A variety of classic and emerging soil-related bacterial and fungal pathogens cause serious human disease that frequently presents in primary care settings. Typically, the growth of these microorganisms is favored by particular soil characteristics and may involve complex life cycles including amoebae or animal hosts. Specific evolved virulence factors or the ability to grow in diverse, sometimes harsh, microenvironments may promote pathogenesis. Infection may occur by direct inoculation or ingestion, ingestion of contaminated food, or inhalation. This narrative review describes the usual presentations and environmental sources of soil-related infections. In addition to tetanus, anthrax, and botulism, soil bacteria may cause gastrointestinal, wound, skin, and respiratory tract diseases that also should be considered, particularly in the case of wound, respiratory tract, or gastrointestinal infections. The purpose of this article is to review bacterial and fungal infections for which the source of contact is primarily the soil (eg, Clostridium tetani) or for which soil is an important or emerging secondary site of contact (eg, Legionella). The emphasis of this article will be on the epidemiology of significant soil-related human pathogens and their common disease presentations such that these entities will be considered promptly during relevant patient evaluations. (The reader is referred to recent texts and manuscripts for details regarding unusual presentations and the diagnosis and treatment of these infections and for discussion of superficial soil-related infections, such as dermatophyte infections, which will not be covered here.) Soil MicrobiologySoil 1,3 is a multilayered surface complex of mineral and organic (humus) constituents present in solid, liquid, and gaseous states. The mineral portion of soil results from the actions of weathering and erosion on rock. Broad soil type-sand, silt, or clay-is defined, largest to smallest, by particle size. These particles pack loosely, and pore spaces of varying sizes are formed. Particle surfaces, pore spaces, and plant roots are particular habitats for microorganisms, often in biofilms. Soil also contains plants, animals, carcasses, and man-made materials.The quantity and type of microorganisms in a particular portion of soil are determined by a complex interaction of varying amounts of sunlight, temperature, moisture, soil pH, nutrients, and reThis article was externally peer reviewed.

The clinical and epidemiologic features of 73 patients with laboratory-confirmed blastomycosis who were identified over an 11-year period in North Central Wisconsin are presented. Pulmonary disease was the sole manifestation in 77% of patients. More than one-half of all patients had symptoms that included fever, cough, weight loss, night sweats, and pleuritic chest pain. Virtually all were previously healthy, and most did not have an outdoor occupation. However, 82% of these patients lived or had visited within 500 m of rivers or associated waterways. The majority experienced the onset of symptoms between December and April. The estimated mean annual incidence rate of infection for Vilas County was 40.4 cases per 100,000 persons, and that for the largest city in the county was 101.3 cases per 100,000 persons. Several areas with an exceptionally high incidence of the infection were observed. We suggest that, in regions where blastomycosis is hyperendemic, clinical disease is most often pulmonary and occurs in immunocompetent individuals and that residence near an ecological focus may be a greater risk factor for acquisition of blastomycosis than is occupation.

Objective To correlate epidemiologic factors with urogenital infections associated with preterm birth. Methods Pregnant women were sequentially included from four Wisconsin cohorts: large urban, midsize urban, small city, and rural city. Demographic, clinical, and current pregnancy data were collected. Cervical and urine specimens were analyzed by microscopy, culture, and polymerase chain reaction for potential pathogens. Results Six hundred seventy-six women were evaluated. Fifty-four (8.0%) had preterm birth: 12.1% (19/157) large urban, 8.8% (15/170) midsize urban, 9.4% (16/171) small city, and 2.3% (4/178) rural city. Associated host factors and infections varied significantly among sites. Urogenital infection rates, especially Mycoplasma hominis and Ureaplasma parvum, were highest at the large urban site. Large urban site, minority ethnicity, multiple infections, and certain historical factors were associated with preterm birth by univariable analysis. By multivariable analysis, preterm birth was associated with prior preterm birth (adjusted odds ratio [aOR] 2.76, 95% confidence interval [CI] 1.27–6.02) and urinary tract infection (aOR 2.62, 95% CI 1.32–519), and negatively associated with provider-assessed good health (aOR 0.42, 95% CI 0.23–0.76) and group B streptococcal infection treatment (surrogate for healthcare utilization) (aOR 0.38, 95% CI 0.15–.99). Risk and protective factors were similar for women with birth at < 35 weeks, and additionally associated with M hominis (aOR 3.6, 95% CI 1.4–9.7). Conclusion These measured differences between sites are consistent with observations that link epidemiologic factors, both environmental and genetic, with minimally pathogenic vaginal bacteria, inducing preterm birth, especially at less than 35 weeks of gestation.

