Last data update: Apr 22, 2024. (Total: 46599 publications since 2009)
Records 1-24 (of 24 Records) |
Query Trace: Truong J [original query] |
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Identification and characterization of ten Escherichia coli strains encoding novel shiga toxin 2 subtypes, Stx2n as well as Stx2j, Stx2m, and Stx2o, in the United States
Lindsey RL , Prasad A , Feldgarden M , Gonzalez-Escalona N , Kapsak C , Klimke W , Melton-Celsa A , Smith P , Souvorov A , Truong J , Scheutz F . Microorganisms 2023 11 (10) The sharing of genome sequences in online data repositories allows for large scale analyses of specific genes or gene families. This can result in the detection of novel gene subtypes as well as the development of improved detection methods. Here, we used publicly available WGS data to detect a novel Stx subtype, Stx2n in two clinical E. coli strains isolated in the USA. During this process, additional Stx2 subtypes were detected; six Stx2j, one Stx2m strain, and one Stx2o, were all analyzed for variability from the originally described subtypes. Complete genome sequences were assembled from short- or long-read sequencing and analyzed for serotype, and ST types. The WGS data from Stx2n- and Stx2o-producing STEC strains were further analyzed for virulence genes pro-phage analysis and phage insertion sites. Nucleotide and amino acid maximum parsimony trees showed expected clustering of the previously described subtypes and a clear separation of the novel Stx2n subtype. WGS data were used to design OMNI PCR primers for the detection of all known stx1 (283 bp amplicon), stx2 (400 bp amplicon), intimin encoded by eae (221 bp amplicon), and stx2f (438 bp amplicon) subtypes. These primers were tested in three different laboratories, using standard reference strains. An analysis of the complete genome sequence showed variability in serogroup, virulence genes, and ST type, and Stx2 pro-phages showed variability in size, gene composition, and phage insertion sites. The strains with Stx2j, Stx2m, Stx2n, and Stx2o showed toxicity to Vero cells. Stx2j carrying strain, 2012C-4221, was induced when grown with sub-inhibitory concentrations of ciprofloxacin, and toxicity was detected. Taken together, these data highlight the need to reinforce genomic surveillance to identify the emergence of potential new Stx2 or Stx1 variants. The importance of this surveillance has a paramount impact on public health. Per our description in this study, we suggest that 2017C-4317 be designated as the Stx2n type-strain. |
High PrEP uptake, adherence, persistence and effectiveness outcomes among young Thai men and transgender women who sell sex in Bangkok and Pattaya, Thailand: findings from the open-label combination HIV prevention effectiveness (COPE) study
Weir BW , Wirtz AL , Chemnasiri T , Baral SD , Decker M , Dun C , Hnin Mon SH , Ungsedhapand C , Dunne EF , Woodring J , Pattanasin S , Sukwicha W , Thigpen MC , Varangrat A , Warapornmongkholkul A , O'Connor S , Ngo JP , Qaragholi N , Sisel HI , Truong JM , Janyam S , Linjongrat D , Sriplienchan S , Sirivongrangson P , Rooney JF , Sullivan P , Chua-Intra B , Hickey AC , Beyrer C . Lancet Reg Health Southeast Asia 2023 15 100217 BACKGROUND: Daily oral pre-exposure prophylaxis (PrEP) is effective in preventing HIV infection, but no study has evaluated combination prevention interventions with PrEP for transgender women (TGW) and men who have sex with men (MSM) who sell sex. METHODS: The Combination Prevention Effectiveness (COPE) study was a community-based, non-randomized implementation study in Bangkok and Pattaya, Thailand. Participants were HIV-negative MSM and TGW aged 18-26 years who reported exchanging sex with men in the prior 12 months and who met 2014 U.S. Public Health Service PrEP eligibility criteria. The intervention included quarterly HIV testing, semiannual testing for sexually transmitted infections, provision of condoms with lubricant, and the opportunity to initiate or end daily oral PrEP use at any time during study participation. Participants taking PrEP received monthly adherence counseling and short message service reminders. The primary outcome was HIV incidence rate ratio (IRR) on PrEP vs. not on PrEP. Secondary outcomes were PrEP initiation, PrEP use at 12 months, and PrEP adherence. FINDINGS: From October 2017 to August 2019, 846 participants were enrolled: 531 (62.8%) immediately initiated PrEP; 104 (12.3%) subsequently initiated PrEP, and 211 (24.9%) never initiated PrEP. Among those initiating PrEP within 30 days of enrollment; 85.9% were on PrEP at the 12-months. When taking PrEP, participants reported adherent PrEP use at 94.2% of quarterly assessments. Ten HIV seroconversions occurred without PrEP use (incidence rate [IR] = 3.42 per 100 person-years [PY]; 95% CI = 1.64-6.30), while zero cases occurred with PrEP use (IR = 0.0 per 100PY; 95% CI = 0.0-0.62), with IRR = 0.0 (95% CI = 0.0-0.22; p < 0.001). INTERPRETATION: Young Thai MSM and TGW who exchange sex can have high PrEP uptake, persistence and adherence, and low HIV incidence when offered in supportive community-based settings. FUNDING: U.S. National Institute of Allergy and Infectious Diseases; Centers for Disease Control and Prevention. |
