Noroviruses are a leading cause of acute gastroenteritis worldwide, yet no licensed vaccines or antivirals are available. A major barrier to broadly protective vaccine development is the extensive genetic and antigenic diversity of these viruses, leading to immune escape. However, the structural mechanisms underlying this immune escape remain incompletely defined. Here, we analyze a panel of monoclonal antibodies generated against a pandemic GII.4 variant to define the molecular determinants of neutralizing immunity. Guided by immunogenetic features and cross-reactivity patterns spanning four decades of viral evolution, we resolved the atomic structures of two neutralizing antibodies targeting the principal immunodominant antigenic sites, A and G. We show that the spatial positioning of antigenic site G shapes neutralizing responses and that coordinated substitutions within these epitopes drove the rapid antigenic transitions observed between 2004 and 2012.Together, these findings establish a structural framework for GII.4 antigenic evolution and inform rational vaccine design.

Chagas disease is a major protozoan infection in the Americas, causing approximately 12,000 deaths each year. It is caused by Trypanosoma cruzi, and can be transmitted transplacentally, leading to congenital Chagas disease, a silent route that carries substantial risk for newborns. However, the mechanisms underlying congenital Chagas transmission are poorly understood. Here, we evaluated whether T. cruzi infection alters the placental microenvironment and systemic physiology, and whether such alterations are associated with congenital transmission. Integrating bulk RNA sequencing, proteomics, and spatial transcriptomics, we show that T. cruzi infection elicits profound molecular remodeling in both placenta and peripheral blood, regardless of transmission status. Transmitting mothers exhibit a distinct transcriptional signature enriched for inflammatory and tissue-remodeling pathways. Notably, peripheral blood profiles mirrored some placental alterations. A panel of inflammatory serum proteins showed promising predictive potential for transmission risk, with implications for prenatal monitoring. Together, these findings support a fundamental shift in the conceptual framework of congenital Chagas disease, from a transmission-centered model to one that recognizes infection-driven placental damage as a pathological spectrum and identifies peripheral blood as a promising, non-invasive source of predictive biomarkers for adverse pregnancy outcomes. This framework motivates the further application of single-cell-resolution approaches to refine models of congenital Chagas pathogenesis and the systematic analysis of maternal peripheral blood during pregnancy to enable early risk stratification and the development of predictive tools for adverse outcomes.

Antibiotic-resistant bacteria are spreading in clinical, industrial, and environmental ecosystems. The spreading dynamics to and from the environment are unknown, largely due to the lack of appropriate (robust, fast, low-cost) analytical assays. In this study, we developed C12a, a versatile molecular toolbox to detect genetic markers of antibiotic resistance using CRISPR/Cas12a. Biochemical characterization show that the C12a toolbox can detect less than 100 attoMolar of pure DNA fragments from the blaCTX-M15 and floR genes, conferring resistance to b-lactams and amphenicols, respectively important for human and veterinary uses. In microbiological assays, C12a detected less than 102 CFU/mL and high concordance was observed if compared to antibiotic susceptibility tests, PCR, or to whole genome sequencing. Additionally, C12a confirmed a high prevalence of the integrase/integron system in E. coli isolates containing multiple antibiotic resistance genes (ARGs). The C12a toolbox shows equivalent detection performance in diverse laboratory settings, results readout (Fluorescence vs. FLA) or input sample. Altogether, this work presents a comprehensive proof-of-concept, development description, and biochemical characterization of a collection of molecular tools to detect antibiotic resistance markers in a one health setup.

