One decade of point-prevalence surveys for carriage of extended-spectrum beta-lactamase-producing enterobacterales: whole genome sequencing based prevalence and genetic characterization in a large Dutch teaching hospital from 2013 to 2022.

OBJECTIVES: To determine the prevalence, trends, and potential nosocomial transmission events of the hidden reservoir of rectal carriage of extended-spectrum beta-lactamase-producing Enterobacterales (ESBL-E). METHODS: From 2013 to 2022, yearly point prevalence surveys were conducted in a large Dutch teaching hospital. On the day of the survey, all admitted patients were screened for ESBL-E rectal carriage using peri-anal swabs and a consistent and sensitive selective culturing method. All Enterobacterales phenotypically suspected of ESBL production were analysed using whole genome sequencing for ESBL gene detection and clonal relatedness analysis. RESULTS: On average, the ESBL-E prevalence was 4.6% (188/4,119 patients), ranging from 2.1 to 6.6% per year. The ESBL-prevalence decreased on average 5.5% per year. After time trend correction, the prevalence in 2016 and 2020 was lower compared to the other year. Among the ESBL-E, Escherichia coli (80%) and CTX-M genes (85%) predominated. Potential nosocomial transmission events could be found in 5.9% (11/188) of the ESBL-E carriers. CONCLUSIONS: The ESBL-E rectal carriage prevalence among hospitalized patients was 4.6% with a downward trend from 2013 to 2022. The decrease in ESBL-E prevalence in 2020 could have been due to the COVID-19 pandemic and subsequent countrywide measures as no nosocomial transmission events were detected in 2020. However, the persistently low ESBL-E prevalences in 2021 and 2022 suggest that the decline in ESBL-E prevalence goes beyond the COVID-19 pandemic, indicating that overall ESBL-E carriage rates are declining over time. Continuous monitoring of ESBL-E prevalence and transmission rates can aid infection control policy to keep antibiotic resistance rates in hospitals low.

Preventing Infections After Prostate Biopsy: Prophylactic Antibiotics, Prebiopsy Rectal Culture, and Biopsy Approach.

Prostate biopsies are commonly performed for the early detection of prostate cancer and yet are associated with risks of life-threatening infections. Drug-resistant strains of Escherichia coli are the most common etiologic agents. Multiple maneuvers can reduce the risk of postbiopsy infections and sepsis during transrectal prostate biopsy including periprocedural empiric or targeted prophylactic antibiotics (based on previous rectal culture) and prebiopsy rectal cleansing with a povidone-iodine solution. The transperineal approach is associated with a very low risk of infection without requiring antibiotic prophylaxis.

Meconium microbiota in naturally delivered canine puppies.

BACKGROUND: Microbial colonization during early life has a pivotal impact on the host health, shaping immune and metabolic functions, but little is known about timing and features of this process in dogs. The objectives of this study were to characterize the first step of intestinal microbiota development in naturally delivered canine puppies and to investigate its relationship with the maternal bacterial flora, using traditional culture and molecular analyses. Sixty puppies of two breeds, Appenzeller Cattle Dog (n = 3 dams) and Lagotto Romagnolo (n = 6), housed in the same breeding kennel, were included in the study. Swabs were collected in duplicate (for culture and for molecular analysis) from the dams' vagina and rectum at the end of parturition, from puppies' rectum, before maternal care, and from the environment (floor of the nursery and parturition box). RESULTS: 93.3% meconium samples showed bacterial growth, limited to a few colonies in 57.0% of cases. High growth was detected for Enterococcus faecalis, which was the most frequently isolated bacterium. The genus Enterococcus was one of the most represented in the dams' rectum and vagina (88.9% and 55.6%, respectively). The genera Staphylococcus, Enterococcus, Escherichia and Proteus were also often isolated in meconium but were usually present in maternal samples as well, together with ubiquitous bacteria (Acinetobacter, Psychrobacter). In the environmental samples, just a few bacterial species were found, all with low microbial load. Additionally, bacteria of the phyla Proteobacteria, Firmicutes, and Actinobacteria were identified in meconium through molecular analysis, confirming the culture results and the early colonization of the newborn gut. Maternal, meconium and environmental samples had similar alpha diversity, while beta-diversity showed differences among families (i.e. a dam and her litter), and association indexes revealed a significant correlation between family members and between sample origin, suggesting a strong contribution of the maternal flora to the initial seeding of the canine neonatal gut and a strong individual dam imprint. CONCLUSION: This study showed that the meconium of vaginally delivered puppies has its own microbiota immediately after birth, and that it is shaped by the dam, which gives a specific imprint to her litter.