Evaluation of the Illumina iSeq whole genome sequencing system for enteric disease surveillance and outbreak detection
Trees E , Poates A , Sabol A , LaFon P , Truong J , Lindsey R . J Microbiol Methods 2023 211 106784 The Illumina iSeq low-capacity sequencing platform was evaluated for use in foodborne disease surveillance and outbreak detection. The platform produced high quality sequence data comparable to that of the Illumina MiSeq and was cost-effective with fast turn-around time in low sample volume environments. |
Impact and effectiveness of Rotavin-M1 under conditions of routine use in two provinces in Vietnam, 2016-2021, an observational and case-control study
Van Trang N , Tate JE , Phuong Mai LT , Vu TD , Quyet NT , Thi Le LK , Thi Chu MN , Ngoc Tran MP , Thi Pham TP , Nguyen HT , Hien ND , Jiang B , Yen C , Tran DN , Anh DD , Parashar UD , Anh LT , Thanh VD , Sanh LV , Dieu Thuy DT , Trang DC , Phong NQ , Truong DH , Tai TV , Dung PV , Van DV . Lancet Reg Health West Pac 2023 37 100789 Background: Half of diarrhea hospitalizations in children aged <5 years in Vietnam are due to rotavirus. Following introduction of a locally developed and licensed oral rotavirus vaccine, Rotavin-M1, into the routine immunization program in two Vietnamese provinces, Nam Dinh and TT Hue, we describe changes in rotavirus positivity among children hospitalized for diarrhea and calculate vaccine effectiveness against moderate-to-severe rotavirus hospitalizations. Methods: Active rotavirus surveillance among children <5 years began in December 2016 at sentinel hospitals in districts where rotavirus vaccine was introduced in December 2017. To estimate reductions in rotavirus detection, we calculated risk ratios comparing rotavirus positivity pre- and post-vaccine introduction. We used a test-negative case–control design to calculate vaccine effectiveness. Findings: From December 2016 to May 2021, 7228 children <5 years hospitalized for diarrhea were enrolled. Following introduction, Rotavin-M1 coverage was 77% (1066/1377) in Nam Dinh and 42% (203/489) in TT Hue. In Nam Dinh, rotavirus positivity among children <5 years significantly declined by 40.6% (95% CI: 34.8%–45.8%) during the three-year post-vaccine introduction period. In TT Hue, no change in rotavirus positivity was observed. Among children aged 6–23 months, a 2-dose series of Rotavin-M1 was 57% (95% CI: 39%–70%) effective against moderate-to-severe rotavirus hospitalizations. Interpretation: Higher vaccination coverage in Nam Dinh than TT Hue likely contributed to substantial declines in rotavirus positivity observed in Nam Dinh following rotavirus vaccine introduction. Robust vaccine effectiveness was observed through the second year of life. National rotavirus vaccine introduction with high coverage may have substantial impact on reducing rotavirus disease burden in Vietnam. Funding: Bill and Melinda Gates Foundation. © 2023 |
Impact and effectiveness of Rotavin-M1 under conditions of routine use in two provinces in Vietnam, 20162021, an observational and casecontrol study
VanTrang N , Tate JE , PhuongMai LT , Vu TD , Quyet NT , ThiLe LK , ThiChu MN , NgocTran MP , ThiPham TP , Nguyen HT , Hien ND , Jiang B , Yen C , Tran DN , Anh DD , Parashar UD , Anh LT , Thanh VD , Sanh LV , DieuThuy DT , Trang DC , Phong NQ , Truong DH , Tai TV , Dung PV , Van DV . Lancet Reg Health West Pac 2023 Background: Half of diarrhea hospitalizations in children aged <5 years in Vietnam are due to rotavirus. Following introduction of a locally developed and licensed oral rotavirus vaccine, Rotavin-M1, into the routine immunization program in two Vietnamese provinces, Nam Dinh and TT Hue, we describe changes in rotavirus positivity among children hospitalized for diarrhea and calculate vaccine effectiveness against moderate-to-severe rotavirus hospitalizations. Methods: Active rotavirus surveillance among children <5 years began in December 2016 at sentinel hospitals in districts where rotavirus vaccine was introduced in December 2017. To estimate reductions in rotavirus detection, we calculated risk ratios comparing rotavirus positivity pre- and post-vaccine introduction. We used a test-negative casecontrol design to calculate vaccine effectiveness. Findings: From December 2016 to May 2021, 7228 children <5 years hospitalized for diarrhea were enrolled. Following introduction, Rotavin-M1 coverage was 77% (1066/1377) in Nam Dinh and 42% (203/489) in TT Hue. In Nam Dinh, rotavirus positivity among children <5 years significantly declined by 40.6% (95% CI: 34.8%45.8%) during the three-year post-vaccine introduction period. In TT Hue, no change in rotavirus positivity was observed. Among children aged 623 months, a 2-dose series of Rotavin-M1 was 57% (95% CI: 39%70%) effective against moderate-to-severe rotavirus hospitalizations. Interpretation: Higher vaccination coverage in Nam Dinh than TT Hue likely contributed to substantial declines in rotavirus positivity observed in Nam Dinh following rotavirus vaccine introduction. Robust vaccine effectiveness was observed through the second year of life. National rotavirus vaccine introduction with high coverage may have substantial impact on reducing rotavirus disease burden in Vietnam. Funding: Bill and Melinda Gates Foundation. 2023 |
Cryptic transmission of SARS-CoV-2 in Washington State.
