Performance of CHROMagar ESBL media for the surveillance of extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE) from rectal swabs in Botswana.

Introduction. Lack of laboratory capacity hampers consistent national antimicrobial resistance (AMR) surveillance. Chromogenic media may provide a practical screening tool for detection of individuals colonized by extended-spectrum beta-lactamase (ESBL)-producing organisms.Hypothesis. CHROMagar ESBL media represent an adequate screening method for the detection of extended-spectrum cephalosporin-resistant Enterobacterales (ESCrE), isolated from rectal swabs.Aim. To evaluate the performance of CHROMagar ESBL media to accurately identify ESCrE isolates from rectal swab samples attained from hospitalized and community participants.Methodology. All participants provided informed consent prior to enrolment. Rectal swabs from 2469 hospital and community participants were inoculated onto CHROMagar ESBL. The performance of CHROMagar ESBL to differentiate Escherichia coli and Klebsiella spp., Enterobacter spp. and Citrobacter spp. (KEC spp.) as well as select for extended-spectrum cephalosporin resistance were compared to matrix-assisted laser desorption/ionization-time-of-flight MS (MALDI-TOF-MS) and VITEK-2 automated susceptibility testing.Results. CHROMagar ESBL had a positive and negative agreement of 91.2 % (95 % CI, 88.4-93.3) and 86.8 % (95 % CI, 82.0-90.7) for E. coli and 88.1 % (95 % CI 83.2-92.1) and 87.6 % (95 % CI 84.7-90.2) for KEC spp. differentiation, respectively, when compared to species ID by MALDI-TOF-MS. When evaluated for phenotypic susceptibilities (VITEK-2), 88.1 % (714/810) of the isolates recovered on the selective agar exhibited resistance to third-generation cephalosporins.Conclusion. The performance characteristics of CHROMagar ESBL media suggest that they may be a viable screening tool for the identification of ESCrE from hospitalized and community participants and could be used to inform infection prevention and control practices in Botswana and potentially other low-and middle-income countries (LMICs). Further studies are required to analyse the costs and the impact on time-to-result of the media in comparison with available laboratory methods for ESCrE surveillance in the country.

Molecular identification of carnivore chaphamaparvovirus 2 (feline chaphamaparvovirus) in cats with diarrhea from China.

Chaphamaparvovirus carnivoran2 (feline chaphamaparvovirus, FeChPV) is a novel feline parvovirus originally detected in Canadian cats in 2019, and it has also been identified in domestic cats in other nations. To evaluate the prevalence and genetic diversity of FeChPV in China, rectal swabs of pet cats from Henan, Guangdong, Anhui, Zhejiang, and Inner Mongolia provinces were collected. Of the 230 samples subjected to nested polymerase chain reaction, 6 (2.6%) tested positive for FeChPV. Although all positive samples were from cats with diarrhea, statistical analyses revealed no correlation between the presence of the virus and clinical symptoms (p > 0.05). Phylogenetic trees of nonstructural protein 1 (NS1) and capsid protein (VP1) demonstrated that these six new strains formed a major branch with other reference FeChPV strains and considerably differed from Chaphamaparvoviru carnivoran1. Moreover, recombination analysis revealed that the FeChPV strain CHN20201025, previously detected in a dog, was a recombinant and strains CHN200228 and CHN180917, identified in this study, were the closest relatives to the parental strains. The findings of this study and a previous study wherein FeChPV was detected in dogs suggest that FeChPV can propagate between species. Additionally, these findings indicate that the genetic diversity of FeChPV can provide an insight into the epidemiological status of FeChPV in China.

Investigating Resistance to Carbapenems in Enterobacterales: A Descriptive Epidemiological Study of 2021 Screening in an Italian Teaching Hospital.

Antimicrobial resistance (AMR) presents a growing threat to global healthcare. This descriptive epidemiological study investigates the prevalence and characteristics of Enterobacterales with AMR factors in a tertiary teaching hospital in Italy over the course of the year 2021. In 2021, the prevalence of colonisation by Enterobacterales with AMR factors in patients was 1.08%. During the observation period, a total of 8834 rectal swabs were performed, with 1453 testing positive. A total of 5639 rectal swabs were performed according to a hospital procedure for the active screening of MDRO colonisation at the time of admission. Of these, 679 were positive for microorganisms under surveillance, and 74 patients were colonised with Enterobacterales, predominantly Klebsiella pneumoniae and Escherichia coli. Antibiotic resistance factors were observed in 61 of these 74 patients (82.43%) of these patients, with NDM and KPC being the most frequent resistance factors. A statistically significant trend in positive swabs was observed across different ward categories (surgery, ICUs, and medical wards). Regarding specific trends, the rate of positive admission screening in medical and surgical wards was higher than in ICU wards. The results highlight the ease with which Enterobacterales develops resistance across different ward categories. The findings underscore the need for adjusted screening protocols and tailored infection prevention strategies in various care settings.

