Stool Swab Research Articles

P-777. Assessment of Epidemiologic Case Definitions for Disseminated Nontuberculous Mycobacterial Disease in Patients Without AIDS

Abstract Background Disseminated Mycobacterium avium complex (MAC) infection rates have declined in persons with HIV; some studies report increasing numbers of disseminated nontuberculous mycobacteria (NTM) infections in other groups of immunocompromised persons. However, no consensus definition exists for disseminated NTM in these populations. We compared characteristics of disseminated NTM in persons without AIDS using different epidemiologic definitions.Table 1.Disseminated nontuberculous mycobacteria definitions.. Methods CDC’s Emerging Infections Program conducted active, laboratory- and population-based NTM surveillance in 4 states (11 counties) during 2021–2022 to identify patients with NTM in clinical specimens, excluding stool or rectal swabs. Clinical and laboratory data were collected via medical record review. Disseminated NTM definitions are shown in Table 1. We determined the numbers of patients without AIDS who met each definition. Among those meeting each definition we calculated the percentages of patients with: 1) selected immunocompromising conditions; 2) MAC infection; and 3) documented clinical diagnosis of any NTM infection (i.e., NTM not likely to represent contamination or colonization).Figure 1.Number of patients meeting each disseminated nontuberculous mycobacteria definition, Emerging Infection Program, 2021–2022 (N=59). Results Among 877 patients with NTM and without AIDS, 15 patients (1.7%) had a documented disseminated NTM clinical diagnosis (definition 1); 59 (6.7%) met ≥1 of the 3 definitions. Although more patients met definition 2 (31, 3.5%) or definition 3 (53, 6.0%) than definition 1, definition 2 only captured 10/15 (66.7%) patients with a documented disseminated NTM clinical diagnosis; definition 3 captured only 9/15 (60.0%) (Figure 1). The proportion of patients with malignancy, immunosuppressive medication, or transplant differed by definition as did the proportion infected with MAC. Seven of 31 patients meeting definition 2 (22.6%) and 14/53 (26.4%) patients meeting definition 3 did not have a clinician documented diagnosis of any NTM infection in the medical record (Figure 2).Figure 2.Proportion of patients with malignancy(a), immunosuppressive medication(b), transplant(c), isolation of M. avium complex, or clinical diagnosis of any type of nontuberculous mycobacteria infection(d), stratified by disseminated NTM definition, Emerging Infections Program, 2021–2022. Conclusion Each disseminated NTM definition identified a different group of patients, limiting their usefulness and comparability. Development of a standard epidemiologic definition for disseminated NTM in persons without AIDS will enable better understanding of disease impact in susceptible populations. Disclosures Kevin L. Winthrop, MD, MPH, AN2: Advisor/Consultant|AN2: Grant/Research Support|Insmed: Advisor/Consultant|Insmed: Grant/Research Support|Mannkind: Advisor/Consultant|Mannkind: Grant/Research Support|Paratek: Advisor/Consultant|Paratek: Grant/Research Support|Renovion: Advisor/Consultant|Renovion: Grant/Research Support|Spero: Advisor/Consultant|Spero: Grant/Research Support

Effects of Vegetable and Fruit Juicing on Gut and Oral Microbiome Composition

Background: In recent years, juicing has often been promoted as a convenient way to increase fruit and vegetable intake, with juice-only diets marketed for digestive cleansing and overall health improvement. However, juicing removes most insoluble fiber, which may diminish the health benefits of whole fruits and vegetables. Lower fiber intake can alter the microbiota, affecting metabolism, immunity, and mental health, though little is known about juicing’s specific effects on the microbiota. This study addresses this gap by exploring how juicing impacts gut and oral microbiome composition in an intervention study. Methods: Fourteen participants followed one of three diets—exclusive juice, juice plus food, or plant-based food—for three days. Microbiota samples (stool, saliva, and inner cheek swabs) were collected at baseline, after a pre-intervention elimination diet, immediately after juice intervention, and 14 days after intervention. Moreover, 16S rRNA gene amplicon sequencing was used to analyze microbiota taxonomic composition. Results: The saliva microbiome differed significantly in response to the elimination diet (unweighted UniFrac: F = 1.72, R = 0.06, p < 0.005; weighted UniFrac: F = 7.62, R = 0.23, p-value = 0.0025) with a significant reduction in Firmicutes (p = 0.004) and a significant increase in Proteobacteria (p = 0.005). The juice intervention diets were also associated with changes in the saliva and cheek microbiota, particularly in the relative abundances of pro-inflammatory bacterial families, potentially due to the high sugar and low fiber intake of the juice-related products. Although no significant shifts in overall gut microbiota composition were observed, with either the elimination diet or the juice intervention diets, bacterial taxa associated with gut permeability, inflammation, and cognitive decline increased in relative abundance. Conclusions: These findings suggest that short-term juice consumption may negatively affect the microbiota.