The potential of residual clinical Group B Streptococcus swabs for assessing the vaginorectal microbiome in late pregnancy.

The maternal pregnancy microbiome (including genitourinary and gut) has been linked to important pregnancy/birth and later childhood health outcomes. However, such sampling as part of large population cohort studies is logistically and financially challenging. Many countries routinely collect vaginal or vaginal-rectal swabs in late pregnancy for Group B Streptococcus (GBS) screening, but their utility for population-based research is still unclear. As part of planning for the Generation Victoria population-based cohort study beginning in pregnancy, we assessed the utility and reliability of residual clinical GBS vaginal/vaginal-rectal swabs for generating late pregnancy microbiome data. We carried out a two-phased pilot study. Phase one assessed the level of microbial diversity apparent in 'residual' clinical vaginal/vaginal-rectal swabs post clinical testing and storage for 7-10 days at 4 °C (routine clinical practice). Phase two directly assessed the impact of storage time and temperature on the microbial composition of vaginal/vaginal-rectal swabs collected specifically for research purposes. The microbiota composition in the 'residual' clinical swabs aligned with published studies. The 'research' swabs, stored at 4 °C for up to ten days, showed minimal changes in microbiota profile, compared to swabs examined on the day of collection. In contrast, significant variation in diversity was seen in swabs stored at room temperature for up to 48 h. Residual clinical material from swabs collected primarily for GBS screening in late pregnancy represent a reliable and abundant source of material for assessing the late pregnancy maternal microbiome for research purposes. This represents a low-burden opportunity for population-representative pregnancy studies to assess the potential of late pregnancy microbiome for prediction and understanding maternal and child health outcomes.

Is screening of patients for Pseudomonas aeruginosa groin/rectal carriage useful in identifying those at risk of bacteraemia in haematology and other high-risk clinical settings?

BACKGROUND: Pseudomonas aeruginosa is a leading cause of healthcare-associated infections in patients exposed to hospital waters. A rising incidence of P. aeruginosa bacteraemia at our tertiary teaching hospital prompted investigation. AIM: Microbiological screening at patient admission to support early identification of acquisition. METHODS: A 41-bed haematology ward (800-bed teaching-hospital, London) was surveyed between January 24th, 2020 and May 13th, 2020. Concurrent rectal and groin swabs were collected in duplicate upon admission weekly. Results were compared with historical shower, drain, and tap water contamination data. FINDINGS: A total of 606 groin/rectal swabs were collected from 154 patients; 61 female and 93 male. Six out of 154 patients admitted (3.9%) were positive for P. aeruginosa. Two patients (1.3%; 95% confidence interval (CI): 0.16 to 4.6) were colonized at admission while four patients (2.6%; CI: 0.7 to 6.5) became colonized by 33 days (interquartile range: 13 to 54) of stay. Concurrent duplicate sampling yielded both positive and negative results in all colonized patient-cases. One patient subsequently developed P. aeruginosa bacteraemia. Shower water and corresponding drains from the four patient rooms where P. aeruginosa was acquired were heavily contaminated (>300 cfu/100 mL) with P. aeruginosa 265 days (median; range: 247-283) before patient admission. CONCLUSION: Rectal/groin swab-screening at admission to hospital might be valuable for early detection of patient colonization but it is intrusive, resource-demanding, and yield may be low. In high-risk settings, enhanced environmental monitoring, decontamination of surfaces and drains, and point-of-use filter-barriers is recommended, especially if expected duration of stay exceeds 30 days.

