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51.
Lulette Tricia C. Bravo Marion J. Tuohy Concepcion Ang Raul V. Destura Myrna Mendoza Gary W. Procop Steven M. Gordon Geraldine S. Hall Nabin K. Shrestha 《Journal of clinical microbiology》2009,47(12):3985-3990
After isoniazid and rifampin (rifampicin), the next pivotal drug class in Mycobacterium tuberculosis treatment is the fluoroquinolone class. Mutations in resistance-determining regions (RDR) of the rpoB, katG, and gyrA genes occur with frequencies of 97%, 50%, and 85% among M. tuberculosis isolates resistant to rifampin, isoniazid, and fluoroquinolones, respectively. Sequences are highly conserved, and certain mutations correlate well with phenotypic resistance. We developed a pyrosequencing assay to determine M. tuberculosis genotypic resistance to rifampin, isoniazid, and fluoroquinolones. We characterized 102 M. tuberculosis clinical isolates from the Philippines for susceptibility to rifampin, isoniazid, and ofloxacin by using the conventional submerged-disk proportion method and validated our pyrosequencing assay using these isolates. DNA was extracted and amplified by using PCR primers directed toward the RDR of the rpoB, katG, and gyrA genes, and pyrosequencing was performed on the extracts. The M. tuberculosis H37Rv strain (ATCC 25618) was used as the reference strain. The sensitivities and specificities of pyrosequencing were 96.7% and 97.3%, 63.8% and 100%, and 70.0% and 100% for the detection of resistance to rifampin, isoniazid, and ofloxacin, respectively. Pyrosequencing is thus a rapid and accurate method for detecting M. tuberculosis resistance to these three drugs.Rifampin (rifampicin), isoniazid, and the fluoroquinolones are the most important initial drug markers for extensively drug-resistant Mycobacterium tuberculosis strains, defined as multidrug-resistant (MDR) isolates (resistant to both isoniazid and rifampin) with additional resistance to a fluoroquinolone and to one of the injectable drugs (2). The fluoroquinolones have become an essential part of treatment regimens for MDR tuberculosis (7, 25). Due to their potency and safety, the new-generation fluoroquinolones are now even being evaluated as first-line medications for tuberculosis (3, 13, 20). Wang et al. further suggested that routine fluoroquinolone resistance testing may have a clinical impact by showing a significant correlation between development of fluoroquinolone and first-line M. tuberculosis drug resistance in an area in which resistant strains are highly endemic (28).The spontaneous acquisition of DNA sequence mutations is the primary genetic basis for the development of M. tuberculosis drug resistance (14). Since sequences are highly conserved, certain mutations correlate well with phenotypic resistance, and a limited number of mutations account for the majority of phenotypic resistance to the important antituberculosis medications, various methods of genotypic testing have successfully been used for the rapid detection of M. tuberculosis resistance (16, 22). The sites that most frequently contain mutations associated with phenotypic resistance, called resistance-determining regions (RDR), differ depending on the drug tested. Among rifampin-resistant isolates worldwide, 95 to 97% harbor mutations in the rifampin RDR, an 81-bp target encompassing codons 507 to 533 of the 3,519-bp rpoB gene (17). Isoniazid resistance has a more complex mechanism, involving several gene targets, the most important of which is codon 315 of the 2,223-bp katG gene, in which mutations are found in up to 50% of resistant isolates (18). Likewise, M. tuberculosis has a quinolone RDR which spans codons 88 to 94 of the 2,517-bp gyrA gene. Mutations in this region, particularly in codon 88, 90, 91, or 94, correlate with high-level resistance and are seen in 42 to 85% of resistant clinical isolates (6).Pyrosequencing, a method of DNA sequencing by synthesis, has been applied to the rapid detection of M. tuberculosis resistance to rifampin, isoniazid, and ethambutol (9, 29). Its main advantage is a much shorter turnaround time than that of conventional drug susceptibility testing, the latter taking 2 to 4 weeks from the time an isolate is obtained in pure culture.After isoniazid and rifampin, the next pivotal drug class in M. tuberculosis treatment is the fluoroquinolone class, as previously discussed (3, 7, 13, 20, 25, 28). Given that most resistance to the latter is determined by mutations that are generally limited to the quinolone RDR of the gyrA gene, it should be feasible and clinically more relevant to develop an assay for rapid resistance testing which includes fluoroquinolone resistance in addition to rifampin and isoniazid resistance.We developed a pyrosequencing assay to determine M. tuberculosis genotypic resistance to rifampin, isoniazid, and fluoroquinolones, which we validated against the conventional submerged-disk proportion method. We also improved on the previously reported pyrosequencing assay by reducing the number of primers required to sequence for rifampin resistance (9). 相似文献
52.
