Clinically relevant antibiotic resistance genes are linked to a limited set of taxa within gut microbiome worldwide.

The acquisition of antimicrobial resistance (AR) genes has rendered important pathogens nearly or fully unresponsive to antibiotics. It has been suggested that pathogens acquire AR traits from the gut microbiota, which collectively serve as a global reservoir for AR genes conferring resistance to all classes of antibiotics. However, only a subset of AR genes confers resistance to clinically relevant antibiotics, and, although these AR gene profiles are well-characterized for common pathogens, less is known about their taxonomic associations and transfer potential within diverse members of the gut microbiota. We examined a collection of 14,850 human metagenomes and 1666 environmental metagenomes from 33 countries, in addition to nearly 600,000 isolate genomes, to gain insight into the global prevalence and taxonomic range of clinically relevant AR genes. We find that several of the most concerning AR genes, such as those encoding the cephalosporinase CTX-M and carbapenemases KPC, IMP, NDM, and VIM, remain taxonomically restricted to Proteobacteria. Even cfiA, the most common carbapenemase gene within the human gut microbiome, remains tightly restricted to Bacteroides, despite being found on a mobilizable plasmid. We confirmed these findings in gut microbiome samples from India, Honduras, Pakistan, and Vietnam, using a high-sensitivity single-cell fusion PCR approach. Focusing on a set of genes encoding carbapenemases and cephalosporinases, thus far restricted to Bacteroides species, we find that few mutations are required for efficacy in a different phylum, raising the question of why these genes have not spread more widely. Overall, these data suggest that globally prevalent, clinically relevant AR genes have not yet established themselves across diverse commensal gut microbiota.

Association of Pregnancy and HIV Status With Molecular-Bacterial Vaginosis in Indian Women.

BACKGROUND: Bacterial vaginosis (BV) is a highly prevalent disorder of the cervicovaginal microbiota. Molecular-BV may put women at increased risk for adverse reproductive and obstetric outcomes. We investigated the association of HIV and pregnancy on the vaginal microbiota and associations with molecular-BV in women of reproductive age from Pune, India. SETTING: We studied vaginal samples from N = 170 women, including N = 44 nonpregnant HIV seronegative, N = 56 pregnant seronegative, N = 47 nonpregnant women with HIV (WWH), and N = 23 pregnant WWH, and collected data on clinical, behavioral, and demographic factors. METHODS: We used 16S rRNA gene amplicon sequencing to characterize the composition of the vaginal microbiota. We classified the vaginal microbiota of these women into community state types based on bacterial composition and relative abundance and further categorized them into molecular-BV versus Lactobacillus -dominated states. To determine associations between pregnancy and HIV status with outcome of molecular-BV, logistic regression models were used. RESULTS: There was a high prevalence of molecular-BV (30%) in this cohort. We found that pregnancy was associated with decreased odds of molecular-BV (adjusted OR = 0.35, 95% CI: 0.14 to 0.87), while HIV was associated with increased odds of molecular-BV (adjusted OR = 2.76, 95% CI: 1.33 to 5.73), even when controlling for multiple relevant factors such as age, number of sexual partners, condom use, and douching. CONCLUSION: Larger and longitudinal studies are needed to further characterize molecular-BV and the vaginal microbiota in pregnant women and WWH and relate these factors to infectious, reproductive, and obstetric outcomes. In the long term, these studies may lead to novel microbiota-based therapeutics to improve women's reproductive and obstetric health.

The Association of Gestational Diabetes with HIV Infection and Tuberculosis in Indian Women.

Infection of HIV is associated with an increased diabetes risk, which also increases tuberculosis risk. It is unknown if similar associations exist with gestational diabetes (GDM). We screened pregnant women living with and without HIV for GDM using oral glucose tolerance testing. In a subgroup of women with latent tuberculosis (positive interferon-gamma [IFN-γ] release assay), we used supernatants from tuberculosis antigen tubes to compare cytokine levels from women with and without GDM, matched by age and HIV status. Of 234 women, 21 (9%) had GDM, 13.9% living with HIV, and 6.5% without HIV (P = 0.06). Compared with women without GDM, women with GDM had lower median IFN-γ (19.1 versus 141.9 pg/mL, P = 0.03) and interleukin-2 (18.7 versus 249 pg/mL, P < 0.01). Our study suggests that HIV infection is associated with an increased risk of GDM, which is associated with decreased Mycobacterium tuberculosis immune responses. Gestational diabetes screening should be prioritized in tuberculosis-endemic countries, especially in women living with HIV.