First-Day-of-Life Rectal Swabs Fail To Represent Meconial Microbiota Composition and Underestimate the Presence of Antibiotic Resistance Genes.

The human gut microbiome plays a vital role in health and disease. In particular, the first days of life provide a unique window of opportunity for development and establishment of microbial community. Currently, stool samples are known to be the most widely used sampling approach for studying the gut microbiome. However, complicated sample acquisition at certain time points, challenges in transportation, and patient discomfort underline the need for development of alternative sampling approaches. One of the alternatives is rectal swabs, shown to be a reliable proxy for gut microbiome analysis when obtained from adults. Here, we compare the usability of rectal swabs and meconium paired samples collected from infants on the first days of life. Our results indicate that the two sampling approaches display significantly distinct patterns in microbial composition and alpha and beta diversity as well as detection of resistance genes. Moreover, the dissimilarity between the two collection methods was greater than the interindividual variation. Therefore, we conclude that rectal swabs are not a reliable proxy compared to stool samples for gut microbiome analysis when collected on the first days of a newborn's life. IMPORTANCE Currently, there are numerous suggestions on how to ease the notoriously complex and error-prone methodological setups to study the gut microbiota of newborns during the first days of life. Especially, meconium samples are regularly failing to yield meaningful data output and therefore have been suggested to be replaced by rectal swabs as done in adults as well. We find this development toward a simplified method to be producing dramatically erroneous results, skewing data interpretation away from the real aspects to be considered for neonatal health during the first days of life. We have put together our knowledge on this critical aspect with careful consideration and identified the failure of rectal swabs to be a replacement for sampling of meconium in term-born newborns.

The potential of rectal swabs to differentiate simple and complex appendicitis in children with a microbiota-based test.

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.

Analyzing the roles of some species of arthropods in the transmission of the Middle East respiratory syndrome coronavirus.

BACKGROUND: The Middle East Respiratory Syndrome coronavirus (MERS-CoV) is still listed on the WHO Research and Development Blueprint of emerging pathogens. Dromedary camels remain the only known animal reservoir of the virus. The animal-to-animal as well as the animal-to-human transmission in the MERS-CoV cycles were reported. However, many aspects of these transmission chains are not well studied. One of these directions is the potential roles of various species of arthropods in the transmission of the virus. OBJECTIVES: The main goal of the current work was to study the roles of several species of arthropods in the transmission of MERS-CoV. METHODOLOGY: To achieve this goal, we identified some MERS-CoV naturally infected dromedary camel populations. We conducted a longitudinal study among these animals for more than 2 months. This was done by repeated testing of nasal swabs biweekly from some selected animals in this population for the presence of MERS-CoV-RNAs by real-time PCR. During the duration of this study, we collected several species of arthropods (Culicoides, Stomoxys, Musca domestica and some Culex species) that shared the habitat and were circulating in this farm during this longitudinal study. RESULTS: Our results showing, despite the detection of the viral RNAs in some animals throughout this study, none of the examined species of arthropods tested positive for the viral RNA. CONCLUSIONS: These results are suggesting that at least the tested species of arthropods may not play roles in the transmission of MERS-CoV. However, more large-scale studies are required to explore any potential roles of arthropods in the transmission cycle of MERS-CoV.

Detection and Genomic Characterization of Canine Circovirus in Iran.

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.

Prolonged SARS-CoV-2 nucleic acid conversion time in military personnel outbreaks with presence of specific IgG antibodies.

