Agricultural and urban practices are correlated to changes in the resistome of riverine systems

The objective of this study was to comprehensively characterise the resistome, the collective set of antimicrobial resistance genes in a given environment, of two rivers, from their source to discharge into the sea, as these flow through areas of different land use. Our findings reveal significant differences in the riverine resistome composition in areas of different land uses, with increased abundance and diversity of AMR in downstream agricultural and urban locations, with the resistome in urban areas more similar to the resistome in wastewater. The changes in resistome were accompanied by changes in microbial communities, with a reduction in microbial diversity in downstream agricultural and urban affected areas, driven mostly by increased relative abundance in the phyla, Bacteroidetes and Proteobacteria. These results provide insight into how pollution associated with agricultural and urban activities affects microbial communities and influences AMR in aquatic water bodies. These results add valuable insights to form effective strategies for mitigating and preserving aquatic ecosystems. Overall, our study highlights the critical role of the environment in the development and dissemination of AMR and underscores the importance of adopting a One Health approach to address this global public health threat.

Bacteriophages from faecal contamination are an important reservoir for AMR in aquatic environments

Bacteriophages have been shown to play an important role in harbouring and propagating antibiotic resistance genes (ARGs). Faecal matter contains high levels of phages, suggesting that faecal contamination of water bodies may lead to increased antimicrobial resistance (AMR) levels due to increased phage loading in aquatic environments. In this study, we assessed whether faecal pollution of three rivers (Rivers Liffey, Tolka, and Dodder) was responsible for increased levels of ARGs in phage particles using established phage-faecal markers, focusing on four ARGs (blaTEM, tet(O), qnrS, and sul1). We observed all four ARGs in phage fractions in all three rivers, with ARGs more frequently observed in agricultural and urban sampling sites compared to their source. These findings highlight the role of faecal pollution in environmental AMR and the impact of agricultural and urban activities on water quality. Furthermore, our results suggest the importance of including phages as indicators when assessing environmental AMR, as they serve as significant reservoirs of resistance genes in aquatic environments. This study provides important insights into the role of faecal pollution and phages in the prevalence of AMR in the environment and the need for their inclusion in future studies to provide a comprehensive understanding of environmental AMR.

Inclusion of hydrodynamic properties of bathing waters is critical in selecting faecal indicators to assess public health impacts of faecal contamination

The EU Bathing Water Directive (BWD) requires member states to assess bathing water quality according to the levels of faecal indicator bacteria (FIB) in designated bathing areas. However, this criterion has two significant limitations given that the BWD does not; (i) account for differences in hydrodynamic properties of bathing waters and, (ii) assumes that all faecal pathogens decay equally in aquatic environments. This study simulated sewage discharge events in three hypothetical aquatic environments characterised by different advection and dispersion parameters in the solute transport equation. Temporal changes in the downstream concentration of six faecal indicators were determined in simulations that utilised measured decay rates of each faecal indicator from a programme of controlled microcosm experiments in fresh and seawater environments. The results showed that the decay rates of faecal indicators are not a critical parameter in advection dominant water bodies, such as in fast-flowing rivers. Therefore, faecal indicator selection is less important in such systems and for these, FIB remains the most cost-effective faecal indicator to monitor the public health impacts of faecal contamination. In contrast, consideration of faecal indicator decay is important when assessing dispersion and advection/dispersion dominant systems, which would pertain to transitional (estuarine) and coastal waterbodies. Results suggest that the inclusion of viral indicators, such as crAssphage and PMMoV, could improve the reliability of water quality modelling and minimise the risk of waterborne illnesses from faecal contamination.

Land use as a critical determinant of faecal and antimicrobial resistance gene pollution in riverine systems

The WHO recognises antimicrobial resistance (AMR) as a global health threat. The environment can act as a reservoir, facilitating the exchange and the physical movement of resistance. Aquatic environments are at particular risk of pollution, with large rivers subject to pollution from nearby human, industrial or agricultural activities. The land uses associated with these activities can influence the type of pollution. One type of pollution and a likely contributor to AMR pollution that lowers water quality is faecal pollution. Both pose an acute health risk and could have implications for resistance circulating in communities. The effects of land use are typically studied using physiochemical parameters or in isolation of one another. However, this study aimed to investigate the impact of different land uses on riverine systems. We explored whether differences in sources of faecal contamination are reflected in AMR gene concentrations across agricultural and urban areas. Water quality from three rivers impacted by different land uses was assessed over one year by quantifying faecal indicator bacteria (FIB), microbial source tracking markers (MST) and AMR genes. In addition, a multiparametric analysis of AMR gene pollution was carried out to understand whether agricultural and urban areas are similarly impacted. Faecal indicators varied greatly, with the highest levels of FIB and the human MST marker observed in urban regions. In addition, these faecal markers correlated with AMR genes. Similarly, significant correlations between the ruminant MST marker and AMR gene levels in agriculture areas were observed. Overall, applying multiparametric analyses to include AMR gene levels, separation and clustering of sites were seen based on land use characterisation. This study suggests that differences in prescription of antimicrobials used in animal and human healthcare may influence environmental resistomes across agricultural and urban areas. In addition, public health risks due to exposure to faecal contamination and AMR genes are highlighted.