A Pilot Study Exploring the Relationship Between Milk Composition and Microbial Capacity in Breastfed Infants.

Maternal obesity may contribute to childhood obesity in a myriad of ways, including through alterations of the infant gut microbiome. For example, maternal obesity may contribute both directly by introducing a dysbiotic microbiome to the infant and indirectly through the altered composition of human milk that fuels the infant gut microbiome. In particular, indigestible human milk oligosaccharides (HMOs) are known to shape the composition of the infant gut microbiome. The goal of this study was to characterize the HMO profiles of normal-weight and overweight mothers and to quantitatively link HMO concentrations to the taxonomic composition and functional potential of the infant gut microbiome. Normal-weight (BMI = 18.5-24.9; n = 9) and overweight/obese (OW/OB; BMI > 25; n = 11) breastfeeding mothers and their infants were enrolled in this single-center, cross-sectional pilot study. Human milk from the mothers and rectal stool swabs from the infants were collected 7-9 weeks postpartum. The HMO composition, microbiome composition, and microbial functions were assessed using HPLC, 16S rRNA gene sequencing, and metagenomic sequencing, respectively. Neither the HMO profiles nor the infant microbiome composition varied according to maternal BMI status. Taxonomically, the gut microbiota of infants were dominated by typical gut lineages including Bifidobacterium. Significant correlations between individual HMOs and bacterial genera were identified, including for Prevotella, a genus of the Bacteroidota phylum that was positively correlated with the concentrations of lacto-N-neotetraose (LNnT) and lacto-N-hexaose (LNH). Using metagenomic assembled genomes, we were also able to identify the broad HMO-degradative capacity across the Bifidobacterium and Prevotella genera. These results suggest that the maternal BMI status does not impact the HMO profiles of human milk. However, select HMOs were correlated with specific bacterial taxa, suggesting that the milk composition influences both the taxonomic composition and the functional capacity of the infant gut microbiome.

Effects of antibiotic therapy on the early development of gut microbiota and butyrate-producers in early infants.

Antibiotics, as the most commonly prescribed class of drugs in neonatal intensive care units, have an important impact on the developing neonatal gut microbiota. Therefore, comprehending the effects of commonly used antibiotic therapy on the gut microbiota and butyrate-producers in early infants could provide information for therapeutic decision-making in the NICU. To explore the effects of antibiotic therapy on the early development of gut microbiota and butyrate-producers in early infants. A total of 72 infants were included in the study. We performed 16S rRNA sequencing on stool swab samples collected from neonatal intensive care unit patients who received amoxicillin-clavulanic acid (AC, n = 10), moxalactam (ML, n = 28) and non-antibiotics (NA, n = 34). We then compared the taxonomic composition between treatment regimens, focusing on differences in butyrate-producers. Our study showed that there were significant differences in Shannon index (p = 0.033) and Beta diversity (p = 0.014) among the three groups. At the family level, compared with the other two groups, the relative abundance of Clostridiaceae (p < 0.001) and Veillonellaceae (p = 0.004) were significantly higher, while the relative abundance of Enterococcidae (p < 0.001) was significantly lower in the NA group. The relative abundance of Enterobacteriaceae (p = 0.022) in the AC group was greater than that in the other two groups. Additionally, butyrate-producers (p < 0.001), especially Clostridiaceae (p < 0.001), were noticeably more abundant in the NA group. The relative abundance of Clostridiaceae and butyrate-producers were the lowest in the ML group (p < 0.001). We found that antibiotic therapy had an adverse impact on the initial development of gut microbiota and leaded to a reduction in the abundance of butyrate-producers, particularly Clostridiaceae. Furthermore, moxalactam had a more pronounced effect on the gut microbiota compared to amoxicillin-clavulanic acid.

Prevalence and pattern of carriage of Enterobacterales isolates among food handlers in Nnewi metropolis, southeast Nigeria

