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Comparing microbiological and molecular diagnostic tools for the surveillance of anthrax
The diagnosis of anthrax, a zoonotic disease caused by Bacillus anthracis can be complicated by detection of closely related species. Conventional diagnosis of anthrax involves microscopy, culture identification of bacterial colonies and molecular detection. Genetic markers used are often virulence gene targets such as B. anthracis protective antigen ( pagA , also called BAPA, occurring on plasmid pXO1), lethal factor ( lef , on pXO1), capsule-encoding capB/C (located on pXO2) as well as chromosomal Ba-1. Combinations of genetic markers using real-time/quantitative polymerase chain reaction (qPCR) are used to confirm B . anthracis from culture but can also be used directly on diagnostic samples to avoid propagation and its associated biorisks and for faster identification. We investigated how the presence of closely related species could complicate anthrax diagnoses with and without culture to standardise the use of genetic markers using qPCR for accurate anthrax diagnosis. Using blood smears from 2012–2020 from wildlife mortalities (n = 1708) in Kruger National Park in South Africa where anthrax is endemic, we contrasted anthrax diagnostic results based on qPCR, microscopy, and culture. From smears, 113/1708 grew bacteria in culture, from which 506 isolates were obtained. Of these isolates, only 24.7% (125 isolates) were positive for B . anthracis based on genetic markers or microscopy. However, among these, merely 4/125 (3.2%) were confirmed B . anthracis isolates (based on morphology, microscopy, and sensitivity testing to penicillin and gamma-phage) from the blood smear, likely due to poor survival of spores on stored smears. This study identified B . cereus sensu lato , which included B . cereus and B . anthracis , Peribacillus spp., and Priestia spp. clusters using gyrB gene in selected bacterial isolates positive for pagA region using BAPA probe. Using qPCR on blood smears, 52.1% (890 samples) tested positive for B . anthracis based on one or a combination of genetic markers which included the 25 positive controls. Notably, the standard lef primer set displayed the lowest specificity and accuracy. The Ba-1+BAPA+ lef combination showed 100% specificity, sensitivity, and accuracy. Various marker combinations, such as Ba-1+ capB , BAPA+ capB , Ba-1+BAPA+ capB + lef , and BAPA+ lef + capB , all demonstrated 100.0% specificity and 98.7% accuracy, while maintaining a sensitivity of 96.6%. Using Ba-1+BAPA+ lef + capB , as well as Ba-1+BAPA+ lef with molecular diagnosis accurately detects B . anthracis in the absence of bacterial culture. Systematically combining microscopy and molecular markers holds promise for notably reducing false positives. This significantly enhances the detection and surveillance of diseases like anthrax in southern Africa and beyond and reduces the need for propagation of the bacteria in culture.
Blue-sac disease investigations: Microbiology and laboratory induction
No abstract available.
Marine recreation and public health microbiology: Quest for the ideal indicator
Four-fifths of the population of the United States live in close proximity to the oceans or Great Lakes, and approximately 100 million Americans use the marine environment for recreation each year ( Thurman 1994 ). Consequently, contamination of lakes, rivers, and coastal waters raises significant public health issues. Among the leading sources of chemical and biological contamination of these waters and associated beaches are sewer systems, septic tanks, stormwater runoff, industrial wastes, wastewater injection wells, cesspits, animal wastes, commercial and private boat wastes, and human recreation. In 1997, 649 beach closings or advisories were caused by sewage spills and overflows ( NRDC 1998 ). In Florida alone, approximately 500 million gallons of sewage were released along the coast each year during the late 1980s ( Neshyba 1987 ). Thus one of the primary concerns in public health is the risk that humans using the marine environment for recreational activities will encounter microbial pathogens.
Chemistry and microbiology of a sewage spill in South San Francisco Bay
During three weeks of September 1979, the breakdown of a waste treatment plant resulted in the discharge of a large volume (1.5×10 7 m 3 ) of primary-treated sewage into a tributary of South San Francisco Bay, California. Chemical and microbial changes occurred within the tributary as decomposition and nitrification depleted dissolved oxygen. Associated with anoxia were relatively high concentrations of particulate organic carbon, dissolved CO 2 , CH 4 , C 2 H 4 , NH + 4 , and fecal bacteria, and low phytoplankton biomass and photosynthetic oxygen production. South San Francisco Bay experienced only small changes in water quality, presumably because of its large volume and the assimilation of wastes that occurred within the tributary. Water quality improved rapidly in the tributary once normal tertiary treatment resumed.
In situ control of groundwater contaminants by microbiological processes
No abstract available.
