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COVID-19 is a severe respiratory disease threatening pregnant women, which increases the possibility of adverse pregnancy outcomes. Several recent studies have demonstrated the ability of SARS-CoV-2 to infect the mother enterocytes, disturbing the gut microbiota diversity. The aim of this study was to characterize the entero-mammary microbiota of women in the presence of the virus during delivery. Fifty mother–neonate pairs were included in a transversal descriptive work. The presence of SARS-CoV-2 RNA was detected in nasopharyngeal, mother rectal swabs (MRS) and neonate rectal swabs (NRS) collected from the pairs, and human colostrum (HC) samples collected from mothers. The microbiota diversity was characterized by high-throughput DNA sequencing of V3-16S rRNA gene libraries prepared from HC, MRS, and NRS. Data were analyzed with QIIME2 and R. Our results indicate that several bacterial taxa are highly abundant in MRS positive for SARS-CoV-2 RNA. These bacteria mostly belong to the Firmicutes phylum; for instance, the families Bifidobacteriaceae, Oscillospiraceae, and Microbacteriaceae have been previously associated with anti-inflammatory effects, which could explain the capability of women to overcome the infection. All samples, both positive and negative for SARS-CoV-2, featured a high abundance of the Firmicutes phylum. Further data analysis showed that nearly 20% of the bacterial diversity found in HC was also identified in MRS. Spearman correlation analysis highlighted that some genera of the Proteobacteria and Actinobacteria phyla were negatively correlated with MRS and NRS (p < 0.005). This study provides new insights into the gut microbiota of pregnant women and their potential association with a better outcome during SARS-CoV-2 infection.

Cattle are regarded as the principle reservoir of O157 and non-O157 shigatoxigenic Escherichia coli (STEC). Spreading of the STEC to human is primarily happens through contaminated meat, milk and their byproducts. The present study was aimed to explore the occurrence of STEC in the rectal swab of apparently healthy cattle. A total of 60 E. coli isolates that were previously isolated from the rectal swab of cattle were used in this study. DNA were extracted from the isolates and screened by PCR to detect E. coli stx (stx1, stx2), ehxA and fO157 genes. Representative amplicons of the PCR products were sequenced. The prevalence of the STEC was determined based on the detection of STEC specific stx genes. The prevalence data were further analyzed by SPSS to elucidate any difference among different demographic groups of the study population. Overall, 43.33% (n=26/60) of the isolates were found carrying stx genes. Based on the presence of stx and ehxA genes, 6 different types of STEC were identified, of which 20% (n=12/26) were carrying both stx1 and stx2 genes. None of the isolates was positive for fbO157. The PCR amplicons were sequenced, and the nucleotide sequences were deposited in GenBank (accession: KM596779KM596784). In this study, non-O157 STEC were found highly prevalent in the local cattle. This study suggests that the apparently healthy cattle may act as a potential source of STEC infection for humans.

Purpose Nosocomial infections caused by carbapenem-resistant bacteria (CRB) present a worldwide threat. We examined the incidence and clinical outcomes of ICU-acquired gastrointestinal colonization with CRB detected through routine weekly surveillance of rectal swabs. Methods This retrospective study included adult patients admitted to the ICU between January 1, 2020 and December 31, 2022, whose rectal swab cultures yielded CRB colonization after at least 72 h of ICU admission. Results Of 4,673 eligible patients, 493 had at least one positive rectal swab culture for CRB (prevalence 10.5%) after a mean of 17.8 days from ICU admission. The most common CRB species was Klebsiella pneumoniae (41.8%), followed by Acinetobacter baumannii (32.3%), Pseudomonas aeruginosa (21.3%) and Escherichia coli (8.1%). Following colonization, 240 patients (48.7%) developed CRB infections after a mean of 11.4 days and 29.2 days from the first positive rectal culture and from ICU admission, respectively. The overall agreement between the baseline rectal and final cultures was 82.1%. CRB-infected patients had higher frequencies of burns at baseline (p < 0.001), carbapenem (p = 0.015) and colistin (p < 0.001) use during ICU stay, need for intubation (p = 0.002) and nasogastric tube (p = 0.021), prolonged ICU stay (p < 0.001), and mortality (p = 0.006). Conclusion Our findings showed that nearly one in every 10 ICU patients acquired CRB colonization despite preventive efforts, ending up with CRB infections in nearly half.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infections have been reported in humans and various wild and domestic animals. The potential for SARS-CoV-2 transmission has been demonstrated in animal models. This study focused on the prevalence of SARS-CoV-2 RNA in domestic dogs and cats in São João de Meriti, Rio de Janeiro, Brazil.This study investigated the potential for domestic dogs and cats to be infected with SARS-CoV-2. Rectal swabs were collected from dogs and cats during routine veterinary visits between December 2020 and June 2021. Viral RNA was detected by real-time PCR, and Sanger sequencing was used to access the viral genome. A total of 650 samples were analyzed, with 48 (7.4%) testing positive for SARS-CoV-2. The positivite rate was 7.7% in dogs and 8.3% in cats. Fourteen animals exhibited clinical signs resembling COVID-19, the most prevalent being lack of appetite, vomiting, and diarrhea. The highest number of positive cases was observed in January 2021. One sample was successfully sequenced and identified as the Gamma (P.1) lineage. To the author’s knowledge, this is the largest Brazilian survey of SARS-CoV-2 in animals. It suggested that dogs and cats might be without clinical signs or present with mild clinical signs. There is no evidence that dogs and cats can spread SARS-CoV-2 back to humans. RESUMO: As infecções pelo coronavírus da síndrome respiratória aguda grave 2 (SARS-CoV-2) foram relatadas não apenas em humanos, mas também em vários animais selvagens e domésticos. O potencial de transmissão do SARS-CoV-2 foi demonstrado em modelos animais. Este estudo enfoca a prevalência do RNA do SARS-CoV-2 em cães e gatos domésticos em São João de Meriti, Rio de Janeiro, Brasil. O objetivo deste estudo foi investigar o potencial de infecção de cães e gatos domésticos pelo SARS-CoV-2. Foram coletados swabs retais de cães e gatos durante visitas veterinárias de rotina entre dezembro de 2020 a junho de 2021. O RNA viral foi detectado por PCR em tempo real, e o sequenciamento de Sanger foi usado para analisar o genoma viral. Um total de 650 amostras foram analisadas, sendo 48 (7,4%) positivas para SARS-CoV-2. A taxa de positividade foi de 7,7% em cães e 8,3% em gatos. Quatorze animais apresentaram sinais clínicos semelhantes aos da COVID-19, sendo os mais prevalentes a falta de apetite, vômitos e diarreia. O maior número de casos positivos foi observado em janeiro de 2021. Uma amostra foi sequenciada com sucesso e identificada como pertencente à linhagem Gamma (P.1). No conhecimento dos autores, esta é a maior pesquisa brasileira sobre o SARS-CoV-2 em animais e sugere que os animais de estimação podem ser sem sinais clínicos ou apresentar sinais clínicos leves. Não há evidências de que cães e gatos possam disseminar o SARS-CoV-2 para os seres humanos.