Bedford T , Greninger AL , Roychoudhury P , Starita LM , Famulare M , Huang ML , Nalla A , Pepper G , Reinhardt A , Xie H , Shrestha L , Nguyen TN , Adler A , Brandstetter E , Cho S , Giroux D , Han PD , Fay K , Frazar CD , Ilcisin M , Lacombe K , Lee J , Kiavand A , Richardson M , Sibley TR , Truong M , Wolf CR , Nickerson DA , Rieder MJ , Englund JA , Hadfield J , Hodcroft EB , Huddleston J , Moncla LH , Müller NF , Neher RA , Deng X , Gu W , Federman S , Chiu C , Duchin J , Gautom R , Melly G , Hiatt B , Dykema P , Lindquist S , Queen K , Tao Y , Uehara A , Tong S , MacCannell D , Armstrong GL , Baird GS , Chu HY , Shendure J , Jerome KR . medRxiv 2020 Following its emergence in Wuhan, China, in late November or early December 2019, the SARS-CoV-2 virus has rapidly spread throughout the world. On March 11, 2020, the World Health Organization declared Coronavirus Disease 2019 (COVID-19) a pandemic. Genome sequencing of SARS-CoV-2 strains allows for the reconstruction of transmission history connecting these infections. Here, we analyze 346 SARS-CoV-2 genomes from samples collected between 20 February and 15 March 2020 from infected patients in Washington State, USA. We found that the large majority of SARS-CoV-2 infections sampled during this time frame appeared to have derived from a single introduction event into the state in late January or early February 2020 and subsequent local spread, strongly suggesting cryptic spread of COVID-19 during the months of January and February 2020, before active community surveillance was implemented. We estimate a common ancestor of this outbreak clade as occurring between 18 January and 9 February 2020. From genomic data, we estimate an exponential doubling between 2.4 and 5.1 days. These results highlight the need for large-scale community surveillance for SARS-CoV-2 introductions and spread and the power of pathogen genomics to inform epidemiological understanding. |
Uptake and continuation of HIV pre-exposure prophylaxis among women of reproductive age in two health facilities in Kisumu County, Kenya
Ogolla M , Nyabiage OL , Musingila P , Gachau S , Odero TMA , Odoyo-June E , Ochanda B , Appolonia A , Katiku E , Joseph R , Ogolla C , Otieno L , Odhiambo F , Truong HM . J Int AIDS Soc 2023 26 (3) e26069 INTRODUCTION: In 2020, Kenya had 19,000 new HIV infections among women aged 15+ years. Studies have shown sub-optimal oral pre-exposure prophylaxis (PrEP) use among sub-populations of women. We assessed the uptake and continuation of oral PrEP among women 15-49 years in two health facilities in Kisumu County, Kenya. METHODS: A retrospective cohort of 262 women aged 15-49 years, initiated into oral PrEP between 12 November 2019 and 31 March 2021, was identified from two health facilities in the urban setting of Kisumu County, Kenya. Data on baseline characteristics and oral PrEP continuation at months 1, 3 and 6 were abstracted from patient records and summarized using descriptive statistics. Missing data in the predictor variables were imputed within the joint modelling multiple imputation framework. Using logistic regression, we evaluated factors associated with the discontinuation of oral PrEP at month 1. RESULTS: Of the 66,054 women screened, 320 (0.5%) were eligible and 262 (82%) were initiated on oral PrEP. Uptake was higher among women 25-29 years as compared to those 15-24 years (77% vs. 33%). Oral PrEP continuation declined significantly with increasing duration of follow-up; 37% at month 1, 21% at month 3 and 12% at month 6 (p<0.05). In the adjusted analysis, women 15-24 years had lower adjusted odds of continuing at month 1 than women ≥25 years (adjusted odds ratio [aOR]: 0.41, 95% CI: 0.21-0.82). There was no association between being sero-discordant and continuation of oral PrEP at month 1 (aOR; 1.21, 95% CI 0.59-2.50). Women from the sub-county hospital were more likely to continue at month 1 of follow-up compared to women enrolled in the county referral hospital (aOR 5.11; 95% CI 2.24-11.70). CONCLUSIONS: The low eligibility for oral PrEP observed among women 15-49 years in an urban setting with high HIV prevalence calls for a review of the screening process to validate the sensitivity of the screening tool and its proper application. The low uptake and continuation among adolescent girls and young women underscores the need to identify and address specific patient- and facility-level barriers affecting different sub-populations at risk for HIV acquisition. |
Systematic sequencing of imported cases leads to detection of SARS-CoV-2 B.1.1.529 (Omicron) variant in central Viet Nam.
Do Thai Hung , Nguyen Bao Trieu , Do Thi Thu Thuy , Olmsted A , Trinh Hoang Long , Nguyen Duc Duy , Huynh Kim Mai , Bui Thi Thu Hien , Nguyen van Van , Tran van Kiem , Vo Thi Thuy Trang , Nguyen Truong Duy , Ton That Thanh , Huynh van Dong , Gould PL , Moore MR . Western Pac Surveill Response J 2022 13 (4) 1-4 As authorities braced for the arrival of the Omicron variant of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), infrastructure investments and government directives prompted action in central Viet Nam to establish capacity for genomic surveillance sequencing. From 17 November 2021 to 7 January 2022, the Pasteur Institute in Nha Trang sequenced 162 specimens from 98 150 confirmed SARS-CoV-2 cases in the region collected from 8 November to 31 December 2021. Of these, all 127 domestic cases were identified as the B.1.617.2 (Delta) variant, whereas 92% (32/35) of imported cases were identified as the B.1.1.529 (Omicron) variant, all among international flight passengers. Patients were successfully isolated, enabling health-care workers to prepare for additional cases. Most (78%) of the 32 Omicron cases were fully vaccinated, suggesting continued importance of public health and social measures to control the spread of new variants. |
SARS-CoV-2 Screening Testing in Schools: A Comparison of School- vs Home-Based Collection Methods.