Transcriptional Analysis for Tuberculosis in Pregnant Women From the PRegnancy Associated Changes In Tuberculosis Immunology (PRACHITi) Study.

A new tuberculosis (TB) diagnostic cartridge assay, which detects a 3-gene TB signature in whole blood, was not diagnostic in women with maternal TB disease in India (area under the curve [AUC] = 0.72). In a cohort of pregnant women, we identified a novel gene set for TB diagnosis (AUC = 0.97) and one for TB progression (AUC = 0.96).

Association of Maternal Inflammation During Pregnancy With Birth Outcomes and Infant Growth Among Women With or Without HIV in India.

Importance: The association of elevated levels of specific inflammatory markers during pregnancy with adverse birth outcomes and infant growth could indicate pathways for potential interventions. Objective: To evaluate whether higher levels of certain inflammatory markers during pregnancy are associated with preterm birth (PTB), low birth weight (LBW), and infant growth deficits. Design, Setting, and Participants: In this cohort study of pregnant women with or without HIV, 218 mother-infant pairs were followed up from pregnancy through 12 months post partum from June 27, 2016, to December 9, 2019. Pregnant women aged 18 to 40 years and between 13 and 34 weeks of gestation who were receiving antenatal care were enrolled in a cohort stratified by HIV status; sampling was based on convenience sampling from women receiving antenatal care at Byramjee Jeejeebhoy Government Medical College. Exposures: Levels of multiple circulating inflammation markers during the third trimester of pregnancy. Main Outcomes and Measures: The primary study outcome was PTB (<37 weeks' gestation). Secondary outcomes were LBW (<2500 g) and repeated measures (delivery; 6 weeks post partum; and 3, 6, and 12 months post partum using multivariable generalized linear models) of infant growth outcomes (length-for-age, weight-for-age, and weight-for-length z scores). Results: The median age of the 218 women at enrollment was 23 years (IQR, 21-27 years). In multivariable models, higher pregnancy levels of interleukin 17A were associated with increased odds of both PTB (adjusted odds ratio [aOR], 2.62; 95% CI, 1.11-6.17) and LBW (aOR, 1.81; 95% CI, 1.04-3.15). Higher levels of interleukin 1ß were associated with increased PTB (aOR, 1.47; 95% CI, 1.15-1.89) and infant growth deficits (lower length-for-age z score: adjusted ß = -0.10; 95% CI, -0.18 to -0.01; lower weight-for-age z score: adjusted ß = -0.07; 95% CI, -0.14 to 0.001). Conclusions and Relevance: This study suggests that increased levels of certain systemic inflammatory markers, including interleukin 1ß and interleukin 17A, during pregnancy were associated with adverse birth outcomes and infant growth deficits. Future studies should evaluate whether potential interventions to modulate specific inflammatory pathways during pregnancy could improve birth outcomes and infant growth.

Stages of pregnancy and HIV affect diagnosis of tuberculosis infection and Mycobacterium tuberculosis (MTB)-induced immune response: Findings from PRACHITi, a cohort study in Pune, India.

BACKGROUND: Accurate tuberculosis infection (TBI) tests are critical for pregnant women, especially those with HIV, who have a high risk of TB disease. METHODS: We enrolled interferon gamma release assay (IGRA)+ pregnant women with and without HIV in a longitudinal study, followed up at delivery and 6 months postpartum. Tuberculin skin test (TST) and IGRA were compared by HIV status at each timepoint. RESULTS: Of 165 enrolled IGRA+ pregnant women: 35 (21%) had HIV and were on antiretroviral therapy with median CD4 of 476 (IQR 399-586). Compared to antepartum, significantly fewer women remained IGRA+ at delivery [HIV+ n=21/35 (62%, p=0.009); HIV- n=100/130 (77%, p=0.002)] and postpartum [HIV+ n=30/35 (87%, p=0.03); HIV- n=116/130 (89%, p=0.01)]. IGRA/TST discordance was high in pregnant women (HIV+: 51%; HIV-: 25%). Median IFN-γ was lowest for all women at delivery; significantly lower in women with HIV at all timepoints compared to women without HIV. TB incidence was 50/ 1000 person-years and 18/1000 person-years among women with and without HIV respectively. CONCLUSIONS: Pregnancy affects TBI test results and reduces IFN-γ response to M. tuberculosis stimulation. Despite adequate CD4 counts, women with HIV express less IFN-γ than women without HIV, which may explain the high TB incidence in postpartum women with HIV.

Impact of HIV status on systemic inflammation during pregnancy.