Coronavirus disease 2019 (COVID-19) is transmitted person-to-person mainly by close contact or droplets from respiratory tract. However, the actual time of viral shedding is still uncertain as well as the different routes of transmission. We aimed to characterize RNA shedding from nasopharyngeal and rectal samples in prolonged cases of mild COVID-19 in young male soldiers. Seventy patients from three different military locations were monitored after recommending to follow more strict isolation measures to prevent the spread of the virus. Then, nasopharyngeal, rectal, and blood samples were taken. SARS-CoV-2 RNA was detected by RT-PCR and specific antibodies by chemiluminescent immunoassays. The median nucleic acid conversion time (NACT) was 60 days (IQR: 7-85 days). Rectal swabs were taken in 60 % of patients. Seven patients (10 %) were positive in nasopharyngeal and rectal swabs, and five (7.14 %) remained positive in rectal swabs, but negative in nasopharyngeal samples. Four patients (5.71 %) that had been discharged, were positive again after 15 days. No significant difference was found in nucleic acid conversion time between age groups nor clinical classification. Maintaining distancing among different positive patients is essential as a possible re-exposure to the virus could cause a longer nucleic acid conversion time in SARS-COV-2 infections.

Rectal colonization by resistant bacteria increases the risk of infection by the colonizing strain in critically ill patients with cirrhosis.

BACKGROUND & AIMS: It remains unclear whether rectal colonization with multidrug-resistant organisms (MDROs) is prevalent and predisposes to infections by the same pathogens in patients with cirrhosis. METHODS: Two series of critically ill patients were evaluated. In the Barcelona cohort, 486 consecutive patients were prospectively evaluated, 129 with and 357 without cirrhosis (2015-2016). Rectal swabs were performed at admission and weekly thereafter (until intensive care unit [ICU] discharge) to detect MDRO colonization. Risk factors for colonization and infection by MDROs were evaluated. A retrospective cohort from Frankfurt (421 patients with cirrhosis; 2010-2018) was investigated to evaluate MDRO rectal colonization in another epidemiological scenario. RESULTS: In the Barcelona cohort, 159 patients were colonized by MDROs (32.7%), 102 (64.2%) at admission and 57 (35.8%) during follow-up. Patients with cirrhosis showed higher rates of rectal colonization at admission than those without cirrhosis (28.7% vs. 18.2%, p = 0.01) but similar colonization rates during ICU stay. Extended-spectrum beta-lactamase-Enterobacterales were the most frequent MDROs isolated in both groups. Colonization by MDROs independently increased the risk of infection by MDROs at admission and during follow-up. Risk of new infection by the colonizing strain was also significantly increased in patients with (hazard ratio [HR] 7.41) and without (HR 5.65) cirrhosis. Rectal colonization by MDROs was also highly prevalent in Frankfurt (n = 198; 47%; 131 at admission [66.2%] and 67 [33.8%] during follow-up), with vancomycin-resistant enterococci being the most frequent colonizing organism. Rectal colonization by MDROs was also associated with an increased risk of infection by MDROs in this cohort. Infections occurring in MDR carriers were mainly caused by the colonizing strain. CONCLUSION: Rectal colonization by MDROs is extremely frequent in critically ill patients with cirrhosis. Colonization increases the risk of infection by the colonizing resistant strain. LAY SUMMARY: Rectal colonization by multidrug-resistant organisms (MDROs) is a prevalent problem in patients with cirrhosis requiring critical care. The pattern of colonizing bacteria is heterogeneous with relevant differences between centers. Colonization by MDROs is associated with increased risk of infection by the colonizing bacteria in the short term. This finding suggests that colonization data could be used to guide empirical antibiotic therapy and de-escalation policies in patients with cirrhosis.

Infectious Etiology of Vomiting in Children With Presumed Acute Gastroenteritis in the Absence of Diarrhea: Protocol for a Cohort Study.

NCT05270291, https://clinicaltrials.gov/ct2/show/. Objectives: In children with acute gastroenteritis (AGE), vomiting often precedes diarrhea. To establish the diagnosis of AGE, enteropathogen detection typically relies on diarrheal stool samples. However, testing requires sufficient stool sample, which may not be easily available. Recent studies suggest that in children presenting to emergency departments with presumed AGE with isolated vomiting, an enteropathogen can be identified using rectal swabs and molecular diagnostic tests. The rate of enteropathogen detection in children with isolated vomiting due to AGE may differ in various populations. Using rectal swabs and molecular diagnostic tests, we plan to assess the proportion of children with isolated vomiting with presumed AGE in whom an enteropathogen can be identified. Methods: This will be a cohort study conducted in the emergency department(s) of one or more pediatric hospital(s) in Poland. Children younger than 5 years with the presence of ≥3 episodes of vomiting due to presumed AGE, lasting no longer than 7 days before enrollment, will be recruited. The primary outcome will be the proportion of children with isolated vomiting in whom an enteropathogen is detected. In all eligible participants, rectal swabs will be taken to perform molecular testing for detection of typical viral and bacterial enteropathogens. All children will be followed-up at 14 days after the initial contact to classify them into one of three groups (i.e., vomiting only, vomiting and diarrhea, and diarrhea only).

