Clinical features, antimicrobial susceptibility patterns and genomics of bacteria causing neonatal sepsis in a children's hospital in Vietnam: protocol for a prospective observational study.

INTRODUCTION: The clinical syndrome of neonatal sepsis, comprising signs of infection, septic shock and organ dysfunction in infants ≤4 weeks of age, is a frequent sequel to bloodstream infection and mandates urgent antimicrobial therapy. Bacterial characterisation and antimicrobial susceptibility testing is vital for ensuring appropriate therapy, as high rates of antimicrobial resistance (AMR), especially in low-income and middle-income countries, may adversely affect outcome. Ho Chi Minh City (HCMC) in Vietnam is a rapidly expanding city in Southeast Asia with a current population of almost 8 million. There are limited contemporary data on the causes of neonatal sepsis in Vietnam, and we hypothesise that the emergence of multidrug resistant bacteria is an increasing problem for the appropriate management of sepsis cases. In this study, we aim to investigate the major causes of neonatal sepsis and assess disease outcomes by clinical features, antimicrobial susceptibility profiles and genome composition. METHOD AND ANALYSIS: We will conduct a prospective observational study to characterise the clinical and microbiological features of neonatal sepsis in a major children's hospital in HCMC. All bacteria isolated from blood subjected to whole genome sequencing. We will compare clinical variables and outcomes between different bacterial species, genome composition and AMR gene content. AMR gene content will be assessed and stratified by species, years and contributing hospital departments. Genome sequences will be analysed to investigate phylogenetic relationships. ETHICS AND DISSEMINATION: The study will be conducted in accordance with the principles of the Declaration of Helsinki and the International Council on Harmonization Guidelines for Good Clinical Practice. Ethics approval has been provided by the Oxford Tropical Research Ethics Committee 35-16 and Vietnam Children's Hospital 1 Ethics Committee 73/GCN/BVND1. The findings will be disseminated at international conferences and peer-reviewed journals. TRIAL REGISTRATION NUMBER: ISRCTN69124914; Pre-results

Tillage and water management for riceland productivity in acid sulfate soils of the Mekong delta, Vietnam.

Acid sulfate soils are characterized by low pH and high concentrations of aluminum, sulfate, iron and hydrogen sulfide. Removal of at least part of these substances is a prerequisite for land use, at least in severely acid soils. In this study, the effectiveness of harrowing and flushing with surface water for the removal of toxic substances from the topsoil of acid sulfate soils (ASS) with different toxicity levels was investigated. During the flood recession period, at three experimental sites ranging from slightly, to moderately to strongly acid, two flushing treatments (once or three times, denoted as F1 and F3, respectively) combined with two harrowing treatments (also once or three times, denoted as H1 and H3, respectively) were applied. Soils were classified as very fine Typic Sulfaquepts. At all three sites, when F1 was practiced, H3 did not have a significantly lower soluble aluminum concentration compared with H1. In slightly ASS, the differences between H1 and H3 and between F1 and F3 were not significant. Under moderately acid conditions, the soluble aluminum concentration after H3 was not significantly different from after H1, but it was significantly lower after F3 compared with F1. In severe ASS, H3 combined with F3 gave a significantly lower soluble aluminum concentration compared with F3H1. In addition to soluble Al, Al at the exchange complex was also investigated. The combinations of flushing and harrowing did not significantly change Al at the exchange complex. The F3H3 treatment resulted in a significantly greater rice yield compared with other treatments (F3H1, F1H3 and F1H1). In order to minimize the contamination of surface water, the flood recession period is the optimal time for flushing aluminum out of ASS

Aluminum-contaminant transport by surface runoff and bypass flow from an acid sulphate soil

Quantifying the process and the amount of acid-contaminant released to the surroundings is important in assessing the environmental hazards associated with reclaiming acid sulphate soils (ASS). The roles of surface runoff and bypass flow (i.e. the rapid downward flow of free water along macropores through an unsaturated soil matrix) in transporting aluminum from three types of raised beds (soil ridges formed by piling up soil materials excavated from adjacent ditches) were studied in a Typic Sulfaquept in Can Tho, Vietnam. During the month of April, 1 h cumulative infiltration of the low raised beds (made only of the topsoil materials) and high raised beds (made of topsoil and jarositic layers) was significantly higher than that of the traditional raised beds (made of topsoil, jarositic and pyritic materials). As the rainfall season progressed, infiltration in July decreased four to seven-fold from the initial values in April, resulting in an increase in runoff. Due to surface crusting, the traditional raised beds yielded the highest runoff (110 versus 50–60 mm in the other types in July). Aluminum concentrations in the bypass flow (6–22 mmol l-1) associated with each of the three bed types were higher than in the runoff (3–14 mmol l-1). In low and high raised beds, the amounts of aluminum transported by bypass flow (15–16 kmol ha-1) was higher than in the runoff (4–6.5 kmol ha-1), while in the traditional type, the two components were similar (11–12 kmol ha-1). The total amount of aluminum released from the low raised beds was lowest. Low raised beds thus pose less environmental hazards to the surroundings compared to the other two types. Interventions that affect the amount of aluminum transport in runoff and in bypass flow are important in balancing agricultural production and environmental protection in ASS area

