Gastrointestinal infection in a New Zealand community : a one year study : a thesis presented in fulfilment of the requirements for the degree of Master of Science in Microbiology at Massey University

Diagnostic medical microbiology laboratories detect and identify pathogens in submitted specimens. The techniques used should maximise the detection of pathogens (sensitivity) while minimising the number of tests for their detection (efficiency). To achieve the best compromise between sensitivity and efficiency, it is necessary to have information on both the relative prevalence and clinical importance of various pathogens within the relevant community, and the relative efficiency of various detection techniques. This investigation had three primary objectives: to establish what pathogens were associated with community-acquired gastrointestinal symptoms in the Eastern Bay of Plenty, and the incidence and relative importance of each; to compare the merits of various methods for detecting these pathogens (in those cases where more than one method was available); and to collect data from patients so as to identify potential sources and/or risk factors for infection. 997 faecal specimens from 716 episodes of illness were tested over a one year period. Patients completed a questionnaire on symptoms, and food and environmental exposures. Using one or more standard techniques, the specimens were tested for bacteria and parasites which may cause gastroenteritis. Specimens from young children were also tested for the presence of rotavirus. The incidence rates of the various pathogens, expressed as a rate per 100 000 persons per year, were as follows: Blastocystis hominis, 358; Campylobacter species, 208; Giardia lamblia, 158; Yersinia species, 87; Cryptosporidium parvum, 67; Salmonella species, 62; Aeromonas species, 62; Dientamoeba fragilis, 29; Plesiomonas shigelloides, 21; Escherichia coli (E coli) O157, 4; Vibrio cholerae non-O1, non-O139, 4; and Shigella species < 4. Faecal specimen macroscopic form, microscopic findings, season, and patient age showed little correlation with the presence of specific pathogens. Consequently the tests selected for the detection of pathogens in faeces should not be based on any of the above parameters. Furthermore, the symptoms associated with parasitic and bacterial infections were similar, so it is not possible to select the appropriate tests on this basis. The presence of rotavirus in patients older than five years was not investigated so incidence in the general population can not be calculated. A study of all age groups for the presence of this organism would be appropriate. From the above findings, and an evaluation of the literature, it is recommended that all specimens should be examined for the following organisms and, on the basis of our observations, the most cost-effective method is shown in brackets: Salmonella (selenite enrichment subcultured to xylose lysine desoxycholate agar); Shigella (none were detected, so a cost-effective medium could not be determined), Campylobacter (5% sheep blood agar supplemented with 32 mg/1 cefoperazone); Yersinia (Yersinia selective agar (YSA), plus selenite enrichment subcultured to YSA); Giardia lamblia (detection of antigen); Cryptosporidium parvum (detection of antigen). While routine testing for E coli O157 is not recommended, laboratories should have the capability to test for this pathogen if a patient presents with haemolytic uraemic syndrome, thrombotic thrombocytopenic purpura or unexplained bloody diarrhoea. Likewise, routine culture for Vibrio species is not recommended; however, laboratories should test specimens using thiosulphate citrate bilesalt sucrose agar if the requesting clinician suspects cholera, or the patient has a recent history of shellfish consumption. A trichome stain for Dientamoeba fragilis is recommended for patients with chronic gastrointestinal symptoms who are to be investigated for neoplastic and other non-infectious conditions. Pathogenic parasites other than those noted above were not detected. However, since such organisms are isolated in New Zealand, usually in association with overseas travel or institutionalisation, it is recommended that a trichrome stain and a faecal concentration technique should be performed on specimens from all cases of gastroenteritis who have recently travelled overseas or who are institutionalised. Close liaison between the laboratory and the clinician is essential to ensure appropriate selective testing for these less common pathogens. The presence of Blastocystis hominis and Aeromonads should be reported, but the report should note that their pathogenicity is uncertain. Dientamoeba fragilis and Plesiomonas shigelloides are probably pathogenic, but further work is needed to clarify this point. Correlation of data from the questionnaires and the laboratory findings identified the following risk factors: (the relative risk, 95% confidence interval and p-value are shown in the brackets). Campylobacter species: consumption of unpasteurised milk (4.67,2.39 - 9.11, p = <0.001); Salmonella species: overseas travel (7.20, 1.67 - 20.9, p = 0.040), eating a barbecued meal (4.55, 1.37 - 15.12, p = 0.026), eating shellfish (3.80, 1.18 - 12.21, p = 0.032); Yersinia species: consumption of water from a home supply (3.46, 1.32 - 9.10, p = 0.016), handling cattle (4.88, 1.73 - 13.76, p = 0.008), handling sheep (14.80. 4.93 - 44.46, p = 0.001); Giardia lamblia: consumption of unpasteurised milk (3.93, 1.63 - 9.46, p = 0.011), attendance at a day care centre (2.70, 1.17 - 6.27, p = 0.033), handling cattle (3.39, 1.59 - 7.22, p = 0.005), handling horses (5.27, 1.85 - 14.97, p = 0.002); Cryptosporidium parvum: consumption of water from a home supply (5.08, 1.88 - 13.71, p = 0.002), consumption of unboiled water from a natural waterway (3.97, 1.29 - 12.24, p = 0.031), attendance at a day care centre (3.30, 1.06 - 10.22, p = 0.054), handling cattle (5.41, 1.88 - 15.58, p = 0.006), owning a cat (4.50,1.02 - 19.91, p = 0.029); Plesiomonas shigelloides: eating shellfish (13.67, 1.44 - 130.13, p = 0.020); and Dientamoeba fragilis: consumption of unboiled water from a natural waterway (7.46, 1.71 - 32.48, p = 0.019). The risk factors suggest the value of the following precautions to prevent gastrointestinal infection: maintaining a high standard of both personal hygiene (particularly in the rural environment) and environmental hygiene in areas that food is prepared; avoiding consumption of untreated water or unpasteurised milk; cooking animal-derived food thoroughly - especially barbecued food and shellfish; and washing hands thoroughly after animal contact. Persons with diarrhoeal symptoms should take particular care with personal hygiene. Those travelling overseas should be conscious of the risk associated with the consumption of food and water which is not properly cooked or treated. These findings should assist New Zealand laboratories to optimise their approach to the detection of faecal pathogens and should also assist in formulating policy for prevention of infection by enteric pathogens

