Subclinical infection and asymptomatic carriage of gastrointestinal zoonoses: occupational exposure, environmental pathways, and the anonymous spread of disease

Machine learning approach as an early warning system to prevent foodborne Salmonella outbreaks in northwestern Italy

Salmonellosis, one of the most common foodborne infections in Europe, is monitored by food safety surveillance programmes, resulting in the generation of extensive databases. By leveraging tree-based machine learning (ML) algorithms, we exploited data from food safety audits to predict spatiotemporal patterns of salmonellosis in northwestern Italy. Data on human cases confirmed in 2015-2018 (n = 1969) and food surveillance data collected in 2014-2018 were used to develop ML algorithms. We integrated the monthly municipal human incidence with 27 potential predictors, including the observed prevalence of Salmonella in food. We applied the tree regression, random forest and gradient boosting algorithms considering different scenarios and evaluated their predictivity in terms of the mean absolute percentage error (MAPE) and R2. Using a similar dataset from the year 2019, spatiotemporal predictions and their relative sensitivities and specificities were obtained. Random forest and gradient boosting (R2 = 0.55, MAPE = 7.5%) outperformed the tree regression algorithm (R2 = 0.42, MAPE = 8.8%). Salmonella prevalence in food; spatial features; and monitoring efforts in ready-to-eat milk, fruits and vegetables, and pig meat products contributed the most to the models' predictivity, reducing the variance by 90.5%. Conversely, the number of positive samples obtained for specific food matrices minimally influenced the predictions (2.9%). Spatiotemporal predictions for 2019 showed sensitivity and specificity levels of 46.5% (due to the lack of some infection hotspots) and 78.5%, respectively. This study demonstrates the added value of integrating data from human and veterinary health services to develop predictive models of human salmonellosis occurrence, providing early warnings useful for mitigating foodborne disease impacts on public health.

Risk factors for food contamination among children discharged from community management of acute malnutrition programmes in South Sudan: A cross-sectional study and hazard analysis critical control point approach

Children under-5 years of age are particularly vulnerable to severe acute malnutrition (SAM), and the risk factors associated with relapse to SAM are poorly understood. Possible causes are asymptomatic or symptomatic infection with enteric pathogens, with contaminated food as a critical transmission route. This cross-sectional study comprised a household survey with samples of child food (n = 382) and structured observations of food preparation (n = 197) among children aged 6-59 months that were discharged from treatment in community management of acute malnutrition (CMAM) programmes in South Sudan. We quantified Escherichia coli and total coliforms (TCs), measured in colony forming units per g of food (CFU/g), as indicators of microbial contamination of child food. A modified hazard analysis critical control point (HACCP) approach was utilised to determine critical control points (CCPs) followed by multivariate logistic regression analysis to understand the risk factors associated with contamination. Over 40% (n = 164) of samples were contaminated with E. coli (43% >0 E. coli CFU/g, 95% CI 38%-48%), and 90% (n = 343) had >10 TCs (CFU/g) (>10 TC CFU/g, 95% CI 87%-93%). Risk factors associated (p < 0.05) with child food contamination included if the child fed themselves (9.05 RR, 95% CI [3.18, 31.16]) and exposure to animals (2.63 RR, 95% CI [1.33, 5.34]). This study highlights the risk factors and potential control strategies that can support interventions that reduce food contamination exposure in young children and help further protect those that are highly vulnerable to recurrent exposure to enteric pathogens.

Patch model for border reopening and control to prevent new outbreaks of COVID-19

In this paper, we propose a two-patch model with border control to investigate the effect of border control measures and local non-pharmacological interventions (NPIs) on the transmission of COVID-19. The basic reproduction number of the model is calculated, and the existence and stability of the boundary equilibria and the existence of the coexistence equilibrium of the model are obtained. Through numerical simulation, when there are no unquarantined virus carriers in the patch-2, it can be concluded that the reopening of the border with strict border control measures to allow people in patch-1 to move into patch-2 will not lead to disease outbreaks. Also, when there are unquarantined virus carriers in patch-2 (or lax border control causes people carrying the virus to flow into patch-2), the border control is more strict, and the slower the growth of number of new infectious in patch-2, but the strength of border control does not affect the final state of the disease, which is still dependent on local NPIs. Finally, when the border reopens during an outbreak of disease in patch-2, then a second outbreak will happen.

High prevalence of small intestine bacteria overgrowth and asymptomatic carriage of enteric pathogens in stunted children in Antananarivo, Madagascar

Environmental Enteric Dysfunction (EED) refers to an incompletely defined syndrome of inflammation, reduced absorptive capacity, and reduced barrier function in the small intestine. It is widespread among children and adults in low- and middle-income countries and is also associated with poor sanitation and certain gut infections possibly resulting in an abnormal gut microbiota, small intestinal bacterial overgrowth (SIBO) and stunting.

