. The current study was designed to determine if these non-matched MRSA (NM-MRSA) were geographically associated with exposure to pig farming in Eastern NC. While residential proximity to farm waste lagoons lacked association with NM-MRSA in a logistic regression model, a spatial cluster was identified in the county with highest pig density. Using MLST, we found a heterogeneous distribution of strain types comprising the NM-MRSA isolates from the most pig dense regions, including ST-5 and ST-398. Our study raises the warning that patients in Eastern NC harbor livestock associated MRSA strains are not easily identifiable by rep-PCR. Future MRSA studies in livestock dense areas in the U.S. should investigate further the role of pig–human interactions.

The feline cutaneous and oral microbiota are influenced by breed and environment

Previous research revealed the feline skin bacterial microbiota to be site-specific and the fungal microbiota to be individual-specific. The effect of other factors, such as genotype and environment, have not yet been studied in cats, but have been shown to be potentially important in shaping the cutaneous microbiota of other animals. Therefore, the objectives of this study were to evaluate the effect of these factors on the bacterial and fungal microbiota of feline skin and oral cavity. The influence of genotype was assessed through the analysis of different cat breeds, and the influence of environment through comparison of indoor and outdoor cats. DNA was extracted from skin and oral swabs, and bacterial and fungal next-generation sequencing were performed. Analysis of the skin microbiota of different cat breeds revealed significant differences in alpha diversity, with Sphynx and Bengal cats having the most diverse communities. Many taxa were found to be differentially abundant between cat breeds, including Veillonellaceae and Malassezia spp. Outdoor environment exposure had considerable influence on beta diversity, especially in the oral cavity, and resulted in numerous differentially abundant taxa. Our findings indicate that the oral bacterial microbiota and both fungal and bacterial microbiota of feline skin are influenced by breed, and to a lesser degree, environment.

Review of Nonfoodborne Zoonotic and Potentially Zoonotic Poultry Diseases

Emerging and re-emerging diseases are continuously diagnosed in poultry species. A few of these diseases are known to cross the species barrier, thus posing a public health risk and an economic burden. We identified and synthesized global evidence for poultry nonfoodborne zoonoses to better understand these diseases in people who were exposed to different poultry-related characteristics (e.g., occupational or nonoccupational, operational types, poultry species, outbreak conditions, health status of flocks). This review builds on current knowledge on poultry zoonoses/potentially zoonotic agents transmitted via the nonfoodborne route. It also identifies research gaps and potential intervention points within the poultry industry to reduce zoonotic transmission by using various knowledge synthesis tools such as systematic review (SR) and qualitative (descriptive) and quantitative synthesis methods (i.e., meta-analysis). Overall, 1663 abstracts were screened and 156 relevant articles were selected for further review. Full articles (in English) were retrieved and critically appraised using routine SR methods. In total, eight known zoonotic diseases were reviewed: avian influenza (AI) virus (n = 85 articles), Newcastle disease virus (n = 8), West Nile virus (WNV, n = 2), avian Chlamydia (n = 24), Erysipelothrix rhusiopathiae (n = 3), methicillin-resistant Staphylococcus aureus (MRSA, n = 15), Ornithonyssus sylvarium (n = 4), and Microsporum gallinae (n = 3). In addition, articles on other viral poultry pathogens (n = 5) and poultry respiratory allergens derived from mites and fungi (n = 7) were reviewed. The level of investigations (e.g., exposure history, risk factor, clinical disease in epidemiologically linked poultry, molecular studies) to establish zoonotic linkages varied across disease agents and across studies. Based on the multiple outcome measures captured in this review, AI virus seems to be the poultry zoonotic pathogen that may have considerable and significant public health consequences; however, epidemiologic reports have only documented severe human cases clustered in Asia and not in North America. In contrast, avian Chlamydia and MRSA reports clustered mainly in Europe and less so in North America and other regions. Knowledge gaps in other zoonoses or other agents were identified, including potential direct (i.e., nonmosquito-borne) transmission of WNV from flocks to poultry workers, the public health and clinical significance of poultry-derived (livestock-associated) MRSA, the zoonotic significance of other viruses, and the role of poultry allergens in the pathophysiology of respiratory diseases of poultry workers. Across all pathogens reviewed, the use of personal protective equipment was commonly cited as the most important preventive measure to reduce the zoonotic spread of these diseases and the use of biosecurity measures to reduce horizontal transmission in flock populations. The studies also emphasized the need for flock monitoring and an integrated approach to prevention (i.e., veterinary-public health coordination with regard to diagnosis, and knowledge translation and education in the general population) to reduce zoonotic transmission.