Background: There is a public health concern about carriage of Enterobacterales among food workers and their potential role for transmission of food-borne illnesses. Food contamination by Enterobacterales could happen at any point of the production, processing, distribution, and preparation processes. This challenge is especially severe in developing countries like Nigeria. The objective of this study is to determine the prevalence and pattern of carriage of Enterobacterales by food handlers in Nnewi metropolis, southeast Nigeria.Methodology: This was a cross-sectional study that employed a non-probability sampling technique to recruit 178 food handlers who gave their consent and were available at the sampling area during the time of the study. Stool, urine, nasal and hand swab samples were collected from 115, 116, 120 and 173 food handlers respectively for microbiological analysis using conventional culture isolation and biochemical identification by Analytical Profile Index (API) 20E (bioMérieux). The antimicrobial susceptibility testing of the isolates was carried out on the identified isolates by the disk diffusion method. Descriptive statistics were carried out on the data.Results: Forty-four (25.4%) of the hand swab samples from 173 food handlers, 39 (32.5%) of the nasal swabs from 120 food handlers, 67 (58.3%) of the stool samples from 115 food handlers, and 29 (25.0%) of the urine samples from 116 food handlers, were positive for Enterobacterales isolates. The frequency of Enterobacterales isolation was significantly higher from stool samples compared to other samples (x2=40.032; p&lt;0.0001), indicating a higher carriage rate in the gastrointestinal tracts of the food handlers. Across all the samples, a total of 179 Enterobacterales were isolated from the 101 (56.7%) positive food handlers. The frequency of isolation in descending order is Escherichia coli 23.2% (n=41), Klebsiella spp 18.1% (n=32), Enterobacter spp 15.3% (n=27), Citrobacter spp 10.7% (n=19), Raoultella spp 7.3% (n=13), Serratia spp 5.6% (n=10), Salmonella spp 3.9% (n=7), Kluyvera spp 3.9% (n=7), Shigella spp 2.8% (n=5), Proteus spp 2.8% (n=5), Cronobacter spp 1.7% (n=3), Erwinia spp 1.1% (n=2), Pantoea spp 1.1% (n=2), Hafnia spp 1.1% (n=2), and Yersinia spp 1.1% (n=2). The Enterobacterales isolates were resistant to cefotaxime (83.0%), amoxicillin-clavulanic acid (79.1%), cefuroxime (76.8%), cefixime (75.1%), imipenem-cilastatin (74.6%), ceftazidime-avibactam (73.3%), ceftriaxone-sulbactam (71.2%) and levofloxacin (70.5%).Conclusion: Food handlers in this study had a high carriage rate of resistant Enterobacterales pathogens, which can be transmitted to unsuspecting consumers, through the food processing and handling chains.

Surveillance of Food and Waterborne Pathogens in North-East India: Protocol for a Laboratory-Based Sentinel Surveillance Study.

Food safety is a global concern, which is often underestimated owing to challenges in investigating foodborne diseases. These challenges arise from the increased globalization of the food trade, advancements in agricultural practices, and shifts in environmental factors. In North-East India, common diarrheal outbreaks from fermented foods pose significant health risks. Despite these challenges, systematic data on foodborne pathogens is lacking in India, highlighting a crucial gap in understanding food safety issues. The aim of this research protocol is to establish an integrated surveillance system to identify enteric pathogens circulating within humans, food animals, and the environment through a health approach in North-East India, and to conduct outbreak investigations. The Indian Council of Medical Research (ICMR) initiated a surveillance study across all 8 North-East states in India, employing a centralized digital database for data collation. The project aims to enhance theinfrastructure for microbial culture, antibiotic sensitivity testing, and molecular epidemiological studies. The study involves laboratory-based surveillance of foodborne pathogens in market foods, hospitalized diarrheal patients, poultry and animal farms, slaughterhouses, butcher shops, and diarrheal outbreaks. A standardized case report form ensures consistent data collection of age, sex, signs, symptoms, and admission dates for diarrheal cases. Stool and rectal swabs will undergo testing for pathogen identification and antimicrobial resistance. Similarly, samples of market foods, food animals, and the environment will be collected. Outbreaks confirmed by the Integrated Disease Surveillance Project (IDSP) will be thoroughly investigated following standardized guidelines. In phase I, 5 surveillance centers were established across 4 states (ie, Assam [Dibrugarh and Guwahati], Tripura, Sikkim, and Arunachal Pradesh) in 2020. Following an interim phase I data assessment and the successful establishment of a streamlined system for data procurement, investigation, recording, and analysis, along with the implementation of regular training and monitoring programs, phase II expansion was initiated in 2023-24. This includes the addition of 7 more centers (including 3 veterinary centers) in the remaining 4 states (ie, Manipur, Meghalaya, Mizoram, and Nagaland), eventually covering the entire North-Eastern Region of India. Food and waterborne diseases are a constant public health problem in many countries. Key challenges to the enhancement of food safety policy include the paucity of systematic data and awareness. With this background, ICMR's initiative is the first systematic surveillance study in the country to adopt a single health approach. Data obtained from this project will help to understand the risk of acquiring food and waterborne pathogens, their transmission pathways, and antimicrobial resistance patterns. The scientific evidence generated through this project will be helpful in formulating and strengthening food safety policy and in initiating government programs to protect the health of the nation. DERR1-10.2196/56469.