Adeno-Associated Virus 2 and Human Adenovirus F41 in Wastewater during Outbreak of Severe Acute Hepatitis in Children, Ireland

During April-July 2022, outbreaks of severe acute hepatitis of unknown etiology (SAHUE) were reported in 35 countries. Five percent of cases required liver transplantation, and 22 patients died. Viral metagenomic studies of clinical samples from SAHUE cases showed a correlation with human adenovirus F type 41 (HAdV-F41) and adeno-associated virus type 2 (AAV2). To explore the association between those DNA viruses and SAHUE in children in Ireland, we quantified HAdV-F41 and AAV2 in samples collected from a wastewater treatment plant serving 40% of Ireland's population. We noted a high correlation between HAdV-F41 and AAV2 circulation in the community and SAHUE clinical cases. Next-generation sequencing of the adenovirus hexon in wastewater demonstrated HAdV-F41 was the predominant HAdV type circulating. Our environmental analysis showed increased HAdV-F41 and AAV2 prevalence in the community during the SAHUE outbreak. Our findings highlight how wastewater sampling could aid in surveillance for respiratory adenovirus species.

SARS-CoV-2 variant trends in Ireland: Wastewater-based epidemiology and clinical surveillance

SARS-CoV-2 RNA quantification in wastewater is an important tool for monitoring the prevalence of COVID-19 disease on a community scale which complements case-based surveillance systems. As novel variants of concern (VOCs) emerge there is also a need to identify the primary circulating variants in a community, accomplished to date by sequencing clinical samples. Quantifying variants in wastewater offers a cost-effective means to augment these sequencing efforts. In this study, SARS-CoV-2 N1 RNA concentrations and daily loadings were determined and compared to case-based data collected as part of a national surveillance programme to determine the validity of wastewater surveillance to monitor infection spread in the greater Dublin area. Further, sequencing of clinical samples was conducted to determine the primary SARS-CoV-2 lineages circulating in Dublin. Finally, digital PCR was employed to determine whether SARS-CoV-2 VOCs, Alpha and Delta, were quantifiable from wastewater. No lead or lag time was observed between SARS-CoV-2 wastewater and case-based data and SARS-CoV-2 trends in Dublin wastewater significantly correlated with the notification of confirmed cases through case-based surveillance preceding collection with a 5-day average. This demonstrates that viral RNA in Dublin's wastewater mirrors the spread of infection in the community. Clinical sequence data demonstrated that increased COVID-19 cases during Ireland's third wave coincided with the introduction of the Alpha variant, while the fourth wave coincided with increased prevalence of the Delta variant. Interestingly, the Alpha variant was detected in Dublin wastewater prior to the first genome being sequenced from clinical samples, while the Delta variant was identified at the same time in clinical and wastewater samples. This work demonstrates the validity of wastewater surveillance for monitoring SARS-CoV-2 infections and also highlights its effectiveness in identifying circulating variants which may prove useful when sequencing capacity is limited.

crAssphage as a human molecular marker to evaluate temporal and spatial variability in faecal contamination of urban marine bathing waters

Bathing water quality may be negatively impacted by diffuse pollution arising from urban and agricultural activities and wildlife, it is therefore important to be able to differentiate between biological and geographical sources of faecal pollution. crAssphage was recently described as a novel human-associated microbial source tracking marker. This study aimed to evaluate the performance of the crAssphage marker in designated bathing waters. The sensitivity and specificity of the crAss_2 marker was evaluated using faecal samples from herring gulls, dogs, sewage and a stream impacted by human pollution (n = 80), which showed that all human impacted samples tested positive for the marker while none of the animal samples did. The crAss_2 marker was field tested in an urban marine bathing water close to the discharge point of human impacted streams. In addition, the bathing water is affected by dog and gull fouling. Analysis of water samples taken at the compliance point every 30 min during a tidal cycle following a rain event showed that the crAss_2 and HF183 markers performed equally well (Spearman correlation ρ = 0.84). The levels of these marker and faecal indicators (Escherichia coli, intestinal enterococci, somatic coliphages) varied by up to 2.5 log₁₀ during the day. Analysis of a high-tide transect perpendicular to the shoreline revealed high levels of localised faecal contamination 1 km offshore, with a concomitant spike in the gull marker. In contrast, both the crAss_2 and HF183 markers remained at a constant level, showing that human faecal contamination is homogenously distributed, while gull pollution is localised. Performance of the crAss_2 and HF183 assay was further evaluated in bimonthly compliance point samples over an 18-month period. The co-occurrence between the crAss_2 and HF183 markers in compliance sampling was 76%. A combination of both markers should be applied in low pollution impacted environments to obtain a high confidence level.

