A Four-Gene Panel in Rectal Swab Samples as a Biomarker for Colorectal Cancer Screening.

BACKGROUND: The dysregulation of gene expression is one of the key molecular features of colorectal cancer (CRC) development. This study aimed to investigate whether such dysregulation is reflected in rectal swab specimens of CRC patients and to evaluate its potential as a non-invasive approach for screening. METHODS: We compared the expression level of 14 CRC-associated genes in tumor and adjacent non-tumor tissue of CRC patients and examined the correlation of their levels in tissue with paired rectal swab specimens. The level of these 14 genes in rectal swab specimens was compared among patients with CRC or polyp and control subjects, and the diagnostic potential of each dysregulated gene and the gene panel were evaluated. RESULTS: The expression of CXCR2, SAA, COX1, PPARδ, PPARγ, Groγ, IL8, p21, c-myc, CD44 and CSF1 was significantly higher in CRC, and there was a significant correlation in the levels of most of them between the CRC and rectal swab specimens. In the training study, we showed that CD44, IL8, CXCR2 and c-myc levels were significantly higher in the rectal swab specimens of the CRC patients. Such result was confirmed in the validation study. A panel of these four genes was developed, and ROC analysis showed that this four-gene panel could identify CRC patients with an AUC value of 0.83 and identify overall polyp and precancerous adenoma patients with AUC values of 0.6522 and 0.7322, respectively. Finally, the predictive study showed that the four-gene panel demonstrated sensitivities of 63.6%, 76.9% and 88.9% in identifying overall polyp, precancerous adenoma and CRC patients, respectively, whereas the specificity for normal subjects was 72.2%. CONCLUSION: The expression of CRC-associated genes in rectal swab specimens reflects the dysregulation status in colorectal tissue, and the four-gene panel is a potential non-invasive biomarker for early precancerous adenoma and CRC screening.

Adherence to universal screening for group B Streptococcus in pregnancy and prevalence of colonised pregnancies in Caserta province, Italy.

Group B Streptococcus (Streptococcus agalactiae; GBS) infection is a significant contributor to neonatal morbidity and mortality. In the early 1970s, the neonatal mortality rate for infants with invasive GBS disease was 55%. With the adoption of the first medical community guidelines to prevent GBS infection in the 1990s, the mortality rate decreased to approximately 5%. The main obstetric procedure for preventing vertical transmission of GBS infection involves universal screening of pregnant women using a vaginal-rectal swab (VRS) to identify those eligible for intrapartum antibiotic prophylaxis (IAP). The study analyzes the adherence of screening and the trend of GBS infection in pregnancy in the province of Caserta, Italy. Data were obtained from pregnant women who gave birth in a first level birthing center in 2022 from birth assistance certificate (CEDAP), obstetric and neonatal record. Postnatal evaluation collected through computer-assisted telephone interviews. 567 women delivered at our center during the study period. The average coverage of GBS testing in pregnancy was 99.2% (562), and the proportion of GBS colonised women was 12.6% (71) according with the national average, which is about 10-20%. The spread of positive cases appears to fluctuate among the various groups of pregnant women studied, indicating no significant statistical variance among presence of a partner, among women who have given birth multiple times, among Italian nationals, or across different ages, but a significant statistical excess is evident among mothers with less education. In 93% (66) of GBS carrier mothers, intrapartum antibiotic prophylaxis (IAP) was administered correctly, regardless of the type of delivery performed. Despite the successful integration of GBS screening, a significant gap remains between the ideal scenario and the actual implementation of IAP. At the three-month assessment, no child required hospitalization, consistent with the relatively low incidence of invasive GBS infection. Nevertheless, for those who are not eligible to VRS screening, such as preterm birth, or IAP, as in precipitous birth, the identification of biomarkers enabling early recognition of invasive GBS disease remains essential. Additionally, the emergence of vaccines administered during gestation, conferring passive immunity to newborns represents a promising possible new direction. Therefore, to ensure the practical application of GBS screening and actual IAP by healthcare providers, periodic audits and regular monitoring should be encouraged.

Rectal swab DNA collection protocol for PCR genotyping in rats.