Cumulative incidence of vancomycin-resistant Enterococcus faecium detection by patient characteristics or possible exposures: prioritization of patients for active screening culture

The target population for active surveillance culture (ASC) of vancomycin-resistant Enterococcus species (VRE) by stool or rectal swabs has not been fully determined during VRE outbreaks in healthcare settings in non-VRE endemic situation. To evaluate cumulative incidences of VRE detection during a vancomycin-resistant Enterococcus faecium outbreak to determine reasonable target populations for ASC. Cases included inpatients whose first VRE-positive sample was obtained at Shizuoka General Hospital between February 2022 and January 2023, during which we conducted admission screening for possible high-risk patients, bi-weekly screening of all inpatients, admission and discharge screening in the high-care unit, and screening of contacts in each ward using stool or rectal samples. We calculated cumulative incidences of VRE detection for those screened by patient characteristics or possible exposure. Among 60 cases identified, 55 (92%) were by ASC. Cumulative incidence was higher for contacts (6.4%, 15/234) than for those identified by other screening methods (0.5%, 40/8565). Among the patients identified through admission screening, those previously hospitalized in areas of reported VRE outbreaks had the highest cumulative incidence (6.6%, 5/78) followed by patients requiring toilet assistance (3.7%, 6/161). A bundle approach including ASC and prompt contact precautions by the hospital infection control team, local public health centre, and local and national infection control experts helped terminate the outbreak in seven months. Patients with contacts, prior hospitalization in areas with known VRE outbreaks, and who need toilet assistance appear to be high-risk populations for VRE detection and are candidates for ASC.

Comparison of intestinal and pharyngeal microbiota in preterm infants on the first day of life and the characteristics of pharyngeal microbiota in infants delivered by cesarean section or vaginally.

This study aimed to explore the distribution of intestinal and pharyngeal microbiota on the first day of life in preterm infants and compare the composition of microbiota in infants delivered by cesarean section or vaginally. This study included 44 late preterm infants with a gestational age of 34-36 + 6 weeks. Stool and throat swab samples were collected from the preterm infants on the first day of life. The infants were divided into cesarean section and vaginal delivery groups. Illumina NovaSeq high-throughput sequencing technology was used to sequence the V3-V4 hypervariable region of the 16S rRNA gene of all bacteria in the samples. Venn diagram was used to identify shared operational taxonomic units (OTUs) in the intestines and pharynges. Microbial analysis was conducted at the phylum and genus levels, and α and β diversity comparisons were performed. (1) Gestational age may have significantly affected the microbial colonization of the intestines and pharynges of preterm infants on the first day after birth (p ≤ 0.001). (2) More OTUs were detected in the pharynx than in the intestines, both have a total of 819 shared OTUs. Proteobacteria, Firmicutes, and Bacteroidota were the dominant phyla in both. At the genus level, Streptococcus had a lower relative abundance in stool samples (0.5%) compared to throat samples (0.5% vs. 22.2%, p = 0.003). 3) The relative abundance of Streptococcus in pharyngeal samples was 26.2% in the cesarean section group much higher than the 3.8% in the vaginal delivery group (p = 0.01). The early postnatal period is a critical time for the establishment of an infant's microbiota. Gestational age at birth may influence microbial colonization, while birth weight, gender, and mode of delivery do not. The intestinal and pharyngeal microbiota composition of preterm infants on the first day after birth showed high similarity, but larger samples are needed for further validation.

Impact of intrapartum antibiotic prophylaxis on the oral and fecal bacteriomes of children in the first week of life

Intrapartum antibiotic prophylaxis (IAP) is commonly used during C-section delivery and in Group B Streptococcus-positive women before vaginal delivery. Here, we primarily aimed to investigate the effect of IAP on the neonatal oral and fecal bacteriomes in the first week of life. In this preliminary study, maternal and neonatal oral swabs and neonatal fecal (meconium and transitional stool) swabs were selected from a pool of samples from healthy mother-neonate pairs participating in the pilot phase of CELSPAC: TNG during their hospital stay. The DNA was extracted and bacteriome profiles were determined by 16S rRNA amplicon sequencing (Illumina). In the final dataset, 33 mother-neonate pairs were exposed to antibiotics during C-section or vaginal delivery (cases; +IAP) and the vaginal delivery without IAP (controls, -IAP) took place in 33 mother-neonate pairs. Differences in alpha diversity (Shannon index, p=0.01) and bacterial composition (PERMANOVA, p<0.05) between the +IAP and -IAP groups were detected only in neonatal oral samples collected ≤48 h after birth. No significant differences between meconium bacteriomes of the +IAP and -IAP groups were observed (p>0.05). However, the IAP was associated with decreased alpha diversity (number of amplicon sequence variants, p<0.001), decreased relative abundances of the genera Bacteroides and Bifidobacterium, and increased relative abundances of genera Enterococcus and Rothia (q<0.01 for all of them) in transitional stool samples. The findings of this study suggest that exposure to IAP may significantly influence the early development of the neonatal oral and gut microbiomes. IAP affected the neonatal oral bacteriome in the first two days after birth as well as the neonatal fecal bacteriome in transitional stool samples. In addition, it highlights the necessity for further investigation into the potential long-term health impacts on children.