Gut colonization with extended-spectrum beta lactamase-producing Enterobacterales (ESBL-E) is increasingly common among children in low- and middle-income countries. Some children nevertheless remain never or rarely colonized during early life. Understanding how this protection is conferred could be helpful for designing future interventions to protect children's health. Here, we investigated whether differences in gut microbiome development could underlie differential susceptibility to ESBL-E gut colonization over time among children in peri-urban Lima. Weekly stool and daily surveys were collected from 345 children < 3 years old during a 2016-19 study of enteric infections. A subset of children (n = 12) was rarely gut-colonized with ESBL-E from 1-16 months of age. We performed short-read metagenomic sequencing of stool collected at 3, 6, 7, 9, 12, and 16 months from these children and a random subset of 42 frequently colonized children, and characterized differences in their exposures and gut microbiomes. No differences in gut taxa or functional pathways were identified over time, though children harbored differentially abundant taxa, more unique E. coli strains, and a higher abundance of blaCTX-M gene copies at ESBL-E-positive versus negative timepoints. Differing patterns of ESBL-E colonization over time among children in peri-urban Lima do not appear to be related to differences in gut microbiome development.

Background:The effects of antibiotic use on children's gut microbiomes and resistomes are not well characterized in middle-income countries, where pediatric antibiotic consumption is exceptionally common. We characterized the effects of antibiotics commonly used by Peruvian children (i.e., amoxicillin, azithromycin, cefalexin, sulfa-trimethoprim) on gut diversity, genera, and antibiotic resistance gene (ARG) abundance from 3-16 months. Methods:This study included 54 children from a prospective cohort of enteric infections in peri-urban Lima, 2016-2019. Stool collected at 3, 6, 7, 9, 12, and 16 months underwent DNA extraction and short-read metagenomic sequencing. We profiled the taxonomy of stool metagenomes and assessed ARG abundance by aligning reads to the ResFinder database. We used daily surveillance data (40,662 observations) to tabulate the number of antibiotic courses consumed in the 30 days prior to stool sampling. Using linear mixed models, the association of recent antibiotic use with species richness, diversity, gut genera, and ARG abundance over time was examined. Results:Most children were vaginally delivered (73%), received breastmilk almost daily over the study period, and belonged to socioeconomically diverse households. Amoxicillin, azithromycin, cefalexin, and sulfa-trimethoprim did not impact gut diversity or genera abundance. Azithromycin use significantly impacted ARGs from the macrolide, aminoglycoside, and folate pathway antagonist classes. Amoxicillin use significantly increased total ARGs. Antibiotics' effects on ARGs appeared to be independent of gut microbiome changes. Conclusion:Common antibiotics like amoxicillin and azithromycin may be key drivers of the gut resistome but not the microbiome during early childhood in this setting with frequent breastfeeding.

As many as one in three people worldwide have anemia, with young children at increased risk of both disease and complications. In settings without clinical laboratories, portable hemoglobinometers serve important roles in diagnosing anemia and estimating prevalence. Here, we assess the validity of two such point-of-care devices-the HemoCue Hb201 and the HemoCue Hb301-relative to the international reference standard, the cyanmethemoglobin method. In total, 428 children ages 6-60 months were recruited at health posts in Lima, Peru, and venous and capillary blood samples were collected from each participant. Venous blood was assessed with the cyanmethemoglobin method, whereas capillary blood was assessed using the Hb201 and the Hb301; 16.1% of participants were found to have anemia using the cyanmethemoglobin method. Both the Hb201 (43.7%) and the Hb301 (20.6%) overestimated this prevalence, with the former reaching statistical significance (P <0.0001 and P = 0.11, respectively). Both devices also tended to underestimate hemoglobin concentration, with the Hb201 (mean difference =-0.99 g/dL; percentage error =-8.1%) being appreciably less accurate than the Hb301 (mean difference =-0.35 g/dL; percentage error =-2.7%). Areas under the curve for the Hb201 (0.92) and the Hb301 (0.93) were statistically similar (P = 0.28); however, the Hb201 incorrectly classified 29.4% of participants compared with 11.0% for the Hb301. Both devices had more false positives than false negatives. In conclusion, the Hb301 was found to be significantly more accurate than the Hb201 at measuring hemoglobin, diagnosing anemia, and estimating anemia prevalence.

