Medical interns in district health services: an evaluation of the new family medicine rotation in the Western Cape of South Africa.

BACKGROUND: In 2021, South Africa introduced a 6-month internship rotation in family medicine, in the second year of a 2-year internship programme for newly qualified doctors. This was a major change from the previous 3-months training in family medicine, and expanded the training platform to smaller district hospitals and primary health care (PHC) facilities, many of which had never had interns. The medical disciplines in South Africa needed to know if this change in the internship programme was worthwhile and successful. The aim of this study was to assess the new family medicine rotation for medical interns at district health facilities in the Western Cape Province. METHODS: Descriptive exploratory qualitative research included six intern programmes across the province. Purposeful sampling identified a heterogeneous group with maximum variation in experience. Overall, eight interns, four managers, four supervisors and four intern curators were included. Individual semi-structured interviews were audio-recorded and the transcripts were thematically analysed using the framework method and Atlas-ti software. RESULTS: Four major themes emerged around the varied structure and organisational characteristics of the rotations, the orientation and arrival of interns, their learning during the rotation, and impact on health services. A programme theory was developed that defined the key inputs (i.e. infrastructure, communication, orientation, preparation, prior learning and guidelines), processes (i.e. model of the rotation, clinical training and supervision, clinical teaching), outputs (i.e. more independent decision making, approach to undifferentiated problems, approach to chronic care and continuity, development of procedural skills, approach to sequential coordination of care and referrals, working in a multidisciplinary team and inter-professional learning, integration of multiple competencies, as well as becoming more person and community orientated). CONCLUSIONS: The new rotation in family medicine was positively experienced by most interns, supervisors and managers. It should lead to improved quality of care, better preparation for obligatory community service, and an increased likelihood of considering a career in district level health services. This study will form part of an exploratory sequential mixed methods study that incorporates the key issues into a questionnaire for a descriptive survey of all interns in a subsequent study.

Consolidating strategic information to monitor progress against the UNAIDS 90-90-90 targets: evaluating the operational feasibility of an electronic HIV testing register in Cape Town, South Africa.

BACKGROUND: HIV diagnosis in South Africa is based on a point-of-care testing (PoCT) algorithm with paper-based record-keeping. Aggregated testing data are reported routinely. To facilitate improved HIV case-based surveillance, the Western Cape Province implemented a unique pilot intervention to digitise PoCT results, at an individual level, and generate an electronic register using the newly developed Provincial Health Data Centre (PHDC). We describe the intervention (phased) and present an evaluation of the operational feasibility of the intervention. We also offer implementation insights into establishing electronic capture of individual level testing data. METHODS: Cross-sectional analyses were conducted on records of all patients attending a local Community Health Centre who had an HIV-PoCT during the study period. Data from the intervention were linked to the PHDC using a unique identifier and compared with aggregate data from the paper-based register. Correlation coefficients were calculated to quantify the correlation between the two monthly datasets. To support an understanding of the findings, the Department of Health project management team generated reflections on the implementation process, which were then grouped thematically into implementation lessons. RESULTS: In total, 11,337 PoCT records were digitised (70% (7954) during Phase I; and 30% (3383) during Phase II). Linkage of forms to the PHDC was 96% in Phase I and 98% in Phase II. Comparison with aggregate data showed high correlation during Phase I, but notable divergence during Phase II. Divergence in Phase II was due to stringent data quality requirements and high clinical staff turnover. Factors supporting implementation success in Phase I included direct oversight of data capturing by a manager with clinical and operational insight. Implementation challenges included operational, health system, and high cost-related issues. CONCLUSIONS: We demonstrate that rapid digitisation of HIV PoCT data, without compromising currently collected aggregate data, is operationally feasible, and can contribute to person-level longitudinal HIV case-based surveillance. To take to scale, we will need to improve PoCT platforms and clerical and administrative systems. Although we highlight challenges, we demonstrate that electronic HIV testing registers can successfully replace manual registers and improve efforts to monitor and evaluate HIV testing strategies.

Patient and clinician priorities for information on treatment outcomes for advanced ovarian cancer: a Delphi exercise.

