Evaluating the cost implications of integrating SARS-CoV-2 genome sequencing for infection prevention and control investigation of nosocomial transmission within hospitals

BACKGROUND

The COG-UK hospital-onset COVID-19 infection (HOCI) trial evaluated the impact of SARS-CoV-2 whole-genome sequencing (WGS) on acute infection, prevention, and control (IPC) investigation of nosocomial transmission within hospitals.

AIM

To estimate the cost implications of using the information from the sequencing reporting tool (SRT), used to determine likelihood of nosocomial infection in IPC practice.

METHODS

A micro-costing approach for SARS-CoV-2 WGS was conducted. Data on IPC management resource use and costs were collected from interviews with IPC teams from 14 participating sites and used to assign cost estimates for IPC activities as collected in the trial. Activities included IPC-specific actions following a suspicion of healthcare-associated infection (HAI) or outbreak, as well as changes to practice following the return of data via SRT.

FINDINGS

The mean per-sample costs of SARS-CoV-2 sequencing were estimated at £77.10 for rapid and £66.94 for longer turnaround phases. Over the three-month interventional phases, the total management costs of IPC-defined HAIs and outbreak events across the sites were estimated at £225,070 and £416,447, respectively. The main cost drivers were bed-days lost due to ward closures because of outbreaks, followed by outbreak meetings and bed-days lost due to cohorting contacts. Actioning SRTs, the cost of HAIs increased by £5,178 due to unidentified cases and the cost of outbreaks decreased by £11,246 as SRTs excluded hospital outbreaks.

CONCLUSION

Although SARS-CoV-2 WGS adds to the total IPC management cost, additional information provided could balance out the additional cost, depending on identified design improvements and effective deployment.

A multicenter prospective hospital-based surveillance to estimate the burden of rotavirus gastroenteritis in children less than five years of age in India

BACKGROUND

Rotavirus is the leading cause of severe, dehydrating diarrhea in children aged <5 years globally, with an estimated 25 million outpatient visits and 2 million hospitalizations attributable to rotavirus infections each year. The aim of this hospital-based surveillance was to summarize the local epidemiological and virological features of rotavirus and to estimate the disease burden in the population under surveillance in India.

METHODS

During the 16 months surveillance period from April 2011 through July 2012, a total of 4711 children under the age of 5 years were admitted with acute diarrhea at 12 medical centers attached to medical schools throughout India. Stool samples were randomly collected from 2051 (43.5%) subjects and were analyzed for rotavirus positivity using commercial enzyme immunoassay kit (Premier Rotaclone Qualitative Elisa) at the respective study centers. Rotavirus positive samples were genotyped for VP7 and VP4 by reverse-transcription polymerase chain reaction (RT-PCR) at a central laboratory.

RESULTS

During the study period, maximum number of rotavirus related hospitalizations were reported from December 2011 through February 2012. Out of the 2051 stool samples tested for rotavirus, overall 541 (26.4%) samples were positive for rotavirus VP6 antigen in stool. The highest positivity was observed in the month of December, 2011 (52.5%) and lowest in the month of May, 2011 (10.3%). We found that majority of the rotavirus positive cases (69.7%) were in children <24 months of age. The most common genotypes reported were G1 (38%), G2 (18%), G9 (18%), G12 (9%) and mixed strains (17%).

CONCLUSIONS

The results of this study confirm the significant burden of acute rotavirus gastroenteritis as a cause of hospitalizations in under five children in India.

Retrospective surveillance for intussusception in children aged less than five years at two tertiary care centers in India

BACKGROUND

A rotavirus vaccine could soon become part of India's national immunization program. However the occurrence of intussusception due to rotavirus vaccine is a potential safety concern. This surveillance aimed at the collection of baseline data on childhood intussusception which would facilitate the monitoring of intussusception cases after the introduction of rotavirus vaccines.

METHODS

We retrospectively reviewed medical records of confirmed intussusception cases in children under the age of five, treated during 2007-2012 at two tertiary care hospitals attached to medical schools in India. Demographic, clinical, diagnostic and treatment practices data were obtained from hospital records.