Decay of infectious SARS-CoV-2 and surrogates in aquatic environments

The introduction of SARS-CoV-2 containing human stool and sewage into water bodies may raise public health concerns. However, assessment of public health risks by faecally contaminated water is limited by a lack of knowledge regarding the persistence of infectious SARS-CoV-2 in water. In the present study the decay rates of viable infectious SARS-CoV-2 and SARS-CoV-2 RNA were determined in river and seawater at 4 and 20°C. These decay rates were compared to S. typhimurium bacteriophage MS2 and pepper mild mottle virus (PMMoV). Persistence of viable SARS-CoV-2 was temperature dependent, remaining infectious for significantly longer periods of time in both freshwater and seawater at 4°C than at 20°C. T₉₀ for infectious SARS-CoV-2 in river water was 2.3 days and 3.8 days at 20°C and 4°C, respectively. The T₉₀ values were 1.1 days and 2.2 days in seawater at 20°C and 4°C, respectively. In contrast to the rapid inactivation of infectious SARS-CoV-2 in river and sea water, viral RNA was relatively stable. The RNA decay rates were increased in non-sterilised river and seawater, presumably due to the presence of microbiota. The decay rates of infectious MS2, MS2 RNA and PMMoV RNA differed significantly from the decay rate of SARS-CoV-2 RNA, suggesting that their use as surrogate markers for the persistence of SARS-CoV-2 in the environment is limited.

Bacterial and Bacteriophage Antibiotic Resistance in Marine Bathing Waters in Relation to Rivers and Urban Streams

Fecal pollution of surface water may introduce bacteria and bacteriophages harboring antibiotic resistance genes (ARGs) into the aquatic environment. Watercourses discharging into the marine environment, especially close to designated bathing waters, may expose recreational users to fecal pollution and therefore may increase the likelihood that they will be exposed to ARGs. This study compares the bacterial and bacteriophage ARG profiles of two rivers (River Tolka and Liffey) and two small urban streams (Elm Park and Trimleston Streams) that discharge close to two marine bathing waters in Dublin Bay. Despite the potential differences in pollution pressures experienced by these waterways, microbial source tracking analysis showed that the main source of pollution in both rivers and streams in the urban environment is human contamination. All ARGs included in this study, bla_TEM, bla_SHV, qnrS, and sul1, were present in all four waterways in both the bacterial and bacteriophage fractions, displaying a similar ARG profile. We show that nearshore marine bathing waters are strongly influenced by urban rivers and streams discharging into these, since they shared a similar ARG profile. In comparison to rivers and streams, the levels of bacterial ARGs were significantly reduced in the marine environment. In contrast, the bacteriophage ARG levels in freshwater and the marine were not significantly different. Nearshore marine bathing waters could therefore be a potential reservoir of bacteriophages carrying ARGs. In addition to being considered potential additional fecal indicators organism, bacteriophages may also be viewed as indicators of the spread of antimicrobial resistance.

Identifying Sources of Faecal Contamination in a Small Urban Stream Catchment: A Multiparametric Approach

Small urban streams discharging in the proximity of bathing waters may significantly contribute to the deterioration of water quality, yet their impact may be overlooked. This study focuses on the Elm Park stream in the city of Dublin that is subject to faecal contamination by unidentified sources. The aim of the study was to identify a minimum number of “sentinel” sampling stations in an urban catchment that would provide the maximum amount of information regarding faecal pollution in the catchment. Thus, high-resolution sampling within the catchment was carried out over the course of 1 year at 11 stations. Faecal indicator bacteria were enumerated and microbial source tracking (MST) was employed to evaluate human pollution. In addition, ammonium, total oxidised nitrogen, and phosphorus levels were monitored to determine if these correlated with faecal indicator and the HF183 MST marker. In addition, the effect of severe weather events on water quality was assessed using automated sampling at one of the identified “sentinel” stations during baseflow and high flow conditions over a 24-h period. Our results show that this urban stream is at times highly contaminated by point source faecal pollution and that human faecal pollution is pervasive in the catchment. Correlations between ammonium concentrations and faecal indicator bacteria (FIB) as well as the human MST marker were observed during the study. Cluster analysis identified four “sentinel” stations that provide sufficient information on faecal pollution in the stream, thus reducing the geographical complexity of the catchment. Furthermore, ammonium levels strongly correlated with FIB and the human HF183 MST marker under high flow conditions at key “sentinel” stations. This work demonstrates the effectiveness of pairing MST, faecal indicators, and ammonium monitoring to identify “sentinel” stations that could be more rapidly assessed using real-time ammonium readouts to assess remediation efforts.

Functional Metagenomic Screening for Antimicrobial Resistance in the Oral Microbiome

A large proportion of bacteria, from a multitude of environments, are not yet able to be grown in the laboratory, and therefore microbiological and molecular biological investigations of these bacteria are challenging. A way to circumvent this challenge is to analyze the metagenome, the entire collection of DNA molecules that can be isolated from a particular environment or sample. This collection of DNA molecules can be sequenced and assembled to determine what is present and infer functional potential, or used as a PCR template to detect known target DNA and potentially unknown regions of DNA nearby those targets; however assigning functions to new or conserved hypothetical, functionally cryptic, genes is difficult. Functional metagenomics allows researchers to determine which genes are responsible for selectable phenotypes, such as resistance to antimicrobials and metabolic capabilities, without the prerequisite needs to grow the bacteria containing those genes or to already know which genes are of interest. It is estimated that a third of the resident species of the human oral cavity is not yet cultivable and, together with the ease of sample acquisition, makes this metagenome particularly suited to functional metagenomic studies. Here we describe the methodology related to the collection of saliva samples, extraction of metagenomic DNA, construction of metagenomic libraries, as well as the description of functional assays that have previously led to the identification of new genes conferring antimicrobial resistance.