OBJECTIVE: Patients with advanced ovarian cancer face a range of treatment options, and there is unwarranted variation in treatment decision-making between UK providers. Decision support tools that produce data on treatment outcomes as a function of individual patient characteristics, would help both patients and clinicians to make informed, preference- and values-based choices. However, data on treatment outcomes to include in such tools are lacking. METHODS: Following a literature review, a questionnaire was designed for use in a Delphi process to establish which treatment outcomes are important to both patients and clinicians in decision-making for treatment for advanced ovarian cancer. Patient and clinician panels were established. RESULTS: Following 2 Delphi rounds, consensus was achieved for 7/11 items in the patient panel and 8/11 items in the clinician panel. Consensus across both panels was achieved for inclusion of both overall survival and progression free survival as important items in the decision-making process, although there remained differences of opinion as to whether these should be presented as relative or absolute values. CONCLUSION: Information needs for treatment decision-making in ovarian cancer differ between and within patient and clinician groups. Whilst overall survival and progression free survival are universally accepted as important data items, decision support tools will need to be nuanced to allow presentation of a range of outcomes and associated probabilities, and in a range of formats, that can be tailored to the preferences of clinician and patients.

Healthcare workers' knowledge of indicators for a palliative care approach.

BACKGROUND:  Palliative care is an essential element of universal healthcare, yet not all people who need palliative care are able to receive it. One of the barriers to ensuring access for people who require palliative care is the identification of those eligible. AIM:  This study evaluated healthcare workers' ability to identify patients who are eligible for palliative care based on their training or experience in palliative care. SETTING:  The setting for the study comprised the Heideveld Emergency Centre and Heideveld Community Day Centre in the Cape Metro, Cape Town, South Africa. METHODS:  This study made use of a cross-sectional survey of healthcare workers. RESULTS:  Of the 55 participants in this study, most were able to correctly identify patients with cancer and chronic kidney disease as needing palliative care, but less accurate with other organ failure categories, trauma indications, or functional assessment of the patient. Participants who reported previous awareness training reported improved knowledge on the indications for a palliative care approach compared to no prior training. CONCLUSION:  Our cohort was too small to analyse the results statistically. From what was analysed, the ability of healthcare workers to identify a person in need of palliative care could be better; more work is needed on our awareness training and basic training courses to improve this vital step.Contribution: This research highlights the fact that existing training for palliative care needs to be more applicable to the setting and that training of staff with existing courses does make a difference in knowledge.

Evaluating the new family medicine internship programmes in the Western Cape, South Africa.

BACKGROUND:  In 2021, South Africa introduced a new 6-month internship in family medicine and primary care. This study aimed to assess the new rotation at district health facilities in the Western Cape. METHODS:  A descriptive survey of interns and supervisors, as phase-two of an exploratory sequential mixed methods study. Questionnaires were developed from a descriptive exploratory qualitative study. Data were analysed with the Statistical Package for Social Sciences. RESULTS:  Questionnaires were completed by 72 interns (response rate 21%) and 36 supervisors (response rate 90%), across 10 training programmes. Interns felt more independent (97.2%), confident (90.3%) and resilient (91.6%). They learnt to manage undifferentiated and chronic conditions (91.6%), to refer patients (94.3%) and conduct procedures (77.8%). Most interns were not exposed to community-based services (68.0%) and continuity of care (54.1%). Supervision was mostly adequate during the day (79.1%) and afterhours (80.6%). Many interns reported no structured teaching programme (41.7% - 55.6%). Most supervision was from medical officers and registrars. Supervisors saw interns as valuable members of the clinical team (100.0%), who required extra support and administration (42.5%). The majority of interns (75.0%) and supervisors (72.7%) thought the rotation was the right length and the best preparation for community service (67.6%). CONCLUSION:  The rotation met most expectations of the Health Professions Council of South Africa. Programmes need to improve exposure to community-orientated primary care, public health medicine, palliative and ongoing care. Supervision and orientation of interns needs improvement.Contribution: This is the first evaluation of the new family medicine internship programme in South Africa.

Meta-analysis of genome-wide association studies of stable warfarin dose in patients of African ancestry.