Microbiota alterations in patients treated for susceptible or drug-resistant TB.

We investigated alterations of human microbiota under anti-TB therapies in relationship to the level of Mycobacterium tuberculosis drug response. Stool, sputum, and oral swab samples were analysed from participants with treatment-naïve TB and participants treated for drug-susceptible TB (DS-TB), drug-resistant TB without injectable drugs (DR-TB-inj-), or with injectable drugs (DR-TB-inj+) at 27-42 days of therapy. From September 2018 to December 2019, 5 participants with treatment-naïve TB, 6 participants with DS-TB, 10 participants with DR-TB-inj-, and 4 participants with DR-TB-inj+ were recruited. Reduced alpha diversities in stool samples indicated more profound dysbiosis in participants treated for DR-TB than in participants treated for DS-TB (-12% (non-significant) for DS-TB, -44% (P < 0.001) for DR-TB-inj-, and -60% (P < 0.05) for DR-TB-inj+ compared to treatment-naïve participants). While reduced abundances were observed in numerous taxa, genus Lactobacillus revealed the most substantial abundance increase in sputa of participants treated for DR-TB compared to treatment-naïve ones (P < 0.05 for DR-TB-inj- and DR-TB-inj+). Notably, a group of nosocomial pneumonia-associated taxa was increased in oral swabs of the DR-TB-inj+ compared to the treatment-naïve group (P < 0.05). Second-line anti-TB therapy in participants with DR-TB results in altered microbiota, including reduced alpha diversity and expansion of phylogenetically diverse taxa, including pathobionts.

Epidemiology of Extrapulmonary Nontuberculous Mycobacterial Disease – 4 Emerging Infection Program Sites, 2021

Background: Extrapulmonary nontuberculous mycobacteria (ENTM) infections are difficult to treat and often require prolonged therapy or surgery. Few population-based studies describe ENTM epidemiology, though well-known healthcare-associated outbreaks have occurred. Using the first year of multi-site ENTM surveillance, we characterized rates and how frequently ENTM infections may be related to healthcare. Methods: CDC’s Emerging Infections Program conducted active, laboratory- and population-based surveillance for ENTM cases in 4 sites (Colorado [5 counties], Minnesota [statewide], New York [1 county], and Oregon [statewide]) in 2021. An incident ENTM case was NTM isolation from a non-pulmonary specimen, excluding stool or rectal swabs, in a resident of the surveillance area without either medical record documentation of prior ENTM infection or isolation of ENTM in the prior 12 months. Demographic, clinical, information on selected healthcare and community exposures, and laboratory data were collected via medical record review. We calculated incidence per 100,000 population using U.S. Census population estimates and performed descriptive analyses. Results: A total of 180 incident ENTM cases were reported in 2021. The crude annual incidence rate was 1.3 per 100,000 persons. Incidence increased with age (from 0.95 per 100,000 among 0–17 year-olds to 2.65 per 100,000 among persons ≥65), ranged from 0.8 among non-Hispanic Asian persons to 1.6 per 100,000 in non-Hispanic Black persons, and was similar among males (1.3 per 100,000) and females (1.4 per 100,000; Figure 1). Mycobacterium avium complex (64 [35.6%]) was the most frequently isolated species group, followed by Mycobacterium chelonae complex (31 [17.2%]). Skin and soft tissue infections were the most frequent infection type (37 [20.6%]); 27 cases (15.0%) were associated with disseminated and/or only bloodstream infection, and 56 cases (31.1%) had no infection type documented. Among 93 cases with localized ENTM infections (i.e., infections that were not disseminated and/or only bloodstream infections), 38.7% had only healthcare-related exposures, 14% had only community-related exposures and 6.5% had both exposure types at the site of infection (Figure 2). Healthcare-related exposures at the infection site included surgery (23.7%), injection/infusion (21.5%), and medical devices (18.3%). The most frequent community-related exposure at the infection site was trauma (17.2%). Only one case was part of a known outbreak, which was healthcare-associated. Conclusions: ENTM infections are relatively rare, but nearly half of patients with localized ENTM infections had prior healthcare-related exposures. This indicates that the burden of ENTM infections related to healthcare may be much larger than what has been suggested from reported outbreaks.

High Prevalence of Colistin-Resistant Encoding Genes Carriage among Patients and Healthy Residents in Vietnam.