Background Studies of the gut microbiome are becoming increasingly important. Such studies require stool collections that can be processed or frozen in a timely manner so as not to alter the microbial content. Due to the logistical difficulties of home-based stool collection, there has been a challenge in selecting the appropriate sample collection technique and comparing results from different microbiome studies. Thus, we compared stool collection and two alternative clinic-based fecal microbiome collection techniques, including a newer glove-based collection method. Results We prospectively enrolled 22 adult men from our prostate cancer screening cohort SABOR (San Antonio Biomarkers of Risk for prostate cancer) in San Antonio, TX, from 8/2018 to 4/2019. A rectal swab and glove tip sample were collected from each participant during a one-time visit to our clinics. A single stool sample was collected at the participant’s home. DNA was isolated from the fecal material and 16 s rRNA sequencing of the V1-V2 and V3-V4 regions was performed. We found the gut microbiome to be similar in richness and evenness, noting no differences in alpha diversity among the collection methods. The stool collection method, which remains the gold-standard method for the gut microbiome, proved to have different community composition compared to swab and glove tip techniques ( p < 0.001) as measured by Bray-Curtis and unifrac distances. There were no significant differences in between the swab and glove tip samples with regard to beta diversity ( p > 0.05). Despite differences between home-based stool and office-based fecal collection methods, we noted that the distance metrics for the three methods cluster by participant indicating within-person similarities. Additionally, no taxa differed among the methods in a Linear Discriminant Analysis Effect Size (LEfSe) analysis comparing all-against-all sampling methods. Conclusion The glove tip method provides similar gut microbiome results as rectal swab and stool microbiome collection techniques. The addition of a new office-based collection technique could help easy and practical implementation of gut microbiome research studies and clinical practice.

Currently, accurate biomarkers differentiating simple (phlegmonous) from complex (gangrenous and/or perforated) appendicitis in children are lacking. However, both types may potentially require different treatment strategies, and the search for diagnostic modalities remains warranted. Previously, we demonstrated a distinct microbiota (both an increased bacterial diversity and abundance) in the appendix of children with complex compared to simple appendicitis. From the same cohort of patients we have collected 35 rectal swabs under general anesthesia prior to appendectomy and microbiota analysis was performed by IS-pro, a 16S-23S rDNA–based clinical microbiota profiling technique. Using the obtained IS-profiles, we performed cluster analyses (UPGMA), comparison of diversity (Shannon Diversity Index) and intensity (abundance in relative fluorescence units) on phylum level, and comparison on species level of bacteria between simple and complex appendicitis. Regarding these analyses, we observed no clear differences between simple and complex appendicitis. However, increased similarity of the microbial composition of the appendix and rectal swab was found within children with complex compared to simple appendicitis. Furthermore, PLS-DA regression analysis provided clear visual differentiation between simple and complex appendicitis, but the diagnostic power was low (highest AUC 0.65).     Conclusion : Microbiota analysis of rectal swabs may be viable to differentiate between simple and complex appendicitis prior to surgery as a supervised classification model allowed for discrimination of both types. However, the current diagnostic power was low and further validation studies are needed to assess the value of this method. What is Known: •   Simple and complex appendicitis in children may require different treatment strategies, but accurate preoperative biomarkers are lacking. •  Clear differentiation can be made between both types in children based upon the microbial composition in the appendix. What is New: •  Increased similarity was found between the microbial composition of the appendix and rectal swab within children with complex compared to simple appendicitis. •   Using a supervised classification model rectal swabs may be viable to discriminate between simple and complex appendicitis, but the diagnostic power was low.