OBJECTIVE: There are limited studies on the association of HIV infection with systemic inflammation during pregnancy. DESIGN: A cohort study (N = 220) of pregnant women with HIV (N = 70) (all on antiretroviral therapy) and without HIV (N = 150) were enrolled from an antenatal clinic in Pune, India. METHODS: The following systemic inflammatory markers were measured in plasma samples using immunoassays: soluble CD163 (sCD163), soluble CD14 (sCD14), intestinal fatty acid-binding protein (I-FABP), C-reactive protein (CRP), alpha 1-acid glycoprotein (AGP), interferon-ß (IFNß), interferon-γ (IFNγ), interleukin (IL)-1ß, IL-6, IL-13, IL-17A, and tumor necrosis factor α (TNFα). Generalized estimating equation (GEE) and linear regression models were used to assess the association of HIV status with each inflammatory marker during pregnancy and by trimester, respectively. RESULTS: Pregnant women with HIV had higher levels of markers for gut barrier dysfunction (I-FABP), monocyte activation (sCD14) and markers of systemic inflammation (IL-6 and TNFα), but surprisingly lower levels of AGP, an acute phase protein, compared with pregnant women without HIV, with some trimester-specific differences. CONCLUSION: Our data show that women with HIV had higher levels of markers of gut barrier dysfunction, monocyte activation and systemic inflammation. These markers, some of which are associated with preterm birth, might help explain the increase in adverse birth outcomes in women with HIV and could suggest targets for potential interventions.

Validation of New Interactive Nutrition Assistant - Diet in India Study of Health (NINA-DISH) FFQ with multiple 24-h dietary recalls among pregnant women in Pune, India.

Adequate dietary intake is critical to prevent adverse pregnancy outcomes. India has a high burden of maternal and child morbidity and mortality, but there is a lack of adequate tools to assess dietary intake. We validate an FFQ, New Interactive Nutrition Assistant - Diet in India Study of Health (NINA-DISH), among pregnant women living with and without HIV in Pune, India. Women were selected from a cohort study investigating immune responses to HIV and latent tuberculosis during pregnancy. The FFQ was administered during the third trimester and validated against multiple 24-h dietary recalls (24-HDR) collected in second and third trimesters. Data for analysis were available from fifty-eight women out of seventy enrolled into this sub-study, after excluding those with incomplete data or implausible energy intake. The median (Q1, Q3) age of study participants was 23 (20, 25) years. Median (Q1, Q3) daily energy intakes were 10 552 (8000, 11 958) and 10 673 (8510, 13 962) kJ by 24-HDR and FFQ, respectively, with FFQ overestimating nutrient intake. Pearson correlations between log-transformed estimates from FFQ and 24-HDR for energy, protein, carbohydrate, fat, Fe and Zn were 0·47, 0·48, 0·45, 0·33, 0·4 and 0·54, respectively. Energy-adjusted and de-attenuated correlations ranged from 0·41 (saturated fat) to 0·73 (Na). The highest misclassification into extreme tertiles was observed for fat (22 %), saturated fat (21 %) and Na (21 %). Bias existed at higher intake levels as observed by Bland-Altman plots. In conclusion, NINA-DISH is a valid and feasible tool for estimating dietary intakes among urban pregnant women in Western India.

Association of Vegetable and Animal Flesh Intake with Inflammation in Pregnant Women from India.

In pregnant women, studies are lacking on the relationship of vegetable and animal flesh (poultry, red meat and seafood) intake with inflammation, especially in low- and middle-income countries. We conducted a cohort study of pregnant women receiving antenatal care at BJ Medical College in Pune, India. The dietary intake of pregnant women was queried in the third trimester using a validated food frequency questionnaire. Twelve inflammatory markers were measured in plasma samples using immunoassays. Only 12% of the study population were vegetarians, although animal flesh intake levels were lower compared to Western populations. In multivariable models, higher intakes of total vegetables were associated with lower levels of the T-helper (Th) 17 cytokine interleukin (IL)-17a (p = 0.03) and the monocyte/macrophage activation marker soluble CD163 (sCD163) (p = 0.02). Additionally, higher intakes of poultry were negatively associated with intestinal fatty-acid binding protein (I-FABP) levels (p = 0.01), a marker of intestinal barrier dysfunction and Th2 cytokine IL-13 (p = 0.03), and higher seafood was associated with lower IL-13 (p = 0.005). Our data from pregnant women in India suggest that a higher quality diet emphasizing vegetables and with some animal flesh is associated with lower inflammation. Future studies should confirm these findings and test if modulating vegetables and animal flesh intake could impact specific aspects of immunity and perinatal health.

