08. EDA

Francesca Schiaffino, Nora Pisanic, Josh M. Colston, Dixner Rengifo, Maribel Paredes Olortegui,
Valentino Shapiama, Pablo Peñataro Yori, Christopher D. Heaney, Meghan F. Davis, Margaret N. Kosek.

F. Schiaffino et al. / Science of the Total Environment 743 (2020) 140531

The performance of eight microbial source tracking (MST) markers was evaluated in a low-resource, tropical community located in Iquitos, Peru. Fecal samples from humans, dogs, cats, rats, goats, buffalos, guinea-pigs, chickens, ducks, pigeons, and parrots were collected (n = 117). All samples were tested with human (BacHum, HF183-Taqman), dog (BactCan), pig (Pig-2-Bac), and avian (LA35, Av4143, ND5, cytB) markers using quantitative PCR (qPCR). Internal validity metrics were calculated using all animal fecal samples, as well as animal fecal samples contextually relevant for the Peruvian Amazon. Overall, Pig-2-Bac performed best, with 100% sensitivity and 88.5% specificity to detect the correct fecal source. Human-associated markers showed a sensitivity of 80.0% and 76.7%, and specificity of 66.2% and 67.6%. When limiting the analysis to contextually relevant animal fecal samples for the Peruvian Amazon, Av143 surpassed cytB with 95.7% sensitivity and 81.8% specificity. BactCan demonstrated 100% sensitivity and 47.4% specificity. The gene copy number detected by BacHum and HF183-Taqman were positively correlated (Pearson’s correlation coefficient: 0.785), as well as avian markers cytB with Av4143 (Pearson’s correlation coefficient: 0.508) and nd5 (Pearson’s correlation coefficient: 0.949). These findings suggest that markers such as Av4143, Pig2Bac, cytb and BacHum have acceptable performance to be impactful in source attribution studies for zoonotic enteric disease transmission in this and similar low-resource communities.

Elizabeth T. Rogawski McQuade, Jie Liu, Gagandeep Kang, Margaret N. Kosek, Aldo A. M. Lima, Pascal O. Bessong, Amidou Samie, Rashidul Haque, Estomih R. Mduma, Sanjaya Shrestha, Jose Paulo Leite, Ladaporn Bodhidatta, Najeeha Iqbal, Nicola Page, Ireen Kiwelu, Zulfiqar Bhutta, Tahmeed Ahmed, Eric R. Houpt, and James A. Platts-Mills.

The Journal of Infectious Diseases 2020;222:1858–68

Background.
The degree of protection conferred by natural immunity is unknown for many enteropathogens, but it is important to support the development of enteric vaccines.
Methods.
We used the Andersen-Gill extension of the Cox model to estimate the effects of previous infections on the incidence of subsequent subclinical infections and diarrhea in children under 2 using quantitative molecular diagnostics in the MAL-ED cohort. We used cross-pathogen negative control associations to correct bias due to confounding by unmeasured heterogeneity of exposure and susceptibility.
Results.
Prior rotavirus infection was associated with a 50% lower hazard (calibrated hazard ratio [cHR], 0.50; 95% confidence interval [CI], 0.41–0.62) of subsequent rotavirus diarrhea. Strong protection was evident against Cryptosporidium diarrhea (cHR, 0.32; 95% CI, 0.20–0.51). There was also protection due to prior infections for norovirus GII (cHR against diarrhea, 0.67; 95% CI, 0.49–0.91), astrovirus (cHR, 0.62; 95% CI, 0.48–0.81), and Shigella (cHR, 0.79; 95% CI, 0.65–0.95). Minimal protection was observed for other bacteria, adenovirus 40/41, and sapovirus.
Conclusions.
Natural immunity was generally stronger for the enteric viruses than bacteria, potentially due to less antigenic diversity. Vaccines against major causes of diarrhea may be feasible but likely need to be more immunogenic than natural infection.

Hannah Karen Mina Labayo, Monica J. Pajuelo, Kentaro Tohma, Lauren A. Ford-Siltz, Robert H. Gilman, Lilia Cabrera, Holger Mayta, Gerardo J. Sanchez, Anniuska Toledo Cornejo, Caryn Bern, Clyde Dapat, Tomonori Nochi, Gabriel I. Parra, Hitoshi Oshitani, Mayuko Saito.