Correlation between antimicrobial resistance and faecal contamination in small urban streams and bathing waters

Antibiotic resistance represents the greatest challenge to healthcare systems around the world. As antibiotic resistance genes (ARGs) are shed in faeces, many studies have focused on how wastewater effluent contributes to ARG pollution in rivers. However, small urban streams and bathing waters not impacted by treated wastewater have received little attention though they may be important reservoirs of ARGs. The main objective of this study was to assess the extent to which ARG and faecal pollution impact small urban streams and bathing waters and to determine if there is a relationship between these contaminants. For one year, bi-monthly water samples were collected from two urban streams and Dublin city's three designated bathing waters. The Liffey Estuary, that receives treated wastewater, was also sampled. The sul1, tet(O), qnrS, bla_TEM, bla_SHV and bla_CTX-M ARGs were quantified. E. coli and intestinal enterococci levels were determined and the source of faecal pollution (human, dog, gull) quantified by microbial source tracking. Our results show that the Liffey Estuary, the urban streams and the bathing waters are highly impacted by ARGs and human faeces. There were clear correlations between all of the studied faecal indicators and ARGs in the Liffey Estuary. In the urban streams relationships were observed for only some of the ARGs and faecal indicators, which is likely a result of non-continuous sewage leaks and overflows to the streams. Similarly, only some ARGs correlated with faecal indicators in the urban bathing waters. The source of ARGs in the bathing waters is likely to be multifaceted as we detected sporadic dog and gull faecal markers. This study demonstrates that small urban streams and bathing waters are reservoirs of ARGs and that they may pose a previously unrecognised public health risk as they have the potential to transmit enteric pathogens and antibiotic resistance determinants.

Efflux in the Oral Metagenome: The Discovery of a Novel Tetracycline and Tigecycline ABC Transporter

Antibiotic resistance in human bacterial pathogens and commensals is threatening our ability to treat infections and conduct common medical procedures. As novel antibiotics are discovered and marketed it is important that we understand how resistance to them may arise and know what environments may act as reservoirs for such resistance genes. In this study a tetracycline and tigecycline resistant clone was identified by screening a human saliva metagenomic library in Escherichia coli EPI300 on agar containing 5 μg/ml tetracycline. Sequencing of the DNA insert present within the tetracycline resistant clone revealed it to contain a 7,765 bp fragment harboring novel ABC half transporter genes, tetAB(60). Mutagenesis studies performed on these genes confirmed that they were responsible for the tetracycline and tigecycline resistance phenotypes. Growth studies performed using E. coli EPI300 clones that harbored either the wild type, the mutated, or none of these genes indicated that there was a fitness cost associated with presence of these genes, with the isolate harboring both genes exhibiting a significantly slower growth than control strains. Given the emergence of E. coli strains that are sensitive only to tigecycline and doxycycline it is concerning that such a resistance mechanism has been identified in the human oral cavity.

Within-day and between-day Reproducibility of Baroreflex Sensitivity in Healthy Adult Males

Within-day and between-day reproducibility of supine and tilt baroreflex sensitivity were investigated utilising sequence and spectral indices in 46 healthy adult males employing 3 repeat measures; baseline, +60 min and +24 h. Reproducibility was assessed via the 95% limits of agreement and by the technical error of the measurement. For spectral parameters, the limits of agreement indicated same day was marginally better than between-day reproducibility. For sequence parameters, between-day had marginally better agreement than same-day reproducibility. Tilt markedly improved reproducibility across all outcome measures. Precision expressed by the technical error of the measurement for all spectral outcomes was good in both supine and tilt baroreflex sensitivity (<6%). Precision was lower, but acceptable, for sequence baroreflex sensitivity outcomes in both positions (<11%). Baroreflex sensitivity transfer gain provided the best agreement and reproducibility during supine and tilt conditions. These findings suggest time and spectral techniques may be employed to assess within-day and between-day baroreflex sensitivity changes in healthy individuals. The inclusion of a tilt manoeuvre may improve the reproducibility of the outcome measure, which may aid in the detection of modest baroreflex sensitivity changes in studies employing limited sample sizes.

The influence of reduced insulin sensitivity via short-term reductions in physical activity on cardiac baroreflex sensitivity during acute hyperglycemia

Reduced insulin sensitivity and impaired glycemic control are among the consequences of physical inactivity and have been associated with reduced cardiac baroreflex sensitivity (BRS). However, the effect of reduced insulin sensitivity and acute hyperglycemia following glucose consumption on cardiac BRS in young, healthy subjects has not been well characterized. We hypothesized that a reduction in insulin sensitivity via reductions in physical activity would reduce cardiac BRS at rest and following an oral glucose tolerance test (OGTT). Nine recreationally active men (23 ± 1 yr; >10,000 steps/day) underwent 5 days of reduced daily physical activity (RA5) by refraining from planned exercise and reducing daily steps (<5,000 steps/day). Spontaneous cardiac BRS (sequence technique) was compared at rest and for 120 min following an OGTT at baseline and after RA5. A substudy (n = 8) was also performed to independently investigate the influence of elevated insulin alone on cardiac BRS using a 120-min hyperinsulinemic-euglycemic clamp. Insulin sensitivity (Matsuda index) was significantly reduced following RA5 (BL 9.2 ± 1.3 vs. RA5 6.4 ± 1.1, P < 0.001). Resting cardiac BRS was unaffected by RA5 and significantly reduced during the OGTT similarly at baseline and RA5 (baseline 0 min, 28 ± 4 vs. 120 min, 18 ± 4; RA5 0 min, 28 ± 4 vs. 120 min, 21 ± 3 ms/mmHg). Spontaneous cardiac BRS was also reduced during the hyperinsulinemic-euglycemic clamp (P < 0.05). Collectively, these data demonstrate that acute elevations in plasma glucose and insulin can impair spontaneous cardiac BRS in young, healthy subjects, and that reductions in cardiac BRS following acute hyperglycemia are unaffected by reduced insulin sensitivity via short-term reductions in physical activity.