The aim of this study was to evaluate different transportation and incubation conditions to test the viability of adult Fasciola hepatica in order to propose a new cultivation workflow. The adult stage of F. hepatica was obtained from naturally infected cattle at a local slaughterhouse in Lima, Peru. Different transport and incubation conditions of F. hepatica were tested, evaluating its viability through a motility scale. DMEM and RPMI 1640 media presented better transport conditions compared to Hedon-Fleig and PBS media (p < 0.001), maintaining the flukes at 37 degrees C. Also, DMEM and RPMI-1640 media presented better incubation conditions compared to Hedon-fleig (p < 0.001). A minimum of 3 ml of medium per fluke was required to maintain best viability (p < 0.001) and no differences in viability were found between the different types of culture plates (p > 0.05). In addition, we found that incubation with DMSO (dimethyl sulfoxide) at concentrations greater than 0.5% v/v for 48 hours generates toxicity (p < 0.001). In conclusion, RPMI 1640 and DMEN media presented better transport and in vitro cultivation conditions for F. hepatica, using DMSO at concentrations lower than 0.5% v/v.

Children living in low-resource settings are frequently gut-colonized with multidrug-resistant bacteria. We explored whether breastfeeding may protect against children's incident gut colonization with extended-spectrum beta-lactamase-producing Escherichia coli (ESBL-Ec) and Klebsiella, Enterobacter, or Citrobacter spp. (ESBL-KEC). We screened 937 monthly stool samples collected from 112 children aged 1-16 months during a 2016-19 prospective cohort study of enteric infections in peri-urban Lima. We used 52,816 daily surveys to examine how exposures to breastfeeding in the 30 days prior to a stool sample were associated with children's risks of incident gut-colonization, controlling for antibiotic use and other covariates. We sequenced 78 ESBL-Ec from 47 children to explore their diversity. Gut-colonization with ESBL-Ec was increasingly prevalent as children aged, approaching 75% by 16 months, while ESBL-KEC prevalence fluctuated between 18% and 36%. Through 6 months of age, exclusively providing human milk in the 30 days prior to a stool sample did not reduce children's risk of incident gut-colonization with ESBL-Ec or ESBL-KEC. From 6 to 16 months of age, every 3 additional days of breastfeeding in the prior 30 days was associated with 6% lower risk of incident ESBL-Ec gut-colonization (95% CI: 0.90, 0.98, p = .003). No effects were observed on incident ESBL-KEC colonization. We detected highly diverse ESBL-Ec among children and few differences between children who were predominantly breastfed (mean age: 4.1 months) versus older children (10.8 months). Continued breastfeeding after 6 months conferred protection against children's incident gut colonization with ESBL-Ec in this setting. Policies supporting continued breastfeeding should be considered in efforts to combat antibiotic resistance.

BackgroundEnterotoxigenic E. coli (ETEC) is a leading cause of diarrheal morbidity and mortality in children, although the data on disease burden, epidemiology, and impact on health at the community level are limited.MethodsIn a longitudinal birth cohort study of 345 children followed until 24 months of age in Lima, Peru, we measured ETEC burden in diarrheal and non-diarrheal samples using quantitative PCR (LT, STh, and STp toxin genes), studied epidemiology and measured anthropometry in children.ResultsAbout 70% of children suffered from one or more ETEC diarrhea episodes. Overall, the ETEC incidence rate (IR) was 73 per 100 child-years. ETEC infections began early after birth causing 10% (8.9–11.1) ETEC-attributable diarrheal burden at the population level (PAF) in neonates and most of the infections (58%) were attributed to ST-ETEC [PAF 7.9% (1.9–13.5)] and LT + ST-ETEC (29%) of which all the episodes were associated with diarrhea. ETEC infections increased with age, peaking at 17% PAF (4.6–27.7%; p = 0.026) at 21 to 24 months. ST-ETEC was the most prevalent type (IR 32.1) with frequent serial infections in a child. The common colonization factors in ETEC diarrhea cases were CFA/I, CS12, CS21, CS3, and CS6, while in asymptomatic ETEC cases were CS12, CS6 and CS21. Only few (5.7%) children had repeated infections with the same combination of ETEC toxin(s) and CFs, suggested genotype-specific immunity from each infection. For an average ETEC diarrhea episode of 5 days, reductions of 0.060 weight-for-length z-score (0.007 to 0.114; p = 0.027) and 0.061 weight-for-age z-score (0.015 to 0.108; p = 0.009) were noted in the following 30 days.ConclusionThis study showed that ETEC is a significant pathogen in Peruvian children who experience serial infections with multiple age-specific pathotypes, resulting in transitory growth impairment.

