Antenatal tobacco use and iron deficiency anemia: integrating tobacco control into antenatal care in urban India

Abstract Background In India, tobacco use during pregnancy is not routinely addressed during antenatal care. We measured the association between tobacco use and anemia in low-income pregnant women, and identified ways to integrate tobacco cessation into existing antenatal care at primary health centers. Methods We conducted an observational study using structured interviews with antenatal care clinic patients (n = 100) about tobacco use, anemia, and risk factors such as consumption of iron rich foods and food insecurity. We performed blood tests for serum cotinine, hemoglobin and ferritin. We conducted in-depth interviews with physicians (n = 5) and auxiliary nurse midwives (n = 5), and focus groups with community health workers (n = 65) to better understand tobacco and anemia control services offered during antenatal care. Results We found that 16% of patients used tobacco, 72% were anemic, 41% had iron deficiency anemia (IDA) and 29% were food insecure. Regression analysis showed that tobacco use (OR = 14.3; 95%CI = 2.6, 77.9) and consumption of green leafy vegetables (OR = 0.6; 95%CI = 0.4, 0.9) were independently associated with IDA, and tobacco use was not associated with consumption of iron-rich foods or household food insecurity. Clinics had a system for screening, treatment and follow-up care for anemic and iron-deficient antenatal patients, but not for tobacco use. Clinicians and community health workers were interested in integrating tobacco screening and cessation services with current maternal care services such as anemia control. Tobacco users wanted help to quit. Conclusion It would be worthwhile to assess the feasibility of integrating antenatal tobacco screening and cessation services with antenatal care services for anemia control, such as screening and guidance during clinic visits and cessation support during home visits.https://deepblue.lib.umich.edu/bitstream/2027.42/143514/1/12978_2018_Article_516.pd

Antenatal tobacco use and iron deficiency anemia: formative research to integrate tobacco cessation into antenatal care for low-income women in Mumbai, India

Background A formative study was conducted at governmental antenatal clinics serving low-income women in Mumbai, India to measure the association of tobacco use with iron deficiency anemia, consumption of iron-rich foods and household food insecurity; and to identify opportunities to integrate tobacco cessation services with existing antenatal care for iron deficiency and anemia control. Methods We administered a structured questionnaire to a sample of 100 pregnant patients at 5 governmental antenatal care clinics that serve low-income communities. Blood tests were done for serum cotinine, hemoglobin and ferritin. We also conducted 10 key informant interviews with physicians and auxiliary nurse midwives, and 5 focus group discussions with community health workers to better understand the services offered during antenatal clinic and home visits. Results Blood test revealed that 16%, 72% and 41% of women used tobacco, were anemic and had iron deficiency anemia (IDA), respectively. Tobacco use was independently associated with IDA (OR=14.3; 95%CI=2.6, 77.9). Tobacco use and IDA were not associated with household food insecurity. Clinics had a system for screening and follow-up care for anemia and iron-deficiency, but not for tobacco use. Antenatal care providers were interested in including services to screen for tobacco use and provide cessation guidance. Patients wanted help to quit. Conclusions It may be worthwhile to assess the feasibility of integrating tobacco use screening and cessation services with antenatal services for anemia and iron deficiency at governmental clinics serving low-income populations in India

Identification of optimum sequencing depth especially for de novo genome assembly of small genomes using next generation sequencing data.

Next Generation Sequencing (NGS) is a disruptive technology that has found widespread acceptance in the life sciences research community. The high throughput and low cost of sequencing has encouraged researchers to undertake ambitious genomic projects, especially in de novo genome sequencing. Currently, NGS systems generate sequence data as short reads and de novo genome assembly using these short reads is computationally very intensive. Due to lower cost of sequencing and higher throughput, NGS systems now provide the ability to sequence genomes at high depth. However, currently no report is available highlighting the impact of high sequence depth on genome assembly using real data sets and multiple assembly algorithms. Recently, some studies have evaluated the impact of sequence coverage, error rate and average read length on genome assembly using multiple assembly algorithms, however, these evaluations were performed using simulated datasets. One limitation of using simulated datasets is that variables such as error rates, read length and coverage which are known to impact genome assembly are carefully controlled. Hence, this study was undertaken to identify the minimum depth of sequencing required for de novo assembly for different sized genomes using graph based assembly algorithms and real datasets. Illumina reads for E.coli (4.6 MB) S.kudriavzevii (11.18 MB) and C.elegans (100 MB) were assembled using SOAPdenovo, Velvet, ABySS, Meraculous and IDBA-UD. Our analysis shows that 50X is the optimum read depth for assembling these genomes using all assemblers except Meraculous which requires 100X read depth. Moreover, our analysis shows that de novo assembly from 50X read data requires only 6-40 GB RAM depending on the genome size and assembly algorithm used. We believe that this information can be extremely valuable for researchers in designing experiments and multiplexing which will enable optimum utilization of sequencing as well as analysis resources

N50 value for the genomes assembled by Velvet, SOAPdenovo, ABySS, Meraculous and IDBA-UD.

<p><b>A</b>) N50 for assembled <i>E.coli</i> genome: N50 is the length of the smallest contig which when added to a set of larger contigs yields at least 50% of the genome. The N50 values for IDBA-UD, Velvet and SOAPdenovo seemed to reach a plateau at 35X, ABySS at 50X depth of coverage. On the other hand, the N50 value of Meraculous generated assembly increased till 150X depth of coverage. <b>B</b>) N50 for assembled <i>S.kudriavzevii</i> genome: IDBA-UD and SOAPdenovo attained peak N50 value at 35X and 100X depth of coverage respectively, whereas the N50 value of Velvet, ABySS and Meraculous generated assembly increased till 150X depth of coverage. <b>C</b>) N50 for assembled <i>C.elegans</i> genome: SOAPdenovo, ABySS and IDBA-UD reached peak N50 value at 100X depth of coverage, whereas the N50 value of Velvet generated assembly increased approximately 1.5 fold until 150X with no change thereafter. Velvet generated assembly had the best N50 values of all the 4 assemblers.</p

Assembly metrics for <i>S.kudriavzevii</i> genome assembled from Illumina paired end data with Velvet, SOAPdenovo, ABySS, Meraculous and IDBA-UD.

<p>The size of the assembled genome we used ZP_591 as reference is 11201698 bases.</p

Assembly metrics for <i>E.coli</i> genome assembled from Illumina paired end data with Velvet, SOAPdenovo, ABySS, Meraculous and IDBA-UD.

<p>The expected genome size for <i>E.coli</i> MG1655 is 4639675 bases.</p

Memory requirement for genome assembly.

<p>Memory required to assemble <i>E.coli</i> (<b>A</b>), <i>S.kudriavzevii</i> (<b>B</b>) and <i>C.elegans</i> (<b>C</b>) genomes increased, although not proportionately, with increasing depth of sequencing.</p