Diagnosing and tracing the pathogens of infantile infectious diarrhea by amplicon sequencing

A 6-year retrospective study of clinical features, microbiology, and genomics of Shiga toxin-producing Escherichia coli in children who presented to a tertiary referral hospital in Costa Rica

Shiga-toxin-producing Escherichia coli (STEC) is associated with diarrhea and hemolytic uremic syndrome (HUS). STEC infections in Costa Rica are rarely reported in children. We gathered all the records of STEC infections in children documented at the National Children's Hospital, a tertiary referral hospital, from 2015 to 2020. Clinical, microbiological, and genomic information were analyzed and summarized. A total of 3,768 diarrheal episodes were reviewed. Among them, 31 STEC were characterized (29 fecal, 1 urine, and 1 bloodstream infection). The prevalence of diarrheal disease due to STEC was estimated at 0.8% (n = 29/3,768), and HUS development was 6.4% (n = 2/31). The stx1 gene was found in 77% (n = 24/31) of STEC strains. In silico genomic predictions revealed a predominant prevalence of serotype O118/O152:H2, accompanied by a cluster exhibiting allele differences ranging from 33 to 8, using a core-genome multilocus sequence typing (cgMLST) approach. This is the first study using a genomic approach for STEC infections in Costa Rica.IMPORTANCEThis study provides a comprehensive description of clinical, microbiological, genomic, and demographic data from patients who attended the only pediatric hospital in Costa Rica with Shiga-toxin-producing Escherichia coli (STEC) infections. Despite the low prevalence of STEC infections, we found a predominant serotype O118/O152:H2, highlighting the pivotal role of genomics in understanding the epidemiology of public health threats such as STEC. Employing a genomic approach for this pathogen for the first time in Costa Rica, we identified a higher prevalence of STEC in children under 2 years old, especially those with gastrointestinal comorbidities, residing in densely populated regions. Limitations such as potential geographic bias and lack of strains due to direct molecular diagnostics are acknowledged, emphasizing the need for continued surveillance to uncover the true extent of circulating serotypes and potential outbreaks in Costa Rica.

The relationship between the gut microbiome and the risk of respiratory infections among newborns

Background

Emerging evidence points to a critical role of the developing gut microbiome in immune maturation and infant health; however, prospective studies are lacking.

Methods

We examined the occurrence of infections and associated symptoms during the first year of life in relation to the infant gut microbiome at six weeks of age using bacterial 16S rRNA V4-V5 gene sequencing (N = 465) and shotgun metagenomics (N = 185). We used generalized estimating equations to assess the associations between longitudinal outcomes and 16S alpha diversity and metagenomics species.

Results

Here we show higher infant gut microbiota alpha diversity was associated with an increased risk of infections or respiratory symptoms treated with a prescription medicine, and specifically upper respiratory tract infections. Among vaginally delivered infants, a higher alpha diversity was associated with an increased risk of all-cause wheezing treated with a prescription medicine and diarrhea involving a visit to a health care provider. Positive associations were specifically observed with Veillonella species among all deliveries and Haemophilus influenzae among cesarean-delivered infants.

Conclusion

Our findings suggest that intestinal microbial diversity and the relative abundance of key taxa in early infancy may influence susceptibility to respiratory infection, wheezing, and diarrhea.

Effects of dietary protein level on small intestinal morphology, occludin protein, and bacterial diversity in weaned piglets

Due to the physiological characteristics of piglets, the morphological structure and function of the small intestinal mucosa change after weaning, which easily leads to diarrhea in piglets. The aim of this study was to investigate effects of crude protein (CP) levels on small intestinal morphology, occludin protein expression, and intestinal bacteria diversity in weaned piglets. Ninety‐six weaned piglets (25 days of age) were randomly divided into four groups and fed diets containing 18%, 20%, 22%, and 24% protein. At 6, 24, 48, 72, and 96 h, changes in mucosal morphological structure, occludin mRNA, and protein expression and in the localization of occludin in jejunal and ileal tissues were evaluated. At 6, 24, and 72 h, changes in bacterial diversity and number of the ileal and colonic contents were analyzed. Results showed that structures of the jejunum and the ileum of piglets in the 20% CP group were intact. The expression of occludin mRNA and protein in the small intestine of piglets in the 20% CP group were significantly higher than those in the other groups. As the CP level increased, the number of pathogens, such as Clostridium difficile and Escherichia coli, in the intestine increased, while the number of beneficial bacteria, such as Lactobacillus, Bifidobacterium, and Roseburia, decreased. It is concluded that maintaining the CP level at 20% is beneficial to maintaining the small intestinal mucosal barrier and its absorption function, reducing the occurrence of diarrhea, and facilitating the growth and development of piglets.

Study on parental satisfaction and clinical treatment outcomes of 128 diarrheic children receiving comprehensive nursing

OBJECTIVE

To explore the clinical treatment outcomes and parental satisfaction of children with diarrhea receiving comprehensive nursing intervention.