DNA collection is essential for genotyping laboratory animals. Common collection methods require tissue amputation, causing discomfort and injury. Rectal swabbing has been proposed as an effective, minimally invasive alternative, but an evidence-backed protocol for the technique remains unavailable. This report evaluates the effects of collection parameters on the quality of PCR results and presents a protocol for genotyping a litter of rats within 3-5 h. Samples with 2-8 scrapes produced enough DNA to amplify targets up to ∼1800 bp long using PCR. Rectal swabbing produced PCR results with similar utility as ear clip samples, and results were unaffected by residual fecal matter or cell debris. The protocol enables fast, minimally invasive and repeatable genotyping using commercial PCR reagents.

DNA collection for genotyping laboratory rodents commonly requires tissue amputation, leading to injury and discomfort. Rectal swabbing can be an effective, minimally invasive alternative, but there is a lack of information on how to apply the technique and the necessary parameters involved. This report assesses collection and processing parameters while combining the rectal swab collection method with commercial PCR reagents to allow for fast genotyping with minimally processed DNA samples. Findings were used to design a protocol for minimally invasive DNA collection and genotyping.

Validation of a rapid molecular detection test for gram-negative multidrug-resistant bacteria in rectal swabs upon admission of patients to the intensive care unit.

In ICU settings, screening patients upon admission for potential multiresistant bacteria (BMR) carriers is crucial. Traditionally, clinical decisions relied on delayed culture results, but a rapid PCR molecular test called RealCycler-Rezero-U/G (Progenie-molecular©), emerged as an alternative. This study aimed to validate its effectiveness in detecting gram-negative BMR in rectal swabs at ICU admission. Over 24 months, an observational study was conducted on 1,234 admitted patients, with 217 meeting isolation criteria and undergoing both PCR and culture tests. Results showed a 17.5 % positive rate for screening. The PCR test exhibited impressive accuracy at 98.6 % and a strong negative predictive value of 99.4 %. The area under the ROC curve (AUC) was 0.98, indicating high reliability. Notably, PCR results were available 44.5 h earlier than culture. In conclusion, PCR-based molecular testing for gram-negative BMR offers excellent diagnostic performance and a valuable negative predictive value, making it a suitable screening tool for ICU admissions.

Antimicrobial prophylaxis protocol based on rectal swab culture before prostate biopsy to prevent infectious complications: a prospective randomized comparative study.

PURPOSE: To evaluate the benefit of targeted antibiotic prophylaxis (TAP) based on rectal swab culture in comparison with standard empiric antimicrobial prophylaxis in patients undergoing transrectal ultrasound-guided needle biopsy of the prostate (TRUS-BP), as well as to assess rate of fecal carriage of Fluoroquinolone-resistant Enterobacterales FQRE. PATIENTS AND METHODS: We prospectively analyzed data that randomized 157 patients within two groups: (G1) TAP according to rectal swab performed 10 days before PB; (G2): empirical antibiotic prophylaxis with ciprofloxacin. Prevalence of FQRE digestive carriage and risk factors were investigated. Incidence of infectious complications after (TRUS-BP) in each group was compared. RESULTS: G2 included 80 patients versus 77 in G1. There was no difference between the two groups regarding age, diabetes, prostate volume, PSA, number of biopsy cores, and risk factors for FQRE. In G2, the prevalence of FQRE digestive carriage was 56.3% all related to E. coli species. In the case of digestive carriage of FQRE, TAP according to the rectal swab culture with third-generation cephalosporins was performed in 73.3%. Patients with FQRE had history of FQ use within the last 6 months in 17.8% (p = 0.03). Rate of febrile urinary tract infection after PB was 13% in G1 and 3.8% in G2 (p = 0.02). CONCLUSIONS: Incidence of FQ resistance in the intestinal flora of our local population was prevalent. Risk factor for resistance was the use of FQ within the last 6 months. TAP adapted to rectal swab, mainly with third-generation cephalosporins, significantly reduced the rate of infectious complications after (TRUS-BP).

Rectal Swab DNA Collection Protocol for PCR Genotyping in Rats.