Rapid identification from rectal swabs of the clinically most relevant carbapenemase genes from gram-negative bacteria using the BD MAX Check-Points CPO Assay.

We conducted an international multicentre evaluation to assess the clinical performance characteristics of the new multiplex PCR-based BD MAX Check-Points CPO assay to detect the 5 major carbapenemase families: KPC, VIM/IMP (tested simultaneously), NDM and OXA-48 compared to a reference method consisting of 2 culture methods (to improve recovery of CPO isolates from the rectal swabs), followed by carbapenem susceptibility testing and sequencing of target carbapenemase genes. Tests were performed from rectal swab specimens in ESwab collection and transport devices. Positive percent agreement (PPA) for BD MAX Check-Points CPO for KPC and OXA-48 were 88.2% (95% CI:72.6-96.7) and 96.2% (95% CI:80.4-99.9), respectively. Negative percent agreement was ≥99% for each gene. Insufficient samples (≤10) were positive for VIM/IMP or NDM tests to calculate meaningful PPA values. The BD MAX Check-Points CPO assay represents an accurate tool for rapid recognition of patients with rectal colonization by the most commonly encountered CPOs.

Usefulness of Xpert® Carba-R on enrichment broth for the early detection of carbapenemase-producing Enterobacterales.

Early detection of patients colonized with carbapenemase-producing Enterobacterales is crucial to limit their spread. Molecular biology tests are rapid but might miss low-level carriage. Culture-based methods using enrichment are cheap and detect low-level carriage but cause delay. Two clinical cases are reported, which demonstrated that molecular biology (Xpert® Carb-R) on enriched broth cumulates advantages of both strategies. In both cases, this strategy enabled early detection of patients colonized at low-level with carbapenemase-producing Enterobacterales because it saved 24 hours in detection time.

Risk factors for norovirus infection in healthcare workers during nosocomial outbreaks: a cross-sectional study.

BACKGROUND: Norovirus outbreaks cause severe medico-socio-economic problems affecting healthcare workers and patients. The aim of the study was to investigate prevalence of norovirus infection and risk factors for infection in healthcare workers during nosocomial outbreaks. METHODS: A cross-sectional study of norovirus infections in healthcare workers was performed in seven outbreak wards in a large university hospital. Packs (swab for rectal sampling, and questionnaire) were posted to healthcare workers on notification of a ward outbreak. Rectal samples were examined with norovirus-specific real-time PCR. Replies from questionnaires were analysed using logistic regression models with norovirus genogroup (G)II positive findings as dependent variable. The results are expressed as odds ratios (OR) with 95% confidence intervals (CI). Sequencing and phylogenetic analyses (1040 nucleotides) were used to characterize norovirus strains from healthcare workers. Cluster analyses included norovirus GII.4 strains detected in ward patients during the ongoing outbreaks. RESULTS: Of 308 packs issued to healthcare workers, 129 (42%) were returned. norovirus GII was detected in 26 healthcare workers (20.2%). Work in cohort care (OR 4.8, 95% CI 1.4-16.3), work in wards for patients with dementia (OR 13.2, 95% CI 1.01-170.7), and having diarrhoea, loose stools or other gastrointestinal symptoms the last week (OR 7.7, 95% CI 2.5-27.2) were associated with increased norovirus prevalence in healthcare workers. Sequencing revealed norovirus GII.4 in healthcare workers samples, and strains detected in healthcare workers and ward patients during a given ward outbreak showed ≥ 99% similarity. CONCLUSION: Norovirus positive findings in healthcare workers were strongly associated with symptomatic infection, close contact with sick patients, and dementia nursing.

Unlikely SARS-CoV-2 Transmission During Vaginal Delivery.

