Assessing pediatric nasal carriage of S. aureus & MRSA

Staphylococcus aureus and methicillin-resistant Staphylococcus aureus (MRSA) has become an increasing problem in the community. Nasal carriage of these bacteria has been shown to be a predisposing factor for infection and environmental contamination. This serious public health concern prompted an investigation to assess the pediatric nasal carriage of these bacteria in an effort to better understand the populations at risk and prevention of infection.^ This prospective study surveys 30 children from the Northwest Assistance Ministries (NAM) pediatric clinic from October 2008 to the present. Two nasal swabs were taken in 2-4 week intervals to determine S. aureus carrier status. Microbiologic tests were conducted to isolate and identify S. aureus from nasal cultures. Children with 2 cultures positive for S. aureus were classified as persistent carriers, those with 1 positive and 1 negative culture were classified as intermittent carriers, and those with 2 negative cultures were classified as noncarriers. This information was related to patient records and statistical analyses (X 2 and t-tests) were performed.^ Distribution of S. aureus carriage related to patient demographics (age, sex, & race) was showed no significant differences between S. aureus positive and S. aureus negative patient populations (p = 0.8). Additionally, the distribution of carrier status related to demographics also showed no significant difference (p = 0.8). Finally, the distribution of carrier status related to relevant medical history (immunizations current, past infection, & antibiotic use at time of swabbing) showed no significant difference (p = 0.4).^ This study is a snapshot of an ongoing study to assess the pediatric nasal carriage of S. aureus and MRSA. The inability to draw any reliable conclusion from the distribution of data is likely a result of an inadequate samples size. This is one of few studies assessing pediatric nasal carriage of S. aureus and targeting an underrepresented, Hispanic population is especially unique. Continuing this study allows for a better understanding of the epidemiology of this bacterium which will hopefully lead to appropriate interventions thus preventing future S. aureus infections.^

An evaluation of a Lake Houston tributary, Cypress Creek, for contamination and water quality

Introduction. Lake Houston serves as a reservoir for both recreational and drinking water for residents of Houston, Texas, and the metropolitan area. The Texas Commission on Environmental Quality (TCEQ) expressed concerns about the water quality and increasing amounts of pathogenic bacteria in Lake Houston (3). The objective of this investigation is to evaluate water quality for the presence of bacteria, nitrates, nitrites, carbon, phosphorus, dissolved oxygen, pH, turbidity, suspended solids, dissolved solids, and chlorine in Cypress Creek. The aims of this project are to analyze samples of water from Cypress Creek and to render a quantitative and graphical representation of the results. The collected information will allow for a better understanding of the aqueous environment in Cypress Creek.^ Methods. Water samples were collected in August 2009 and analyzed in the field and at UTSPH laboratory by spectrophotometry and other methods. Mapping software was utilized to develop novel maps of the sample sites using coordinates attained with the Global Positioning System (GPS). Sample sites and concentrations were mapped using Geographic Information System (GIS) software and correlated with permitted outfalls and other land use characteristic.^ Results. All areas sampled were positive for the presence of total coliform and Escherichia coli (E. coli). The presences of other water contaminants varied at each location in Cypress Creek but were under the maximum allowable limits designated by the Texas Commission on Environmental Quality. However, dissolved oxygen concentrations were elevated above the TCEQ limit of 5.0 mg/L at majority of the sites. One site had near-limit concentration of nitrates at 9.8 mg/L. Land use above this site included farm land, agricultural land, golf course, parks, residential neighborhoods, and nine permitted TCEQ effluent discharge sites within 0.5 miles upstream.^ Significance. Lake Houston and its tributary, Cypress Creek, are used as recreational waters where individuals may become exposed to microbial contamination. Lake Houston also is the source of drinking water for much of Houston/Harris and Galveston Counties. This research identified the presence of microbial contaminates in Cypress Creek above TCEQ regulatory requirements. Other water quality variables measured were in line with TCEQ regulations except for near-limit for nitrate at sample site #10, at Jarvis and Timberlake in Cypress Texas.^