DNA collection is essential for genotyping laboratory animals. However, common collection methods require tissue amputation, causing discomfort and injury. Rectal swabbing has been proposed as an effective non-invasive alternative, but an evidence-backed protocol for the technique remains unavailable. We evaluate the effect of collection parameters on PCR result quality and present a genotyping protocol that can yield results for a litter of rats within 3-5 hours. We found that samples with 2-8 scrapes produced enough DNA to amplify targets up to ~1800bp long using PCR. Rectal swabbing produced PCR results with similar quality to ear clip samples, and results were unaffected by residual fecal matter or cell debris. Our protocol enables fast, non-invasive, and repeatable genotyping using commercial PCR reagents.

Shigella Detection and Molecular Serotyping With a Customized TaqMan Array Card in the Enterics for Global Health (EFGH): Shigella Surveillance Study.

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.

Relationship Between Rectal Swab and Tissue Samples in Mucosa-associated Microbiota in Patients With Inflammatory Bowel Disease.

BACKGROUND: Gut mucosa-associated microbiota is more closely correlated with disease phenotypes than fecal microbiota; however sampling via tissue biopsy is more invasive and uncomfortable. Rectal swab may be a suitable substitute for tissue biopsy, but its effectiveness is controversial. This study aimed to evaluate differences in the microbiota at these sites in patients with inflammatory bowel disease (IBD). METHODS: Inflammatory bowel disease patients and a control group were enrolled when surveillance colonoscopy was scheduled. Samples of colon biopsy tissues, rectal swabs during colonoscopy, and feces before bowel preparation were collected to analyze microbial composition. To explore the short-term effects of bowel preparation on swab microbiota, prepreparation swab samples were also collected from 27 IBD patients. RESULTS: A total of 33 Crohn's disease, 54 ulcerative colitis, and 21 non-IBD patients were enrolled. In beta diversity analysis, fecal microbiota clearly differed from swab and tissue microbiota in the 3 disease groups. The swab microbiota was closer to, but still different from, the tissue microbiota. Consistently, we identified that swab samples differed more in abundant genera from feces than from tissue. Beta diversity analysis did not reveal a difference in swab microbiota before and after bowel preparation, but the genus composition of most individuals varied markedly. CONCLUSIONS: Swab microbiota more closely resembled tissue microbiota relative to fecal microbiota, but there were still differences. Bowel preparation did not alter the overall swab microbiota in the short term but markedly changed the microbial composition in most patients.

Investigation of the prevalence of carbapenem resistance genes in faecal carriage of carbapenem resistant Klebsiella spp. isolates by multiplex real-time PCR method.

INTRODUCTION: Increased carbapenem resistance in Klebsiella spp. strains causes high morbidity and mortality. The genes encoded for carbapenemaseare transferrable between different bacterial species. In the present study, we aimed to investigate carbapenem resistance genes in Klebsiella spp. strains. METHODOLOGY: Fifty Klebsiella spp. strains were isolated from rectal swabs of patients hospitalized in the neonatal intensive care unit (NICU). All strains were identified with API20E. The minimum inhibitory concentrations (MICs) of carbapenems were determined by the broth dilution method. The major five carbapenem genes (OXA-48, NDM, VIM, KPC, and IMP) were detected by the multiplex real-time PCR method. RESULTS: It was found that 49 (98%) of the strains were resistant to ertapenem (MIC ≥ 2µg/mL) and imipenem(MIC ≥ 4 µg/mL), and 47 (94%) of the strains were resistant to doripenem (MIC ≥ 4 µg/mL)and meropenem(MIC ≥ 4 µg/mL).NDM was detected in 42%, OXA-48 in 16%, and VIM in one (2%) isolate, and NDM + OXA-48 co-existed in 36% of the isolates. The KPC and IMP genes were not detected. CONCLUSIONS: NDM and NDM co-existing with OXA-48 were prevalent in the NICU of Istanbul Medical Faculty Hospital. Paying attention to the hand hygiene of healthcare workers, screening of rectal swabs of hospitalized patients for the presence of carbapenem resistance strains, and isolation of infected patients can effectively control the spread of carbapenem-resistant strains.