Pregnant women display a higher risk of progression to disease and higher viral loads during infections due to their more permissive, tolerogenic immune system. However, only few studies have focused on SARS-CoV-2 intrapartum vertical transmission via vaginal secretions or faeces. The aim of this study was to investigate the presence of the virus in vaginal, rectal and blood specimens from pregnant women characterized by different COVID-19 disease severity. We enrolled 56 SARS-CoV-2-positive pregnant women, of which 46 (82%) were in the third trimester of pregnancy, 6 (10%) in the second and 4 (7%) in the first. QPCR was performed to detect the virus in vaginal and rectal swabs and in plasma samples. SARS-CoV-2 was detected in 27% of rectal swabs of pregnant women in the third trimester, while no virus particles were detected in vaginal swabs of the same patients. Furthermore, only 4% plasma samples tested positive to SARS-CoV-2. No virus was detected in newborn's nasopharyngeal swabs. Despite the low number of subjects enrolled, our data suggest that, while theoretically possible, intrapartum vaginal or orofecal SARS-CoV-2 transmission seems to be unlikely.

Case report of gastrointestinal localization of SARS-CoV-2 and open abdomen technique in an Italian emergency surgery department for gastrointestinal bleeding.

This article aims to present the case of a man affected by SARS CoV-2 and to discuss the association between this manifestation, viral infection and Open Abodmen. A 52 years old Caucasian man, affected by SARS CoV-2 infection, was admitted to the Emergency department of Arcispedale Sant'Anna of Ferrara for epigastralgia followed by syncopal episode, vomiting and diarrhea with bloody stools. The next day the patient underwent colonoscopy, which detected an ulceration proximally to the ileocecal valve without active bleeding. Subsequently an initial non-operative management and two pharyngeal swabs negative, for another rectorrhagia and hypotensive episode, underwent emerging surgery and an Open Abdomen was performed. The patient was discharged in 12th post-surgery day without complications. The IHC analysis with anti-SARS-CoV-2 nucleocapsid-protein revealed the presence of viral protein expression in epithelial cell of ulcerated intestinal mucosa. In this case report, we showed the presence of viral inclusion in small intestinal wall after two negative pharyngeal swabs for SARS-CoV-2 RNA. We can also say that the largest amount of viral inclusions was in the tissue of ulceration of the last ileal loop. This case report showed that SARS-CoV-2 can be unseen also after clinical healing. It's probably can be expelled with stools and rectal swabs search for SARS-Cov-2 RNA after pharyngeal swabs could be mandatory for declare heled a patient. Moreover, damage control surgery and Open Abdomen as a surgical technique can be a valid alternative in case of uncertainty of the bleeding source and when a second surgical look is necessary.

Exploring the potential roles of some rodents in the transmission of the Middle East respiratory syndrome coronavirus.

Middle East respiratory syndrome coronavirus (MERS-CoV) is one of the recently identified zoonotic coronaviruses. The one-hump camels are believed to play important roles in the evolution and transmission of the virus. The animal-to-animal, as well as the animal-to-human transmission in the context of MERS-CoV infection, were reported. The camels shed the virus in some of their secretions, especially the nasal tract. However, there are many aspects of the transmission cycle of the virus from animals to humans that are still not fully understood. Rodents played important roles in the transmission of many pathogens, including viruses and bacteria. They have been implicated in the evolution of many human coronaviruses, especially HCoV-OC43 and HCoV-HKU1. However, the role of rodents in the transmission of MERS-CoV still requires more exploration. To achieve this goal, we identified MERS-CoV that naturally infected dromedary camel by molecular surveillance. We captured 15 of the common rodents (rats, mice, and jerboa) sharing the habitat with these animals. We collected both oral and rectal swabs from these animals and then tested them by the commercial MERS-CoV real-time-PCR kits using two targets. Despite the detection of the viral shedding in the nasal swabs of some of the dromedary camels, none of the rodents tested positive for the virus during the tenure of this study. We concluded that these species of rodents did not harbor the virus and are most unlikely to contribute to the transmission of the MERS-CoV. However, further large-scale studies are required to confirm the potential roles of rodents in the context of the MERS-CoV transmission cycle, if any.

Comparison of rectal swab, glove tip, and participant-collected stool techniques for gut microbiome sampling.

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.

Detection and Genetic Characterization of Viruses Present in Free-Ranging Snow Leopards Using Next-Generation Sequencing.