Chloe Andrews Robin Shrestha Shibani Ghosh Katherine Appel Sabi Gurung Lynne M. Ausman Elizabeth Marino Costello Patrick Webb 《Maternal & child nutrition》2022,18(1):e13287
In rural Bangladesh, intake of nutrient-rich foods, such as animal source foods (ASFs), is generally suboptimal. Diets low in nutrients and lacking in diversity put women of reproductive age (WRA) at risk of malnutrition as well as adverse birth outcomes. The objective of this study was to assess the relationship between maternal dietary diversity, consumption of specific food groups and markers of nutritional status, including underweight [body mass index (BMI) < 18.5 kg/m2], overweight (BMI ≥ 23 kg/m2) and anaemia (haemoglobin < 120 g/dl) among WRA in Bangladesh. This analysis used data from the third round of a longitudinal observational study, collected from February through May of 2017. Dietary data were collected with a questionnaire, and Women's Dietary Diversity Score (WDDS) was calculated. Associations between WDDS, food group consumption and markers of nutritional status were assessed with separate adjusted logistic regression models. Among WRA, the prevalence of underweight, overweight and anaemia was 13.38%, 40.94% and 39.99%, respectively. Women who consumed dark green leafy vegetables (DGLV) or eggs were less likely to be anaemic or underweight, respectively, and women who consumed ASFs, particularly fish, were less likely to be underweight compared with women who did not consume these foods. WDDS did not show any consistent relationship with WRA outcomes. Interventions that focus on promoting optimal nutritional status among WRA in Bangladesh should emphasise increasing consumption of specific nutrient-rich foods, including ASFs, DGLV and eggs, rather than solely focusing on improving diet diversity in general. 相似文献
53.
Stewart CP Katz J Khatry SK LeClerq SC Shrestha SR West KP Christian P 《Maternal & child nutrition》2007,3(3):174-185
Pregnancy during adolescence is associated with adverse birth outcomes, including preterm delivery and low birthweight. The nutrient availability to the fetus may be limited if the mother is still growing. This research aims to study the effects of pregnancy during adolescence in a nutritionally poor environment in rural Nepal. This study utilized data from a randomized controlled trial of micronutrient supplementation during pregnancy in south-eastern Nepal. Women of parity 0 or 1 and of age 相似文献
54.
Daum LT Canas LC Klimov AI Shaw MW Gibbons RV Shrestha SK Myint KS Acharya RP Rimal N Reese F Niemeyer DM Arulanandam BP Chambers JP 《Archives of virology》2006,151(9):1863-1874
Summary. Currently circulating influenza B viruses can be divided into two antigenically and genetically distinct lineages referred
to by their respective prototype strains, B/Yamagata/16/88 and B/Victoria/2/87, based on amino acid differences in the hemagglutinin
surface glycoprotein. During May and July 2005, clinical specimens from two early season influenza B outbreaks in Arizona
and southeastern Nepal were subjected to antigenic (hemagglutinin inhibition) and nucleotide sequence analysis of hemagglutinin
(HA1), neuraminidase (NA), and NB genes. All isolates exhibited little reactivity with the B/Shanghai/361/2002 (B/Yamagata-like)
vaccine strain and significantly reduced reactivity with the previous 2003/04 B/Hong Kong/330/2001 (B/Victoria-like) vaccine
strain. The majority of isolates were antigenically similar to B/Hawaii/33/2004, a B/Victoria-like reference strain. Sequence
analysis indicated that 33 of 34 isolates contained B/Victoria-like HA and B/Yamagata-like NA and NB proteins. Thus, these
outbreak isolates are both antigenically and genetically distinct from the current Northern Hemisphere vaccine virus strain
as well as the previous 2003–04 B/Hong Kong/330/2001 (B/Victoria lineage) vaccine virus strain but are genetically similar
to B/Malaysia/2506/2004, the vaccine strain proposed for the coming seasons in the Northern and Southern Hemispheres. Since
these influenza B outbreaks occurred in two very distant geographical locations, these viruses may continue to circulate during
the 2006 season, underscoring the importance of rapid molecular monitoring of HA, NA and NB for drift and reassortment. 相似文献
55.
High prevalence of hepatitis B virus pre-s mutant in countries where it is endemic and its relationship with genotype and chronicity 总被引:7,自引:0,他引:7 下载免费PDF全文
Huy TT Ushijima H Win KM Luengrojanakul P Shrestha PK Zhong ZH Smirnov AV Taltavull TC Sata T Abe K 《Journal of clinical microbiology》2003,41(12):5449-5455
It has been reported that hepatitis B virus (HBV) mutants carrying mutations in the pre-S region can be found in infected patients. In this study, we investigated the prevalence of the HBV variant with the pre-S mutant in different geographic regions, including countries with low and high levels of endemic HBV infection, and analyzed the correlation with clinical findings. We examined 387 HBV DNA-positive serum samples from individuals among 12 countries, consisting of Vietnam, Myanmar, Thailand, China, Korea, Nepal, Japan, Russia, Spain, United States, Bolivia, and Ghana. HBV pre-S mutants were detected in 71 (18.3%) of 387 serum samples tested. This mutant was the most prevalent in Vietnam (36%), followed by Nepal (27.3%), Myanmar (23.3%), China (22.4%), Korea (14.3%), Thailand (10.5%), Japan (7.7%), and Ghana (4.3%). In contrast, no case with this mutation was found in Russia, Spain, United States, and Bolivia. Among the HBV deletion mutations, 15.5% (11 of 71) occurred in the pre-S1 and 46.5% (33 of 71) in the pre-S2 regions. Eight (11.3%) cases had a mutation in both the pre-S1 and pre-S2 regions. In addition, a point mutation at the pre-S2 starting codon was observed in 19 (26.7%) cases. The detection rate of the HBV mutant in patients with hepatocellular carcinoma was significantly higher than in other patients (P < 0.05). Furthermore, these mutants were found more frequently in genotype B (25%) and genotype C (24.5%) than in the other genotypes (P < 0.05). Our results indicated that there was a high prevalence of HBV pre-S mutation in regions of endemic HBV infection in Asia. Furthermore, the pre-S mutation appeared to be correlated with hepatocellular carcinoma and HBV genotypes. 相似文献
56.