Implementation of Daily Multidisciplinary Rounding Audits of Adherence to an Indwelling Catheter Protocol Impact on Catheter-Associated Urinary Tract Infections

Problem Statement: Catheter-associated urinary tract infections (CAUTIs) among critical care patients negatively impact the trajectory of the patient’s hospitalization through increased mortality, morbidity, length of stay, and cost. To combat this, hospitals have implemented bundles in compliance with evidence-based practice models to reduce CAUTIs. Purpose: Determine if implementing a daily multidisciplinary rounding audit of established CAUTI prevention protocol decreases the occurrence of CAUTIs in critical care patients with indwelling urinary catheters. Methods: Participants in this quality improvement project included critical care nurses and providers participating in daily multidisciplinary rounds on all critical care patients with indwelling urinary catheters admitted to the surgical intensive care unit (SICU) during a three-month timeframe. Staff compliance was ensured through the completion of daily audits and electronic health record documentation. Rates of urinary catheter use and incidence of CAUTIs were evaluated monthly following the Centers for Disease Control and Prevention (CDC) criteria throughout the study period. Results: Before implementation of the strategy, six catheter-associated urinary catheter tract infections were reported for 2021 and five for 2022. Established best practice protocols, supported by daily multidisciplinary rounding audits decreased CAUTIs to zero not only during the project implementation but also following, up to the current date. Conclusion: Daily multidisciplinary rounding audits on ICU patients with urinary catheters resulted in a decrease in standard utilization ratios as well as zero catheter-associated urinary tract infections with a standardized infection ratio of 0.00. These findings support the feasibility of incorporating daily audits, of established best practice protocols, in the ICU

The impact of Katse Dam water on water quality in the Ash, Liebenbergsvlei and Wilge Rivers and the Vaal Dam