Colonization of multidrug-resistant Gram-negative bacteria increases risk of surgical site infection after hemorrhoidectomy: a cross-sectional study of two centers in southern China.

PURPOSE: The present study aims to determine the rectoanal colonization rate and risk factors for the colonization of present multidrug-resistant bacteria (MDRBs). In addition, the relationship between MDRB colonization and surgical site infection (SSI) following hemorrhoidectomy was explored. METHODS: A cross-sectional study was conducted in the Department of Colorectal Surgery of two hospitals. Patients with hemorrhoid disease, who underwent hemorrhoidectomy, were included. The pre-surgical screening of multidrug-resistant Gram-negative bacteria (MDR-GNB) colonization was performed using rectal swabs on the day of admission. Then, the MDRB colonization rate was determined through the rectal swab. Logistic regression models were established to determine the risk factors for MDRB colonization and SSI after hemorrhoidectomy. A p-value of < 0.05 was considered statistically significant. RESULTS: A total of 432 patients met the inclusion criteria, and the MDRB colonization prevalence was 21.06% (91/432). The independent risk factors for MDRB colonization were as follows: patients who received ≥ 2 categories of antibiotic treatment within 3 months (odds ratio (OR): 3.714, 95% confidence interval (CI): 1.436-9.605, p = 0.007), patients with inflammatory bowel disease (IBD; OR: 6.746, 95% CI: 2.361-19.608, p < 0.001), and patients with high serum uric acid (OR: 1.006, 95% CI: 1.001-1.010, p = 0.017). Furthermore, 41.57% (37/89) of MDRB carriers and 1.81% (6/332) of non-carriers developed SSIs, with a total incidence of 10.21% (43/421). Based on the multivariable model, the rectoanal colonization of MDRBs (OR: 32.087, 95% CI: 12.052-85.424, p < 0.001) and hemoglobin < 100 g/L (OR: 4.130, 95% CI: 1.556-10.960, p = 0.004) were independently associated with SSI after hemorrhoidectomy. CONCLUSION: The rectoanal colonization rate of MDRBs in hemorrhoid patients is high, and this was identified as an independent risk factor for SSI after hemorrhoidectomy.

FDA trial regulation of laboratory developed tests (LDTs): An academic medical center's experience with Mpox in-house testing.

The 2022 mpox outbreak presented a familiar challenge to clinical laboratories. Accordingly, our institution was able to swiftly implement in-house mpox testing to meet the imminent diagnostic needs of the public health emergency. While the FDA authorized laboratory-developed tests (LDTs) for lesion specimens, however, it restricted the testing of rectal swabs despite mounting evidence of its clinical utility. Notably, within the short timeframe when rectal testing was available, we identified a high-risk patient without apparent lesions who tested monkeypox-positive only by our in-house rectal swab assay. In order for our institution to continue testing non-lesion samples, The FDA required a separate Emergency Use Authorization (EUA) application that demanded additional resource-costly validation studies despite utilizing the same testing platform as lesion samples. Here, we provide a brief review of the history, current status, and legal scope surrounding LDT validations, with an in-depth comparison of the technical requirements by CLIA, CAP and the FDA. Importantly, we provide our experience with the mpox EUA submission process to serve as context for the challenges that may be imposed by the new FDA regulations. We hope that our experience will offer a valuable perspective that promotes constructive discourse towards addressing the imperative to offer high-quality laboratory diagnostics without compromising on the need of the medical laboratory community to provide effective patient care.

Safety of mid-thigh exit site venous catheters in multidrug resistant colonized patients.