RESULTS

Over a five to six year observation period, we identified 187 confirmed cases of intussusception, of which 75% were males. The median age of intussusception was 8 months, and we observed a possible trend in the distribution of cases with the highest number of cases being reported in the month of April and lowest in the month of October. The most common diagnostic methods used were ultrasonography and abdominal radiography with most cases being treated surgically (71%). The median length of hospital stay was 8 days (range 1-40) and mean was 10.2 days. Records of any fatality due to intussusception were not found during the review of the records.

CONCLUSIONS

This analysis provides an estimate of the baseline data of childhood intussusception prior to the introduction of the rotavirus vaccination as a part of routine immunization in India. A prospective surveillance system using a standardized case definition is needed in order to better examine the incidence of intussusception in developing countries.

Relation between plasma leptin and anthropometric and metabolic covariates in lean and obese diabetic and hyperlipidaemic Asian Northern Indian subjects

This study investigated the relationship of plasma leptin to obesity, diabetes and hyperlipidaemia in Asian Northern Indian subjects, considered to have a predisposition to abdominal obesity and metabolic syndrome. A total of 72 subjects, subcategorised into lean and obese healthy subjects, lean and obese Type 2 diabetic and lean and obese non-diabetic hyperlipidaemic subjects were recruited. High leptin values were observed in all obese groups, and obese diabetic patients showed the highest levels. In lean and obese diabetic subjects, plasma leptin did not show any correlation to any index of glycaemia. When all lean and all obese subjects were analysed in two separate groups, body mass index (BMI), percent total body fat, and body density significantly correlated with the plasma leptin levels (p<0.05). Leptin values, when correlated to all variables in all patients taken together, showed the greatest magnitude of correlation with BMI (r=0.64), percent total body fat (r=0.67), and waist circumference (r=0.51). Strong inverse correlation was seen with body density (r=-0.67). Levels of serum insulin did not show any correlation with leptin levels in all subjects combined, and separately in various groups. Multiple linear regression analysis performed in obese, non-diabetic and normolipidaemic subjects, all Type 2 diabetic and all non-diabetic hyperlipidaemic subjects separately showed that percent total body fat is the only significant predictor of plasma leptin concentration in all the 3 groups. The present study suggests that plasma leptin has a strong positive correlation with percent total body fat in Asian Northern Indian subjects. Among other components of metabolic syndrome, only abdominal obesity is weakly correlated to serum leptin levels.

Assessment Of Nutritive Value In Milled Rice Grain Of Some Indian Rice Landraces And Their Molecular Characterization

The study was aimed at the evaluation of nutritive values in terms of total protein and some essential amino acid content of a set of 258 diverse rice landraces maintained in the Germplasm Section of Indira Gandhi Agricultural University at Raipur, Chhattisgarh. Protein content of milled grains ranged from 4.91% to 12.08% with the mean of 6.63%. Similarly wide variation was recorded in lysine content which varied from 1.73 to 7.13 g/l6g N, the mean being 4.62 g/I6g N. Grain protein and lysine levels varied two to three folds. Variation for lysine content (CV 23.68%) was higher than that of protein content (CV 12.45%). This clearly indicated the existence of wide genetic variability for protein and lysine contents in rice. Two sets of ten elite lines each containing high levels of protein and lysine were further analyzed separately for another essential amino acid tryptophan. In the set with high protein, the tryptophan levels varied from 0.36-0.88 g/16 g N, the mean being 0.642 g/l6 g N. Among the landraces containing high levels of lysine, the tryptophan content ranged from 0.256 to 0.86 g/16 g N, the average being 0.514. A positive correlation of tryptophan with lysine content (r = 0.076) and a strong negative correlation with total protein content (r = - 0.923) were recorded. Donor lines for breeding rice varieties with optimum protein quality were identified as potential donor parents for genetic improvement of rice for nutritious grains. Fourteen SSR primer sets were used to investigate the level of polymorphism among the ten elite landraces of extra early maturity group. The estimated similarity ranged from 20.18 to 69.00% reflecting much variation at the DNA level. Keywords: Milled rice grain; protein; lysine; tryptophan; nutritive value of rice. DOI: http://dx.doi.org/10.3329/bjar.v36i3.9265 BJAR 2011; 36(3): 369-380