Abstract Background Despite widespread vaccination, pertussis has re-emerged as a serious public health concern worldwide. Since 2017, Peru has experienced an increase in pertussis cases exhibiting a higher risk of severity and death in young infants. Thus, a dose of the tetanus, diphtheria, and acellular pertussis (Tdap) vaccine is recommended for pregnant women in the third trimester. Although evidence suggests the maternal Tdap vaccine is safe and effective, its association with a reduced risk of pertussis in developing countries remains poorly investigated. Methods We conducted a case-control study to evaluate the association between Tdap vaccination during pregnancy and reduction in the risk of pertussis among infants aged <2 months in Peru. Pertussis cases and controls treated in healthcare facilities nationwide between 2019 and 2021 and confirmed by real-time polymerase chain reaction were included. The controls were randomly selected from test-negative patients. Odds ratios (ORs) and vaccine effectiveness (VE) were calculated using a multiple logistic regression model and 1 − (OR) × 100%, respectively. Results Fifty cases and 150 controls were included in the analysis. The mothers of 4% of cases and 16.7% of controls received Tdap vaccination during pregnancy, resulting in an OR of 0.19 (95% confidence interval [CI], .04–.86) and VE of 81% (95% CI, 14%–96%) for preventing pertussis in infants. Conclusions Peruvian infants <2 months old whose mothers received the Tdap vaccine in the third trimester of pregnancy had a significantly lower risk of pertussis. The Tdap vaccination is thus an effective intervention to reduce the burden of pertussis in at-risk populations.

Rapid molecular testing for severe acute respiratory coronavirus 2 (SARS-CoV-2) variants may contribute to the development of public health measures, particularly in resource-limited areas. Reverse transcription recombinase polymerase amplification using a lateral flow assay (RT-RPA-LF) allows rapid RNA detection without thermal cyclers. In this study, we developed two assays to detect SARS-CoV-2 nucleocapsid (N) gene and Omicron BA.1 spike (S) gene-specific deletion–insertion mutations (del211/ins214). Both tests had a detection limit of 10 copies/µL in vitro and the detection time was approximately 35 min from incubation to detection. The sensitivities of SARS-CoV-2 (N) RT-RPA-LF by viral load categories were 100% for clinical samples with high (>9015.7 copies/µL, cycle quantification (Cq): < 25) and moderate (385.5–9015.7 copies/µL, Cq: 25–29.9) viral load, 83.3% for low (16.5–385.5 copies/µL, Cq: 30–34.9), and 14.3% for very low (<16.5 copies/µL, Cq: 35–40). The sensitivities of the Omicron BA.1 (S) RT-RPA-LF were 94.9%, 78%, 23.8%, and 0%, respectively, and the specificity against non-BA.1 SARS-CoV-2-positive samples was 96%. The assays seemed more sensitive than rapid antigen detection in moderate viral load samples. Although implementation in resource-limited settings requires additional improvements, deletion–insertion mutations were successfully detected by the RT-RPA-LF technique.