ABSTRACT: Warfarin dose requirements are highly variable because of clinical and genetic factors. Although genetic variants influencing warfarin dose have been identified in European and East Asian populations, more work is needed to identify African-specific genetic variants to help optimize warfarin dosing. We performed genome-wide association studies (GWASs) in 4 African cohorts from Uganda, South Africa, and Zimbabwe, totaling 989 warfarin-treated participants who reached stable dose and had international normalized ratios within therapeutic ranges. We also included 2 African American cohorts recruited by the International Warfarin Pharmacogenetics Consortium (n = 316) and the University of Alabama at Birmingham (n = 199). After the GWAS, we performed standard error-weighted meta-analyses and then conducted stepwise conditional analyses to account for known loci in chromosomes 10 and 16. The genome-wide significance threshold was set at P < 5 × 10-8. The meta-analysis, comprising 1504 participants, identified 242 significant SNPs across 3 genomic loci, with 99.6% of these located within known loci on chromosomes 10 (top SNP: rs58800757, P = 4.27 × 10-13) and 16 (top SNP: rs9925964, P = 9.97 × 10-16). Adjustment for the VKORC1 SNP -1639G>A revealed an additional locus on chromosome 2 (top SNPs rs116057875/rs115254730/rs115240773, P = 3.64 × 10-8), implicating the MALL gene, that could indirectly influence warfarin response through interactions with caveolin-1. In conclusion, we reaffirmed the importance of CYP2C9 and VKORC1 in influencing warfarin dose requirements, and identified a new locus (MALL), that still requires direct evidence of biological plausibility.

A Delphi study to guide the development of a clinical indicator tool for palliative care in South Africa.

BACKGROUND:  The South African National Policy Framework and Strategy on Palliative Care (NPFSPC) recommends that when integrating palliative care (PC) into the health system, a PC indicators tool should be used to guide clinicians to recognise a patient who should receive PC. The policy document recommends 'a simple screening tool developed for use in South Africa that would assist healthcare professionals (HCPs) to recognise patients who may have unmet palliative care needs'. AIM:  This research study sought to develop South African consensus on indicators for PC to assist clinicians to recognise a patient in need of PC. SETTING:  The South African healthcare setting. METHODS:  A Delphi study was considered suitable as a methodology to develop consensus. The methodology was based on the Conducting and REporting of DElphi studies (CREDES) guidance on Delphi studies to ensure rigour and transparency in conducting and reporting. Six different Delphi rounds were used to develop consensus. Each round allowed participants to anonymously rate statements with predefined rating scales. RESULTS:  Cognisant of the disparities in healthcare provision and access to equitable healthcare in South Africa, the expert advisory group recommended, especially for South Africa, that 'this tool is for deteriorating patients with an advanced life-limiting illness where all available and appropriate management for underlying illnesses and reversible complications has been offered'. The expert advisory group felt that disease-specific indicators should be described before the general indicators in the South African indicators tool, so all users of the tool orientate themselves to the disease categories first. This study included three new domains to address the South African context: trauma, infectious diseases and haematological diseases. General indicators for PC aligned with the original Supportive and Palliative Care Indicators Tool (SPICT) tool. CONCLUSION:  The Supportive and Palliative Care Indicators Tool for South Africa (SPICTTM-SA) is a simple screening tool for South Africa that may assist HCPs to recognise patients who may have unmet PC needs.

Stable warfarin dose prediction in sub-Saharan African patients: A machine-learning approach and external validation of a clinical dose-initiation algorithm.

Warfarin remains the most widely prescribed oral anticoagulant in sub-Saharan Africa. However, because of its narrow therapeutic index, dosing can be challenging. We have therefore (a) evaluated and compared the performance of 21 machine-learning techniques in predicting stable warfarin dose in sub-Saharan Black-African patients and (b) externally validated a previously developed Warfarin Anticoagulation in Patients in Sub-Saharan Africa (War-PATH) clinical dose-initiation algorithm. The development cohort included 364 patients recruited from eight outpatient clinics and hospital departments in Uganda and South Africa (June 2018-July 2019). Validation was conducted using an external validation cohort (270 patients recruited from August 2019 to March 2020 in 12 outpatient clinics and hospital departments). Based on the mean absolute error (MAE; mean of absolute differences between the actual and predicted doses), random forest regression (12.07 mg/week; 95% confidence interval [CI], 10.39-13.76) was the best performing machine-learning technique in the external validation cohort, whereas the worst performing technique was model trees (17.59 mg/week; 95% CI, 15.75-19.43). By comparison, the simple, commonly used regression technique (ordinary least squares) performed similarly to more complex supervised machine-learning techniques and achieved an MAE of 13.01 mg/week (95% CI, 11.45-14.58). In summary, we have demonstrated that simpler regression techniques perform similarly to more complex supervised machine-learning techniques. We have also externally validated our previously developed clinical dose-initiation algorithm, which is being prospectively tested for clinical utility.

