Impacts of small-scale chicken farming activity on antimicrobial-resistant Escherichia coli carriage in backyard chickens and children in rural Ecuador.

The emergence, spread, and persistence of antimicrobial resistance (AMR) remains a pressing global concern. Increased promotion of commercial small-scale agriculture within low-resource settings has facilitated an increased use in antimicrobials as growth promoters globally, creating antimicrobial-resistant animal reservoirs. We conducted a longitudinal field study in rural Ecuador to monitor the AMR of Escherichia coli populations from backyard chickens and children at three sample periods with approximately 2-month intervals (February, April, and June 2017). We assessed AMR to 12 antibiotics using generalized linear mixed effects models (GLMM). We also sampled and assessed AMR to the same 12 antibiotics in one-day-old broiler chickens purchased from local venders. One-day-old broiler chickens showed lower AMR at sample period 1 compared to sample period 2 (for 9 of the 12 antibiotics tested); increases in AMR between sample periods 2 and 3 were minimal. Two months prior to the first sample period (December 2016) there was no broiler farming activity due to a regional collapse followed by a peak in annual farming in February 2017. Between sample periods 1 and 2, we observed significant increases in AMR to 6 of the 12 antibiotics in children and to 4 of the 12 antibiotics in backyard chickens. These findings suggest that the recent increase in farming, and the observed increase of AMR in the one-day old broilers, may have caused the increase in AMR in backyard chickens and children. Small-scale farming dynamics could play an important role in the spread of AMR in low- and middle-income countries.

Latent variable modeling to develop a robust proxy for sensitive behaviors: application to latrine use behavior and its association with sanitation access in a middle-income country.

BACKGROUND: Globally, diarrhea is a leading cause of child morbidity and mortality. Although latrines are integral for reducing enteric pathogen transmission, several studies have shown no evidence that latrine ownership improved child health. There are a number of explanations for these results. One explanation is that latrine access does not equate to latrine use. Latrine use, however, is difficult to accurately ascertain, as defecation behavior is often stigmatized. To address this measurement issue, we measure latrine use as a latent variable, indicated by a suite of psychosocial variables. METHODS: We administered a survey of 16 defecation-related psychosocial questions to 251 individuals living in rural Ecuador. We applied latent class analysis (LCA) to these data to model the probability of latrine use as a latent variable. To account for uncertainty in predicted latent class membership, we used a pseudo-class approach to impute five different probabilities of latrine use for each respondent. Via regression modeling, we tested the association between household sanitation and each imputed latrine use variable. RESULTS: The optimal model presented strong evidence of two latent classes (entropy = 0.86): consistent users (78%) and inconsistent users (22%), predicted by 5 of our 16 psychosocial variables. There was no evidence of an association between the probability of latrine use, predicted from the LCA, and household access to basic sanitation (OR = 1.1, 95% CI = 0.6-2.1). This suggests that home access to a sanitation facility may not ensure the use of the facility for every family member at all times. CONCLUSION: Effective implementation and evaluation of sanitation programs requires accurate measurement of latrine use. Psychosocial variables, such as norms, perceptions, and attitudes may provide robust proxy-measures. Future longitudinal studies will help to strengthen the use of these surrogate measures, as many of these factors may be subject to secular trends. Additionally, subgroup analyses will elucidate how our  proxy indicators of latrine defecation vary by individual-level characteristics.

Heterogeneity in norovirus shedding duration affects community risk.

Norovirus is a common cause of gastroenteritis in all ages. Typical infections cause viral shedding periods of days to weeks, but some individuals can shed for months or years. Most norovirus risk models do not include these long-shedding individuals, and may therefore underestimate risk. We reviewed the literature for norovirus-shedding duration data and stratified these data into two distributions: regular shedding (mean 14-16 days) and long shedding (mean 105-136 days). These distributions were used to inform a norovirus transmission model that predicts the impact of long shedders. Our transmission model predicts that this subpopulation increases the outbreak potential (measured by the reproductive number) by 50-80%, the probability of an outbreak by 33%, the severity of transmission (measured by the attack rate) by 20%, and transmission duration by 100%. Characterizing and understanding shedding duration heterogeneity can provide insights into community transmission that can be useful in mitigating norovirus risk.

Norovirus outbreaks: a systematic review of commonly implicated transmission routes and vehicles.