Gestational diabetes as a risk factor for GBS maternal rectovaginal colonization: a systematic review and meta-analysis.

BACKGROUND: Maternal rectovaginal colonization by group B Streptococcus (GBS) increases the risk of perinatal GBS disease that can lead to death or long-term neurological impairment. Factors that increase the risk of rectovaginal GBS carriage are incompletely understood resulting in missed opportunities for detecting GBS in risk-based clinical approaches. There is a lacking consensus on whether gestational diabetes mellitus (GDM) is a risk factor for rectovaginal GBS. This systematic review and meta-analysis aims to address current conflicting findings and determine whether GDM should be clinically considered as a risk factor for maternal GBS colonization. METHODS: Peer-reviewed studies that provided GDM prevalence and documented GBS vaginal and/or rectal colonization in women with and without GDM were included in this analysis. From study inception to October 30, 2023, we identified 6,275 relevant studies from EMBASE and PUBMED of which 19 were eligible for inclusion. Eligible studies were analyzed and thoroughly assessed for risk of bias with a modified Newcastle-Ottawa Scale that interrogated representativeness and comparability of cohorts, quality of reporting for GDM and GBS status, and potential bias from other metabolic diseases. Results were synthesized using STATA 18 and analyzed using random-effects meta-analyses. RESULTS: Studies encompassed 266,706 women from 10 different countries, with study periods spanning from 1981 to 2020. Meta-analysis revealed that gestational diabetes is associated with a 16% increased risk of rectovaginal GBS carriage (OR 1.16, CI 1.07-1.26, P = 0.003). We also performed subgroup analyses to assess independent effects of pregestational vs. gestational diabetes on risk of maternal GBS carriage. Pregestational diabetes (Type 1 or Type 2 diabetes mellitus) was also associated with an increased risk of 76% (pooled OR 1.76, CI 1.27-2.45, P = 0.0008). CONCLUSIONS: This study achieved a consensus among previously discrepant observations and demonstrated that gestational diabetes and pregestational diabetes are significant risk factors for maternal rectovaginal carriage of GBS. Recognition of GDM as a risk factor during clinical decisions about GBS screening and intrapartum antibiotic prophylaxis may decrease the global burden of GBS on maternal-perinatal health.

Linking active rectal mucosa-attached microbiota to host immunity reveals its role in host-pathogenic STEC O157 interactions.

The rectal-anal junction (RAJ) is the major colonization site of Shiga toxin-producing Escherichia coli (STEC) O157 in beef cattle, leading to transmission of this foodborne pathogen from farms to food chains. To date, there is limited understanding regarding whether the mucosa-attached microbiome has a profound impact on host-STEC interactions. In this study, the active RAJ mucosa-attached microbiota and its potential role in host immunity-STEC commensal interactions were investigated using RAJ mucosal biopsies collected from calves orally challenged with two STEC O157 strains with or without functional stx2a (stx2a+ or stx2a-). The results revealed that shifts of microbial diversity, topology, and assembly patterns were subjected to stx2a production post-challenge and Paeniclostridium and Gallibacterium were the keystone taxa for both microbial interactions and assembly. Additional mucosal transcriptome profiling showed stx2a-dependent host immune responses (i.e. B- and T-cell signaling and antigen processing and presentation) post-challenge. Further integrated analysis revealed that mucosa-attached beneficial microbes (i.e. Provotella, Faecalibacterium, and Dorea) interacted with host immune genes pre-challenge to maintain host homeostasis; however, opportunistic pathogenic microbes (i.e. Paeniclostridium) could interact with host immune genes after the STEC O157 colonization and interactions were stx2a-dependent. Furthermore, predicted bacterial functions involved in pathogen (O157 and Paeniclostridium) colonization and metabolism were related to host immunity. These findings suggest that during pathogen colonization, host-microbe interactions could shift from beneficial to opportunistic pathogenic bacteria driven and be dependent on the production of particular virulence factors, highlighting the potential regulatory role of mucosa-attached microbiota in affecting pathogen-commensal host interactions in calves with STEC O157 infection.