Viability of enteric bacterial pathogens in transport media

Bacterial pathogens such as enterotoxigenic Escherichia coli, Salmonella, and Campylobacter spp. are associated with up to 80% of diarrheal illness to travelers from developed countries to developing countries. In order to study acute gastrointestinal diseases, researchers from developed countries such as the United States rely on transporting clinical specimens from the developing countries to laboratories in the U.S. in transport media systems. There are few commercially available transport media systems cited in the literature or designated by transport system manufacturers for the transport of enteric bacteria. Therefore a laboratory-based study was conducted to assess three commercial available transport media systems, two gel swabs and one liquid vial, to determine the most appropriate for the maintenance and recovery of common enteric bacterial pathogens. A total of 13 bacterial enteropathogens were recovered from 25°C and 4°C storage temperatures at time points up to 21 days. The results demonstrated that the gel swab and liquid vial transport systems performed similarly for all isolates at both temperatures. All three transport media systems struggled to maintain the isolates at recoverable concentrations when stored at 4°C and it is recommended that isolates be stored at 25°C in transport media systems. Lastly, swab transport systems are recommend for transport since they are small and easy to pack, resist leakage, and are less expensive than similarly performing liquid vial transport media systems.^

The evidence for groundwater as a source of enteric illness in developing countries: A systematic review of the literature

Groundwater constitutes approximately 30% of freshwater globally and serves as a source of drinking water in many regions. Groundwater sources are subject to contamination with human pathogens (viruses, bacteria and protozoa) from a variety of sources that can cause diarrhea and contribute to the devastating global burden of this disease. To attempt to describe the extent of this public health concern in developing countries, a systematic review of the evidence for groundwater microbially-contaminated at its source as risk factor for enteric illness under endemic (non-outbreak) conditions in these countries was conducted. Epidemiologic studies published in English language journals between January 2000 and January 2011, and meeting certain other criteria, were selected, resulting in eleven studies reviewed. Data were extracted on microbes detected (and their concentrations if reported) and on associations measured between microbial quality of, or consumption of, groundwater and enteric illness; other relevant findings are also reported. In groundwater samples, several studies found bacterial indicators of fecal contamination (total coliforms, fecal coliforms, fecal streptococci, enterococci and E. coli), all in a wide range of concentrations. Rotavirus and a number of enteropathogenic bacteria and parasites were found in stool samples from study subjects who had consumed groundwater, but no concentrations were reported. Consumption of groundwater was associated with increased risk of diarrhea, with odds ratios ranging from 1.9 to 6.1. However, limitations of the selected studies, especially potential confounding factors, limited the conclusions that could be drawn from them. These results support the contention that microbial contamination of groundwater reservoirs—including with human enteropathogens and from a variety of sources—is a reality in developing countries. While microbially-contaminated groundwaters pose risk for diarrhea, other factors are also important, including water treatment, water storage practices, consumption of other water sources, water quantity and access to it, sanitation and hygiene, housing conditions, and socio-economic status. Further understanding of the interrelationships between, and the relative contributions to disease risk of, the various sources of microbial contamination of groundwater can guide the allocation of resources to interventions with the greatest public health benefit. Several recommendations for future research, and for practitioners and policymakers, are presented.^

Changes of dissolved organic matter compositions in artifical and natural seawater during Pseudovibrio growth experiment

To study the consumption of dissolved organic matter (DOM) by bacteria living in untra-oligotrophic artificial or natural seawater, we analyzed the composition of DOM before (timepoint t0, directly after inoculation) and after (timepoint t2, 3 weeks of incubation) growth of the bacteria using Fourier transform ion cyclotron mass spectrometry (ESI FT-ICR-MS). The oligotrophic natural seawater used originates from the South Pacific Gyre. Our data show that the bacteria were able to utilize a variety of different organic compounds. These compounds belong to different chemical compound groups and likely fuel the bacterial energy, carbon and nitrogen requirements under the ultra-oligotrophic conditions.

Fatty acids and intact polar lipids of laminated microbial sediments from St. Peter Ording, German Wadden Sea