Chung E , Magedson A , Emanuels A , Luiten K , Pfau B , Truong M , Chow EJ , Hughes JP , Uyeki TM , Englund JA , Nickerson DA , Lockwood CM , Shendure J , Starita LM , Chu HY . J Pediatric Infect Dis Soc 2022 11 (11) 522-524 We implemented a voluntary SARS-CoV-2 screening testing study for kindergarten-2nd grade students in a Washington School district. Weekly SARS-CoV-2 testing participation was higher for students with staff-collected nasal swabs at school than for students with parent-collected swabs at home. |
Sequencing of Enteric Bacteria: Library Preparation Procedure Matters for Accurate Identification and Characterization.
Poates A , Truong J , Lindsey R , Griswold T , Williams-Newkirk AJ , Carleton H , Trees E . Foodborne Pathog Dis 2022 19 (8) 569-578 Enzymatic library preparation kits are increasingly used for bacterial whole genome sequencing. While they offer a rapid workflow, the transposases used in the kits are recognized to be somewhat biased. The aim of this study was to optimize and validate a protocol for the Illumina DNA Prep kit (formerly Nextera DNA Flex) for sequencing enteric pathogens and compare its performance against the Nextera XT kit. One hundred forty-three strains of Campylobacter, Escherichia, Listeria, Salmonella, Shigella, and Vibrio were prepared with both methods and sequenced on the Illumina MiSeq using 300 and/or 500 cycle chemistries. Sequences were compared using core genome multilocus sequence typing (cgMLST), 7-gene multilocus sequence typing (MLST), and detection of markers encoding serotype, virulence, and antimicrobial resistance. Sequences for one Escherichia strain were downsampled to determine the minimum coverage required for the analyses. While organism-specific differences were observed, the Prep libraries generated longer average read lengths and less fragmented assemblies compared to the XT libraries. In downstream analysis, the most notable difference between the kits was observed for Escherichia, particularly for the 300 cycle sequences. The O group was not predicted in 32% and 4% of XT sequences when using blast and kmer algorithms, respectively, while the O group was predicted from all Prep sequences regardless of the algorithm. In addition, the ehxA gene was not detected in 6% of XT sequences and 34% were missing one or more of the type III secretion systems and/or plasmid-associated genes, which were detected in the Prep sequences. The coverage downsampling revealed that acceptable assembly quality and allele detection was achieved at 30 × coverage with the Prep libraries, whereas 40-50 × coverage was required for the XT libraries. The better performance of the Prep libraries was attributed to more even coverage, particularly in genome regions low in GC content. |
Establishing a standardized surveillance system for health care-associated infections in Vietnam
Coker D , Phuong HTK , Nguyen LTP , Ninh T , Gupta N , Ha TTT , Truong NT , Van Thanh H , Vasquez A , Bui HTT , Malpiedi P . Glob Health Sci Pract 2022 10 (3) Standardized surveillance for health care-associated infections (HAI) is critical to understand HAI burden and inform prevention strategies at a national level. Due to differing and generally limited resources in Vietnam’s health care facilities, implementation of HAI surveillance has been variable and data quality has not been systematically assessed. In 2016, the Vietnam Administration for Medical Services (VAMS) under the Ministry of Health, with the support of partners, began to establish a context-appropriate, standardized HAI surveillance system for bloodstream infections (BSI) and urinary tract infections (UTI) among 6 pilot hospitals in Vietnam. We identified 5 key elements of our HAI surveillance implementation process that have been conducive to ensuring data quality and program sustainability and scalability. These include: (1) engaging stakeholders, (2) designating roles and responsibilities, (3) developing context-sensitive, standardized surveillance protocols, (4) creating a surveillance implementation strategy, and (5) linking HAI surveillance and prevention activities. With the active participation of infection prevention and control staff from the 6 pilot hospitals, standardized HAI surveillance for BSIs and UTIs was expanded to 12 additional hospitals in 2019. Together, VAMS and partners are helping Vietnam fulfill its commitment to safe health care for all patients. © Coker et al. |
A pretest-posttest design to assess the effectiveness of an intervention to reduce HIV-related stigma and discrimination in healthcare settings in Vietnam
Pollack TM , Duong HT , Nhat Vinh DT , Phuong DT , Thuy DH , Nhung VTT , Uyen NK , Linh VT , Van Truong N , Le Ai KA , Ninh NT , Nguyen A , Canh HD , Cosimi LA . J Int AIDS Soc 2022 25 Suppl 1 e25932 INTRODUCTION: Stigma and discrimination are important barriers to HIV epidemic control. We implemented a multi-pronged facility-level intervention to reduce stigma and discrimination at health facilities across three high-burden provinces. Key components of the intervention included measurement of stigma, data review and use, participatory training of healthcare workers (HCWs), and engagement of people living with HIV and key populations in all stigma reduction activities. METHODS: From July 2018 to July 2019, we assessed HIV-related stigma and discrimination among patients and HCWs at 10 facilities at baseline and 9 months following an intervention. A repeated measures design was used to assess the