Microbial signatures and continuum in endometrial cancer and benign patients.

BACKGROUND: Endometrial cancer is a multifactorial disease with inflammatory, metabolic and potentially microbial cues involved in disease pathogenesis. The endometrial cancer microbiome has been poorly characterised so far and studies have often overestimated bacterial biomass due to lack of integration of appropriate contamination controls. There is also a scarcity of evidence on the functionality of microbial microenvironments in endometrial cancer. This work addresses that knowledge gap by interrogating the genuine, contamination-free microbial signatures in the female genital tract and rectum of women with endometrial cancer and the mechanistic role of microbiome on carcinogenic processes. RESULTS: Here we sampled different regions of the reproductive tract (vagina, cervix, endometrium, fallopian tubes and ovaries) and rectum of 61 patients (37 endometrial cancer; 24 benign controls). We performed 16S rRNA gene sequencing of the V1-V2 hypervariable regions and qPCR of the 16S rRNA gene to qualitatively and quantitatively assess microbial communities and used 3D benign and endometrial cancer organoids to evaluate the effect of microbial products of L. crispatus, which was found depleted in endometrial cancer patients following primary analysis, on endometrial cell proliferation and inflammation. We found that the upper genital tract of a subset of women with and without endometrial cancer harbour microbiota quantitatively and compositionally distinguishable from background contaminants. Endometrial cancer was associated with reduced cervicovaginal and rectal bacterial load together with depletion of Lactobacillus species relative abundance, including L. crispatus, increased bacterial diversity and enrichment of Porphyromonas, Prevotella, Peptoniphilus and Anaerococcus in the lower genital tract and endometrium. Treatment of benign and malignant endometrial organoids with L. crispatus conditioned media exerted an anti-proliferative effect at high concentrations but had minimal impact on cytokine and chemokine profiles. CONCLUSIONS: Our findings provide evidence that the upper female reproductive tract of some women contains detectable levels of bacteria, the composition of which is associated with endometrial cancer. Whether this is a cause or consequence of cancer pathophysiology and what is the functional significance of this finding remain to be elucidated to guide future screening tools and microbiome-based therapeutics. Video Abstract.

Prevalence of rectal carbapenem resistant Enterobacterales carriage among patients attending healthcare facilities in Ibadan, Nigeria: a descriptive study.

BACKGROUND: Carbapenem Resistant Enterobacterales (CRE) infections are increasingly associated with or directly responsible for morbidity and mortality from bacterial infections in sub-Saharan Africa where there are limited antibiotic options. CRE rectal colonization of patients in healthcare facilities provides a reservoir of these organisms and could potentially cause invasive infections in these settings. The prevalence of rectal carriage among patients attending healthcare facilities in Nigeria has not been previously described. We set out to assess the prevalence of rectal CRE carriage and their antibiotic susceptibility patterns among patients attending healthcare facilities in Nigeria. METHODS: A descriptive cross-sectional study was carried out from December 2021 to September 2022 in Ibadan, in which patients attending primary, secondary and tertiary healthcare facilities were screened for rectal carriage of CRE by microscopy, culture and sensitivity of rectal swab specimens. RESULTS: A total of 291 patients were screened; 45 (15.5%), 66 (22.7%) and 180 (61.8%) at primary, secondary and tertiary healthcare facilities, respectively. All but one of them had received a third-generation cephalosporin or carbapenem in the preceding 30 days. The mean age was 28.8 years and 55.7% were male. Overall, 51 (17.5%) participants had CRE colonization, with 5(11.1%), 9(13.6%) and 37(20.6%) at primary, secondary and tertiary healthcare facilities, respectively (p = 0.243). Regarding antimicrobial susceptibility, 43(84.3%) CRE isolates were resistant to at least 3 different classes of antibiotics while two Escherichia coli isolates were resistant to all 5 classes of antibiotics tested. The lowest rates of CRE resistance were to tigecycline (6, 11.5%) and colistin (8, 15.7%). CONCLUSIONS: In this first study on CRE colonization in Nigeria, we found that a substantial proportion of patients in three levels of healthcare facilities had rectal carriage of CRE, including pan-resistant isolates. Active surveillance and appropriate infection prevention and control practices (IPC) need to be urgently strengthened to mitigate the risk of active CRE infection. TRIAL REGISTRATION: Not applicable.