The main purpose of this study is to determine the difference in water quality of the rivers between the Katse and Vaal Dams (Wilge River and Vaal Dam reservoir sub-catchments) after the construction of the Lesotho Highlands Water Project. These rivers include the Ash, Liebenbergsvlei and Wilge Rivers. The temporal changes in water constituents, namely: electrical conductivity, chemical oxygen demand, pH, turbidity, ammonia, calcium, manganese and chlorophyll a, at selected water sampling points were analysed to clarify if Katse Dam water has had any impact on the water quality of the Ash, Liebenbergsvlei and Wilge Rivers and the Vaal Dam. The water quality was studied over an eleven-year period from November 1994 until December 2005. This includes a five-year period prior to, and a six-year period following the completion of the Katse Dam. The Ash, Liebenbergsvlei and Wilge Rivers fall within the Wilge sub-catchment, and the Vaal Dam falls within the Vaal Dam reservoir sub-catchment. Both the aforementioned sub-catchments form part of the Vaal River catchment. Physical, chemical and microbiological sampling results were obtained from Rand Water. The results were compared with the in-stream water quality guidelines as set by the Vaal Barrage Catchment Executive Committee. The results of the selected constituents were depicted visually in the form of graphs. Trends in the constituents over the period were then determined. The graphs were divided into two sections namely, pre-Katse Dam (before 1999) and post-Katse Dam (1999 to 2005). Differences in water quality before and after the construction of the Katse Dam were determined from sampling and chemical analysis at six locations, and hence evaluations were made whether the release of Katse Dam water has had a significant effect on the water quality results in the Vaal River System. The water quality results with respect to the different water constituents illustrated a distinct change in water quality over the period. Northwards, towards the Vaal Dam, the difference in water quality became less apparent. Sampling points throughout the study area experienced decreases in: electrical conductivity, chemical oxygen demand, turbidity, ammonia, and manganese. Hence, the release of Katse Dam water into the Vaal River system has had a ii positive influence on the water quality and thus changed the riverine environments in the Vaal River system. The high quality water from the Katse Dam that enters the Vaal River system thus initially increases the quality of the water in the recipient system with a lesser effect downstream. The result is an improvement of water quality in the upper reaches of the Vaal River system and no significant influence on the Vaal Dam itself. However, the change in water quality may have a detrimental effect on the river environment as a result of the increased volume of water entering the system and the resultant soil erosion, which serves for further studies. Consequently, the advantageous high quality water from the Lesotho Highlands is not being optimally utilised, hence the proposed recommendation by Rand Water to alternatively transfer Katse Dam water via a gravity-fed pipeline to the Vaal Dam thereby receiving the full benefit of high quality water, leaving river environments unaltered and possibly lowering purification costs.Prof. J. T. Harmse Prof. H. J. Annegar

Use of the Strengths & Difficulties Questionnaire to identify treatment needs in looked after children referred to CAMHS

© The Author(s) 2019Background: In England and Wales, the Strengths & Difficulties Questionnaire (SDQ) is used to assess and monitor looked after children’s (LAC) mental health; and some targeted CAMHS teams use it to decide who can access services. However, the ability of the single-informant SDQ to identify LAC who need mental health treatment is insufficiently understood. Methods: 144 LAC referrals to a Targeted CAMHS Team were screened as part of a larger study. To establish how well the SDQ identified children who required treatment, Total Difficulties Scores (TDS) from single-informant SDQs submitted at referral were compared to treatment recommendations following routine CAMHS assessment in a real-world setting. To explain the results, clinicians (n=9) from the team were interviewed and key themes identified using Thematic Analysis. Results: Optimal accuracy calculations for SDQs completed by carers (TDS=17, sensitivity .67, specificity .57), teachers (TDS=17, sensitivity .79, specificity .71) and young people (TDS=14, sensitivity.79, specificity .42) compared to the outcome of routine CAMHS assessments indicated that the number of children whose treatment needs were not identified by their SDQ score may be unacceptably high. Key themes from clinician interviews identified possible gaps and limitations: Developmental Trauma and Attachment Difficulties, A different kind of ‘patient?’, Seeing the bad but neglecting the sad, and The importance of clinical judgement. Conclusions: Contrary to UK Government policy, this study suggests that the single-report SDQ should not be relied upon as a sole means of identifying mental health difficulties in this vulnerable, high-risk population.Peer reviewedFinal Accepted Versio

One-third of U.S. adults embraced most heart healthy behaviors in 1999-2002

"A number of U.S. Department of Health and Human Services programs recommend behaviors to reduce risk of cardiovascular disease (CVD), including the National High Blood Pressure Education Program (NHBPEP) and the National Cholesterol Education Program (NCEP) (1-6). The objective of this report is to estimate the prevalence of persons engaging in multiple behaviors recommended to reduce risk of CVD. Behaviors identified by NHBPEP and NCEP as primary lifestyle modifications to reduce CVD risk include physical activity, four dietary recommendations, smoking abstention, moderate alcohol consumption, and screening for high blood pressure and high blood cholesterol."Jacqueline D. Wright, Rosemarie Hirsch and Chia-Yih Wang.Title from title screen (viewed on May 27, 2009)."May 2009."Mode of access: Internet from the CDC web site. Address as of 5/27/2009: http://www.cdc.gov/nchs/data/databriefs/db15.pdf; current access available via PURL.Includes bibliographical references (p. 7-[8])

The guanine nucleotide exchange factor RIC8 regulates conidial germination through Gα proteins in Neurospora crassa.