A genome-wide association study of plasma concentrations of warfarin enantiomers and metabolites in sub-Saharan black-African patients.

Diversity in pharmacogenomic studies is poor, especially in relation to the inclusion of black African patients. Lack of funding and difficulties in recruitment, together with the requirement for large sample sizes because of the extensive genetic diversity in Africa, are amongst the factors which have hampered pharmacogenomic studies in Africa. Warfarin is widely used in sub-Saharan Africa, but as in other populations, dosing is highly variable due to genetic and non-genetic factors. In order to identify genetic factors determining warfarin response variability, we have conducted a genome-wide association study (GWAS) of plasma concentrations of warfarin enantiomers/metabolites in sub-Saharan black-Africans. This overcomes the issue of non-adherence and may have greater sensitivity at genome-wide level, to identify pharmacokinetic gene variants than focusing on mean weekly dose, the usual end-point used in previous studies. Participants recruited at 12 outpatient sites in Uganda and South Africa on stable warfarin dose were genotyped using the Illumina Infinium H3Africa Consortium Array v2. Imputation was conducted using the 1,000 Genomes Project phase III reference panel. Warfarin/metabolite plasma concentrations were determined by high-performance liquid chromatography with tandem mass spectrometry. Multivariable linear regression was undertaken, with adjustment made for five non-genetic covariates and ten principal components of genetic ancestry. After quality control procedures, 548 participants and 17,268,054 SNPs were retained. CYP2C9*8, CYP2C9*9, CYP2C9*11, and the CYP2C cluster SNP rs12777823 passed the Bonferroni-adjusted replication significance threshold (p < 3.21E-04) for warfarin/metabolite ratios. In an exploratory GWAS analysis, 373 unique SNPs in 13 genes, including CYP2C9*8, passed the Bonferroni-adjusted genome-wide significance threshold (p < 3.846E-9), with 325 (87%, all located on chromosome 10) SNPs being associated with the S-warfarin/R-warfarin outcome (top SNP rs11188082, CYP2C19 intron variant, p = 1.55E-17). Approximately 69% of these SNPs were in linkage disequilibrium (r 2 > 0.8) with CYP2C9*8 (n = 216) and rs12777823 (n = 8). Using a pharmacokinetic approach, we have shown that variants other than CYP2C9*2 and CYP2C9*3 are more important in sub-Saharan black-Africans, mainly due to the allele frequencies. In exploratory work, we conducted the first warfarin pharmacokinetics-related GWAS in sub-Saharan Africans and identified novel SNPs that will require external replication and functional characterization before they can be considered for inclusion in warfarin dosing algorithms.

Point-of-care HbA1c testing in an urban primary care diabetes clinic in South Africa: a mixed methods feasibility study.

INTRODUCTION: Monitoring and treatment of type 2 diabetes in South Africa usually takes place in primary care using random blood glucose testing to guide treatment decisions. This study explored the feasibility of using point-of-care haemoglobin A1c (HbA1c) testing in addition to glucose testing in a busy primary care clinic in Cape Town, South Africa. SUBJECTS: 185 adults aged 19-88 years with type 2 diabetes. MATERIALS AND METHODS: Participants recruited to this mixed methods cohort study received a point-of-care HbA1c test. Doctors were asked to use the point-of-care HbA1c result for clinical decision-making. Qualitative interviews were held with clinical staff. RESULTS: Point-of-care HbA1c test results were obtained for 165 participants of whom 109 (65%) had poor glycaemic control (>8% HbA1c, 64 mmol/mol). Medical officers reported using a combination of HbA1c and blood glucose 77% of the time for clinical decision-making. Nurses found the analyser easy to use and doctors valued having the HbA1c result to help with decision-making. DISCUSSION: Our results suggest that 30% of patients may have received inappropriate medication or not received necessary additional medication if random blood glucose alone had been used in routine appointments. Clinicians valued having access to the HbA1c test result to help them make treatment decisions.