INTRODUCTION: Venous catheters inserted in superficial femoral vein and with mid-thigh exit site have emerged as a feasible and safe technique for central or peripheral tip's venous access, especially in agitated, delirious patients. The spread of multidrug-resistant bacterial (MDR) strains is an emerging clinical problem and more and more patients are being colonized by these types of bacteria. The aim of this study is to evaluate the incidence of central line associated bloodstream infections (CLABSI) or catheter related bloodstream infections (CRBSI) in mid-thigh catheters in patients with positive rectal swabs to evaluate the safety of this procedure and the real infection risk. METHODS: In this retrospective observational study, we analyzed data on patients with mid-tight catheters inserted from May 2021 to November 2022. All surveillance rectal swabs were recorded. In addition, to collect data on CLABSI and CRBSI, the results of all blood and catheter tip cultures performed during the hospital stay were acquired. RESULTS: Six hundred two patients were enrolled, 304 patients (50.5%) had a rectal swab; 128 (42.1%) swabs were positive for MDR. Nine CLABSI (only two in patients with a positive rectal swab) and three CRBSI were detected. No statistical difference in the absolute number of CLABSI and CRBSI and in the number of infections per 1000 catheter days emerged between the overall population and patients with positive rectal swabs (respectively p = 0.45 and p = 0.53). Similarly, no statistical difference in the number of CLABSI and CRBSI was found among patients with a negative swab and patients with a positive one (respectively p = 0.43 and p = 0.51). CONCLUSIONS: According to our data, cannulation of the superficial femoral vein represents a safe location in patients with positive rectal swabs.

Comparing the broth enrichment-multiplex lateral flow immunochromatographic assay with real time quantitative PCR for the rapid detection of carbapenemase-producing organisms in rectal swabs.

BACKGROUND: Rapid and accurate identification of carbapenemase-producing organism (CPO) intestinal carriers is essential for infection prevention and control. Molecular diagnostic methods can produce results in as little as 1 h, but require special instrumentation and are expensive. Therefore, it is urgent to find an alternative method. The broth enrichment-multiplex lateral flow immunochromatographic assay was recently reported, but using it to directly detect CPO intestinal carriers in rectal swabs still requires the evaluation of many samples. The aim of this study was to compare the performance of these two methods, and to explore the control measures of CPO infection. METHODS: Through CPO selective culture, PCR and DNA sequencing, 100 rectal swabs confirmed to be CPO-positive and 100 rectal swabs with negative results were collected continuously. After eluting the rectal swabs with saline, three aliquots were used: one for counting, one for detection by Xpert Carba-R, and one for culture in broth for 0 h, 1 h, 2 h, 3 h and 4 h, followed by NG-Test CARBA 5 assessment. The sensitivity and specificity of the NG-Test CARBA 5 method after different incubation times were calculated. The limit of detection (LoD) of this assay after 4 h broth incubation was estimated by examining the bacterial suspensions and simulated faecal suspensions prepared with CPOs producing different types of carbapenemases. RESULTS: Xpert Carba-R demonstrated a combined sensitivity of 99.0% and specificity of 98.0%. The sensitivity and specificity were higher than 90.0% for the different enzyme types. The specificities of five common carbapenemases detected by the broth enrichment NG-Test CARBA 5 combined method after different incubation times were 100%. The sensitivities increased with increasing incubation time. At 4 h, the Klebsiella pneumoniae carbapenemase (KPC), New Delhi metallo-beta-lactamase (NDM), imipenemase (IMP), Verona integron-encoded metallo-beta-lactamase (VIM), and oxacillinase (OXA) -48 detection sensitivities were 93.0%, 96.3%, 100%, 100% and 85.7%, respectively. The LoDs were between 102 and 104 CFU/mL for all five enzymes after 4 h of incubation. CONCLUSIONS: This investigation highlighted that the broth enrichment-multiplex lateral flow immunochromatographic assay can be used as a new method for screening CPOs in rectal swabs.

Isolation of Multidrug-Resistant Organisms in Surveillance Stool Culture at Diagnosis Fails to Predict Mortality or Subsequent Sepsis due to Multidrug-Resistant Organisms in Children with Acute Leukemia: A Single-Center, Prospective, Observational Study.