OBJECTIVE:The aim of the study was to describe the clinicopathological profile of patients diagnosed with liver, bile ducts or gallbladder cancer.MATERIALS AND METHODS:Between 2006 and 2017, 89 patients (57% female; mean age: 62 years-old) with these cancers were diagnosed at two national hospitals in Lima, Peru.RESULTS:Most patients (64%) had advanced stages of disease. Anemia was more frequent in patients with bile duct and liver cancer and in advanced stages. Hypertension (HTN) was frequent among liver cancer patients (32%). The analysis by age showed that HTN was more frequent in patients over 50 years. Likewise, people under 50 years had more frequent history of previous infections (50%), Hepatitis B (HBV) being the most common.CONCLUSIONS:This study describes the baseline clinicopathological characteristics of a malignancy poorly studied in Peru.

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OBJECTIVE:To assess oral health-related quality of life (OHRQoL) changes before and after the primary surgical treatment in infants with cleft lip and/or palate (CL/P).DESIGN:Quasi-experimental study.METHODS:A total of 106 infants with CL/P younger than 2 years undergoing primary surgical treatment in the Plastic Surgery Service of the Instituto Nacional de Salud del Niño in Peru. The parent/caregiver answered a questionnaire about OHRQoL named the Peruvian version of the Early Childhood Oral Health Impact Scale (P-ECOHIS) in the pretreatment (baseline) and follow-up post-treatment. The total score of P-ECOHIS and their 2 sections (child impact and family impact) in the baseline and each follow-up period post-treatment scores were assessed. As well as, the type of the CL/P on OHRQoL, standardized effect sizes (ES) based on mean total change scores (difference between baseline and 12th month) were analyzed.RESULTS:Improvements in infant's OHRQoL after treatment were reflected in each follow-up period P-ECOHIS score compared to the baseline score. The total P-ECOHIS scores decreased significantly from 28.07 (baseline) to 7.7 (12th month; P < .0001), as did the individual domain scores (P < .0001). There were significant differences in the baseline and follow-up post-treatment scores of infants who reported improvement of the OHRQoL (P < .0001). The ES was large (3.79). The cleft lip had an improvement in the OHRQoL at 12th month post-treatment (P < .0001).CONCLUSIONS:Primary surgical post-treatment resulted in significant improvement of the infant's OHRQoL with CL/P.

Objetivo: El objetivo del estudio fue describir las características clínico-patológicas de individuos diagnosticados de cáncer de hígado, vías biliares o vesícula. Materiales y métodos: Entre el 2006 y 2017, se diagnosticaron 89 pacientes (57% mujeres; media: 62 años) con estos canceres en dos hospitales nacionales de Lima, Perú. Resultados: Los resultados mostraron que, independientemente del tipo de cáncer, 64% de los participantes habían sido diagnosticados en estadios avanzados. La anemia fue más frecuente en los pacientes con cáncer de vías biliares e hígado y en estadios avanzados. Se observó mayor frecuencia (32%) de hipertensión arterial (HTA) en el grupo con cáncer de hígado. El análisis por edad mostró que en los pacientes mayores de 50 años la HTA fue más frecuente. Asimismo, sujetos menores de 50 años reportaron antecedentes de infecciones previas en mayor frecuencia (50%), siendo Hepatitis B (HBV) la más común. Conclusiones: Este estudio describe las características clínico-patológicas de base de una neoplasia poco estudiada en el ámbito nacional.