change in stigma and discrimination among HCWs and a repeated cross-sectional design assessed the change in stigma and discrimination experienced by PLHIV. HCWs at target facilities were invited at random and PLHIV were recruited when presenting for care during the two assessment periods. McNemar's test was used to compare paired proportions among HCWs, and chi-square test was used to compare proportions among PLHIV. Mixed models were used to compare outcomes before and after the intervention. RESULTS: Semi-structured interviews were conducted with 649 and 652 PLHIV prior to and following the intervention, respectively. At baseline, over the previous 12 months, 21% reported experiencing discrimination, 16% reported self-stigma, 14% reported HIV disclosure without consent and 7% had received discriminatory reproductive health advice. Nine months after the intervention, there was a decrease in reported stigma and discrimination across all domains to 15%, 11%, 7% and 3.5%, respectively (all p-values <0.05). Among HCWs, 672 completed the pre- and post-intervention assessment. At baseline, 81% reported fear of HIV infection, 69% reported using unnecessary precautions when caring for PLHIV, 44% reported having observed other staff discriminate against PLHIV, 54% reported negative attitudes towards PLHIV and 41% felt uncomfortable working with colleagues living with HIV. The proportions decreased after the intervention to 52%, 34%, 32%, 35% and 24%, respectively (all p-values <0.05). CONCLUSIONS: A multi-pronged facility-level intervention was successful at reducing healthcare-associated HIV-related stigma in Vietnam. The findings support the scale-up of this intervention in Vietnam and highlight key components potentially applicable in other settings. |
Inactivated poliovirus vaccine closing the type 2 immunity gap in Vietnam
Huyen DTT , Anh DD , Trung NT , Hong DT , Thanh TT , Truong LN , Jeyaseelan V , Lopez Cavestany R , Hendley WS , Mainou BA , Mach O . J Pediatric Infect Dis Soc 2022 11 (9) 413-416 This was a cross-sectional community-based serological survey of polio antibodies assessing the immunogenicity of inactivated poliovirus vaccine (IPV) focusing on poliovirus serotype 2. IPV was administered to 5-month-old children. Type 2 antibody seroprevalence when measured 1 month after IPV administration was >95%. One IPV dose successfully closed the immunity gap. |
SARS-CoV-2 Outbreak Investigation in a Hospital Emergency Department - California, December 2020 - January 2021.
Li R , Beshearse E , Malden D , Truong H , Kraushaar V , Bonin BJ , Kim J , Kennedy I , McNary J , Han GS , Rudman SL , Perz JF , Perkins KM , Glowicz J , Epson E , Benowitz I , Villarino E . Infect Control Hosp Epidemiol 2022 1-21 We describe a large SARS-CoV-2 outbreak involving an acute care hospital emergency department during December 2020 and January 2021, in which 27 healthcare personnel worked while infectious, resulting in multiple opportunities for SARS-CoV-2 transmission to patients and other healthcare personnel. We provide recommendations for improving infection prevention and control. |
Diverse contexts and social factors among young cisgender men and transgender women who sell or trade sex in Bangkok and Pattaya, Thailand: formative research for a PrEP program implementation study
Truong JM , Chemnasiri T , Wirtz AL , Mon SHH , Varangrat A , Decker M , Janyam S , Linjongrat D , Sirivongrangson P , Hickey AC , Weir BW , Beyrer C . AIDS Care 2022 34 (11) 1-9 HIV incidence is high and persistent among cisgender men who have sex with men (MSM) and transgender women (TGW) who have sex with men, particularly among those who sell or trade sex. In preparation for an open-label combination HIV pre-exposure prophylaxis (PrEP) program for these groups, we conducted formative research to explore the context of sex work/trade and factors that affect implementation of PrEP interventions. This study analyzed interviews with 20 young (aged 18-26 years) MSM and TGW who sell/trade sex and three sex work venue managers in Bangkok and Pattaya, Thailand. Participants described diverse contexts of sex work/trade, including in multiple informal and formal sex venues. Several participants reported mobility across provinces and out of the country, which led to intermittent sex work/trade. TGW sex workers reported challenges with access and cost of femininizing hormones and limited employment opportunities. Factors that could facilitate or challenge PrEP program implementation included HIV stigma, the role of venue management in sexual health practice, lack of PrEP knowledge, lower perceived HIV risk, and interest in personal health and wellbeing. Program implementers must consider myriad factors to successfully implement PrEP among young MSM and TGW engaged in sex work or trade in Thailand. |
Comparison of four enzymatic library preparation kits for sequencing Shiga toxin-producing Escherichia coli for surveillance and outbreak detection.
Truong J , Poates A , Joung YJ , Sabol A , Griswold T , Williams-Newkirk AJ , Lindsey R , Trees E . J Microbiol Methods 2021 190 106329 Four enzymatic DNA library preparation kits were compared for sequencing Shiga toxin-producing E. coli. All kits produced high quality sequence data which performed equally well in the downstream analyses for surveillance and outbreak detection. Important differences were noted in the workflow user-friendliness and per sample cost. |
Cryptic transmission of SARS-CoV-2 in Washington state.