Intensified Short Symptom Screening Program for Dengue Infection during Pregnancy, India.

Mosquitoborne diseases (e.g., malaria, dengue, and chikungunya) are endemic to India and pose diagnostic challenges during pregnancy. We evaluated an intensified short symptom screening program in India to diagnose dengue during pregnancy. During October 2017-January 2018, we screened pregnant women during antenatal surveillance for symptoms of mosquitoborne diseases (fever only, fever with conjunctivitis, fever with rash, or all 3 symptoms) within the previous 15 days. Of 5,843 pregnant women screened, 52 were enrolled and tested for dengue, chikungunya, and Zika viruses by using a Trioplex real-time reverse transcription PCR. Of 49 who had complete results, 7 (14%) were dengue positive. Of these ocular pain was seen in 4 (57%) and conjunctivitis in 7 (100%). Intensified symptom screening using conjunctivitis, in addition to rash, in pregnant women with fever might improve dengue case detection and can be included in routine symptom screening during pregnancy.

Systemic Inflammation in Pregnant Women With Latent Tuberculosis Infection.

Background: Recent studies in adults have characterized differences in systemic inflammation between adults with and without latent tuberculosis infection (LTBI+ vs. LTBI-). Potential differences in systemic inflammation by LTBI status has not been assess in pregnant women. Methods: We conducted a cohort study of 155 LTBI+ and 65 LTBI- pregnant women, stratified by HIV status, attending an antenatal clinic in Pune, India. LTBI status was assessed by interferon gamma release assay. Plasma was used to measure systemic inflammation markers using immunoassays: IFNß, CRP, AGP, I-FABP, IFNγ, IL-1ß, soluble CD14 (sCD14), sCD163, TNF, IL-6, IL-17a and IL-13. Linear regression models were fit to test the association of LTBI status with each inflammation marker. We also conducted an exploratory analysis using logistic regression to test the association of inflammatory markers with TB progression. Results: Study population was a median age of 23 (Interquartile range: 21-27), 28% undernourished (mid-upper arm circumference (MUAC) <23 cm), 12% were vegetarian, 10% with gestational diabetes and 32% with HIV. In multivariable models, LTBI+ women had significantly lower levels of third trimester AGP, IL1ß, sCD163, IL-6 and IL-17a. Interestingly, in exploratory analysis, LTBI+ TB progressors had significantly higher levels of IL1ß, IL-6 and IL-13 in multivariable models compared to LTBI+ non-progressors. Conclusions: Our data shows a distinct systemic immune profile in LTBI+ pregnant women compared to LTBI- women. Data from our exploratory analysis suggest that LTBI+ TB progressors do not have this immune profile, suggesting negative association of this profile with TB progression. If other studies confirm these differences by LTBI status and show a causal relationship with TB progression, this immune profile could identify subsets of LTBI+ pregnant women at high risk for TB progression and who can be targeted for preventative therapy.

Screening and diagnosis of gestational diabetes in India: a systematic review and meta-analysis.

AIMS: Although diabetes is rapidly increasing in India, there is no national consensus on best practices for screening, diagnosis, and management of gestational diabetes mellitus (GDM). The goal of this study was to systematically review the literature for studies reporting the prevalence and screening and diagnostic methods for gestational diabetes in India. METHODS: We searched MEDLINE, Embase, and POPLINE for studies on screening for GDM in India. We included English-language full reports and conference abstracts of cross-sectional studies, prospective, and retrospective cohorts that reported the screening method and prevalence of GDM. We performed descriptive analysis on all studies and meta-analysis, meta-regression, and subgroup meta-analysis on studies with medium or low risk of bias. RESULTS: We included 64 studies reporting 90 prevalence estimates. Prevalence estimates ranged from 0 to 41.9%. Subset meta-analyses showed that the IADPSG diagnostic criteria found significantly more GDM cases (prevalence = 19.19% [15.5, 23.6], p < 0.05) than the WHO 1999 criteria (10.13% [8.17, 12.50]) and DIPSI criteria (7.37% [5.2, 10.16]). Studies that compared the IADPSG and WHO 1999 criteria showed poor positive agreement (33-79%). Studies specifying time of GDM diagnosis showed that patients (11-60%) develop GDM as early as the first trimester, but many GDM cases (16-40%) are missed if screened only at first visit. CONCLUSIONS: In India, prevalence estimates of GDM vary substantially by diagnostic criteria. When evaluating screening and diagnostic criteria for GDM, providers should consider their patients' needs and correlate screening criteria with pregnancy outcomes.

Heterosexual anal sex among female sex workers in high HIV prevalence states of India: need for comprehensive intervention.