3D printed rectal swabs for assessing the gut microbiome, metabolome and inflammation.

Investigating the gut microbiome and metabolome frequently requires faecal samples, which can be difficult to obtain. Previous studies have shown that rectal swabs are comparable to faecal samples for analysing gut microbiota composition and key metabolites. In this study, 3D printed rectal swabs were compared with conventional flocked swabs and faecal samples, due to the potential advantages 3D printing as a technique offers for swab production and development. 16S rRNA gene sequencing, qPCR and metabolite profiling (using 1H-NMR spectroscopy) were performed on swab and faecal samples from healthy participants. Faecal calprotectin and total protein analysis were performed on samples from inflammatory bowel disease (IBD) patients. There were no significant differences between both swab types and faecal samples when assessing key measures of alpha and beta diversity, and differences in the abundance of major phyla. There was a strong correlation between both swab types and faecal samples for all combined metabolites detected by NMR. In IBD patients, there was no significant difference in faecal calprotectin and total protein levels between both swab types and faecal samples. These data lead us to conclude that 3D printed swabs are equivalent to flocked swabs for the analysis of the gut microbiome, metabolome and inflammation.

Enrichment culture evaluation and characterization of Streptococcus agalactiae among pregnant women in Japan.

Introduction. Maternal screening tests and prophylactic antibiotics are important to prevent neonatal and infant group B streptococcal (GBS) infections.Hypothesis/Gap Statement. The performance of enrichment broth media for GBS screening that are available in Japan is unclear. Whole-genome data of GBS isolates from pregnant women in Japan is lacking.Aim. The aim of this study was to compare the protocol performance of six enrichment broths and two subculture agar plates, which were all available in Japan, for GBS detection. In addition, we showed whole-genome data of GBS isolates from pregnant women in Japan.Methodology. We collected 133 vaginal-rectal swabs from pregnant women visiting clinics and hospitals in Nagasaki Prefecture, Japan, and compared the protocol performance of 6 enrichment broths and 2 subculture agar plates. All GBS isolates collected in this study were subjected to whole-genome sequencing analysis.Results. We obtained 133 vaginal-rectal swabs from pregnant women at 35-37 weeks of gestation from 8 private clinics and 2 local municipal hospitals within Nagasaki Prefecture, Japan. The detection rate of the protocol involving the six enrichment broths and subsequent subcultures varied between 95.5 and 100 %, depending on the specific choice of enrichment broth. The GBS carriage rate among pregnant women in this region was 18.8 %. All 25 isolates derived from the swabs were susceptible to penicillin, whereas 48 and 36 % of the isolates demonstrated resistance to erythromycin and clindamycin, respectively. The distribution of serotypes was highly diverse, encompassing seven distinct serotypes among the isolates, with the predominant serotype being serotype V (n = 8). Serotype V isolates displayed a tendency towards increased resistance to erythromycin and clindamycin, with all resistant isolates containing the ermB gene.Conclusion. There was no difference in performance among the culture protocols evaluated in this study. GBS strains isolated from pregnant women appeared to have greater genomic diversity than GBS strains detected in neonates/infants with invasive GBS infections. To confirm this result, further studies with larger sample sizes are needed.