The utility of surveillance stool culture (SSC) to guide antibiotics for febrile neutropenia (FN) is unresolved in non-transplant settings. The prospective study explored the prevalence of multidrug-resistant organisms (MDRO) in SSCs, its correlation with mortality, and the concordance of SSCs with cultures obtained during subsequent episodes of FN amongst children with acute leukemia. SSCs were obtained at presentation and 2 mo into chemotherapy. Seventy-nine patients (mean age: 5.9±3.2 y) with acute lymphoblastic leukemia (ALL) (80%), acute myeloid leukemia (AML) (16%), or biphenotypic leukemia (4%) were enrolled. MDROs were isolated from 14 (17.5%) patients in the first SSCs, including E.coli (80%), K. pneumoniae (10%), and E. faecium (10%). Three (3.8%) patients developed MDRO sepsis; none concorded with the SSCs. Eleven (14%) patients died; 4/14 (28.5%) with MDRO-colonization vis-à-vis 7/66 (10.6%) without MDRO-colonization (OR: 3.37, 95% CI: 0.8-13.6; p = 0.095). MDRO-colonization failed to predict MDRO-sepsis, bloodstream infection, or mortality. SSC failed to guide the choice of antibiotics for FN in children with acute leukemia.

Evidence of Mpox Virus Infection Among Persons Without Characteristic Lesions or Rash Presenting for First Dose of JYNNEOS Vaccine-District of Columbia, August 2022.

We assessed mpox virus prevalence in blood, pharyngeal, and rectal specimens among persons without characteristic rash presenting for JYNNEOS vaccine. Our data indicate that the utility of risk-based screening for mpox in persons without skin lesions or rash via pharyngeal swabs, rectal swabs, and/or blood is likely limited.

Mpox Presenting as Proctitis in Men Who Have Sex With Men.

In our cohort of 70 patients of men who have sex with men (MSM) with mpox, more than one-third presented with proctitis. In two-thirds of proctitis patients, there was no typical rash upon presentation, and in one-fifth, there was no rash at all, making the diagnosis a challenge. A rectal swab for mpox polymerase chain reaction (PCR) can be diagnostic.

The incidence of intestinal colonization of carbapenem-resistant Enterobacterales and its risk factors for bloodstream infection / 中华检验医学杂志

Objective:The aim of this study was to determine the colonization rate of carbapenem-resistant Enterobacterales (CRE) and identify the proportion and risk factors for bloodstream infection.Methods:This was a retrospective study conducted at the Department of Clinical Laboratory, Peking University People′s Hospital from January 2018 to December 2021. A total of 4 993 patients underwent rectal swab CRE screening for CRE, of which 137 were found to be positive. Clinical and laboratory data of the positive patients were collected, and the following parameters were analyzed: the positive rate of CRE screening in high-risk population, the species of colonized bacteria, antimicrobial resistance and the risk factors of CRE bloodstream infection in colonized patients. Statistical analysis was performed using SPSS 26.0 software. Univariate analysis was conducted using the chi-square (χ 2) test, while multivariate analysis was performed using binary logistic regression. The results were expressed as relative risk (odds ratio, OR) and 95% confidence interval ( CI). A significance level of 0.05 was considered statistically significant. The drug resistance rate of pathogen was analyzed by WHONET 5.6 software. Results:During the study period, a total of 4 991 patients who underwent rectal swab screening were eligible for inclusion, of which 137 patients were screened positive, resulting in a positive rate of 2.7% (137/4 991). The positive rates were higher in the intensive care ward and hematology ward, with rates of 5.5% (27/493) and 3.3% (109/3 321), respectively. A total of 145 colonization strains were isolated from patients with positive CRE screening, including 63 strains of Klebsiella pneumoniae (43.4%, 63/145), 52 strains of Escherichia coli (35.9%, 52/145), 16 strains of Enterobacter cloacae (11.0%, 16/145) and 14 strains of other Enterobacterales (9.7%, 14/145). The metal β-lactamase production type was the main component of CRE positive colonizing bacteria. The antimicrobial resistance of 145 strains to 22 antibacterial agents revealed that amikacin and tigacycline were the most sensitive. Among 137 CRE screening-positive patients, 14 (10.2%, 14/137) developed bloodstream infection. The isolated pathogenic bacteria included 10 Klebsiella pneumoniae strains and 4 Escherichia coli strains, with a predominant serine carbapenemase producing. Notably, the enzyme type and antimicrobial resistance of the bloodstream infection isolates in the same patient were highly consistent with those of the previous screening strains. Comparison was made between patients with positive CRE screening and those with CRE conversion to bloodstream infection. The unifactor analysis revealed significant differences in surgical history, neutropenia, hematopoietic stem cell transplantation, history of antibiotic use before rectal swab screening, screening within 48 hours after admission, and serine carbapenemase production by strains ( P<0.05). The multivariate analysis indicated that surgical history ( OR 24.659, 95% CI 2.540-239.411, P=0.006) and neutropenia ( OR 93.796, 95% CI 6.294-1 397.804, P=0.001) remained significantly associated with the risk of CRE bloodstream infection ( P<0.05). Conclusions:The CRE colonization rate was low in our hospital, but the proportion of patients with positive screening converted to bloodstream infection was high. Surgical history and neutropenia are risk factors for bloodstream infection transmission. Thus, it is essential to enhance monitoring in high-risk areas and susceptible patients.