Background and Objectives: We aimed to investigate the carriage of colistin-resistant genes among both patients with a history of antibiotic exposure and apparently healthy adults with no recent healthcare contact. Materials and Methods: Stool swabs were collected from healthy people, and specimens were collected at the infection foci from the patients. Eleven primer/probe sets were used to perform the Multiplex Real-Time PCR assay with the QuantiNova Multiplex Probe PCR kit for screening the carriage of colistin-resistant genes (mcr-1 to mcr-10) and 16S rRNA gene as internal control. Results: In total, 86 patients and 96 healthy residents were included. Twenty two patients (25.9%) were positive with at least one colistin-resistance encoding gene. The mcr-1 gene was the most frequent (16.5%), followed by mcr-9, mcr-6, and mcr-4 genes, where the prevalence was 11.8%, 10.6%, and 9.4%, respectively. No patient was positive with mcr-3, mcr-7, and mcr-8 genes. Eight patients (9.4%) were positive with multiple colistin-encoding genes. Twenty-three healthy people (24.0%) were positive with at least one colistin-resistance encoding gene, and the mcr-10 gene was the most frequent (27.0%), followed by the mcr-1, mcr-8, and mcr-9 genes, where the prevalence was 24.3%, 21.6%, and 13.5%, respectively. No person was positive with the mcr-2 and mcr-5 genes. Conclusions: Our findings underscore the urgent need for enhanced surveillance, infection control measures, and stewardship interventions to mitigate the spread of colistin resistance in Vietnam.

Gut microbiota composition in recurrent acute otitis media: a cross-sectional observational study.

Recurrent acute otitis media (rAOM) poses a significant challenge in children aged 1 to 6 years, characterized by frequent and treatment-resistant ear infections. While existing studies predominantly focus on alterations in the nasopharyngeal microbiome associated with rAOM, our research explores the understudied association with the gut microbiome.In this cross-sectional observational prospective study, we enrolled 35 children aged 1 to 6 years during the 2021/2022 cold season. The test group comprised children with rAOM (n = 16), and the control group consisted of generally healthy children (n = 19). Samples (stool and nasopharyngeal swabs) were collected in late spring to ensure an antibiotic-free period. Detailed metadata was gathered through a questionnaire examining factors potentially influencing microbiota. Microbiota composition was assessed through amplicon sequencing of the V3-V4 region of the 16S rRNA gene. Our findings revealed limited alterations in gut microbiota composition among children with rAOM compared to healthy controls. Six bacterial taxa (Veillonella, Lachnospiraceae, Ruminococcaceae, Lachnospiraceae, Bacteroides and Blautia) were differentially represented with weak statistical significance. However, several bacterial taxa displayed correlations with multiple consecutive infections, with Turicibacter showing the most significant association. Additionally, day care centre attendance emerged as a potent gut microbiota modifier, independent of rAOM. Although our study identified limited differences in gut microbiota composition between children with rAOM and healthy controls, the observed correlations between the number of infections and specific bacterial taxa suggest a potential link between rAOM and the gut microbiota, warranting further investigation.

Molecular Epidemiology of Clostridioides difficile Colonization in Families With Infants.

Community-associated Clostridioides difficile infection is a major public health hazard to adults and older children. Infants frequently excrete toxigenic C difficile asymptomatically in their stool, but their importance as a community reservoir of C difficile is uncertain. Families of healthy infants were recruited at the baby's 4-month well child visit and were followed longitudinally until the baby was approximately 9 months old. Babies and mothers submitted stool or rectal swabs every 2 weeks that were cultivated for C difficile; fathers' participation was encouraged but not required. Clostridioides difficile isolates were strain-typed by fluorescent polymerase chain reaction ribotyping and by core genome multilocus sequence typing, and the number of families in whom the same strain was cultivated from >1 family member ("strain sharing") was assessed. Thirty families were enrolled, including 33 infants (3 sets of twins) and 30 mothers; 19 fathers also participated. Clostridioides difficile was identified in 28 of these 30 families over the course of the study, and strain sharing was identified in 17 of these 28. In 3 families, 2 separate strains were shared. The infant was involved in 17 of 20 instances of strain sharing, and in 13 of these, the baby was identified first, with or without a concomitantly excreting adult. Excretion of shared strains usually was persistent. Clostridioides difficile strain sharing was frequent in healthy families caring for an infant, increasing the likelihood that asymptomatically excreting babies and their families represent a reservoir of the organism in the community.

Bacterial foodborne illness and Escherichia coli O157:H7 strain infection among asymptomatic food handlers in Northeast Ethiopia: Implication for hygienic practices and mass-screening.