Microbiology of the aquatic environment
This is the third of several compilations of briefing papers on water quality by the U.S. Geological Survey. Each briefing paper is prepared in a simple, nontechnical, easy-to-understand manner. This U.S. Geological Survey Circular contains papers on selected organic substances in water. Briefing papers are included on ' Why study organic substances in water. ', ' Taste and odor in water ', and ' Classification and fractionation of organic solutes in natural waters'. (USGS)
Assessment of microbiological contamination of the Jacks Fork within the Ozark National Scenic Riverways, Missouri—phase I
The Ozark National Scenic Riverways (ONSR), the Nation's first scenic riverway, was created by an Act of Congress (Public Law 88-492) on August 24, 1964, for "the purpose of conserving and interpreting unique scenic and other natural values and objects of historic interest, including preservation of parts of the Current River and the Jacks Fork River in Missouri as free-flowing streams, preservation of springs and caves, management of wildlife, and provisions for use and enjoyment of the outdoor recreation resources thereof by the people of the United States" (National Park Service, 1981). The primary natural resources protected by the park are 134 miles of the Current and Jacks Fork Rivers. About 1.5 million people visit the ONSR annually to take advantage of excellent recreational opportunities, including canoeing, johnboating, swimming, fishing, tubing, camping, hiking, caving, horseback riding, and hunting.
Microbiological quality of public-water supplies in the Ozark Plateaus aquifer system, Missouri
In 1986, Congress amended the Safe Drinking Water Act (SDWA) requiring the U.S. Environmental Protection Agency (USEPA) to promulgate disinfection requirements for all public-water supplies. The USEPA promulgated the Surface Water Treatment Rule (SWTR) in June 1989 to establish disinfection requirements for surface-water supplies and for ground water under the direct influence of surface water. To complete the requirements of the SDWA, the USEPA plans to propose and promulgate disinfection requirements for ground water not under the direct influence of surface water to protect the public health of persons served by those systems.
Ohio water microbiology laboratory
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Microbiology and public beach safety: integrated science for the protection of public health
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Assessment of groundwater pathways and contaminant transport in Florida and Georgia using multiple chemical and microbiological indicators
The hydrogeology of Florida, especially in the northern part of the state, and southwestern Georgia is characterized by a predominance of limestone aquifers overlain by varying amounts of sands, silts, and clays. This karstic system of aquifers and their associated springs is particularly vulnerable to contamination from various anthropogenic activities at the land surface. Numerous sinkholes, disappearing streams, and conduit systems or dissolution pathways, often associated with large spring systems, allow rapid movement of contaminants from the land surface to the groundwater system with little or no attenuation or degradation. The fate of contaminants in the groundwater system is not fully understood, but traveltimes from sources are greatly reduced when conduits are intercepted by pumping wells and springs. Contaminant introduction to groundwater systems in Florida and Georgia is not limited to seepage from land surface, but can be associated with passive (drainage wells) and forced subsurface injection (aquifer storage and recovery, waste-water disposal).
Preliminary geochemical, microbiological, and epidemiological investigations into possible linkages between lignite aquifers, pathogenic microbes, and kidney disease in northwestern Louisiana
In May 2002, 15 wells and four surface water sites were sampled, and in September 2002, those same wells and sites plus four additional surface sites were sampled in five parishes of northwestern Louisiana. A geographic information system (GIS) was used to select residential water wells for sampling. Well water samples were analyzed for pH, conductivity, organic compounds, and nutrient and anion concentrations. All samples were further tested for presence of fungi (maintained for up to 28 days and colonies counted and identified microscopically), and metal and trace element concentration by inductively-coupled plasma mass spectrometry and atomic emission spectrometry. Surface water samples were tested for dissolved oxygen and evidence of leptospiral bacterial presence. A polymerase chain reaction protocol was optimized for detection of pathogenic leptospires, and the sensitivity of the assay was determined. The Spearman correlation method was used to assess the association between the endpoints for these field/laboratory analyses and the incidence of cancer of the renal pelvis obtained from the Louisiana Tumor Registry. Significant associations were revealed between the cancer rate and the overall number of organic compounds, the fungi Zygomycetes, the nutrients PO4 and NH3, and thirteen chemical elements (As, B, Br, Cl, Cr, F, Li, Na, P, Rb, Se, Sr, W) from the well water as compared to the controls. Among the species of fungi from the total of 136 isolates were 12 Penicillium spp., at least two Aspergillus spp., a number of other genera (Alternaria sp., Eupenicillium lapidosum, Cladosporium sp., Epicoccum sp., Trichoderma sp., Paecilomyces sp., Chrysosporium sp., Chloridium sp.), and Zygomycetes, and Coelmycetes -- some of which are known mycotoxin producers. The two control wells yielded a mean of 6.5 (SD = 3.5355) individual isolates, while the mean number of isolates from all other sites was 7.6 (SD = 4.4866). Presence of human pathogenic leptospires was detected in 4/8 (50 percent) of the surface water sites sampled. These initial results suggest that additional investigation into these relationships is warranted.