Vaginal and rectal microbiome contribute to genital inflammation in chronic pelvic pain.

BACKGROUND: Chronic pelvic pain (CPP) is a multifactorial syndrome that can substantially affect a patient's quality of life. Endometriosis is one cause of CPP, and alterations of the immune and microbiome profiles have been observed in patients with endometriosis. The objective of this pilot study was to investigate differences in the vaginal and gastrointestinal microbiomes and cervicovaginal immune microenvironment in patients with CPP and endometriosis diagnosis compared to those with CPP without endometriosis and no CPP. METHODS: Vaginal swabs, rectal swabs, and cervicovaginal lavages (CVL) were collected among individuals undergoing gynecologic laparoscopy. Participants were grouped based on patients seeking care for chronic pain and/or pathology results: CPP and endometriosis (CPP-Endo) (n = 35), CPP without endometriosis (n = 23), or patients without CPP or endometriosis (controls) (n = 15). Sensitivity analyses were performed on CPP with endometriosis location, stage, and co-occurring gynecologic conditions (abnormal uterine bleeding, fibroids). 16S rRNA sequencing was performed to profile the microbiome, and a panel of soluble immune mediators was quantified using a multiplex assay. Statistical analysis was conducted with SAS, R, MicrobiomeAnalyst, MetaboAnalyst, and QIIME 2. RESULTS: Significant differences were observed between participants with CPP alone, CPP-Endo, and surgical controls for body mass index, ethnicity, diagnosis of ovarian cysts, and diagnosis of fibroids. In rectal microbiome analysis, both CPP alone and CPP-Endo exhibited lower alpha diversity than controls, and both CPP groups revealed enrichment of irritable bowel syndrome-associated bacteria. CPP-Endo exhibited an increased abundance of vaginal Streptococcus anginosus and rectal Ruminococcus. Patients with CPP and endometrioma (s) demonstrated increased vaginal Streptococcus, Lactobacillus, and Prevotella compared to other endometriosis sites. Further, abnormal uterine bleeding was associated with an increased abundance of bacterial vaginosis-associated bacteria. Immunoproteomic profiles were distinctly clustered by CPP alone and CPP-Endo compared to controls. CPP-Endo was enriched in TNF⍺, MDC, and IL-1⍺. CONCLUSIONS: Vaginal and rectal microbiomes were observed to differ between patients with CPP alone and CPP with endometriosis, which may be useful in personalized treatment for individuals with CPP and endometriosis from those with other causes of CPP. Further investigation is warranted in patients with additional co-occurring conditions, such as AUB/fibroids, which add additional complexity to these conditions and reveal the enrichment of distinct pathogenic bacteria in both mucosal sites. This study provides foundational microbiome-immunoproteomic knowledge related to chronic pelvic pain, endometriosis, and co-occurring gynecologic conditions that can help improve the treatment of patients seeking care for pain.

Ligilactobacillus salivarius V4II-90 eradicates Group B Streptococcus colonisation during pregnancy: a randomised, double-blind, placebo-controlled trial.

Group B Streptococcus (GBS) is the leading cause of bacterial neonatal sepsis. This study aimed to confirm the effect of Ligilactobacillus salivarius V4II-90 on GBS colonisation during pregnancy. A randomised, multicentre, double-blind, placebo-controlled, parallel-group study was conducted in seven hospitals in Madrid, Spain. The sample was broken down into two groups with 20 participants each (n = 40) in order to show reduced GBS colonisation frequency in the probiotic versus the placebo group. Pregnant participants positive for vaginal-rectal colonisation before or during the 13th week of gestation were randomly assigned to either the placebo or the probiotic group. The probiotic, L. salivarius V4II-90 at 1 × 109 cfu/day was administered for 12 weeks, starting at week 21-23 of gestation. The primary outcome was the percentage of participants with vaginal and/or rectal GBS colonisation at the end of the intervention period (35 weeks of gestation). Secondary outcomes were changes in the microbial composition of vaginal and rectal exudates; premature delivery; premature rupture of membranes; intrapartum antibiotics; new-borns with early or late-onset GBS sepsis; adverse events (AEs); and GBS test results performed at the hospital at week 35 of gestation. Of the 481 participants included, 44 were vaginal-rectal colonised with GBS and randomised. 43 completed the study (20 in the probiotic group and 23 in the placebo group). After intervention, GBS was eradicated in six participants (27%) from the placebo group and in twelve participants (63%) from the probiotic group ( P = 0.030). None of the 185 AEs reported were identified as possibly, probably, or definitely related to the investigational product. In conclusion, oral administration of L. salivarius V4II-90 is a safe and successful strategy to significantly decrease the rates of GBS colonisation at the end of pregnancy and, therefore, to reduce the exposure of subjects and their infants to intrapartum antibiotic prophylaxis. Trial registered at ClinicalTrials.gov: number NCT03669094.