Food-borne illness is a public health concern in developing countries because of improper food handling and sanitation practices, irregular medical checkups, lack of clean water supplies, and inadequate education among food handlers. This study investigated the burden of bacterial food-borne illness, antibiotic resistance patterns, and associated factors among food handlers in prison and nonprison food establishment settings. A cross-sectional study was conducted from August 2022 to January 2023 among asymptomatic food handlers in Shewa Robit town. A total of 384 food handlers participated. Data were collected using structured questionnaires. Stool and hand swab samples were collected and cultivated onto MacConkey agar, xylose-lysine-deoxycholate, Mannitol salt agar, and blood agar, and incubated at 37°C. Bacterial species were identified using biochemical tests and gram staining. Mueller-Hinton agar was used in Kirby Bauer's disk diffusion method. Data were entered and analyzed using SPSS. Descriptive and logistic regression analysis were performed. Fecal and hand carriage rate of bacterial isolates were 106 (27.6%), and 214 (55.7%), respectively. Out of the 102 bacterial isolates, the most common ones from stool samples were Escherichia coli 71 (18.5%), Klebsiella aerogenes 12 (3.1%), and Salmonella spp. 7 (1.8%). Among 214 bacterial isolates, coagulase-negative Staphylococci 115 (29.9%) and Staphylococci aureus 66 (17.3%) were identified from hand swab samples. Hand washing practice after restroom with water (adjusted odds ratio [AOR] = 2; 95% confidence interval [CI]: 1.16-3.45), irregular medical checkups (AOR = 2.49; 95% CI: 1.35-4.59), and did not receive food safety and hygiene training (AOR = 2.33; 95% CI: 1.34-4.05) were statistically significant association with food-borne illness. Foodborne pathogens pose a serious health risk in the study areas. The level of antimicrobial resistance are also concerning. Food handlers should therefore get strict regular health education, medical checkups, and training programs to prevent the spread of infections to the customers.

Microbiome Review: Ethnicity, Diet, and Lifestyle in Bad Obstetric History

This systematic review explores the intricate relationship between the maternal microbiome and adverse obstetric outcomes in women with a history of recurrent miscarriages, preterm birth, or stillbirth, collectively known as Bad Obstetric History (BOH). The microbiome, encompassing bacteria, viruses, and fungi, within the reproductive tract is increasingly recognized as a crucial factor in pregnancy maintenance and complications. The study explores BOH's multifactorial causes—genetic, anatomical, endocrine, thrombophilic, immunological, and environmental. Despite one-third of cases being unexplained, it underscores the importance of evaluating uterine macro and microenvironments. Emerging evidence challenges prior beliefs by supporting the existence of an endometrial microbiome, hinting at its impact on pregnancy outcomes. The methodology follows a systematic approach adhering to PRISMA guidelines, incorporating electronic database searches yielding 125 relevant articles, with 47 meeting inclusion criteria. The selected studies focus on human samples from stool, oral, or vaginal swabs, including randomized clinical trials, systematic reviews, and meta-analyses. In conclusion, the review emphasizes the significance of understanding the microbial changes in pregnant females and their potential impact on obstetric outcomes. The findings propose a connection between altered microbiota and maternal complications, highlighting the potential for personalized medicine interventions. Additionally, the study delves into the nuanced relationship between ethnicity, dietary patterns, and the microbiome, underscoring the importance of personalized and culturally sensitive healthcare interventions. Overall, this comprehensive review provides valuable insights into the role of the microbiome in obstetric outcomes, paving the way for future research and targeted interventions to optimize pregnancy outcomes globally.

Presence of SARS-CoV-2 RNA in COVID-19 survivors with post-COVID symptoms 2 years after hospitalization: The VIPER study.

The SARS-CoV-2 VIrus PERsistence (VIPER) study investigated the presence of long-lasting SARS-CoV-2 RNA in plasma, stool, urine, and nasopharyngeal samples in COVID-19 survivors. The presence of SARS-CoV-2 RNA reverse transcription polymerase chain reactions (RT-PCR) were analyzed within plasma, stool, urine, and nasopharyngeal swab samples in COVID-19 survivors with post-COVID symptoms and a comparison group of COVID-19 survivors without post-COVID symptoms matched by age, sex, body mass index and vaccination status. Participants self-reported the presence of any post-COVID symptom (defined as a symptom that started no later than 3 months after the initial infection). Fifty-seven (57.9% women, age: 51.1, standard deviation [SD]: 10.4 years) previously hospitalized COVID-19 survivors with post-COVID symptoms and 55 (56.4% women, age: 50.0, SD: 12.8 years) matched individuals who had a past SARS-CoV-2 infection without post-COVID symptoms were evaluated 27 (SD 7.5) and 26 (SD 8.7) months after hospital discharge, respectively. The presence of SARS-CoV-2 RNA was identified in three nasopharyngeal samples of patients with post-COVID symptoms (5.2%) but not in plasma, stool, or urine samples. Thus, SARS-CoV-2 RNA was not identified in any sample of survivors without post-COVID symptoms. The most prevalent post-COVID symptoms consisted of fatigue (93%), dyspnea, and pain (both, 87.7%). This study did not find SARS-CoV-2 RNA in plasma, stool, or urine samples, 2years after the infection. A prevalence of 5.2% of SARS-CoV-2 RNA in nasopharyngeal samples, suggesting a potential active or recent reinfection, was found in patients with post-COVID symptoms. These results do not support the association between SARS-CoV-2 RNA in plasma, stool, urine, or nasopharyngeal swab samples and post-COVID symptomatology in the recruited population.