Bedford T , Greninger AL , Roychoudhury P , Starita LM , Famulare M , Huang ML , Nalla A , Pepper G , Reinhardt A , Xie H , Shrestha L , Nguyen TN , Adler A , Brandstetter E , Cho S , Giroux D , Han PD , Fay K , Frazar CD , Ilcisin M , Lacombe K , Lee J , Kiavand A , Richardson M , Sibley TR , Truong M , Wolf CR , Nickerson DA , Rieder MJ , Englund JA , Hadfield J , Hodcroft EB , Huddleston J , Moncla LH , Müller NF , Neher RA , Deng X , Gu W , Federman S , Chiu C , Duchin JS , Gautom R , Melly G , Hiatt B , Dykema P , Lindquist S , Queen K , Tao Y , Uehara A , Tong S , MacCannell D , Armstrong GL , Baird GS , Chu HY , Shendure J , Jerome KR . Science 2020 370 (6516) 571-575 Following its emergence in Wuhan, China, in late November or early December 2019, the SARS-CoV-2 virus has rapidly spread globally. Genome sequencing of SARS-CoV-2 allows reconstruction of its transmission history, although this is contingent on sampling. We have analyzed 453 SARS-CoV-2 genomes collected between 20 February and 15 March 2020 from infected patients in Washington State, USA. We find that most SARS-CoV-2 infections sampled during this time derive from a single introduction in late January or early February 2020 which subsequently spread locally before active community surveillance was implemented. |
Prescribers and naloxone pharmacy claims
Smart R , Geiger CK , Jones CM , Stein BD . J Gen Intern Med 2020 35 (8) 2475 We appreciate the response from Truong, Patil, and Rich to our study regarding retail pharmacy naloxone prescriptions1 and thank them for highlighting the importance of patient and caregiver education for individuals receiving naloxone. While naloxone is generally considered a safe medication, like almost all medications, there are risks of unintended adverse consequences if not used as intended. It is essential that prescribers educate patients and caregivers regarding the circumstances when naloxone should be administered, and the procedures for administering it, when writing a naloxone prescription. In addition, since nearly all states have laws or policies that allow individuals to obtain naloxone from a pharmacist without a prescription from a physician, pharmacists also play a critical role in counseling patients and caregivers regarding the circumstances when naloxone should be administered and proper procedures for administration.2 |
Testing for Coccidioidomycosis among community-acquired pneumonia patients, southern California, USA
Tartof SY , Benedict K , Xie F , Rieg GK , Yu KC , Contreras R , Truong J , Fong K , Tseng HF , Jacobsen SJ , Mody RK . Emerg Infect Dis 2018 24 (4) 779-781 We conducted a cohort study to identify characteristics associated with testing for, and testing positive for, coccidioidomycosis among patients with community-acquired pneumonia in southern California, USA. Limited and delayed testing probably leads to underdiagnosis among non-Hispanic black, Filipino, or Hispanic patients and among high-risk groups, including persons in whom antimicrobial drug therapy has failed. |
Phylodynamics of Enterovirus A71-Associated Hand, Foot and Mouth Disease in Viet Nam.
Geoghegan JL , Van Tan L , Kuhnert D , Halpin RA , Lin X , Simenauer A , Akopov A , Das SR , Stockwell TB , Shrivastava S , Ngoc NM , Uyen LT , Tuyen NT , Thanh TT , Hang VT , Qui PT , Hung NT , Khanh TH , Thinh LQ , Nhan LN , Van HM , Viet DC , Tuan HM , Viet HL , Hien TT , Chau NV , Thwaites G , Grenfell BT , Stadler T , Wentworth DE , Holmes EC , Van Doorn HR . J Virol 2015 89 (17) 8871-9 Enterovirus A71 (EV-A71) is a major cause of hand, foot and mouth disease (HFMD) and is particularly prevalent in parts of Southeast Asia, affecting thousands of children and infants each year. Revealing the evolutionary and epidemiological dynamics of EV-A71 through time and space is central to understanding its outbreak potential. We generated the full genome sequences of 200 EV-A71 strains sampled from various locations in Viet Nam between 2011-2013, and used these sequence data to determine the evolutionary history and phylodynamics of EV-A71 in Viet Nam, providing estimates of the effective reproduction number (Re) of the infection through time. In addition, we described the phylogeography of EV-A71 throughout Southeast Asia, documenting patterns of viral gene flow. Accordingly, our analysis reveals that a rapid genogroup switch from C4 to B5 likely took place during 2012 in Viet Nam. We show that the Re of subgenogroup C4 decreased during the time-frame of sampling, while that of B5 increased and remained >1 at the end of 2013, corresponding to a rise in B5 prevalence. Our study reveals that the subgenogroup B5 virus that emerged into Viet Nam is closely related to variants that were responsible for large epidemics in Malaysia and Taiwan and therefore extends our knowledge regarding its associated endemic area. Subgenogroup B5 evidently has the potential to cause more widespread outbreaks across Southeast Asia. IMPORTANCE: EV-A71 is one of many viruses that cause HFMD, a common syndrome that largely affects infants and children. HFMD usually causes only mild illness with no long-term consequences. Occasionally, however, severe infection may arise, especially in very young children, causing neurological complications and even death. EV-A71 is highly contagious and is associated with the most severe HFMD cases, with large and frequent epidemics of the virus recorded worldwide. Although major advances have been made in the development of a potential EV-A71 vaccine, there is no current prevention and little is known about the patterns and dynamics of EV-A71 spread. In this study we utilize full-length genome sequence data obtained from HFMD patients in Viet Nam, a geographical region where the disease has been endemic since 2003, to characterize the phylodynamics of this important emerging virus. |
Geographic and temporal trends in the molecular epidemiology and genetic mechanisms of transmitted HIV-1 drug resistance: an individual-patient- and sequence-level meta-analysis.