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The TaqMan real-time PCR assay was developed from the Blastomyces dermatitidis BAD1 gene promoter. The assay identified all haplotypes of B. dermatitidis and five of six positive paraffin-embedded tissues. The assay sensitivity threshold was 1 pg genomic DNA of the mold form and 2 CFU of the yeast form of B. dermatitidis. No cross-reactivity was observed against other fungal DNA. The assay allowed rapid (5-h) identification of B. dermatitidis from culture and from clinical specimens. Blastomyces dermatitidis is a dimorphic fungal pathogen that causes blastomycosis. The infection generally starts by inhalation of spores of the mold form of the fungus, found in the environment. Upon entry into the hosts, the spores convert to the yeast form. The infection can be self-limiting to the lungs, or it can disseminate to other body parts, mainly to bones and skin. Apart from humans, dogs are highly susceptible to B. dermatitidis infection. Blastomycosis is endemic in the midwestern and southeastern United States and around the Great Lakes (4). Interestingly, blastomycosis has also been reported in humans and dogs in New York State (6,8), but the ecological niche of this fungus has yet to be established in this region. Similarly, blastomycosis has been reported from Colorado and Nebraska, which are all outside known zones where the infection is endemic (7, 13).The laboratory methods most frequently used to diagnose blastomycosis include serology, direct smear, and histopathology. However, the gold standard for diagnosis remains a positive culture. Traditional confirmation of a suspect culture of B. dermatitidis by conversion to the yeast form in the laboratory can take weeks, but identification can be confirmed on the same day by Gen-Probe (Gen-Probe, Inc., San Diego, CA). The Gen-Probe test can be used only with pure cultures of B. dermatitidis (yeast or mold); hence, it has limited application. To overcome these problems, several conventional PCR assays have been developed for the identification of B. dermatitidis from clinical specimens and soil samples (2, 5). These assays used identical primer pair sequences targeting the putative promoter region of the BAD1 (earlier known as WI-1) gene, which codes for an important adhesin molecule and virulence factor (10). Recently, it has been shown that the BAD1 promoter region has a number of nucleotide polymorphisms, which resulted in the identification of four haplotypes of B. dermatitidis (11,12). In addition to nucleotide polymorphism, a major size disparity due to two large insertions in the BAD1 promoter was also found in many B. dermatitidis strains (12). This can complicate the conventional PCR assay due to either insufficient amplification efficiency or misinterpretation as a nonspecific product.In this study, we describe the development of a TaqMan real-time PCR assay using a specific region of the BAD1 promoter to encompass all known haplotypes of B. dermatitidis. Our results indicate that the BAD1 real-time PCR assay is highly specific and rapid, with a turnaround t...

Aims: To understand which clinical criteria physicians use to diagnose pneumonia compared to bronchitis and upper respiratory tract infection (URTI).Methods: Retrospective chart review of adults diagnosed with pneumonia, bronchitis, or URTI.Results: Logistic regression analysis identified rales, a temperature > 100°F (37.8°C), chest pain, dyspnoea, rhonchi, heart rate, respiratory rate, and rhinorrhoea, as the best explanation for the variation in diagnosis of pneumonia compared to either of the alternative diagnoses (R 2 = 59.3), with rales and a temperature > 100°F explaining 30% of the variation. Rales, chest pain, and a temperature > 100°F best predicted the ordering of a chest x-ray (R 2 = 20.0). However, 35% (59/175) of patients diagnosed with pneumonia had a negative chest x-ray. Abnormal breath sounds were the best predictors for prescribing antibiotics (R 2 = 38%). A significant number of patients with acute bronchitis (93% excluding sinusitis) and URTI (42%) were given antibiotics. Conclusions:The presence of abnormal breath sounds and a temperature > 100°F were the best predictors of a diagnosis of pneumonia.

The presence of various pathogenic fungi in rather unsuspected hosts and environments has always attracted the attention of the scientific community. Reports on the putative role of animals in fungal infections of humans bear important consequences on public health as well as on the understanding of fungal ecology. Fungi are ubiquitous in nature and their great capacity for adaptation allows them to survive and indeed, to thrive, in plants, trees and other natural substrata. Nonetheless, we are just beginning to learn the significance that these diverse fungal habitats have on the increasing number of immunosuppressed individuals. The accidental or permanent presence of fungi in animals, plants, soils and watercourses should not be taken too lightly because they constitute the source where potential pathogens will be contracted. If those fungal habitats that carry the largest risks of exposure could be defined, if seasonal variations in the production of infectious propagules could be determined, and if their mode of transmission were to be assessed, it would be possible to develop protective measures in order to avoid human infection. Additionally, unsuspected avenues for the exploration of fungal survival strategies would be opened, thus enhancing our capacity to react properly to their advancing limits. This paper explores several ecological connections between human pathogenic fungi and certain animals, trees, waterways and degraded organic materials. The occurrence of such connections in highly endemic areas will hopefully furnish more precise clues to fungal habitats and allow the design of control programs aimed at avoiding human infection.