H.K.M. Labayo et al. / EClinicalMedicine 27 (2020) 100561

Background: Norovirus (NV) causes acute gastroenteritis in infants. Humoral and fecal immunoglobulin A(IgA) responses have been correlated with protection against NV; however, the role of breast milk IgA against NV infection and associated diarrhea is still unknown. This study aimed to evaluate the protective role of NVspecific IgA (NV-IgA) in breast milk.

Methods: Ninety-five breast milk samples collected from mothers enrolled in a 2016
2017 Peruvian birth cohort study were tested for total IgA and NV-IgA by ELISA using GII¢4 variants and non-GII¢4 genotype virus-like particles (VLPs). Breast milk samples were grouped according to the NV infection and diarrheal status of infants: NV positive with diarrhea (NV+D+, n=18); NV positive without diarrhea (NV+D-, n=37); and NV negative without diarrhea (NV-D-, n=40). The percent positivity and titer of NV-IgA were compared among groups. The cross-reactivity was estimated based on the correlation of ratio between NV-IgA against GII¢4 variants and non-GII¢4 genotype VLPs.

Findings: NV-IgA had high positivity rates against different VLPs, especially against GII (89-100%). The NV+Dgroup had higher percent positivity (89% vs. 61%, p=0¢03) and median titer (1:100 vs 1:50, p=0¢03) of NV-IgA than the NV+D+ group against GI¢1 VLPs. A relatively high correlation between different GII¢4 variants (0¢87) and low correlation between genogroups (0¢23
0¢37) were observed.
Interpretation: Mothers with high positivity rates and titers of NV-IgA in breast milk had NV infected infants with reduced diarrheal symptoms. Antigenic relatedness to the genetic diversity of human norovirus was suggested.

Josh Colston, Maribel Paredes Olortegui, Benjamin Zaitchik, Pablo Peñataro Yori, Gagandeep Kang, Tahmeed Ahmed, Pascal Bessong, Esto Mduma, Zulfiqar Bhutta, Prakash Sunder Shrestha, Aldo Lima and Margaret Kosek.

Int. J. Environ. Res. Public Health 2020, 17, 487

Abstract:
Extreme floods pose multiple direct and indirect health risks. These risks include contamination of water, food, and the environment, often causing outbreaks of diarrheal disease. Evidence regarding the effects of flooding on individual diarrhea-causing pathogens is limited, but is urgently needed in order to plan and implement interventions and prioritize resources before climate-related disasters strike. This study applied a causal inference approach to data from a multisite study that deployed broadly inclusive diagnostics for numerous high-burden common enteropathogens. Relative risks (RRs) of infection with each pathogen during a flooding disaster that occurred at one of the sites—Loreto, Peru—were calculated from generalized linear models using a comparative interrupted time series framework with the other sites as a comparison group and adjusting for background seasonality. During the early period of the flood, increased risk of heat-stable enterotoxigenic E. coli (ST-ETEC) was identified (RR = 1.73 [1.10, 2.71]) along with a decreased risk of enteric adenovirus (RR = 0.36 [0.23, 0.58]). During the later period of the flood, sharp increases in the risk of rotavirus (RR = 5.30 [2.70, 10.40]) and sapovirus (RR = 2.47 [1.79, 3.41]) were observed, in addition to increases in transmission of Shigella spp. (RR = 2.86 [1.81, 4.52]) and Campylobacter spp. (RR = 1.41 (1.01, 1.07). Genotype-specific exploratory analysis reveals that the rise in rotavirus transmission during the flood was likely due to the introduction of a locally atypical, non-vaccine (G2P[4]) strain of the virus. Policy-makers should target interventions towards these pathogens—including vaccines as they become available—in settings where vulnerability to flooding is high as part of disaster preparedness strategies, while investments in radical, transformative, community-wide, and locally-tailored water and sanitation interventions are also needed.

Elizabeth T. Rogawski McQuade, Fariha Shaheen, Furqan Kabir, Arjumand Rizvi, James A. Platts-Mills, Fatima Aziz, Adil Kalam, Shahida Qureshi, Sarah Elwood, Jie Liu, Aldo A. M. Lima, Gagandeep Kang, Pascal Bessong, Amidou Samie, Rashidul Haque, Estomih R. Mduma, Margaret N. Kosek, Sanjaya Shrestha, Jose Paulo Leite, Ladaporn Bodhidatta, Nicola Page, Ireen Kiwelu, Sadia Shakoor,
Ali Turab, Sajid Bashir Soofi, Tahmeed Ahmed, Eric R. Houpt, Zulfiqar Bhutta, Najeeha Talat Iqba.