Rhee SY , Blanco JL , Jordan MR , Taylor J , Lemey P , Varghese V , Hamers RL , Bertagnolio S , de Wit TF , Aghokeng AF , Albert J , Avi R , Avila-Rios S , Bessong PO , Brooks JI , Boucher CA , Brumme ZL , Busch MP , Bussmann H , Chaix ML , Chin BS , D'Aquin TT , De Gascun CF , Derache A , Descamps D , Deshpande AK , Djoko CF , Eshleman SH , Fleury H , Frange P , Fujisaki S , Harrigan PR , Hattori J , Holguin A , Hunt GM , Ichimura H , Kaleebu P , Katzenstein D , Kiertiburanakul S , Kim JH , Kim SS , Li Y , Lutsar I , Morris L , Ndembi N , Ng KP , Paranjape RS , Peeters M , Poljak M , Price MA , Ragonnet-Cronin ML , Reyes-Teran G , Rolland M , Sirivichayakul S , Smith DM , Soares MA , Soriano VV , Ssemwanga D , Stanojevic M , Stefani MA , Sugiura W , Sungkanuparph S , Tanuri A , Tee KK , Truong HH , van de Vijver DA , Vidal N , Yang C , Yang R , Yebra G , Ioannidis JP , Vandamme AM , Shafer RW . PLoS Med 2015 12 (4) e1001810 BACKGROUND: Regional and subtype-specific mutational patterns of HIV-1 transmitted drug resistance (TDR) are essential for informing first-line antiretroviral (ARV) therapy guidelines and designing diagnostic assays for use in regions where standard genotypic resistance testing is not affordable. We sought to understand the molecular epidemiology of TDR and to identify the HIV-1 drug-resistance mutations responsible for TDR in different regions and virus subtypes. METHODS AND FINDINGS: We reviewed all GenBank submissions of HIV-1 reverse transcriptase sequences with or without protease and identified 287 studies published between March 1, 2000, and December 31, 2013, with more than 25 recently or chronically infected ARV-naive individuals. These studies comprised 50,870 individuals from 111 countries. Each set of study sequences was analyzed for phylogenetic clustering and the presence of 93 surveillance drug-resistance mutations (SDRMs). The median overall TDR prevalence in sub-Saharan Africa (SSA), south/southeast Asia (SSEA), upper-income Asian countries, Latin America/Caribbean, Europe, and North America was 2.8%, 2.9%, 5.6%, 7.6%, 9.4%, and 11.5%, respectively. In SSA, there was a yearly 1.09-fold (95% CI: 1.05-1.14) increase in odds of TDR since national ARV scale-up attributable to an increase in non-nucleoside reverse transcriptase inhibitor (NNRTI) resistance. The odds of NNRTI-associated TDR also increased in Latin America/Caribbean (odds ratio [OR] = 1.16; 95% CI: 1.06-1.25), North America (OR = 1.19; 95% CI: 1.12-1.26), Europe (OR = 1.07; 95% CI: 1.01-1.13), and upper-income Asian countries (OR = 1.33; 95% CI: 1.12-1.55). In SSEA, there was no significant change in the odds of TDR since national ARV scale-up (OR = 0.97; 95% CI: 0.92-1.02). An analysis limited to sequences with mixtures at less than 0.5% of their nucleotide positions-a proxy for recent infection-yielded trends comparable to those obtained using the complete dataset. Four NNRTI SDRMs-K101E, K103N, Y181C, and G190A-accounted for >80% of NNRTI-associated TDR in all regions and subtypes. Sixteen nucleoside reverse transcriptase inhibitor (NRTI) SDRMs accounted for >69% of NRTI-associated TDR in all regions and subtypes. In SSA and SSEA, 89% of NNRTI SDRMs were associated with high-level resistance to nevirapine or efavirenz, whereas only 27% of NRTI SDRMs were associated with high-level resistance to zidovudine, lamivudine, tenofovir, or abacavir. Of 763 viruses with TDR in SSA and SSEA, 725 (95%) were genetically dissimilar; 38 (5%) formed 19 sequence pairs. Inherent limitations of this study are that some cohorts may not represent the broader regional population and that studies were heterogeneous with respect to duration of infection prior to sampling. CONCLUSIONS: Most TDR strains in SSA and SSEA arose independently, suggesting that ARV regimens with a high genetic barrier to resistance combined with improved patient adherence may mitigate TDR increases by reducing the generation of new ARV-resistant strains. A small number of NNRTI-resistance mutations were responsible for most cases of high-level resistance, suggesting that inexpensive point-mutation assays to detect these mutations may be useful for pre-therapy screening in regions with high levels of TDR. In the context of a public health approach to ARV therapy, a reliable point-of-care genotypic resistance test could identify which patients should receive standard first-line therapy and which should receive a protease-inhibitor-containing regimen. |
Telomere Length as an Indicator of the Robustness of B- and T-Cell Response to Influenza in Older Adults.