Selected procedures for biological and microbiological investigations
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Chemical, isotopic, and microbiological evidence for denitrification during transport of domestic wastewater through a thick unsaturated zone in the Mojave Desert, San Bernardino County, California
Nitrogen in downward-infiltrating wastewater discharged from seepage pits (dry wells) at residences in the upper Mojave River Basin, California represents a significant potential source of nitrate contamination to the underlying ground water. However, increases in nitrate concentration in the ground water have not yet been observed. The low nitrate concentration in the ground water may be the result of lateral dispersion in the unsaturated zone, dilution below the water table, or denitrification of wastewater nitrate in the unsaturated zone. Measured vertical rates indicate that some wastewater has reached the water table beneath communities that are older than 5 to 10 years. As wastewater percolates from seepage pits into the unsaturated zone, reduced nitrogen is converted rapidly to nitrate at shallow depths and the nitrate concentrations commonly decrease with depth. The largest nitrate decreases seem to coincide with increased content of fine-grained sediments or with proximity to the water table. Between lysimeters at 160 and 199 feet at one residence, the decrease in nitrate concentration coincided with a large increase in sulfate, decrease in alkalinity, and increase in 815N in nitrate. Those data are consistent with denitrification by oxidation of iron sulfide to produce ferric oxides; but if such a reaction occurs, it must be in domains that are small in comparison with the sampled volumes because the waters also contain substantial quantities of dissolved oxygen. The predominantly low nitrate concentrations in the area's ground water are consistent with the operation of a nitrogen-removal mechanism, possibly denitrification; however, the reducing capacity of the sediments to maintain denitrification is not known.
Microbiological effects of recharging the Magothy Aquifer, Bay Park, New York, with tertiary-treated sewage
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Assessment of the use of selected chemical and microbiological constituents as indicators of wastewater in curtain drains from home sewage-treatment systems in Medina County, Ohio
Many home sewage-treatment systems (HSTS) in Ohio use curtain or perimeter drains to depress the level of the subsurface water in and around the systems. These drains could possibly intercept partially untreated wastewater and release potential pathogens to ground-water and surface-water bodies. The quality of water in curtain drains from two different HSTS designs in Medina County, Ohio, was investigated using several methods. Six evaporation-transpiration-absorption (ETA) and five leach-line (LL) systems were investigated by determining nutrient concentrations, chloride/bromide ratios (Cl/Br), Escherichia coli (E. coli ) concentrations, coliphage genotyping, and genetic fingerprinting of E. coli. Water samples were collected at 11 sites and included samples from curtain drains, septic tanks, and residential water wells. Nitrate concentrations in the curtain drains ranged from 0.03 to 3.53 mg/L (milligrams per liter), as N. Concentrations of chloride in 10 of the 11 curtain drains ranged from 5.5 to 21 mg/L; the chloride concentration in the eleventh curtain drain was 340 mg/L. Bromide concentrations in 11 curtain drains ranged from 0.01 to 0.22 mg/L. Cl/Br ratios ranged from 86 to 2,000. F-specific coliphage were not found in any curtain-drain samples. Concentrations of E. coli in the curtain drains ranged from 1 to 760 colonies per 100 milliliters. The curtain-drain water-quality data were evaluated to determine whether HSTS-derived water was present in the curtain drains. Nutrient concentrations were too low to be of use in the determination. The Cl/Br ratios appear promising. Coliphage was not detected in the curtain drains, so genotyping could not be attempted. E. coli concentrations in the curtain drains were all less than those from the corresponding HSTS; only one sample exceeded the Ohio secondary-contact water-quality standard. The genetic fingerprinting data were inconclusive because multiple links between unrelated sites were found. Although the curtain-drain samples from the ETA systems showed somewhat more evidence of the presence of HSTS water than did the LL systems, most of the approaches were inconclusive by themselves. The best evidence of HSTS water, from the Cl/Br ratios, indicates that the water in 10 of the 11 curtain drains, at both HSTS types, was a mixture of dilute ground water and HSTS-derived water; the 11th drain also show some effects of the HSTS, although road salt-affected water may be present. Therefore, it appears that there is no difference between the ETA and LL systems with respect to the water quality in curtain drains.
Methods for collection and analysis of aquatic biological and microbiological samples
No abstract available.