Gut microbiome alterations in Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal Infections (PANDAS) suggests variation in the gut-brain axis and gut metabolic potential

PANDAS, or Pediatric Autoimmune Neuropsychiatric Disorders Associated with Streptococcal Infections is a form of Children’s Post infectious Autoimmune Encephalopathy (CPAE), a neuropsychiatric condition characterized by the abrupt onset of diverse neuropsychiatric manifestations following streptococcal infection. It is an increasingly recognized neuropsychiatric disorder that affects a subset of children whose underlying etiology remains unclear. Gut microbiome plays a crucial role in its host brain development and is implicated throughout the life in neurobehavior and neurological disorders. Emerging evidence suggest gut dysbiosis resulting in altered intestinal flora can impair gut barrier and increase leakiness in the blood-brain barrier leading to inflammation. We aimed to investigate if the microbiome is altered in pediatric patients with PANDAS. Stool (n=19), oral (n=20) and nasal swabs (n=18) were collected from patients diagnosed with PANDAS or healthy controls (HC) and used for 16S analysis. 13 stool samples (7 HC and 6 PANDAS) samples were further used for shogun metagenomics and 17 for untargeted metabolomics (8 HC and 9 PANDAS). 16S rRNA gene sequencing identified significant difference in microbial α diversity, with lower Shannon H’ in PANDAS compared to HC (Welch’s t-test t(16.95)=-2.6, p=0.02), and in β-diversity (PERMANOVA R2=0.08 p=0.04) between PANDAS and HC fecal but not throat and nasal samples. Shotgun metagenomics identified a significant reduction in gene diversity (Welch’s t-test t(9.9)=-3.06, p=0.01) and changes in various KEGG ortholog modules involved in gut metabolism and gut-brain axis. Significant differences were also detected in metabolite composition (PERMANOVA R2=0.10, p=0.02). We also identified a set of microbial groups and metabolites enriched or depleted in CPAE patients, involved in different aspects of host physiology and gut metabolism. Our results show that PANDAS patients have an altered gut microbial community, which may exacerbate their behavioral symptoms and it should be taken into consideration in unveiling the complex pathogenesis and selection of treatment options. Arizona Department of Health Services RFGA2022-010-23 (PK) and ADHS17-00007403 (SR, MD); The Alex Manfull Fund (PK). This is the full abstract presented at the American Physiology Summit 2024 meeting and is only available in HTML format. There are no additional versions or additional content available for this abstract. Physiology was not involved in the peer review process.

Comparison of rectal swabs and fecal samples for the detection of Clostridioides difficile infections with a new in-house PCR assay.

Clostridioides difficile infection (CDI) is the leading cause of healthcare-associated diarrhea, resulting in high morbidity, mortality, and economic burden. In clinical laboratories, CDI testing is currently performed on stool samples collected from patients with diarrhea. However, the diagnosis of CDI can be delayed by the time required to collect stool samples. Barriers to sample collection could be overcome by using a rectal swab instead of a stool sample. Our study showed that CDI can be identified rapidly and reliably by a new PCR assay developed in our laboratory on both stool and rectal swab specimens. The use of PCR tests on rectal swabs could reduce the time for the detection of CDI and improve the management of this infection. It should also provide a useful alternative for infection-control practitioners to better control the spread of C. difficile.

Occurrence of Clostridium perfringens in Wild Mammals in the Amazon Biome.

The objective of this study was to evaluate the occurrence of Clostridium perfringens in stool samples and swabs collected from wild mammals in the Amazon biome. Sixty-five faecal and swab samples were collected in situ and ex situ from 16 species and three genera of wild mammals, some of which were in good health and some of which had diarrhoea. After pre-enrichment, the samples were plated on selective agar for C. perfringens. Characteristic colonies were subjected to multiplex PCR for the detection of genes encoding the main C. perfringens toxins (alpha, beta, epsilon, and iota toxin and enterotoxin). Among the 65 samples, 40 (61.5%) were positive for the gene encoding the alpha toxin and were classified as type A, 36 of which were asymptomatic animals and four were diarrheal. No other toxinotypes were found. The findings of this study suggest that C. perfringens type A is commonly found in mammal species of the Amazon biome. This seems to be the first study to identify C. perfringens type A in species such as B. variegatus (common ground sloth), C. didactylus (two-toed sloth), P. flavus (Jupará), T. tetradactyla (anteater), S. collinsi (squirrel monkey), S. niger (black marmoset), and S. apella (Guyana capuchin) and in the genus Didelphis sp. (opossum).