Causal mechanisms of norovirus outbreaks are often not revealed. Understanding the transmission route (e.g. foodborne, waterborne, or environmental) and vehicle (e.g. shellfish or recreational water) of a norovirus outbreak, however, is of great public health importance; this information can facilitate interventions for an ongoing outbreak and regulatory action to limit future outbreaks. Towards this goal, we conducted a systematic review to examine whether published outbreak information was associated with the implicated transmission route or vehicle. Genogroup distribution was associated with transmission route and food vehicle, but attack rate and the presence of GII.4 strain were not associated with transmission route, food vehicle, or water vehicle. Attack rate, genogroup distribution, and GII.4 strain distribution also varied by other outbreak characteristics (e.g. setting, season, hemisphere). These relationships suggest that different genogroups exploit different environmental conditions and thereby can be used to predict the likelihood of various transmission routes or vehicles.

The epidemiology of published norovirus outbreaks: a review of risk factors associated with attack rate and genogroup.

The purpose of this study was to examine global epidemiological trends in human norovirus (NoV) outbreaks by transmission route and setting, and describe relationships between these characteristics, viral attack rates, and the occurrence of genogroup I (GI) or genogroup II (GII) strains in outbreaks. We analysed data from 902 reverse transcriptase-polymerase chain reaction-confirmed, human NoV outbreaks abstracted from a systematic review of articles published from 1993 to 2011 and indexed under the terms 'norovirus' and 'outbreak'. Multivariate regression analyses demonstrated that foodservice and winter outbreaks were significantly associated with higher attack rates. Foodborne and waterborne outbreaks were associated with multiple strains (GI+GII). Waterborne outbreaks were significantly associated with GI strains, while healthcare-related and winter outbreaks were associated with GII strains. These results identify important trends for epidemic NoV detection, prevention, and control.

Associations between water-treatment methods and diarrhoea in HIV-positive individuals.

This manuscript extends our previously published work (based on data from one clinic) on the association between three drinking water-treatment modalities (boiling, filtering, and bottling) and diarrhoeal disease in HIV-positive persons by incorporating data from two additional clinics collected in the following year. We conducted a cross-sectional survey of drinking water patterns, medication usage, and episodes of diarrhoea among HIV-positive persons attending clinics associated with the San Francisco Community Consortium. We present combined results from our previously published work in one clinic (n = 226) with data from these two additional clinics (n = 458). In this combined analysis we employed logistic regression and marginal structural modelling of the data. The relative risk of diarrhoea for 'always' vs. 'never' drinking boiled water was 0.68 (95% CI 0.45-1.04) and for 'always' vs. 'never' drinking bottled water was 1.22 (95 % CI 0.82-1.82). Drinking filtered water was unrelated to diarrhoea (1.03 (95% CI 0.78, 1.35) for 'always' vs. 'never' drinking filtered water]. Adjustment for confounding did not have any notable effect on the point estimates (0.61, 1.35 and 0.98 for boiled, bottled, and filtered water respectively, as defined above). The risk of diarrhoea was lower among those consuming boiled water but this finding was not statistically significant. Because of these findings, the importance of diarrhoea in immunocompromised individuals, and the limitations of cross-sectional data further prospective investigations of water consumption and diarrhoea among HIV-positive individuals are needed.

Risk factors in HIV-associated diarrhoeal disease: the role of drinking water, medication and immune status.

In a cross-sectional survey of 226 HIV-infected men, we examined the occurrence of diarrhoea and its relationship to drinking water consumption patterns, risk behaviours, immune status and medication use. Diarrhoea was reported by 47% of the respondents. Neither drinking boiled nor filtered water was significantly associated with diarrhoea (OR = 0.5 [0.2, 1.6], 1.2 [0.6, 2.5] respectively), whereas those that drank bottled water were at risk for diarrhoea (OR = 3.0 [1.1, 7.8]). Overall, 47% always or often used at least one water treatment. Of the 37% who were very concerned about drinking water, 62% had diarrhoea, 70% always or often used at least one water treatment. An increase in CD4 count was protective only for those with a low risk of diarrhoea associated with medication (OR = 0.6 [0.5, 0.9]). A 30% attributable risk to diarrhoea was estimated for those with high medication risk compared to those with low medication risk. The significant association between concern with drinking water and diarrhoea as well as between concern with drinking water and water treatment suggests awareness that drinking water is a potential transmission pathway for diarrhoeal disease. At the same time we found that a significant portion of diarrhoea was associated with other sources not related to drinking water such as medication usage.