Aluminum-contaminant transport by surface runoff and bypass flow from an acid sulphate soil

Quantifying the process and the amount of acid-contaminant released to the surroundings is important in assessing the environmental hazards associated with reclaiming acid sulphate soils (ASS). The roles of surface runoff and bypass flow (i.e. the rapid downward flow of free water along macropores through an unsaturated soil matrix) in transporting aluminum from three types of raised beds (soil ridges formed by piling up soil materials excavated from adjacent ditches) were studied in a Typic Sulfaquept in Can Tho, Vietnam. During the month of April, 1 h cumulative infiltration of the low raised beds (made only of the topsoil materials) and high raised beds (made of topsoil and jarositic layers) was significantly higher than that of the traditional raised beds (made of topsoil, jarositic and pyritic materials). As the rainfall season progressed, infiltration in July decreased four to seven-fold from the initial values in April, resulting in an increase in runoff. Due to surface crusting, the traditional raised beds yielded the highest runoff (110 versus 50–60 mm in the other types in July). Aluminum concentrations in the bypass flow (6–22 mmol l-1) associated with each of the three bed types were higher than in the runoff (3–14 mmol l-1). In low and high raised beds, the amounts of aluminum transported by bypass flow (15–16 kmol ha-1) was higher than in the runoff (4–6.5 kmol ha-1), while in the traditional type, the two components were similar (11–12 kmol ha-1). The total amount of aluminum released from the low raised beds was lowest. Low raised beds thus pose less environmental hazards to the surroundings compared to the other two types. Interventions that affect the amount of aluminum transport in runoff and in bypass flow are important in balancing agricultural production and environmental protection in ASS area

Tillage and water management for riceland productivity in acid sulfate soils of the Mekong delta, Vietnam.

Acid sulfate soils are characterized by low pH and high concentrations of aluminum, sulfate, iron and hydrogen sulfide. Removal of at least part of these substances is a prerequisite for land use, at least in severely acid soils. In this study, the effectiveness of harrowing and flushing with surface water for the removal of toxic substances from the topsoil of acid sulfate soils (ASS) with different toxicity levels was investigated. During the flood recession period, at three experimental sites ranging from slightly, to moderately to strongly acid, two flushing treatments (once or three times, denoted as F1 and F3, respectively) combined with two harrowing treatments (also once or three times, denoted as H1 and H3, respectively) were applied. Soils were classified as very fine Typic Sulfaquepts. At all three sites, when F1 was practiced, H3 did not have a significantly lower soluble aluminum concentration compared with H1. In slightly ASS, the differences between H1 and H3 and between F1 and F3 were not significant. Under moderately acid conditions, the soluble aluminum concentration after H3 was not significantly different from after H1, but it was significantly lower after F3 compared with F1. In severe ASS, H3 combined with F3 gave a significantly lower soluble aluminum concentration compared with F3H1. In addition to soluble Al, Al at the exchange complex was also investigated. The combinations of flushing and harrowing did not significantly change Al at the exchange complex. The F3H3 treatment resulted in a significantly greater rice yield compared with other treatments (F3H1, F1H3 and F1H1). In order to minimize the contamination of surface water, the flood recession period is the optimal time for flushing aluminum out of ASS

Bypass flow and its role in leaching of raised beds under different land use types on an acid sulphate soil.

A better understanding of leaching processes in raised beds is useful in assessing management options for acid sulphate soils. Field and laboratory studies were carried out to quantify the effects of soil physical properties and bypass flow on leaching processes of new, 1-year-old and 2-year-old raised beds for yam and pineapple cultivation in a Typic Sulfaquept in Tien Giang, Vietnam. The methylene blue staining technique was used to characterize the water-conducting pores in terms of number, stained area, and total pore perimeter at 10 cm depth intervals of six 1 x 1 m subplots. Undisturbed 20 cm x 25 cm soil cores taken from the raised beds were subjected to three 30 mm h-1 rains. Volume, aluminum and sulphate concentration of the outflows were monitored. Consolidation with time decreased the area and perimeter of water-conducting pores in 2-year-old pineapple beds to about a third, and bypass flow rate to about 80% of those in newly constructed beds. Consolidation did not affect macropore network geometry in yam beds because they were subjected to annual tillage and yam tubers were uprooted regularly. Al3 and SO4/2- concentrations in the outflows of the newly constructed and 1-year-old raised beds were higher in pineapple, while those in 2-year raised beds were higher in ya