A pilot study examining the effects of consuming a high-protein vs normal-protein breakfast on free-living glycemic control in overweight/obese 'breakfast skipping' adolescents

To examine whether the daily consumption of normal-protein (NP) vs higher-protein (HP) breakfasts improve free-living glycemic control in overweight/obese, 'breakfast skipping' adolescents. Twenty-eight healthy, but overweight, teens (age: 19±1 year; BMI: 29.9±0.8 kg m(-2)) completed a 12-week randomized parallel-arm study in which the adolescents consumed either a 350 kcal NP breakfast (13 g protein) or HP breakfast (35 g protein). Pre- and post-study 24-h blood glucose measures were assessed using continuous glucose monitoring. Although no main effects of time or group were detected, time by group interactions were observed. Post hoc pairwise comparisons assessing the post-pre changes revealed that the daily consumption of the HP breakfasts tended to reduce the 24-h glucose variability (s.d.) vs NP (-0.17±0.09 vs +0.09±0.10 s.d.; P=0.06) and tended to reduce the time spent above the high glucose limit (-292±118 vs -24±80 min; P=0.09). The consumption of the HP breakfasts also reduced the 24-h maximal (peak) glucose response (-0.94±0.36 vs +0.30±0.18 mmol l(-1); P<0.01) and reduced postprandial glucose fluctuations (-0.88±0.44 vs +0.49±0.34 mmol l(-1); P<0.03) vs NP. These data suggest that the daily addition of a HP breakfast, containing 35 g of high-quality protein, has better efficacy at improving free-living glycemic control compared with a NP breakfast in overweight/obese, but otherwise healthy, 'breakfast skipping' adolescents.

Conventional and toxicogenomic assessment of the acute pulmonary damage induced by the instillation of Cardiff PM10 into the rat lung

There is strong epidemiological evidence of association between PM10 (particulate matter with an aerodynamic diameter less than or equal to 10 microm) and adverse health outcomes including death and increased hospital admissions for cardiopulmonary conditions. Ambient PM10 surrogates such as diesel exhaust particles (DEP), a common component of UK PM10 have been shown to induce lung inflammation in both humans and rodents. To date, few studies have reported on the toxicological response of UK PM10 in experimental animals. This study examines the pulmonary toxicological responses in male Sprague Dawley rats following the intratracheal instillation of Cardiff urban PM10. A mild but significant change in lung permeability was observed in the lung post-instillation of a high (10 mg) dose of the whole PM10 as adjudged by increases in lung to body weight ratio and total acellular lavage protein. Such effects were less marked following instillation of a water-soluble fraction (80% of the total mass) but histological examination showed that lung capillaries were swollen in size with this treatment. In conclusion, conventional toxicological, histological and toxicogenomic studies have indicated that Cardiff PM10 exhibits low bioreactivity in the form of mild permeability changes. Differential gene expression was observed when the lung was treated with whole PM10, containing durable particles, in comparison with the water-soluble fraction of PM10 that was devoid of particles. Such changes were linked to different histopathological events within the lung.

Can toxicogenomics provide information on the bioreactivity of diesel exhaust particles?

Epidemiologists have linked increased cardio-respiratory hospital admissions, morbidity and mortality rates and increases in particulate matter with an aerodynamic diameter less than 10 microns (PM10) concentrations (Anderson et al., 1991). PM10 consist of a heterogeneous mixture of particles that include minerals, metal oxides, sea salt, biological components and soot. In urban locations, soot, especially ultrafine diesel exhaust particles (DEP), accounts for 20-80% by mass of the airborne PM10 arising from vehicular activities. In the experiment described here, control [NaCl] and 1.25 mg of DEP were instilled into rat lung and the responses assessed using changes in lung permeability, inflammation and epithelial cell markers in lavage fluid, with the addition of a new technique of gene expression profiling using macroarrays. The aim of the study was to use these macroarrays as a sensitive measurement of acute up- or down-regulation of genes that were taking place in the rat lung in response to the small instilled mass of DEP. DEP instillation caused a slight oedematous lung with no overt inflammation and ten out of a possible 207 (5%) rat stress genes were repeatedly changed in response to DEP instillation. Therefore, the conclusion from the macroarray analysis is in agreement with the conventional toxicology and suggest that DEP elicits a low bioreactive response in a healthy rat lung.