Hidden for the untrained eye through a thin layer of sand, laminated microbial sediments occur in supratidal beaches along the North Sea coast. The inhabiting microbial communities organize themselves in response to vertical gradients of light, oxygen or sulfur compounds. We performed a fine-scale investigation on the vertical zonation of the microbial communities using a lipid biomarker approach, and assessed the biogeochemical processes using a combination of microsensor measurements and a 13C-labeling experiment. Lipid biomarker fingerprinting showed the overarching importance of cyanobacteria and diatoms in these systems, and heterocyst glycolipids revealed the presence of diazotrophic cyanobacteria even in 9 to 20 mm depth. High abundance of ornithine lipids (OL) throughout the system may derive from sulfate reducing bacteria, while a characteristic OL profile between 5 and 8 mm may indicate presence of purple non-sulfur bacteria. The fate of 13C-labeled bicarbonate was followed by experimentally investigating the uptake into microbial lipids, revealing an overarching importance of cyanobacteria for carbon fixation. However, in deeper layers, uptake into purple sulfur bacteria was evident, and a close microbial coupling could be shown by uptake of label into lipids of sulfate reducing bacteria in the deepest layer. Microsensor measurements in sediment cores collected at a later time point revealed the same general pattern as the biomarker analysis and the labeling experiments. Oxygen and pH-microsensor profiles showed active photosynthesis in the top layer. The sulfide that diffuses from deeper down and decreases just below the layer of active oxygenic photosynthesis indicates the presence of sulfur bacteria, like anoxygenic phototrophs that use sulfide instead of water for photosynthesis.

(Table S1) Molecular analyses and morphological comparisons of deep-sea clams

Large vesicomyid clams are common inhabitants of sulphidic deep-sea habitats such as hydrothermal vents, hydrocarbon seeps and whale-falls. Yet, the species- and genus-level taxonomy of these diverse clams has been unstable due to insufficiencies in sampling and absence of detailed taxonomic studies that would consistently compare molecular and morphological characters. To clarify uncertainties about species-level assignments, we examined DNA sequences from mitochondrial cytochrome-c-oxidase subunit I (COI) in conjunction with morphological characters. New and published COI sequences were used to create a molecular database for 44 unique evolutionary lineages corresponding to species. Overall, the congruence between molecular and morphological characters was good. Several discrepancies due to synonymous species designations were recognized, and acceptable species names were rectified with published COI sequences in cases where morphological specimens were available. We identified seven species with trans-Pacific distributions, and two species with Indo-Pacific distributions. Presently, 27 species have only been documented from one region, which might reflect limited ranges, or insufficient geographical sampling. Vesicomyids exhibit the greatest species diversity along the northwest Pacific ridge systems and in the eastern Pacific, along the western America margin, where depth zonation typically results in segregation of closely related species. The broad distributions of several vesicomyid species suggest that their required chemosynthetic habitats might be more common than previously recognized and occur along most continental margins.

Molecular differentiation by PCR-RFLP technique shows that Antarctic fishes of the genus Notothenia, claimed to be two species, are phenotypic varieties with the same genetic pattern (Table 1)

The taxonomy of Antarctic fishes has been predominantly based on morphological characteristics rather than on genetic criteria. A typical example is the Notothenia group, which includes N. coriiceps Richardson, 1844, N. neglecta Nybelin, 1951 and N. rossii Richardson, 1844. The Polymerase Chain Reaction and Restriction Fragment Length Polymorphism (PCR-RFLP) technique was used to determine whether N. coriiceps Richardson, 1844 and N. neglecta Nybelin, 1951 are different or whether they are the same species with morphological, physiological and behavioural variability. N. rossii was used as control. Mitochondrial DNA (mtDNA) was isolated from muscle specimens of N. coriiceps Richardson, 1844, N. neglecta Nybelin, 1951 and N. rossii, which were collected in Admiralty Bay, King George Island. The DNA was used to amplify a fragment (690 base pairs) of the mitochondrial gene coding region of NADH dehydrogenase subunit 2. Further, the amplicon was digested with the following restriction enzymes: DdeI, HindIII and RsaI. The results showed a variation of the digestion pattern of the fragment amplified between N. rossii, and N. coriiceps Richardson, 1844 or N. neglecta Nybelin, 1951. However, no differences were found between N. coriiceps Richardson, 1844 and N. neglecta Nybelin, 1951, on the grounds of the same genetic pattern shown by the two fish.