The microbiome compositional and functional differences between rectal mucosa and feces.

In recent years, most studies on the gut microbiome have primarily focused on feces samples, leaving the microbial communities in the intestinal mucosa relatively unexplored. To address this gap, our study employed shotgun metagenomics to analyze the microbial compositions in normal rectal mucosa and matched feces from 20 patients with colonic polyps. Our findings revealed a pronounced distinction of the microbial communities between these two sample sets. Compared with feces, the mucosal microbiome contains fewer genera, with Burkholderia being the most discriminating genus between feces and mucosa, highlighting its significant influence on the mucosa. Furthermore, based on the microbial classification and KEGG Orthology (KO) annotation results, we explored the association between rectal mucosal microbiota and factors such as age, gender, BMI, and polyp risk level. Notably, we identified novel biomarkers for these phenotypes, such as Clostridium ramosum and Enterobacter cloacae in age. The mucosal microbiota showed an enrichment of KO pathways related to sugar transport and short chain fatty acid metabolism. Our comprehensive approach not only bridges the knowledge gap regarding the microbial community in the rectal mucosa but also underscores the complexity and specificity of microbial interactions within the human gut, particularly in the Chinese population. IMPORTANCE: This study presents a system-level map of the differences between feces and rectal mucosal microbial communities in samples with colorectal cancer risk. It reveals the unique microecological characteristics of rectal mucosa and its potential influence on health. Additionally, it provides novel insights into the role of the gut microbiome in the pathogenesis of colorectal cancer and paves the way for the development of new prevention and treatment strategies.

The association of maternal factors with the neonatal microbiota and health.

The human microbiome plays a crucial role in human health. However, the influence of maternal factors on the neonatal microbiota remains obscure. Herein, our observations suggest that the neonatal microbiotas, particularly the buccal microbiota, change rapidly within 24-48 h of birth but begin to stabilize by 48-72 h after parturition. Network analysis clustered over 200 maternal factors into thirteen distinct groups, and most associated factors were in the same group. Multiple maternal factor groups were associated with the neonatal buccal, rectal, and stool microbiotas. Particularly, a higher maternal inflammatory state and a lower maternal socioeconomic position were associated with a higher alpha diversity of the neonatal buccal microbiota and beta diversity of the neonatal stool microbiota was influenced by maternal diet and cesarean section by 24-72 h postpartum. The risk of admission of a neonate to the newborn intensive care unit was associated with preterm birth as well as higher cytokine levels and probably higher alpha diversity of the maternal buccal microbiota.

Investigation of prevalence and antimicrobial resistance of Salmonella in pet dogs and cats in Turkey.