INTRODUCTION: Role of vaginal sex in heterosexual transmission of HIV has been investigated but that of heterosexual anal sex (HAS) is not fully understood. This paper examines practice of HAS among Female Sex Workers (FSWs) and its correlates in India where the HIV epidemic is being primarily driven by core groups like FSWs. METHODS: Data for this paper are drawn from Round I survey of 9667 FSWs in the Integrated Biological and Behavioral Assessment (IBBA) from 23 districts of 4 high HIV prevalent states of India. Bivariate and multivariate analysis identified factors associated with HAS. RESULTS: Ever having anal sex was reported by 11.9% FSWs (95% CI: 11.3%-12.6%). Typology (AOR 2.20, 95% CI 1.64-2.95) and literacy (AOR 1.28, 95% CI 1.10-1.49) were positively associated with practice of HAS. Longer duration in sex trade (AOR 1.69, 95% CI 1.44-1.99), entertaining larger number of clients the previous week (AOR 1.78, 95% CI 1.47-2.15), alcohol consumption (AOR 1.21, 95% CI 1.03-1.42) and inability to negotiate condom use (AOR 1.53, 95% CI 1.28-1.83) were also correlated with HAS. Self-risk perception for HIV (AOR 1.46, 95% CI 1.25-1.71) did not impede HAS. Although symptoms of sexually transmitted infections (STIs) in the last 12 months were associated with anal sex (AOR 1.39, 95% CI 1.13-1.72) there was no significant association between laboratory confirmed HIV and other STIs with HAS. CONCLUSION: Practice of HAS by FSWs might significantly contribute to HIV transmission in India. This study also shows that despite self-risk perception for HIV, even literate FSWs with longer duration in sex work report HAS. General messages on condom use may not influence safe HAS. FSWs need to be targeted with specific messages on HIV transmission during anal sex. Women controlled prevention methods, such as rectal microbicides and vaginal microbicides are needed.

Correlates of premarital relationships among unmarried youth in Pune district, Maharashtra, India.

CONTEXT: Although premarital partnerships-whether or not they involve sex-are widely discouraged in India, some youth do form such partnerships. It is important to know more about the nature of and the factors associated with these relationships. METHODS: Data are drawn from a community-based study of 15-24-year-olds in urban slum and rural settings in Pune District, Maharashtra. Multivariate analyses were conducted to identify associations between youths' individual, peer and family factors and their experience of romantic relationships and physical intimacy, including intercourse. RESULTS: Among young men, 17-24% had had a romantic relationship, 20-26% had engaged in some form of physical intimacy and 16-18% had had sex; the proportions among young women were 5-8%, 4-6% and 1-2%, respectively. Exposure to alcohol, drugs or pornographic films and having more frequent interaction with peers were positively associated with romantic and sexual relationships for both young women and young men. Educational attainment was negatively associated with both types of relationships for young women, but only with sexual relationships for young men. Closeness to parents was negatively associated with relationships only for young women. Young women whose father beat their mother were more likely than other young women to form romantic partnerships, and those beaten by their family had an elevated risk of entering romantic and sexual partnerships. Youth who reported strict parental supervision were no less likely than others to enter relationships. CONCLUSIONS: Program interventions should ensure that youth are fully informed and equipped to make safe choices and negotiate wanted outcomes, while positively influencing their peer networks; encourage closer interaction between parents and children; and be tailored to the different circumstances and experiences of young women and men.

Romance and sex: pre-marital partnership formation among young women and men, Pune district, India.

Using qualitative and survey data in a rural and an urban slum setting in Pune district, India, this paper describes patterns of pre-marital romantic partnerships among young people aged 15-24, in spite of norms that discourage opposite-sex interaction before marriage. 25-40% of young men and 14-17% of young women reported opposite-sex friends. Most young people devised strategies to interact with others, largely from the same neighbourhood. There were wide gender differences with regard to making or receiving romantic proposals, having a romantic partner and experiencing hand-holding, kissing and sexual relations. For those who engaged in sexual relations, the time from the onset of the partnership to having sexual relations was short. Sex most often took place without protection or communication, and for a disturbing minority of young women only after persuasion or without consent. Among those who were unmarried, a large percentage had expected to marry their romantic partner, but for a third of young women and half of young men the relationship had been discontinued. Partnership formation often leads to physical intimacy, but intimacy should be wanted, informed and safe. Findings call for programmes that inform youth in non-threatening, non-judgmental and confidential ways, respect their sexual rights and equip them to make safe choices and negotiate wanted outcomes.