Impact of environmental microbiota on human microbiota of workers in academic mouse research facilities: An observational study

Objectives

To characterize the microbial environment of workers in academic mouse research facilities using endotoxin, 16S qPCR, and 16S amplicon sequencing. To determine whether the work microbiome contributes to the human microbiome of workers.

Methods

We performed area air sampling from the animal rooms, dirty, middle, and setup cage wash locations in four academic mouse research facilities. 10 workers in the dirty cage wash area underwent personal air sampling as well as repeated collection of nasal, oral, and skin samples before and after the work shift. Environmental samples underwent measurement of endotoxin, mouse allergen, bacteria copy number via 16S qPCR, and microbial identification via 16S rDNA sequencing. 16S rDNA sequencing was also performed on human samples before and after the work shift. SourceTracker was used to identify the contribution of the work microbiome to the human microbiome.

Results

Median endotoxin levels ranged from undetectable to 1.0 EU/m³. Significant differences in mouse allergen levels, bacterial copy number, microbial richness, and microbial community structure were identified between animal, dirty, middle, and setup cage wash locations. Endotoxin levels had only a moderate correlation with microbial composition. Location within a facility was a stronger predictor of microbial community composition (R² = 0.41, p = 0.002) than facility. The contribution of the work microbiome to the pre-shift human microbiome of workers was estimated to be 0.1 ± 0.1% for the oral microbiome; 3.1 ± 1.9% for the nasal microbiome; and 3.0 ± 1.5% for the skin microbiome.

Conclusions

The microbial environment of academic animal care facilities varies significantly by location rather than facility. Endotoxin is not a proxy for assessment of environmental microbial exposures using 16S qPCR or 16S rDNA sequencing. The work microbiome contributes to the composition of the nasal and skin microbiome of workers; the clinical implications of this observation should be further studied.

Identification of novel risk factors for community-acquired Clostridium difficile infection using spatial statistics and geographic information system analyses

Background

The rate of community-acquired Clostridium difficile infection (CA-CDI) is increasing. While receipt of antibiotics remains an important risk factor for CDI, studies related to acquisition of C. difficile outside of hospitals are lacking. As a result, risk factors for exposure to C. difficile in community settings have been inadequately studied.

Main objective

To identify novel environmental risk factors for CA-CDI

Methods

We performed a population-based retrospective cohort study of patients with CA-CDI from 1/1/2007 through 12/31/2014 in a 10-county area in central North Carolina. 360 Census Tracts in these 10 counties were used as the demographic Geographic Information System (GIS) base-map. Longitude and latitude (X, Y) coordinates were generated from patient home addresses and overlaid to Census Tracts polygons using ArcGIS; ArcView was used to assess “hot-spots” or clusters of CA-CDI. We then constructed a mixed hierarchical model to identify environmental variables independently associated with increased rates of CA-CDI.

Results

A total of 1,895 unique patients met our criteria for CA-CDI. The mean patient age was 54.5 years; 62% were female and 70% were Caucasian. 402 (21%) patient addresses were located in “hot spots” or clusters of CA-CDI (p<0.001). “Hot spot” census tracts were scattered throughout the 10 counties. After adjusting for clustering and population density, age ≥ 60 years (p = 0.03), race (<0.001), proximity to a livestock farm (0.01), proximity to farming raw materials services (0.02), and proximity to a nursing home (0.04) were independently associated with increased rates of CA-CDI.

Conclusions

Our study is the first to use spatial statistics and mixed models to identify important environmental risk factors for acquisition of C. difficile and adds to the growing evidence that farm practices may put patients at risk for important drug-resistant infections.

Updated systematic review: associations between proximity to animal feeding operations and health of individuals in nearby communities

OBJECTIVE

The objective of this review was to update a systematic review of associations between living near an animal feeding operation (AFO) and human health.

METHODS

The MEDLINE® and MEDLINE® In-Process, Centre for Agricultural Biosciences Abstracts, and Science Citation Index databases were searched. Reference lists of included articles were hand-searched. Eligible studies reported exposure to an AFO and an individual-level human health outcome. Two reviewers performed study selection and data extraction.

RESULTS

The search returned 3702 citations. Sixteen articles consisting of 10 study populations were included in the analysis. The health outcomes were lower and upper respiratory tracts, MRSA, other infectious disease, neurological, psychological, dermatological, otologic, ocular, gastrointestinal, stress and mood, and other non-infectious health outcomes. Most studies were observational and used prevalence measures of outcome. An association between Q fever risk and proximity to goat production was reported. Other associations were unclear. Risk of bias was serious or critical for most exposure-outcome associations. Multiplicity (i.e., a large number of potentially correlated outcomes and exposures assessed on the same study subjects) was common in the evidence base.