METHODS

A total of 128 diarrheic children treated in our hospital from June 2016 to June 2017 were recruited and divided into a control group (n=64) receiving conventional nursing and an observation group (n=64) receiving comprehensive nursing intervention, as per a random number table. The clinical outcomes, electrolyte disorders, recovery of gastrointestinal function, quality of life and parental satisfaction were compared between the two groups after nursing.

RESULTS

The overall response rate of the observation group was higher than that of the control group (81.25% vs. 51.56%) (P < 0.05). Nursing satisfaction in the observation group was higher than that in the control group (100.00% vs. 75.00%) (P < 0.05). However, the time to resolution of clinical symptoms and time to return of bowel sounds in the observation group were shorter than those in the control group (P < 0.05). After nursing, the incidence of electrolyte disorders in the observation group was lower than that in the control group. The scores of physical symptoms, physical functioning, emotional functioning, cognitive functioning and social functioning in PedsQLTM Measurement Model were higher than those in the control group, and the electrolyte index monitoring results were better than those in the control group (P < 0.05).

CONCLUSION

Comprehensive nursing intervention can effectively reduce the incidence of electrolyte disorders, improve parental satisfaction, accelerate the recovery of gastrointestinal function and improve the quality of life in the treatment of pediatric diarrhea.

Managing Contamination and Diverse Bacterial Loads in 16S rRNA Deep Sequencing of Clinical Samples: Implications of the Law of Small Numbers

In this article, we investigate patterns of microbial DNA contamination in targeted 16S rRNA amplicon sequencing (16S deep sequencing) and demonstrate how this can be used to filter background bacterial DNA in diagnostic microbiology. We also investigate the importance of sequencing depth. We first determined the patterns of contamination by performing repeat 16S deep sequencing of negative and positive extraction controls. This process identified a few bacterial species dominating across all replicates but also a high intersample variability among low abundance contaminant species in replicates split before PCR amplification. Replicates split after PCR amplification yielded almost identical sequencing results. On the basis of these observations, we suggest using the abundance of the most dominant contaminant species to define a threshold in each clinical sample from where identifications with lower abundances possibly represent contamination. We evaluated this approach by sequencing of a diluted, staggered mock community and of bile samples from 41 patients with acute cholangitis and noninfectious bile duct stenosis. All clinical samples were sequenced twice using different sequencing depths. We were able to demonstrate the following: (i) The high intersample variability between sequencing replicates is caused by events occurring before or during the PCR amplification step. (ii) Knowledge about the most dominant contaminant species can be used to establish sample-specific cutoffs for reliable identifications. (iii) Below the level of the most abundant contaminant, it rapidly becomes very demanding to reliably discriminate between background and true findings. (iv) Adequate sequencing depth can be claimed only when the analysis also picks up background contamination.

Using next-generation sequencing to develop a Shigella species threshold and profile faecal samples from suspected diarrhoea cases

Globally, it is estimated that there are 2 billion cases of diarrhoeal disease each year, with 525,000 children under the age of 5 years, dying from diarrhoea. This also affects 1 in 5 people in the UK each year. Rapid diagnosis, appropriate treatment and infection control measures are, therefore, particularly important. Currently, Public Health Wales and England Microbiology Division test for five key bacterial gastrointestinal pathogens, i.e. Escherichia coli O157 (VTEC), Shigella dysenteriae, Salmonella spp., Campylobacter spp. and Clostridioides difficile. There is, however, a poor success rate with identification of these pathogens, leaving the patient at risk from untreated infections. This study has developed effective and reliable tools with a high positive outcome for diagnosis of diarrhoeal infection. The study blindly analysed 592 samples, with the most abundant species being Shigella sonnei at 15%, and the top genus Bacteroides at 26%. Campylobacter spp. had an abundance of 4%, Clostridium difficile 3%, and Salmonella spp. 0.2%. There were also significant differences in abundance at genus level, between the Flemish Gut project and diarrhoea samples, with respect to Shigella (0.2%) and Campylobacter (0.1%). The project introduced a novel Shigella spp. (Escherichia) threshold of 5.32% to determine (Escherichia) a healthy or unhealthy community. A DMBiome model was developed to integrate the 5.32% threshold of Shigella spp., the Public Health laboratory tested pathogens, and two emerging enteropathogens. The overall positive outcome was that 89% of all samples were diagnosed with diarrhoea infections, leaving 11% unknown.

Childhood diarrhoeal diseases in developing countries

Diarrhoeal diseases collectively constitute a serious public health challenge globally, especially as the leading cause of death in children (after respiratory diseases). Childhood diarrhoea affecting children under the age of five accounts for approximately 63% of the global burden. Accurate and timely detection of the aetiology of these diseases is very crucial; but conventional methods, apart from being laborious and time-consuming, often fail to identify difficult-to-culture pathogens. The aetiological agent of an average of up to 40% of cases of diarrhoea cannot be identified. This review gives an overview of the recent trends in the epidemiology and treatment of diarrhoea and aims at highlighting the potentials of metagenomics technique as a diagnostic method for enteric infections.