Utility of digitising point of care HIV test results to accurately measure, and improve performance towards, the UNAIDS 90-90-90 targets.

INTRODUCTION: High rates of pre-treatment loss to care among persons diagnosed with HIV persist. Linkage to care can be improved through active digitally-based surveillance. Currently, record-keeping for HIV diagnoses in South Africa is paper-based. Aggregated testing data are reported routinely, and only discordant findings result in a specimen being tested at a laboratory and digitised. The Western Cape Province in South Africa has a Provincial Health Data Centre (PHDC) where person-level routine electronic data are consolidated in a single database, leveraging the existence of a unique patient identifier. To facilitate improved HIV surveillance, a pre-carbonated point-of-care test (PoCT) form was piloted, where one copy was routed to a central point and digitised for PHDC inclusion. METHODS: We evaluated the utility of the intervention using cross-sectional and retrospective cohort analyses, as well as comparisons with aggregate data. Data were linked to the Patient Master Index of the PHDC using unique identifiers. Prior evidences of HIV within the PHDC were used to differentiate newly diagnosed patients and those retesting, as well as linkage to care and treatment. RESULTS: From May 2017 to June 2018, 11337 digitised point-of-care HIV testing records were linked to the PHDC. Overall, 96% of records in the aggregate dataset were digitised, with 97% linked to the PHDC. Of those tested, 79% were female (median age 27 years). Linkage demonstrated that 51.3% (95% CI 48.4-54.1%) of patients testing HIV-positive were retesting. Of those newly diagnosed, 81% (95% CI 77.9-84.3%) were linked to HIV care and 25% (95% CI 21.6-28.7%) were initiated on antiretroviral therapy immediately. CONCLUSION: Digitisation of PoCT results provides individuated HIV testing data to assist in linkage to care and in differentiating newly diagnosed patients from positive patients retesting. Actionable and accurate data can improve the measurement of performance towards the UNAIDS 90-90-90 targets.

Thermal inactivation of Escherichia coli O157:H7 in cow manure compost.

Rates of inactivation of a five-strain mixture of green fluorescent protein-labeled Escherichia coli O157:H7 in autoclaved and unautoclaved commercial cow manure compost with a moisture content of ca. 38% were determined at temperatures of 50, 55, 60, 65, and 70 degrees C. Trypticase soy agar with ampicillin was determined to be the best medium for the enumeration of heat-injured and uninjured cells of green fluorescent protein-labeled E. coli O157:H7. The results obtained in this study revealed that in autoclaved compost, E. coli O157:H7 reductions of ca. 4 log CFU/g occurred within 8 h, 3 h, 15 min, 2 min, and < 1 min at 50, 55, 60, 65, and 70 degrees C, respectively. At 65 and 70 degrees C, considerably less time was required to kill the pathogen in unautoclaved compost than in autoclaved compost. Decimal reduction times (D-values) for autoclaved compost at 50, 55, 60, 65, and 70 degrees C were 137, 50.3, 4.1, 1.8, and 0.93 min, respectively, and D-values for unautoclaved compost at 50, 55, and 60 degrees C were 135, 35.4, and 3.9 min, respectively. Considerable tailing was observed for inactivation curves, especially at 60, 65, and 70 degrees C. These results are useful for identifying composting conditions that will reduce the risk of the transmission of E. coli O157:H7 to foods produced in the presence of animal fecal waste.

Fate of Escherichia coli O157:H7 during composting of bovine manure in a laboratory-scale bioreactor.