Martagon-Villamil J Shrestha N Sholtis M Isada CM Hall GS Bryne T Lodge BA Reller LB Procop GW 《Journal of clinical microbiology》2003,41(3):1295-1298
We designed and tested a real-time LightCycler PCR assay for Histoplasma capsulatum that correctly identified the 34 H. capsulatum isolates in a battery of 107 fungal isolates tested and also detected H. capsulatum in clinical specimens from three patients that were culture positive for this organism. 相似文献
57.
Shrestha SM Shrestha S Tsuda F Nishizawa T Gotanda Y Takeda N Okamoto H 《Journal of medical virology》2003,69(2):207-214
One hundred fifty-four consecutive patients with sporadic acute hepatitis, who were seen at a city hospital in the Kathmandu valley of Nepal in 1997, were studied. IgM antibodies to hepatitis A virus were detected in four patients (3%), IgM antibodies to hepatitis B core in four patients (3%), hepatitis B surface antigen in 20 (13%), and hepatitis C virus RNA in four patients (3%). IgM antibodies to hepatitis E virus (HEV) (anti-HEV IgM) and HEV RNA were detected in 77 (50%) and 48 (31%), respectively. Consequently, 86 patients (56%) including nine HEV-viremic patients without anti-HEV IgM, were diagnosed with hepatitis E. The cause of hepatitis was not known in 53 patients (34%). All 48 HEV RNA-positive samples were genotyped as 1, and subtyped further as 1a in 17 (35%), 1c in 29 (60%), and mixed infection of 1a and 1c in 2 (4%). A seasonal difference in the prevalence of HEV subtypes was recognized. Before the rainy season (January to July), both 1a and 1c isolates were found: the intrasubtypic difference was up to 9.0% and 1.7%, respectively, in the 412-nucleotide sequence of open reading frame 2. During the rainy season (August), only 1c isolates (n = 17) with 99.5-100% identity were found; 13 of 17 isolates had the same sequence, being identical to the 3 isolates that emerged at the end of July. These results suggest that a particular HEV 1c strain spread widely during the rainy season and was implicated in a small epidemic in the Kathmandu valley in August 1997. 相似文献
58.
Shrestha S Smith MW Broman KW Farzadegan H Vlahov D Strathdee SA 《Journal of acquired immune deficiency syndromes (1999)》2006,43(3):335-343
Syringe-sharing behaviors among injection drug users (IDUs) are typically based on self-reports and subject to socially desirable responding. We used 3 short tandem repeat (STR) genetic biomarkers to detect sharing in 2,512 syringes exchanged by 315 IDUs in the Baltimore needle exchange program (NEP; 738 person-visits). Demographic characteristics as well as direct and indirect needle-sharing behaviors corresponding to the closest AIDS Link to Intravenous Experience (ALIVE) study visits were examined for association with multiperson use (MPU) of syringes. Overall, 56% of the syringes exchanged at the Baltimore NEP had evidence of MPU. Less MPU of syringes (48% vs. 71%; P < 0.0001) was seen with more rapid syringe turnaround (<3 days). IDUs always exchanging their own syringes ("primary" syringes) were less likely to return syringes with evidence of MPU (52%) than those who exchanged syringes for others ("secondary" syringes; 64%; P = 0.0001) and those exchanging primary and secondary syringes (58%; P = 0.004). In a multivariate analysis restricted to primary exchangers, MPU of syringes was associated with sharing cotton (adjusted odds ratio [AOR] = 2.06, 95% confidence interval [CI]: 1.30 to 3.28), lending syringes (AOR = 1.70, 95% CI: 1.24 to 2.34), and injecting less than daily (AOR = 0.64, 95% CI: 0.43 to 0.95). These findings support additional public health interventions such as expanded syringe access to prevent HIV and other blood-borne infections. Testing of STRs represents a promising approach to examining and accessing complex behavioral data, including syringe sharing. 相似文献
59.
Maria Mathisen Tor A Strand Biswa N Sharma Ram K Chandyo Palle Valentiner-Branth Sudha Basnet Ramesh K Adhikari Dag Hvidsten Prakash S Shrestha Halvor Sommerfelt 《BMC medicine》2009,7(1):35
Background
Pneumonia is among the main causes of illness and death in children <5 years of age. There is a need to better describe the epidemiology of viral community-acquired pneumonia (CAP) in developing countries. 相似文献60.