Background Sample collection for gut microbiota analysis from in-patients can be challenging. Collection method and storage conditions are potential sources of variability. In this study, we compared the bacterial microbiota from stool stored under different conditions, as well as stool and swab samples, to assess differences due to sample storage conditions and collection method. Methods Using bacterial 16S rRNA gene sequence analysis, we compared the microbiota profiles of stool samples stored and collected under various conditions. Stool samples (2 liquid, 1 formed) from three different patients at two hospitals were each evaluated under the following conditions: immediately frozen at -80°C, stored at 4°C for 12-48 hours before freezing at -80°C and stored at -20°C with 1-2 thaw cycles before storage at -80°C. Additionally, 8 stool and 30 rectal swab samples were collected from 8 in-patients at one hospital. Microbiota differences were assessed using the Yue and Clayton dissimilarity index (θ YC distance) and analysis of molecular variance (AMOVA). Results Regardless of the storage conditions, the bacterial communities of aliquots from the same stool samples were very similar based on θ YC distances (median intra-sample θ YC distance: 0.035, IQR: 0.015-0.061) compared to aliquots from different stool samples (median inter-sample θ YC distance: 0.93, IQR: 0.85-0.97) (Wilcoxon test p -value: <0.0001). For the stool and rectal swab comparison, samples from different patients, regardless of sample collection method, were significantly different (AMOVA p -values: <0.001-0.029) compared to no significant difference between all stool and swab samples (AMOVA p -value: 0.976). The θ YC dissimilarity index between swab and stool samples was significantly lower within individuals (median 0.17, IQR: 0.10-0.27) than between individuals (median 0.93, IQR: 0.85-0.97) (Wilcoxon test p -value: <0.0001), indicating minimal differences between stool and swab samples collected from the same individual over the sampling period. Conclusion For gastrointestinal microbiota studies based on bacterial 16S rRNA gene sequence analysis, interim stool sample storage at 4 °C or -20 °C, rather than immediate storage at -80 °C, does not significantly alter results. Additionally, stool and rectal swab microbiotas from the same subject were highly similar, indicating that these sampling methods could be used interchangeably to assess the community structure of the distal GI tract.

Canine circovirus (CaCV) is a single-stranded DNA virus that globally circulates in dogs and wild carnivores. Although the pathogenic potential of the virus has not been fully understood yet, CaCV has been suggested to exacerbate the clinical course of other canine viral infections but also to circulate in dogs without clinical signs. In this study, we carried out real-time PCR assays to detect enteric pathogens from 156 canine rectal swabs collected from dogs without enteritis in 3 different regions in Iran. A total of 14 samples tested positive for CaCV and full-length genome sequences were obtained from 6 of the detected strains. Sequence and phylogenetic analyses showed that, despite the distance between the different sample collection sites, all Iranian CaCV strains were closely related and formed a separate clade from extant CaCVs. The present study shows that CaCV is circulating in non-diarrheic dogs in Iran, thus highlighting the need for further epidemiological investigations in Iranian domestic and wild carnivores.

Abstract Background Quantitative polymerase chain reaction (qPCR) targeting ipaH has been proven to be highly efficient in detecting Shigella in clinical samples compared to culture-based methods, which underestimate Shigella burden by 2- to 3-fold. qPCR assays have also been developed for Shigella speciation and serotyping, which is critical for both vaccine development and evaluation. Methods The Enterics for Global Health (EFGH) Shigella surveillance study will utilize a customized real-time PCR–based TaqMan Array Card (TAC) interrogating 82 targets, for the detection and differentiation of Shigella spp, Shigella sonnei, Shigella flexneri serotypes, other diarrhea-associated enteropathogens, and antimicrobial resistance (AMR) genes. Total nucleic acid will be extracted from rectal swabs or stool samples, and assayed on TAC. Quantitative analysis will be performed to determine the likely attribution of Shigella and other particular etiologies of diarrhea using the quantification cycle cutoffs derived from previous studies. The qPCR results will be compared to conventional culture, serotyping, and phenotypic susceptibility approaches in EFGH. Conclusions TAC enables simultaneous detection of diarrheal etiologies, the principal pathogen subtypes, and AMR genes. The high sensitivity of the assay enables more accurate estimation of Shigella-attributed disease burden, which is critical to informing policy and in the design of future clinical trials. Shigella spp, Shigella flexneri serotypes, and other diarrhea-associated enteropathogens are detected and quantified with a customized real-time polymerase chain reaction–based TaqMan Array Card in the Enterics for Global Health: Shigella surveillance study. Shigella burden will be estimated with a quantitative methodology.