Inactivation profiles of Escherichia coli O157:H7 in inoculated bovine manure-based compost ingredients were determined by composting these ingredients in a bioreactor under controlled conditions. A 15-liter bioreactor was constructed to determine the fate of E. coli O157:H7 and changes in pH, moisture content, temperature, and aerobic mesophilic and thermophilic bacterial counts during composting. Fresh cow manure, wheat straw, cottonseed meal, and ammonium sulfate were combined to obtain a moisture content of ca. 60% and a carbon/nitrogen ratio of 29:1. The compost ingredients were held in the bioreactor at a constant external temperature of 21 or 50 degrees C. Self-heating of the ingredients due to microbial activity occurred during composting, with stratified temperatures occurring within the bioreactor. At an external temperature of 21 degrees C, self-heating occurred for 0 to 3 days, depending on the location within the bioreactor. E. coli O157:H7 populations increased by 1 to 2 log10 CFU/g during the initial 24 h of composting and decreased by ca. 3.5 log10 CFU/g near the bottom of the bioreactor and by ca. 2 log10 CFU/g near the middle and at the top during 36 days of composting. At an external temperature of 50 degrees C. E. coli O157:H7 was inactivated rapidly (by ca. 4.9 log10 CFU/g at the top of the bioreactor, by 4.0 log10 CFU/g near the middle, and by 5.9 log10 CFU/g near the bottom) within 24 h of composting. When inoculated at an initial level of ca. 10(7) CFU/g. E. coli O157:H7 survived for 7 days but not for 14 days at all three sampling locations, as indicated by either direct plating or enrichment culture. At the top of the bioreactor a relatively constant moisture content of 60% was maintained, whereas the moisture content near the bottom decreased steadily to 37 to 45% over 14 days of composting. The pH of the composting mixture decreased to ca. 6 within 1 to 3 days and subsequently increased to 8 to 9. Results obtained in this study indicate that large populations (10(4) to 10(7) CFU/g) of E coli O157:H7 survived for 36 days during composting in a bioreactor at an external temperature of 21 degrees C but were inactivated to undetectable levels after 7 to 14 days when the external temperature of the bioreactor was 50 degrees C. Hence, manure contaminated with large populations (e.g., 10(7) CFU/g) of E. coli O157:H7 should be composted for more than 1 week, and preferably for 2 weeks, when held at a minimum temperature of 50 degrees C.

Fate of Listeria monocytogenes in bovine manure-amended soil.

The survival and growth of Listeria monocytogenes in soil amended with bovine manure was studied under different environmental conditions of temperature, nutrients, and soil microflora. Autoclaved soil was compared with unautoclaved soil for assessing the influence of competitive soil microflora on the survival of L. monocytogenes. Initial L. monocytogenes cell numbers of 5 to 6 log CFU/g survived for up to 43, 43, and 14 days in manure-amended autoclaved soil at 5, 15, and 21 degrees C, respectively. In manure-amended unautoclaved soil, the pathogen was detectable for up to 43, 21, and 21 days at 5, 15, and 21 degrees C, respectively. L. monocytogenes was inactivated more rapidly in autoclaved soil amended with manure at a manure/soil ratio of 1:10 than in the more dilute (1:100) manure in soil samples at both 15 and 21 degrees C. However, in manure-amended unautoclaved soil, L. monocytogenes survived longer in samples with ratios of 1:10 than in the more dilute (1:100) manure-amended soil. The persistence of L. monocytogenes for several weeks in manure-amended soil suggests listeriae could be transmitted through soil to fresh produce or to shoes, clothing, and hands of field workers, especially during the cold months.

Fate of Escherichia coli O157:H7 in manure compost-amended soil and on carrots and onions grown in an environmentally controlled growth chamber.

Studies were done to determine the fate of Escherichia coli O157:H7 in manure compost-amended soil and on carrots and green onions grown in an environmentally controlled growth chamber. Commercial dairy cattle manure compost was inoculated with a five-strain mixture of green fluorescent protein-labeled E. coli O157:H7 at 10(7) CFU g(-1) and mixed with unsterilized Tifton sandy loam soil at a ratio of 1:5. Baby carrot or green onion seedlings were planted into the manure compost-amended soil in pots, and soil samples surrounding the plant, edible carrot roots and onion bulb samples, and soil immediately beneath the roots were assayed for E. coli O157:H7 in triplicate at weekly intervals for the first 4 weeks, and every 2 weeks for the remainder of the plant growth cycle (up to 3 months). E. coli O157:H7 cell numbers decreased within 64 days by 3 log CFU/g in soil and soil beneath the roots of green onions and by more than 2 log CFU/g on onions. E. coli O157:H7 survived better during the production of carrots, with a 2.3-log CFU/g reduction in soil and a 1.7-log CFU/g reduction on carrots within 84 days. These results indicate that the type of plant grown is an important factor influencing the survival of E. coli O157:H7 both on the vegetable and in the soil in which the vegetable is grown.