Najarro K , Nguyen H , Chen G , Xu M , Alcorta S , Yao X , Zukley L , Metter EJ , Truong T , Lin Y , Li H , Oelke M , Xu X , Ling SM , Longo DL , Schneck J , Leng S , Ferrucci L , Weng NP . J Infect Dis 2015 212 (8) 1261-9 BACKGROUND: Telomeres provide a key mechanism for protecting the integrity of chromosomes and their attrition after cell division and during aging are evident in lymphocytes. However, the significance of telomere shortening in age-associated decline of immune function is unknown. METHODS: We selected 22 HLA-A2+ healthy older adults who have relatively short or long telomere lengths to compare their antibody response against the influenza vaccine, and their CD8+ T cell response against an influenza antigen. RESULTS: B cells from individuals with a robust antibody response to the influenza vaccine had significantly longer telomeres than those with a poor antibody response. Monocyte-derived antigen-presenting cells of both short and long telomere groups induced similar expansions of influenza M1-specific CD8+ T cells. Vaccination did not increase M1-specific CD8+ T cells in blood, however, M1-specific CD8+ T cells from the long telomere group exhibited significantly better expansion in vitro compared to those from the short telomere group. Finally, M1-specific CD8+ T cells that underwent more expansions had significantly longer telomeres compared to cells with fewer divisions. CONCLUSIONS: Telomere length is positively associated with a robust lymphocyte response and telomere attrition may contribute to the age-associated decline of adaptive immunity. |
Pretreatment HIV-1 drug resistance to first-line drugs: results from a baseline assessment of a large cohort initiating ART in Vietnam, 2009-10
Pham QD , Do NT , Le YN , Nguyen TV , Nguyen DB , Huynh TK , Bui DD , Khuu NV , Nguyen PD , Luong AQ , Bui HT , Nguyen HH , McConnell M , Nguyen LT , Zhang L , Truong LX . J Antimicrob Chemother 2014 70 (3) 941-7 OBJECTIVES: The objective of this study was to determine the prevalence and correlates of pretreatment drug resistance (PDR) to first-line antiretroviral drugs among people initiating therapy for HIV in Vietnam. METHODS: Blood was collected during November 2009 to October 2010 from people consecutively initiating ART in four purposively selected public outpatient clinics in three Vietnamese cities. At each study site, recruitment lasted for 6-10 months until the target sample size (range 120-130 individuals) had been reached. The viral load was measured in 501 samples; 490 samples (viral load ≥1000 copies/mL) were genotyped using a nucleotide population-based sequencing assay. Self-reported demographic and clinical data were elicited through interviews. We classified drug-resistance-associated mutations (DRMs) according to the 2009 WHO surveillance list. RESULTS: DRMs were identified in 17/490 participants (3.5%; 95% CI 2.2%-5.5%). The prevalence of DRMs was 1.6% (8/490) against NRTIs, 1.6% (8/490) against NNRTIs and 0.8% (4/490) against PIs; three (0.6%) participants were resistant to both NRTIs and NNRTIs. The overall prevalence of PDR to first-line drugs was low [2.7% (13/490); 95% CI 1.6%-4.4%]. The prevalence of PDR to first-line drugs was greater among 198 HIV-infected participants who injected drugs than among 286 participants who reported risks for sexually acquired HIV (4.0% versus 1.4%, P = 0.079). Multivariable logistic regression analysis suggested that PDR to first-line drugs was significantly higher among people who injected drugs (OR = 3.94; 95% CI 1.13-13.68). CONCLUSIONS: With low PDR, first-line ART may be effective in Vietnam and pretreatment genotyping may be unnecessary. Continuing strategies for the prevention and surveillance of antiretroviral resistance are important for maintaining a low prevalence of antiretroviral resistance in Vietnam. The association between resistance and injection drug use warrants further research. |
Genomic comparison of Escherichia coli O104:H4 isolates from 2009 and 2011 reveals plasmid, and prophage heterogeneity, including shiga toxin encoding phage stx2.
Ahmed SA , Awosika J , Baldwin C , Bishop-Lilly KA , Biswas B , Broomall S , Chain PS , Chertkov O , Chokoshvili O , Coyne S , Davenport K , Detter JC , Dorman W , Erkkila TH , Folster JP , Frey KG , George M , Gleasner C , Henry M , Hill KK , Hubbard K , Insalaco J , Johnson S , Kitzmiller A , Krepps M , Lo CC , Luu T , McNew LA , Minogue T , Munk CA , Osborne B , Patel M , Reitenga KG , Rosenzweig CN , Shea A , Shen X , Strockbine N , Tarr C , Teshima H , van Gieson E , Verratti K , Wolcott M , Xie G , Sozhamannan S , Gibbons HS . PLoS One 2012 7 (11) e48228 In May of 2011, an enteroaggregative Escherichia coli O104:H4 strain that had acquired a Shiga toxin 2-converting phage caused a large outbreak of bloody diarrhea in Europe which was notable for its high prevalence of hemolytic uremic syndrome cases. Several studies have described the genomic inventory and phylogenies of strains associated with the outbreak and a collection of historical E. coli O104:H4 isolates using draft genome assemblies. We present the complete, closed genome sequences of an isolate from the 2011 outbreak (2011C-3493) and two isolates from cases of bloody diarrhea that occurred in the Republic of Georgia in 2009 (2009EL-2050 and 2009EL-2071). Comparative genome analysis indicates that, while the Georgian strains are the nearest neighbors to the 2011 outbreak isolates sequenced to date, structural and nucleotide-level differences are evident in the Stx2 phage genomes, the mer/tet antibiotic resistance island, and in the prophage and plasmid profiles of the strains, including a previously undescribed plasmid with homology to the pMT virulence plasmid of Yersinia pestis. In addition, multiphenotype analysis showed that 2009EL-2071 possessed higher resistance to polymyxin and membrane-disrupting agents. Finally, we show evidence by electron microscopy of the presence of a common phage morphotype among the European and Georgian strains and a second phage morphotype among the Georgian strains. The presence of at least two stx2 phage genotypes in host genetic backgrounds that may derive from a recent common ancestor of the 2011 outbreak isolates indicates that the emergence of stx2 phage-containing E. coli O104:H4 strains probably occurred more than once, or that the current outbreak isolates may be the result of a recent transfer of a new stx2 phage element into a pre-existing stx2-positive genetic background. |
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