Density and substrata are important in lung type II cell transdifferentiation in vitro

Morphological techniques and metabolic cell marker assays were used to study the transdifferentiation of pulmonary type II epithelial cells to type I-like cells in vitro. In the lung this process is important during remodelling and alveolar repair. Type II cell phenotype was best maintained over eight days when densely packed cells were plated out on a commercially available extracellular matrix. Such cells retained type II cell characteristics (lamellar bodies, high activities of gamma glutamyl transpeptidase and alkaline phosphatase) but expressed low levels of rT1(40) a surface protein marker of type I cells. In contrast, low density cultures, irrespective of substratum, exhibited rapid cell spreading, loss of lamellar bodies, loss of type II cell enzyme markers and expressed high levels or rT1(40). Conditions have been described whereby the same isolate of type II cells can be used to produce differential epithelial phenotypes and use can be made of this for further characterisation or to investigate the effect of toxins on different lung cell types in vitro.

Activation, inhibition, and regiospecificity of the lysophospholipase activity of the 85-kDa group IV cytosolic phospholipase A2

The 85-kDa Group IV calcium-dependent cytosolic phospholipase A2 (cPLA2) catalyzes the hydrolysis of palmitoylglycero-3-phosphocholine to palmitic acid and glycero-3-phosphocholine. Palmitoylglycero-3-phosphocholine exists as a 9:1 equilibrium mixture of the sn-1 and sn-2 isomers, with the fatty acid predominately at the sn-1 position. We have monitored this reaction by 31P NMR to determine which palmitoylglycero-3-phosphocholine isomer is processed by cPLA2. When both lysophospholipid isomers are present in a 1:1 mixture under conditions in which acyl migration is minimized, cPLA2 rapidly consumes both isomers. However, 1-palmitoylglycero-3-phosphocholine is consumed seven times faster than the 2-palmitoylglycero-3-phosphocholine isomer. We have previously reported that this lysophospholipase reaction is accelerated in the presence of glycerol. We now find that this apparent increase in activity is accounted for, in part, by glycerol acting as an alternative acceptor for the cleaved fatty acid, as is the case for this enzyme's phospholipase A2 (PLA2) activity. In contrast, dioleoylglycerol, which accelerates the PLA2 activity, does not act as an acceptor in either the lysophospholipase or the PLA2 reaction, but can affect enzyme activities by altering substrate presentation. We also show that a known inhibitor of the PLA2 activity of cPLA2 is able to inhibit its lysophospholipase activity with a similar IC50 to its PLA2 activity. However, the effect of inhibitors is dependent on the manner in which they are presented to the enzyme.

Identification of essential residues for the catalytic function of 85-kDa cytosolic phospholipase A2. Probing the role of histidine, aspartic acid, cysteine, and arginine

Cytosolic phospholipase A2 (cPLA2) hydrolyzes the sn-2-acyl ester bond of phospholipids and shows a preference for arachidonic acid-containing substrates. We found previously that Ser-228 is essential for enzyme activity and is likely to function as a nucleophile in the catalytic center of the enzyme (Sharp, J. D., White, D. L., Chiou, X. G., Goodson, T., Gamboa, G. C., McClure, D., Burgett, S., Hoskins, J., Skatrud, P. L., Sportsman, J. R., Becker, G. W., Kang, L. H., Roberts, E. F., and Kramer, R. M.(1991) J. Biol. Chem. 266, 14850-14853). cPLA2 contains a catalytic aspartic acid motif common to the subtilisin family of serine proteases. Substitution within this motif of Ala for Asp-549 completely inactivated the enzyme, and substitutions with either glutamic acid or asparagine reduced activity 2000- and 300-fold, respectively. Additionally, using mutants with cysteine replaced by alanine, we found that Cys-331 is responsible for the enzyme's sensitivity to N-ethylmaleimide. Surprisingly, substituting alanine for any of the 19 histidines did not produce inactive enzyme, demonstrating that a classical serine-histidine-aspartate mechanism does not operate in this hydrolase. We found that substituting alanine or histidine for Arg-200 did produce inactive enzyme, while substituting lysine reduced activity 200-fold. Results obtained with the lysine mutant (R200K) and a coumarin ester substrate suggest no specific interaction between Arg-200 and the phosphoryl group of the phospholipid substrate. Arg-200, Ser-228, and Asp-549 are conserved in cPLA2 from six species and also in four nonmammalian phospholipase B enzymes. Our results, supported by circular dichroism, provide evidence that Asp-549 and Arg-200 are critical to the enzyme's function and suggest that the cPLA2 catalytic center is novel.

Irreversible inhibition of Ca(2+)-independent phospholipase A2 by methyl arachidonyl fluorophosphonate

Methyl arachidonyl fluorophosphonate (MAFP) has been recently reported to be a selective, active-site directed, irreversible inhibitor of the Group IV 85 kDa cytosolic phospholipase A2 (cPLA2). We have now shown that this compound also potently inhibits the Ca(2+)-independent cytosolic phospholipase A2 (iPLA2). MAFP inhibited iPLA2 in a concentration-dependent manner with half-maximal inhibition observed at 0.5 microM after a 5 min preincubation at 40 degrees C. This inhibition was not reversed upon extensive dilution of the enzyme into the assay mixture. Preincubation of iPLA2 with MAFP resulted in a linear, time-dependent inactivation of enzyme activity, and the enzyme was protected from inactivation by the reversible inhibitor PACOCF3. The ability of MAFP to inhibit the iPLA2 suggests that this enzyme proceeds through an acyl-enzyme intermediate as has been proposed for the cPLA2. Further testing indicated that MAFP did not inhibit the arachidonoyl-CoA synthetase, CoA-dependent acyltransferase, or CoA-independent transacylase activities from P388D1 cells. Thus, MAFP is not a general inhibitor for enzymes which act on arachidonoyl substrates. Instead, the inhibitor appears to show some selectivity for PLA2, although it does not discriminate between cPLA2 and iPLA2. Particular caution must be exercised to distinguish these activities if this inhibitor is used in intact cells.