Snow leopards inhabit the cold, arid environments of the high mountains of South and Central Asia. These living conditions likely affect the abundance and composition of microbes with the capacity to infect these animals. It is important to investigate the microbes that snow leopards are exposed to detect infectious disease threats and define a baseline for future changes that may impact the health of this endangered felid. In this work, next-generation sequencing is used to investigate the fecal (and in a few cases serum) virome of seven snow leopards from the Tost Mountains of Mongolia. The viral species to which the greatest number of sequences reads showed high similarity was rotavirus. Excluding one animal with overall very few sequence reads, four of six animals (67%) displayed evidence of rotavirus infection. A serum sample of a male and a rectal swab of a female snow leopard produced sequence reads identical or closely similar to felid herpesvirus 1, providing the first evidence that this virus infects snow leopards. In addition, the rectal swab from the same female also displayed sequence reads most similar to feline papillomavirus 2, which is the first evidence for this virus infecting snow leopards. The rectal swabs from all animals also showed evidence for the presence of small circular DNA viruses, predominantly Circular Rep-Encoding Single-Stranded (CRESS) DNA viruses and in one case feline anellovirus. Several of the viruses implicated in the present study could affect the health of snow leopards. In animals which are under environmental stress, for example, young dispersing individuals and lactating females, health issues may be exacerbated by latent virus infections.

Evaluation of Quadruple Real-Time PCR Method to Detect Enterococci Carrying Vancomycin-Resistant Genes vanA, vanB, vanM in Rectal Swabs.

Purpose: To evaluate the sensitivity and accuracy of the quadruple real-time PCR method for the detection of enterococci carrying vancomycin-resistant genes vanA, vanB, and vanM in rectal swabs. Methods: Choosing PCR-sequenced DNA extracted directly from rectal swabs as the gold standard, the results of the quadruple real-time PCR method and the traditional method (screening culture combined PCR-sequencing method whose DNA extracted from single colony) were compared with the gold standard. The sensitivity, specificity, positive predictive value (PPV), negative predictive value (NPV), and accuracy of the quadruple real-time PCR method and the traditional method were obtained. The time required for the three methods was calculated. Results: The results between gold standard and the quadruple real-time PCR method were similar. Compared to the traditional method, the quadruple real-time PCR method had a much higher sensitivity, specificity, PPV, NPV, and consistency. Our study found that the quadruple real-time PCR method is beneficial for detection of enterococci carrying vanM with vancomycin heteroresistance. The traditional method had high specificity and NPV, but its sensitivity and PPV were not ideal. The time needed for gold standard is a minimum of 28 h; the quadruple real-time PCR method takes 2-3 h while the traditional method consumes a minimum of 72 h. Conclusion: The quadruple real-time PCR method can provide a rapid and reliable result for the diagnosis of patients with colonized vancomycin-resistant enterococci. This new method is beneficial for the active screening, timely clinical treatment measures, epidemiological research, and hospital monitoring of the enterococci carrying vancomycin-resistant gene, especially for the enterococci with vancomycin heteroresistance carrying vanM.

Evaluation of the FecalSwab for Stool Specimen Storage and Molecular Detection of Enteropathogens on the BD Max System.

The FecalSwab system (Copan Italia, Brescia, Italy) is a convenient alternative to bulk stool for the diagnosis of enteric pathogens. Although the U.S. Food and Drug Administration (FDA) approved for transport and culture of enteric bacterial pathogens, the FecalSwab has not been well assessed for its suitability with molecular platforms. In this study, we evaluated the FecalSwab as a specimen type for the BD Max system using the viral and bacterial enteric panels (BD Diagnostics, Baltimore, MD, USA). A total of 186 unpreserved stool specimens were collected and used to prepare matched bulk stool and FecalSwab samples. Performance was equivalent (P > 0.48) to bulk stool for all targets when 50 µl of FecalSwab specimen was loaded onto the BD Max assays. As stool specimens are often collected off-site from the clinical microbiology laboratory and require transport, we assessed the stability of stool specimens stored for up to 14 days at 4°C, 22°C, or 35°C to account for varying transportation conditions. Molecular detection for the majority of viral targets (excluding astrovirus) was unaffected (change in cycle threshold [ΔCT ] ≤ 1) by sample storage temperature over the 2-week period; however, detection of enteric bacteria was variable if specimens were not refrigerated (22°C or 35°C). By demonstrating equivalent performance to matched bulk stool and maintaining molecular detection sensitivity when stored at 4°C, we suggest that the FecalSwab is a suitable specimen type for enteropathogen diagnostics on the BD Max system.