Heterotrimeric G protein signaling is essential for normal hyphal growth in the filamentous fungus Neurospora crassa. We have previously demonstrated that the non-receptor guanine nucleotide exchange factor RIC8 acts upstream of the Gα proteins GNA-1 and GNA-3 to regulate hyphal extension. Here we demonstrate that regulation of hyphal extension results at least in part, from an important role in control of asexual spore (conidia) germination. Loss of GNA-3 leads to a drastic reduction in conidial germination, which is exacerbated in the absence of GNA-1. Mutation of RIC8 leads to a reduction in germination similar to that in the Δgna-1, Δgna-3 double mutant, suggesting that RIC8 regulates conidial germination through both GNA-1 and GNA-3. Support for a more significant role for GNA-3 is indicated by the observation that expression of a GTPase-deficient, constitutively active gna-3 allele in the Δric8 mutant leads to a significant increase in conidial germination. Localization of the three Gα proteins during conidial germination was probed through analysis of cells expressing fluorescently tagged proteins. Functional TagRFP fusions of each of the three Gα subunits were constructed through insertion of TagRFP in a conserved loop region of the Gα subunits. The results demonstrated that GNA-1 localizes to the plasma membrane and vacuoles, and also to septa throughout conidial germination. GNA-2 and GNA-3 localize to both the plasma membrane and vacuoles during early germination, but are then found in intracellular vacuoles later during hyphal outgrowth

Understanding the decline in prevalence of hypertension in US adults between 1976-80 and 1999-02

The National Health and Nutrition Examination Survey (NHANES) is conducted to monitor the health and nutrition status of the United States (US) population. Results from the NHANES indicate that between 1976-80 and 1999-02 the prevalence of obesity doubled in the US while hypertension declined by 25 percent. Much attention has been focused on obesity as a risk factor for hypertension and on programs to reduce obesity prevalence in the population. The objective of the first paper was to estimate the effect of two sources of measurement error on the estimated prevalences of hypertension in the two surveys. In the second paper I estimated the effect of measurement error and selected risk factors on the difference in hypertension prevalence between 1976-80 and 1999-02. Blood pressure measurements were adjusted for use of inappropriate cuff size using previously published correction equations. I modeled the effect of zero end digit preference using different sets of assumptions. The adjustment for cuff size changed the age-adjusted prevalence of hypertension in 1976-80 from 34 to 31% and in 1999-02 from 25 to 26%. After the adjustment for cuff size, adjustment for end digit preference reduced the prevalence in 1976-80 slightly more from 31 to 30% and in 1999-02 the prevalence was unchanged at 26%. The prevalence difference was -8.6 percentage points (-11.4, -5.8) after standardization for age alone compared with -8.0 percentage points (-10.8, -5.1) after standardization for age, body mass index (BMI), sex, race-ethnicity, smoking, and education. This should not be interpreted as meaning that none of these factors affected the difference. The difference decreased to -4.8 percentage points (-7.5, -2.0) after correction for cuff size and increased to -14.7 percentage points (-17.6, -11.7) after standardization for BMI and age. Using observed blood pressure prevalence differences were greater in overweight and obese persons than in normal weight persons but were similar after adjustment for measurement error. Zero end digit preference and lack of adjustment for cuff size contributed to the apparent decline in hypertension prevalence. Standardization for BMI, age, sex, race-ethnicity, education, and smoking did not explain the decline in hypertension seen between 1976-80 and 1999-02

Phylogeny and potential virulence of cryptic clade Escherichia coli species complex isolates derived from an arable field trial

Analysis of Escherichia coli taxonomy has expanded into a species-complex with the identification of divergent cryptic clades. A key question is the evolutionary trajectory of these clades and their relationship to isolates of clinical or veterinary importance. Since they have some environmental association, we screened a collection of E. coli isolated from a long-term spring barley field trial for their presence. While most isolates clustered into the enteric-clade, four of them clustered into Clade-V, and one in Clade-IV. The Clade -V isolates shared >96% intra-clade average nucleotide sequence identity but <91% with other clades. Although pan-genomics analysis confirmed their taxonomy as Clade -V (E. marmotae), retrospective phylogroup PCR did not discriminate them correctly. Differences in metabolic and adherence gene alleles occurred in the Clade -V isolates compared to E. coli sensu scricto. They also encoded the bacteriophage phage-associated cyto-lethal distending toxin (CDT) and antimicrobial resistance (AMR) genes, including an ESBL, blaOXA-453. Thus, the isolate collection encompassed a genetic diversity, and included cryptic clade isolates that encode potential virulence factors. The analysis has determined the phylogenetic relationship of cryptic clade isolates with E. coli sensu scricto and indicates a potential for horizontal transfer of virulence factors