Fate of Escherichia coli O157:H7 in manure-amended soil.

Escherichia coli O157:H7 cells survived for up to 77, >226, and 231 days in manure-amended autoclaved soil held at 5, 15, and 21 degrees C, respectively. Pathogen populations declined more rapidly in manure-amended unautoclaved soil under the same conditions, likely due to antagonistic interactions with indigenous soil microorganisms. E. coli O157:H7 cells were inactivated more rapidly in both autoclaved and unautoclaved soils amended with manure at a ratio of 1 part manure to 10 parts soil at 15 and 21 degrees C than in soil samples containing dilute amounts of manure. The manure-to-soil ratio, soil temperature, and indigenous microorganisms of the soil appear to be contributory factors to the pathogen's survival in manure-amended soil.

Persistence of Salmonella enterica serovar typhimurium on lettuce and parsley and in soils on which they were grown in fields treated with contaminated manure composts or irrigation water.

There are many sources of pathogen contamination of vegetable crops in the field that include manure used as fertilizer and irrigation water. An avirulent strain of Salmonella enterica serovar Typhimurium was added to three different types of composts-PM-5 (poultry manure compost), 338 (dairy manure compost), and NVIRO-4 (alkaline stabilized dairy manure compost)-and irrigation water at 10(7) colony forming units (cfu)/g and 10(5) cfu/mL, respectively, to determine under field conditions the persistence of salmonellae in soils treated with these composts or irrigation water, and also on leaf lettuce and parsley grown on such treated soil. Contaminated compost was applied to soil in the field as a strip at a rate of 4.5 metric tons/hectare on the day before lettuce and parsley seedlings were transplanted. Contaminated irrigation water was applied only once on the plants at the rate of 2 liters per plot on the same day after the seedlings were transplanted. Twenty-five plots, each measuring 1.8 x 4.6 meters, were used for each crop, with five treatments (one without compost, three with each of the three composts, and one without compost but applied with contaminated water) and five replication plots for each treatment. Salmonella persisted for 161 and up to 231 days in soils amended with contaminated composts on which lettuce and parsley, respectively, were grown, and was detected for up to 63 days and 231 days on lettuce and parsley, respectively. The type of contaminated compost had minimal effect on the persistence of S. Typhimurium in soil. Occurrence of Salmonella on vegetables and survival in soil on which these vegetables were grown, irrespective of source of contamination through irrigation water or compost, were similar, suggesting both contaminated manure compost and irrigation water can play important roles in contaminating soil and vegetables with Salmonella for an extended period of time.

Fate of Salmonella enterica serovar Typhimurium on carrots and radishes grown in fields treated with contaminated manure composts or irrigation water.

Three different types of compost, PM-5 (poultry manure compost), 338 (dairy cattle manure compost), and NVIRO-4 (alkaline-pH-stabilized dairy cattle manure compost), and irrigation water were inoculated with an avirulent strain of Salmonella enterica serovar Typhimurium at 10(7) CFU g(-1) and 10(5) CFU ml(-1), respectively, to determine the persistence of salmonellae in soils containing these composts, in irrigation water, and also on carrots and radishes grown in these contaminated soils. A split-plot block design plan was used for each crop, with five treatments (one without compost, three with each of the three composts, and one without compost but with contaminated water applied) and five replicates for a total of 25 plots for each crop, with each plot measuring 1.8 x 4.6 m. Salmonellae persisted for an extended period of time, with the bacteria surviving in soil samples for 203 to 231 days, and were detected after seeds were sown for 84 and 203 days on radishes and carrots, respectively. Salmonella survival was greatest in soil amended with poultry compost and least in soil containing alkaline-pH-stabilized dairy cattle manure compost. Survival profiles of Salmonella on vegetables and soil samples contaminated by irrigation water were similar to those observed when contamination occurred through compost. Hence, both contaminated manure compost and irrigation water can play an important role in contaminating soil and root vegetables with salmonellae for several months.