We investigated bacterial pathogen exposure in stunted and non-stunted children in Antananarivo, Madagascar by collecting fecal samples from 464 children (96 severely stunted, 104 moderately stunted and 264 non-stunted) and the prevalence of SIBO in 109 duodenal aspirates from stunted children (61 from severely stunted and 48 from moderately stunted children). SIBO assessed by both aerobic and anaerobic plating techniques was very high: 85.3% when selecting a threshold of ≥10⁵ CFU/ml of bacteria in the upper intestinal aspirates. Moreover, 58.7% of the children showed more than 10⁶ bacteria/ml in these aspirates. The most prevalent cultivated genera recovered were Streptococcus, Neisseria, Staphylococcus, Rothia, Haemophilus, Pantoea and Branhamella. Feces screening by qPCR showed a high prevalence of bacterial enteropathogens, especially those categorized as being enteroinvasive or causing mucosal disruption, such as Shigella spp., enterotoxigenic Escherichia coli, enteropathogenic E. coli and enteroaggregative E. coli. These pathogens were detected at a similar rate in stunted children and controls, all showing no sign of severe diarrhea the day of inclusion but both living in a highly contaminated environment (slum-dwelling). Interestingly Shigella spp. was the most prevalent enteropathogen found in this study (83.3%) without overrepresentation in stunted children.

About 2 million children under the age of 5 suffer from stunted growth in Madagascar. Although deficient diet is the major cause of undernutrition, impaired absorption or assimilation caused by Environmental Enteric dysfunction (EED) has been proposed to play an important role in stunting. EED is widespread among children and adults in low- and middle-income countries (LMIC) and is also associated with undernutrition, poor sanitation, certain gut infections resulting in an abnormal gut microbiota and small intestinal bacterial overgrowth (SIBO) although the role of SIBO in EED remains unclear. The current study highlights the presence at high concentrations of bacterial taxa usually found in the oro-pharyngeal sphere in a high number of duodenal fluids of stunted children. This uncommon presence suggests a decompartmentalization of the gastrointestinal tract and a possible pro-inflammatory effect due to the ectopic presence of some of these bacteria in the duodenum.

The study also points to a high prevalence of enteropathogens (especially Shigella spp.) in the feces of both stunted and control children, hence preventing from proposing a direct association with stunting. This suggests that, beside combatting poverty and improving diet, environmental sanitation, quality of water sources, hygiene promotion and health education are key points to mitigate stunting and restore nutritional benefits.

COVID 19 mortality: Probable role of microbiome to explain disparity

There is a significant difference between COVID 19 associated mortality between different countries. Generally the number of deaths per million population are higher in the developed countries despite better health care efficiency, drinking water quality and expected healthy life span (HALE) at the time of birth. Developing and underdeveloped countries on the other hand have lower mortality even with higher rural and slum populations along with incidence of diarrhea because of lack of sanitation. We analyzed data from 122 countries out of which 80 were high or upper middle income and 42 were low or low middle income countries. There was statistically significant positive correlation between COVID 19 deaths /million population and water current score, health efficiency, and HALE. Statistically significant negative correlation was observed with % rural population and fraction of diarrhea because of inadequate sanitation for all ages. Moreover analysis of 51 countries showed that there is significant negative correlation between COVID 19 deaths /million population and proportion of total population living in slums. We propose that high microbial exposure particularly gram negative bacteria can possibly induce interferon type I which might have a protective effect against COVID 19 since the countries with less mortality also tend to have lack of sanitation and high incidence of attendant diseases. So, far none of the predictive models have taken into account immune status of populations engendered by environmental microbial exposure or microbiome. There might be a need to look at dynamics of COVID 19 pandemic using immune perspective. The approach can potentially inform better policies including interventions.

Municipal Wastewater Surveillance Revealed a High Community Disease Burden of a Rarely Reported and Possibly Subclinical Salmonella enterica Serovar Derby Strain

Clinical surveillance of enteric pathogens like Salmonella is integral to track outbreaks and endemic disease trends. However, clinic-centered disease monitoring biases toward detection of severe cases and underestimates the incidence of self-limiting gastroenteritis and asymptomatic strains. Monitoring pathogen loads and diversity in municipal wastewater (MW) can provide insight into asymptomatic or subclinical infections which are not reflected in clinical cases. Subclinical infection patterns may explain the unusual observation from a year-long sampling campaign in Hawaii: Salmonella enterica serovar Derby was the most abundant pulsotype in MW but was detected infrequently in clinics over the sampling period. Using whole-genome sequencing data of Salmonella isolates from MW and public databases, we demonstrate that the Derby serovar has lower virulence potential than other clinical serovars, particularly based on its reduced profile of genes linked with immune evasion and symptom production, suggesting its potential as a subclinical salmonellosis agent. Furthermore, MW had high abundance of a rare Derby sequence type (ST), ST-72 (rather than the more common ST-40). ST-72 isolates had higher frequencies of fimbrial adherence genes than ST-40 isolates; these are key virulence factors involved in colonization and persistence of infections. However, ST-72 isolates lack the Derby-specific Salmonella pathogenicity island 23 (SPI-23), which invokes host immune responses. In combination, ST-72's genetic features may lead to appreciable infection rates without obvious symptom production, allowing for subclinical persistence in the community. This study demonstrated wastewater's capability to provide community infectious disease information-such as background infection rates of subclinical enteric illness-which is otherwise inaccessible through clinical approaches.IMPORTANCE Wastewater-based epidemiology (WBE) has been conventionally used to analyze community health via the detection of chemicals, such as legal and illicit drugs; however, municipal wastewater contains microbiological determinants of health and disease as well, including enteric pathogens. Here, we demonstrate that WBE can be used to examine subclinical community salmonellosis patterns. Derby was the most abundant Salmonella serovar detected in Hawaii wastewater over a year-long sampling study, with few corresponding clinical cases. Comparative genomics analyses indicate that the normally rare strain of S Derby found in wastewater has a unique combination of genes which allow it to persist as a subclinical infection without producing symptoms of severe gastroenteritis. This study shows that WBE can be used to explore trends in community infectious disease patterns which may not be reflected in clinical monitoring, shedding light on overall enteric disease burden and rates of asymptomatic cases.