Composition of organic matter from samples of massive sulfides, bottom sediments, and seawater collected within the Logachev and Broken Spur hydrothermal fields, Mid-Atlantic Ridge

Lipid components of hydrothermal deposits from the unusual field at 14°45'N MAR and from the typical field at 29°N MAR were studied. For the first time mixed nature of organic matter (OM) from hydrothermal sulfide deposits was established with use of biochemical, gas chromatographic, and molecular methods of studies. In composition of OM lipids of phytoplankton, those of chemosynthesis bacteria and non-biogenic synthesis lipids were determined. Specific conditions of localization of sulfide deposits originated from ''black smokers'' (reducing conditions, absence of free oxygen, presence of reduced sulfur preventing OM from decomposition) let biogenic material, including bacterial one, be preserved in sulfide deposits. The hydrothermal system at 14°45'N MAR is characterized by geological, geochemical and thermodynamic conditions allowing abiogenic synthesis of methane and petroleum hydrocarbons. For sulfide deposits at 29°N and other active hydrothermal fields known at MAR, abiogenic synthesis of hydrocarbons occurs in lower scales.

Biogeochemistry of sediments in the Aegean Sea

Biochemical composition of sedimentary organic matter (OM), vertical fluxes and bacterial distribution were studied at 15 stations (95-2270 m depth) in the Aegean Sea during spring and summer. Downward fluxes of labile OM were significantly higher in the northern than in the southern part and were higher in summer than in spring. Primary inputs of OM were not related to sedimentary OM concentrations, which had highest values in summer. Sedimentary chlorophyll-a concentrations were similar in the northern and southern parts. Carbohydrates, the main component of sedimentary OM, were about 1.2 times higher in the southern part than in the northern, without significant temporal changes. Total proteins were higher in summer and about double in the northern part. Sedimentary proteins appeared more dependent upon the downward flux of phytopigment than of proteins. Sedimentary OM was characterised by a relatively large fraction of soluble compounds and showed better quality in the northern part. The lack of a depth-related pattern in sedimentary OM and the similar concentrations in the two areas suggest that differences in sedimentary OM quality in the Aegean basin are dependent on system productivity; the bulk of sedimentary OM is largely conservative. Sedimentary bacterial density was about double in the northern part and higher in spring than in summer, but bacterial size was about three times higher in summer, resulting in a larger bacterial biomass in summer. Bacterial density was coupled with total and protein fluxes, indicating a rapid bacterial response to pelagic production. Bacterial biomass was significantly correlated with sedimentary protein and phytopigment concentrations, indicating a clear response to accumulation of labile OM in the sediments. In all cases bacteria accounted for <5% of the organic C and N pools. The efficiency of benthic bacteria in exploiting protein pools, estimated as amounts of protein available per unit bacterial biomass, indicates a constant ratio of about 70 µg proteins/µg C. This suggests a similar bacterial efficiency all over the area studied, unaffected by different trophic conditions.

Paleocene and Eocene diatom biosttarigraphy of ODP Hole 121-752A, eastern Indian Ocean

The Paleocene/Eocene boundary was recovered for the first time in diatom-bearing sediments at Broken Ridge, Site 752. Diatom assemblages are documented throughout the 180-m-thick sequence of upper Paleocene to lower Eocene sediments. Age control available from magnetostratigraphy, calcareous nannofossils, and planktonic foraminifers allows calibration of diatom datum levels to absolute time. A partly new/partly revised diatom zonation is proposed for the Paleocene/early Eocene based on the results of Site 752 and consideration of other studies. The diatom zones are defined as follows (from the youngest to the oldest): Pyxilla gracilis Zone (first occurrence of Craspedodiscus undulatus to first occurrence Pyxilla gracilis); Hemiaulus incurvus Zone (first occurrence Pyxilla gracilis to first occurrence Hemiaulus incurvus); Hemiaulus peripterus Zone (first occurrence Hemiaulus incurvus to first occurrence Hemiaulus peripterus var. peripterus). Three new taxa are described: Anaulus fennerae n. sp., Stictodiscus bipolaris n. sp., and Hemiaulus peripterus var. longispinus n. var.

Oligocene and lowermost Miocene diatom stratigraphy and datums of ODP Site 199-1220 sediments

Completion of studies on material collected during Ocean Drilling Program Leg 199 at Site 1220 in the equatorial Pacific allows calibration of the ranges of >35 stratigraphically important diatoms to paleomagnetic stratigraphy for the Oligocene and earliest Miocene (~33.5-21.5 Ma). The taxonomy of these taxa is reviewed, and age estimates of their first and last occurrences are compiled. The diatom zonation for the Oligocene and earliest Miocene of the equatorial Pacific is revised and correlated with paleomagnetic stratigraphy. This biostratigraphy is likely to be applicable throughout the low-latitude regions of the world's oceans.