CONCLUSIONS

Few studies reported an association between surrogate clinical outcomes and AFO proximity for respiratory tract-related outcomes. There were no consistent dose-response relationships between surrogate clinical outcome and AFO proximity. A new finding was that Q fever in goats is likely associated with an increased Q fever risk in community members. The review results for the non-respiratory health outcomes were inconclusive because only a small number of studies were available or the between-study results were inconsistent.

SYSTEMATIC REVIEW REGISTRATION

PROSPERO CRD42014010521.

Antibiotic discovery throughout the Small World Initiative: A molecular strategy to identify biosynthetic gene clusters involved in antagonistic activity

The emergence of bacterial pathogens resistant to all known antibiotics is a global health crisis. Adding to this problem is that major pharmaceutical companies have shifted away from antibiotic discovery due to low profitability. As a result, the pipeline of new antibiotics is essentially dry and many bacteria now resist the effects of most commonly used drugs. To address this global health concern, citizen science through the Small World Initiative (SWI) was formed in 2012. As part of SWI, students isolate bacteria from their local environments, characterize the strains, and assay for antibiotic production. During the 2015 fall semester at Bowling Green State University, students isolated 77 soil‐derived bacteria and genetically characterized strains using the 16S rRNA gene, identified strains exhibiting antagonistic activity, and performed an expanded SWI workflow using transposon mutagenesis to identify a biosynthetic gene cluster involved in toxigenic compound production. We identified one mutant with loss of antagonistic activity and through subsequent whole‐genome sequencing and linker‐mediated PCR identified a 24.9 kb biosynthetic gene locus likely involved in inhibitory activity in that mutant. Further assessment against human pathogens demonstrated the inhibition of Bacillus cereus, Listeria monocytogenes, and methicillin‐resistant Staphylococcus aureus in the presence of this compound, thus supporting our molecular strategy as an effective research pipeline for SWI antibiotic discovery and genetic characterization.

Prospective multicenter surveillance identifies Staphylococcus aureus infections caused by livestock-associated strains in an agricultural state

We conducted a surveillance study to investigate the epidemiology of Staphylococcus aureus infections in Iowa, using a convenience sample. Diagnostic laboratories submitted 20 S. aureus isolates per month for a 20-month period between 2011 and 2013. Of the 2226 isolates analyzed, 73.6% were methicillin-resistant S. aureus (MRSA) and 26.4% were methicillin-susceptible S. aureus (MSSA). S. aureus infections in 25 patients (1%) were caused by ST398- and ST9-associated strain types, and appeared to be a common occurrence in areas of the state with the highest numbers of hogs and hog farms. Twenty nine (5.1%) of MSSA isolates and 10 (40.0%) livestock-associated strains were multi-drug resistant.

Molecular characterization of methicillin-resistant Staphylococcus aureus (MRSA) nasal colonization and infection isolates in a Veterans Affairs hospital

Background

Nasal colonization with methicillin-resistant Staphylococcus aureus (MRSA) is associated with increased infection risk, yet colonization and infection isolates are rarely compared within the same study. The objectives of this study were to compare colonization and infection isolates from a Veterans Administration hospital in Iowa, and to determine the prevalence of livestock-associated MRSA (LA-MRSA) colonization and infection in a state with high livestock density.

Methods

All patients with available MRSA isolates collected through routine nasal screening (73%; n = 397) and from infections (27%; n = 148) between December 2010 and August 2012 were included and tested for spa type and presence of PVL and mecA genes. Clinical isolates were tested for antibiotic resistance patterns. Paired colonization and infection isolates were compared for genetic and phenotypic congruity.

Results

The most common spa types were t002 (and other CC5-associated strains; 65%) and t008 (and other CC8-associated strains; 20%). No classic LA-MRSA spa types were identified. CC5-associated strains were less likely to be associated with infections (22%; 77/353) compared with CC8-associated strains (49%; 53/109). MRSA colonization was more common among patients with infections (71%) compared with the general screening population (7%). In most cases (82%; 28/34), paired colonization and infection isolates were genetically and phenotypically indistinguishable.

Conclusions

Our data demonstrate a direct link between antecedent nasal colonization and subsequent MRSA infection. Further, our data indicate variability in colonization and infection efficiency among MRSA genotypes, which points to the need to define the molecular determinants underlying emergence of S. aureus strains in the community and nosocomial setting.