PLoS Negl Trop Dis 14(8): e0008536.

Culture-independent diagnostics have revealed a larger burden of Shigella among children in low-resource settings than previously recognized. We further characterized the epidemiology of Shigella in the first two years of life in a multisite birth cohort. We tested 41,405 diarrheal and monthly non- diarrheal stools from 1,715 children for Shigella by quantitative PCR. To assess risk factors, clinical factors related to age and culture positivity, and associations with inflammatory biomarkers, we used log-binomial regression with generalized estimating equations. The prevalence of Shigella varied from 4.9%-17.8% in non-diarrheal stools across sites, and the incidence of Shigella-attributable diarrhea was 31.8 cases (95% CI: 29.6, 34.2) per 100 child-years. The sensitivity of culture compared to qPCR was 6.6% and increased to 27.8% in Shigella-attributable dysentery. Shigella diarrhea episodes were
more likely to be severe and less likely to be culture positive in younger children. Older age (RR: 1.75, 95% CI: 1.70, 1.81 per 6-month increase in age), unimproved sanitation (RR: 1.15, 95% CI: 1.03, 1.29), low maternal education (<10 years, RR: 1.14, 95% CI: 1.03, 1.26), initiating complementary foods before 3 months (RR: 1.10, 95% CI: 1.01, 1.20), and malnutrition (RR: 0.91, 95% CI: 0.88, 0.95 per unit increase in weight-for-age z-score) were risk factors for Shigella. There was a linear dose-response between Shigella quantity and myeloperoxidase concentrations. The burden of Shigella varied widely across sites, but uniformly increased through the second year of life and was associated with intestinal inflammation. Culture missed most clinically relevant cases of severe diarrhea and dysentery.

Timothy L. McMurry, Elizabeth T. Rogawski McQuade, Jie Liu, Gagandeep Kang, Margaret N. Kosek, Aldo A. M. Lima, Pascal O. Bessong, Amidou Samie, Rashidul Haque, Estomih R. Mduma, Jose Paulo Leite, Ladaporn Bodhidatta, Najeeha T. Iqbal, Nicola Page, Ireen Kiwelu, Zulfiqar A. Bhutta, Tahmeed Ahmed, Eric R. Houpt, and James A. Platts-Mills.

Clinical Infectious Diseases 2021;72(11):e806–14

Background.
Prolonged enteropathogen shedding after diarrhea complicates the identification of etiology in subsequent episodes and is an important driver of pathogen transmission. A standardized approach has not been applied to estimate the duration of shedding for a wide range of pathogens.

Methods.
We used a multisite birth cohort of children 0–24 months of age from whom diarrheal and monthly nondiarrheal stools were previously tested by quantitative polymerase chain reaction for 29 enteropathogens. We modeled the probability of detection of the etiologic pathogen before and after diarrhea using a log-normal accelerated failure time survival model and estimated the median duration of pathogen carriage as well as differences in subclinical pathogen carriage 60 days after diarrhea onset in comparison to a prediarrhea baseline.

Results.
We analyzed 3247 etiologic episodes of diarrhea for the 9 pathogens with the highest attributable burdens of diarrhea. The median duration of postdiarrheal carriage varied widely by pathogen, from about 1 week for rotavirus (median, 8.1 days [95% confidence interval {CI}, 6.2–9.6]) to >1 month for Cryptosporidium (39.5 days [95% CI, 30.6–49.0]). The largest increases in subclinical pathogen carriage before and after diarrhea were seen for Cryptosporidium (prevalence difference between 30 days prior and 60 days after diarrhea onset, 0.30 [95% CI, .23–.39]) and Shigella (prevalence difference, 0.21 [95% CI, .16–.27]).

Conclusions.
Postdiarrheal shedding was widely variable between pathogens, with strikingly prolonged shedding seen for Cryptosporidium and Shigella. Targeted antimicrobial therapy and vaccination for these pathogens may have a relatively large impact on transmission.