This cross-sectional study evaluated epidemiologic characteristics of persons living with HIV (PWH) coinfected with Trypanosoma cruzi in Cochabamba, Bolivia, and estimated T. cruzi parasitemia by real-time quantitative polymerase chain reaction (qPCR) in patients with and without evidence of reactivation by direct microscopy. Thirty-two of the 116 HIV patients evaluated had positive serology for T. cruzi indicative of chronic Chagas disease (27.6%). Sixteen of the 32 (50%) patients with positive serology were positive by quantitative polymerase chain reaction (qPCR), and four of the 32 (12.5%) were positive by direct microscopy. The median parasite load by qPCR in those with CD4+ < 200 was 168 parasites/mL (73-9951) compared with 28.5 parasites/mL (15-1,528) in those with CD4+ ≥ 200 (P = 0.89). There was a significant inverse relationship between the degree of parasitemia estimated by qPCR from blood clot and CD4+ count on the logarithmic scale (rsBC= -0.70, P = 0.007). The correlation between T. cruzi estimated by qPCR+ blood clot and HIV viral load was statistically significant with rsBC = 0.61, P = 0.047. Given the significant mortality of PWH and Chagas reactivation and that 57% of our patients with CD4+ counts < 200 cells/mm3 showed evidence of reactivation, we propose that screening for chronic Chagas disease be considered in PWH in regions endemic for Chagas disease and in the immigrant populations in nonendemic regions. Additionally, our study showed that PWH with advancing immunosuppression have higher levels of estimated parasitemia measured by qPCR and suggests a role for active surveillance for Chagas reactivation with consideration of treatment with antitrypanosomal therapy until immune reconstitution can be achieved.

The role of domestic cats in the dynamics of SARS-CoV-2 remains poorly characterized, especially in epidemiologic contexts of countries with high viral transmission. Here, we report the first evidence of SARS-CoV-2 Lambda variant of interest in symptomatic domestic cats whose owners were diagnosed with COVID-19 in Lima, Peru, providing evidence that transmission of this new variant in domestic cats is occurring. More epidemiological studies are required to further characterize the role of domestic animals in the transmission dynamics of SARS-CoV-2.

The widespread and poorly regulated use of antibiotics in animal production in low- and middle-income countries (LMICs) is increasingly associated with the emergence and dissemination of antibiotic resistance genes (ARGs) in retail animal products. Here, we compared Escherichia coli from chickens and humans with varying levels of exposure to chicken meat in a low-income community in the southern outskirts of Lima, Peru. We hypothesize that current practices in local poultry production result in highly resistant commensal bacteria in chickens that can potentially colonize the human gut. E. coli was isolated from cloacal swabs of non-organic (n = 41) and organic chickens (n = 20), as well as from stools of market chicken vendors (n = 23), non-vendors (n = 48), and babies (n = 60). 315 E. coli isolates from humans (n = 150) and chickens (n = 165) were identified, with chickens showing higher rates of multidrug-resistant and extended-spectrum beta-lactamase phenotypes. Non-organic chicken isolates were more resistant to most antibiotics tested than human isolates, while organic chicken isolates were susceptible to most antibiotics. Whole-genome sequencing of 118 isolates identified shared phylogroups between human and animal populations and 604 ARG hits across genomes. Resistance to florfenicol (an antibiotic commonly used as a growth promoter in poultry but not approved for human use) was higher in chicken vendors compared to other human groups. Isolates from non-organic chickens contained genes conferring resistance to clinically relevant antibiotics, including mcr-1 for colistin resistance, blaCTX-M ESBLs, and blaKPC-3 carbapenemase. Our findings suggest that E. coli strains from market chickens are a potential source of ARGs that can be transmitted to human commensals.

Vaccine implementation planning in low- and middle-income countries (LMIC) often focuses on children without considering special adult populations. We adapted an economic model developed by the United States Department of Defense (DoD) to evaluate the cost-effectiveness of vaccine acquisition strategies for Campylobacter-, ETEC-, Shigella-, and norovirus-associated gastroenteritis. We compared implementation costs with current medical management in the Peruvian armed forces, a special population of low- and middle-income (LMIC) adults with a high incidence of infectious gastroenteritis. Pathogen-specific vaccine implementation resulted in calculated cost-effectiveness ratio (CER) per duty day lost averted (CERDDL) of $13,741; $1,272; $301; and $803, and a CER per diarrhea day averted of $2,130; $215; $51; and $199 for Campylobacter, ETEC, Shigella, and norovirus, respectively. These estimates compare favorably to CERDDL estimates from high-income military population and suggest that implementing vaccines gastroenteritis may be cost-effective in the Peruvian military population.