Inactivation of secretory phospholipase A2 by ionizing radiation

The extracellular phospholipase A2s (PLA2) from cobra venom, rattlesnake venom, and porcine pancreas were analyzed by radiation inactivation to determine their functional aggregation states. The analysis was performed in the presence of the protein transferrin at two different concentrations of PLA2: 5 micrograms/ml. The small size of these proteins necessitated the use of high radiation dosages. The catalytic activity of all samples decreased as a single exponential as a function of radiation dosage, to > 97% inactivation. Target size analysis of these curves yielded sizes corresponding to dimers for all three PLA2s, indicating that all three enzymes exist as dimers or larger aggregates under the conditions studied. An analysis of the amount of intact protein remaining by sodium dodecyl sulphate-polyacrylamide gel electrophoresis showed that the loss of protein also followed a dimeric size for all three PLA2s. The loss of protein as a dimer indicates that transfer of radiation energy is occurring between polypeptides.

1-Hexadecyl-2-arachidonoylthio-2-deoxy-sn-glycero-3-phosphorylcholine as a substrate for the microtiterplate assay of human cytosolic phospholipase A2

Human cytosolic phospholipase A2 (cPLA2) is an 85-kDa protein which displays a preference for arachidonoyl phospholipids as substrates. This substrate preference and the assay characteristics of the enzyme are quite different from those of the smaller, more well-studied extracellular PLA2s. We now report the development of a nonradioactive, spectrophotometric, microtiterplate assay for human cPLA2 using a novel synthetic thio-phospholipid analog as a substrate. This substrate is a phosphatidylcholine derivative with an arachidonoylthioester in the sn-2 position and an alkyl-ether in the sn-1 position. The use of an sn-1 alkyl-ether in the substrate ensures that the assay will only measure PLA2 activity and will not be complicated by the metabolism of the lysophospholipid product by the enzyme's lysophospholipase activity. cPLA2 is assayed at pH 7.4 and 37 degrees C with a mixed micellar substrate consisting of 2 mM thio-phospholipid and 4 mM Triton X-100 in 30% glycerol. Under these conditions, the assay is fairly linear for over 1 h.

Metal ion and salt effects on the phospholipase A2, lysophospholipase, and transacylase activities of human cytosolic phospholipase A2

Human cytosolic phospholipase A2 (cPLA2) is an arachidonic acid specific enzyme which may play a role in arachidonic acid release, eicosanoid production, and signal transduction. The PLA2 activity of this enzyme is stimulated by microM levels of Ca2+. Using a pure recombinant enzyme, we have confirmed that cPLA2 is not absolutely dependent on Ca2+, since Sr2+, Ba2+ and Mn2+ also gave full enzyme activity. Heavy metals, in contrast, inhibited enzyme catalysis suggesting the involvement of an essential cysteine residue. In the absence of Ca2+, high salt concentrations overcame the requirement for divalent metals, indicating that Ca2+ is not required for PLA2 catalytic activity. cPLA2 also displays a lysophospholipase (lyso PLA) activity with lysophosphatidylcholine micelles as a substrate. Unlike the PLA2 activity, the lyso PLA activity toward these micelles is not stimulated by Ca2+. However, upon the addition of glycerol or Triton X-100 to the assay, Ca2+ activation is observed, indicating that substrate presentation can affect the apparent Ca2+ dependence. Glycerol was found to be a potent stimulator of lyso PLA activity and specific activities up to 50 mumol min-1 mg-1 were observed. In addition to the PLA2 and lyso PLA activities, we report that cPLA2 displays a relatively low, CoA-independent transacylase activity which produces phosphatidylcholine from lysophosphatidylcholine substrate. The observation of this novel transacylase activity is consistent with the formation of an acyl-enzyme intermediate.

Analysis of human synovial fluid phospholipase A2 on short chain phosphatidylcholine-mixed micelles: development of a spectrophotometric assay suitable for a microtiterplate reader

The development of a reliable assay for human synovial fluid phospholipase A2 (HSF PLA2) is important for the kinetic characterization of the enzyme and for the identification of enzyme inhibitors. This enzyme behaves differently from other extracellular PLA2s in many standard phospholipase assays and is generally assayed using radiolabeled, autoclaved Escherichia coli as a substrate. We have now developed a nonradioactive, continuous, spectrophotometric assay for this enzyme that is adaptable for use with a microtiterplate reader and is suitable for screening enzyme inhibitors. The assay uses a thioester derivative of diheptanoyl phosphatidylcholine as a substrate, with which the enzyme displays a specific activity of about 25 mumol min-1 mg-1. The substrate concentration curve fits a Hill equation with an apparent Km of 500 microM and a Hill coefficient of two. The enzyme has a pH optimum of 7.5 in this assay and requires about 10 mM Ca2+ for maximal activity. The presence of 0.3 mM Triton X-100 was necessary to solubilize the substrate; however, higher concentrations of the detergent inhibited enzyme activity. Using this spectrophotometric assay, inhibition of HSF PLA2 by a thioether phosphonate phosphatidylethanolamine analog was observed with an IC50 of 18 microM.