Clinically Unreported Salmonellosis Outbreak Detected via Comparative Genomic Analysis of Municipal Wastewater Salmonella Isolates

Municipal wastewater includes human waste that contains both commensal and pathogenic enteric microorganisms, and this collective community microbiome can be monitored for community diseases. In a previous study, we assessed the salmonellosis disease burden using municipal wastewater from Honolulu, Hawaii, which was monitored over a 54-week period. During that time, a strain of Salmonella enterica serovar Paratyphi B variant L(+) tartrate(+) (also known as Salmonella enterica serovar Paratyphi B variant Java) was identified; this strain was detected simultaneously with a clinically reported outbreak, and pulsed-field gel electrophoresis patterns were identical for clinical and municipal wastewater isolates. Months after the outbreak subsided, the same pulsotype was detected as the dominant pulsotype in municipal wastewater samples, with no corresponding clinical cases reported. Using genomic characterization (including core single-nucleotide polymorphism alignment, core genome multilocus sequence typing, and screening for virulence and antibiotic resistance genes), all S Java municipal wastewater isolates were determined to be clonal, indicating a resurgence of the original outbreak strain. This demonstrates the feasibility and utility of municipal wastewater surveillance for determining enteric disease outbreaks that may be missed by traditional clinical surveillance methods.IMPORTANCE Underdetection of microbial infectious disease outbreaks in human communities carries enormous health costs and is an ongoing problem in public health monitoring (which relies almost exclusively on data from health clinics). Surveillance of municipal wastewater for community-level monitoring of infectious disease burdens has the potential to fill this information gap, due to its easy access to the mixed community microbiome. In the present study, the genomes of 21 S Java isolates (collected from municipal wastewater in Honolulu) were analyzed; results showed that the same Salmonella strain that caused a known salmonellosis clinical outbreak in spring 2010 remerged as the most dominant strain in municipal wastewater in spring 2011, indicating a new outbreak that was not detected by health clinics. Our results show that wastewater monitoring holds great promise to inform the field of public health regarding outbreak status within communities.

Antimicrobial resistant Helicobacter fennelliae isolated from non-diarrheal child stool sample in Battambang, Cambodia

Helicobacter fennelliae (H. fennelliae) is associated with human gastroenteritis; however, H. fennelliae was isolated and confirmed by phenotypic and genotypic identification from a non-diarrheal child stool sample in Cambodia. Antimicrobial susceptibility testing demonstrated that this isolate had a high minimal inhibitory concentration against macrolides and quinolones, which are first-line antibiotic treatment choices for Campylobacter infections. Consequently, macrolides and quinolones were likewise expected to be ineffective against Campylobacter-like organisms such as H. fennelliae. This isolate warranted further genetic characterization to better understand associated antibiotic resistance mechanisms. Resistant pathogens from asymptomatic diarrheal cases are likely underestimated, and as such colonized individuals may spread resistant organisms to local community members and the environment.

Prevalence of Asymptomatic Brucellosis in Children 7 to 12 Years Old

Background. Brucellosis is one of the most common diseases of humans and animals and its clinical manifestations differ from asymptomatic infection to chronic illness associated with recurrence of symptoms. This study aimed to evaluate the prevalence of brucellosis in asymptomatic children 7 to 12 years old in Kahak, Iran. Methods. In this study, 186 children 7 to 12 years old were evaluated. Demographic data and exposure to the brucellosis agent were recorded and blood samples for the Wright, Coombs, and 2ME tests were collected. All the study subjects were followed up for one year about the appearance of symptoms. Results. The mean age was 10 ± 1.72 years and 51% were boys. Family history was positive for brucellosis in 15% of children. A total of 8 children were brucellosis seropositive and, in subsequent follow-up, 6 of them showed the disease symptoms. Conclusion. This study showed that approximately 4.3% of children in endemic areas can have asymptomatic brucellosis and many of these children may be symptomatic in short term.