BACKGROUND: Although salmonellosis is considered to be a foodborne zoonotic disease, pets can play a significant role in the dissemination of antimicrobial-resistant Salmonella organisms to humans because of close contact with their owners. OBJECTIVES: To determine the prevalence, risk factors, virulence factors, serotypes, and antimicrobial resistance profile of Salmonella in pet dogs and cats in Turkey and to assess the public health risk. Furthermore, to perform macroscopic comparison of lactic acid bacteria (LAB) in Salmonella-positive and Salmonella-negative animals. METHODS: International Standards Organization (ISO) 6579-1:2017 and Food and Drug Administration (FDA) methods were used to compare the effectiveness of culture methods in the identification of Salmonella in 348 rectal swabs. Positive isolates were serotyped using the slide agglutination method according to the White-Kauffmann-Le Minor scheme and the presence of virulence genes (invA and stn) were evaluated by polymerase chain reaction (PCR). Antimicrobial activity was tested by Kirby-Bauer disk diffusion method according to Clinical and Laboratory Standards Institute (CLSI) guidelines. RESULTS: Salmonella prevalence was 5.73% (9/157) in dogs and 0.0% (0/191) in cats. Eight (8/9) isolates were cultured with the ISO method and 5 (5/9) isolates were cultured with the FDA method. Macroscopic results revealed that Salmonella agents had no effect on LAB. Three different serotypes were detected and all isolates were positive for virulence genes. Antibiotic resistance profiling indicated that 11.1% of the isolates were MDR and the highest resistance was found for ciprofloxacin. MDR-resistant S. Virchow and carbapenem-resistant S. Enteritidis were detected from dog isolates. There was a significant difference between raw meat consumption and Salmonella carriage (p < 0.01). CONCLUSIONS: Dogs could be potential carriers of Salmonella infection. The isolation of Salmonella in healthy dogs instead of dogs suffering from diarrhoea indicates that attention should be paid to asymptomatic carriage. The emergence of resistance among zoonotic Salmonella isolates poses a significant threat to public health.

Overcoming analytical and preanalytical challenges associated with extragenital home collected STI specimens.

Home sample collection for sexually transmitted infection (STI) screening options can improve access to sexual healthcare across communities. For Chlamydia trachomatis (CT) and Neisseria gonorrhoeae (NG), genital infections have classically been the focus for remote collection options. However, infections may go undiagnosed if sampling is limited to urogenital sites because some individuals only participate in oral and/or anal intercourse. Here we evaluated samples for CT/NG detection after several pre-analytical collection challenges. A paired provider to self-collection validation was performed on rectal [n = 162; 22 + for CT and 9 + for NG by provider-collected (PC)] and throat (N = 158; 2 + for CT and 11 + for NG by provider-collected) swabs. The positive percent agreement for CT and NG ranged from 90.9% to 100%. The discrepancies were more often positive on self-collected (SC) (n = 9 SC+/PC-; n = 1 PC+/SC-; n = 1 PC+/SC Equiv.; n = 2 PC-/SC Equiv.). An empirical limit of detection (LoD) lower than the manufacturer's claim (0.031 vs 2.5 IFU/mL for CT and 0.063 vs 124.8 CFU/ml for NG, respectively) was used to challenge additional variables. Common hand contaminants, including soap, hand sanitizer, lotion, and sunscreen were added to known positive (3× empirical LoD) or negative samples and did not influence detection. Samples at 2× and 10× the empirical LoD were challenged with extreme temperature cycling and extended room temperature storage. Detection was not affected by these conditions. These results indicate that remote self-collection is an appropriate method of sample acquisition for detecting extragenital CT/NG infections. Additionally, they provide a foundation towards meeting the regulatory standards for commercial testing of home collected extragenital samples. IMPORTANCE: There is a clinical need for expanded extragenital bacterial sexually transmitted infection (STI) testing options, but the current regulatory landscape limits the wide-spread promotion and adoption of such services. Improved access, particularly for the LGBTQ+ community, can be achieved by validating testing for specimens that are self-collected at a remote location and arrive at the laboratory via a postal carrier or other intermediary route. Here we provide valuable data showing that self-collected samples for anal and oropharyngeal STI testing are equally or increasingly sensitive compared with those collected by a provider. We systematically consider the effects of storage time, exposure to temperature extremes, and the addition of common toiletries on results.