Inhibition of venom phospholipases A2 by manoalide and manoalogue. Stoichiometry of incorporation

We have previously described the irreversible inhibition of cobra venom phospholipase A2 (PLA2) by the marine natural product manoalide (MLD) (Lombardo, D., and Dennis, E. A. (1985) J. Biol. Chem. 260, 7234-7240) and by its synthetic analog, manoalogue (MLG) (Reynolds L. J., Morgan, B. P., Hite, G. A., Mihelich, E. D., and Dennis, E. A. (1988) J. Am. Chem. Soc. 110, 5172-5177). We have now made a direct comparison of the action of these two inhibitors on PLA2 from cobra, bee, and rattlesnake venoms and have found that MLG behaves kinetically similarly to MLD in all cases with only minor differences. The time courses of inactivation differ significantly between the three enzymes, however, with the inactivation of bee and rattlesnake PLAs2, occurring much faster than does the inactivation of the cobra venom enzyme. The enzymes also differ in their sensitivity to the presence of Ca2+ during the inactivation. Of the three enzymes, the most Ca(2+)-sensitive is the rattlesnake enzyme, which shows a much faster rate of inactivation in the presence of Ca2+ than in the presence of EGTA. However, the same rate of inactivation was also observed when the inhibitor Ba2+ was substituted for Ca2+, indicating that catalytic activity is not required for inactivation of the enzyme. To probe the mechanism of inactivation and to determine the stoichiometry of incorporation, we have synthesized 3H-labeled MLG and have found that inactivation of cobra PLA2 is accompanied by an incorporation of 3.8 mol of [3H]MLG/mol of enzyme. The same amount of 3H incorporation was observed when p-bromophenacyl bromide-inactivated PLA2 was incubated with [3H]MLG, again indicating that catalytic activity is not required for the reaction of PLA2 with MLG. All together, these results suggest that MLD and MLG are not suicide inhibitors of PLA2. A portion of the incorporated radioactivity was acid-labile, and dialysis of the radiolabeled PLA2 under acidic conditions resulted in a loss of about one-third of the enzyme-associated radioactivity, leaving 2.4 mol of [3H]MLG/mol of PLA2. In previous studies, amino acid analysis, which also included acid treatment, indicated that MLG-modified cobra phospholipase A2 contained 2.8 mol of Lys less than the native enzyme. Thus, 1 mol of [3H]MLG is incorporated per mol of Lys lost. The implications of this 1:1 stoichiometry of MLG to Lys on the mechanism of reaction of these inhibitors is discussed.

Assay strategies and methods for phospholipases

Of the general considerations discussed, the two issues which are most important in choosing an assay are (1) what sensitivity is required to assay a particular enzyme and (2) whether the assay must be continuous. One can narrow the options further by considering substrate availability, enzyme specificity, assay convenience, or the presence of incompatible side reactions. In addition, the specific preference of a particular phospholipase for polar head group, micellar versus vesicular substrates, and anionic versus nonionic detergents may further restrict the options. Of the many assays described in this chapter, several have limited applicability or serious drawbacks and are not commonly employed. The most commonly used phospholipase assays are the radioactive TLC assay and the pH-stat assay. The TLC assay is probably the most accurate, sensitive assay available. These aspects often outweigh the disadvantages of being discontinuous, tedious, and expensive. The radioactive E. coli assay has become popular recently as an alternative to the TLC assay for the purification of the mammalian nonpancreatic phospholipases. The assay is less time consuming and less expensive than the TLC assay, but it is not appropriate when careful kinetics are required. Where less sensitivity is needed, or when a continuous assay is necessary, the pH-stat assay is often employed. With purified enzymes, when free thiol groups are not present, a spectrophotometric thiol assay can be used. This assay is approximately as sensitive as the pH-stat assay but is more convenient and more reproducible, although the substrate is not available commercially. Despite the many assay choices available, the search continues for a convenient, generally applicable assay that is both sensitive and continuous. The spectrophotometric SIBLINKS assay and some of the fluorescent assays show promise of filling this need.

Differential reactivity in the processing of [p-(halomethyl)benzoyl] formates by benzoylformate decarboxylase, a thiamin pyrophosphate dependent enzyme

A series of [p-(halomethyl)benzoyl]formates have been investigated as substrates for benzoylformate decarboxylase. These analogues vary from acting as normal substrates to acting as potent competitive inhibitors. The fluoro analogue is a substrate with Km (190 microM) and turnover number (20 s-1) similar to those of benzoylformate (Km = 340 microM; 81 s-1). The bromo analogue is a competitive inhibitor (Ki = 0.3 microM) and exhibits processing to eliminate bromide and form (p-methylbenzoyl)thiamin pyrophosphate. This modified cofactor hydrolyzes to form the p-methylbenzoate in quantitative yield. The chloro analogue [Km(app) = 21 microM] partitions between these two pathways such that 0.6% of the analogue ultimately forms p-methylbenzoate. These data are consistent with the interpretation that the leaving group potential of the halogen determines the enzymic fate of the analogue and that the potent inhibition observed for the bromo analogue is due to covalent modification of the cofactor.