Impact of a multi-strain probiotic administration on peri-rectal colonization with drug-resistant Gram-negative bacteria in preterm neonates.

Background: Infections caused by drug resistant Gram-negative bacteria (DR-GNB) are a major health concern for hospitalized preterm neonates, globally. The aim of this study was to investigate the effect of a multi-strain probiotic on the incidence of rectal colonization with DR-GNB in preterm neonates. Methods: A double-blind, placebo-controlled, randomized clinical trial was conducted including 200 neonates, randomly allocated to a multi-strain probiotic (n = 100) or placebo (n = 100). Results: Fifteen percent of the neonates showed peri-rectal colonization with DR-GNB on the day of enrolment indicating probable maternal-to-neonate (vertical) bacterial transmission or environmental acquisition at time of delivery, with no difference between groups. Acquisition of further DR-GNB colonization was rapid, with an increase from 15% on the day enrolment to 77% by day 7 and 83% by day 14 of life. By day 7 (corresponding to early gut colonization), neonates in the probiotic group were 57% less likely to have peri-rectal DR-GNB colonization [OR: 0.43 (0.20-0.95); p = 0.04] and by day 14 (corresponding to late gut colonization), neonates in the probiotic group were 93% less likely to have peri-rectal DR-GNB colonization [OR: 0.07 (0.02-0.23); p < 0.001]. Conclusion: Hospitalized neonates showed substantial peri-rectal colonization with DR-GNB at enrolment and further rapid acquisition of DR-GNB in the first 2 weeks of life. The use of a multi-strain probiotic was effective in reducing early and late neonatal gut colonization with DR-GNB. Clinical Trial Registration: The trial was registered at the Pan African Clinical Trial Registry (PACTR202011513390736).

Clinical Impact of Colonization with Carbapenem-Resistant Gram-Negative Bacteria in Critically Ill Patients Admitted for Severe Trauma.

Multidrug-resistant (MDR) Gram-negative bacteria (GNB) have raised concerns as common, frequent etiologic agents of nosocomial infections, and patients admitted to intensive care units (ICUs) present the highest risk for colonization and infection. The incidence of colonization and infection in trauma patients remains poorly investigated. The aim of this study was to assess the risk factors for Carbapenem-resistant (CR)-GNB colonization and the clinical impact of colonization acquisition in patients with severe trauma admitted to the ICU in a CR-GNB hyperendemic country. This is a retrospective observational study; clinical and laboratory data were extracted from the nosocomial infection surveillance system database. Among 54 severe trauma patients enrolled in the study, 28 patients were colonized by CR-GNB; 7 (12.96%) patients were already colonized at ICU admission; and 21 (38.89%) patients developed a new colonization during their ICU stay. Risk factors for colonization were the length of stay in the ICU (not colonized, 14.81 days ± 9.1 vs. colonized, 38.19 days ± 27.9; p-value = 0.001) and days of mechanical ventilation (not colonized, 8.46 days ± 7.67 vs. colonized, 22.19 days ± 15.09; p-value < 0.001). There was a strong statistical association between previous colonization and subsequent development of infection (OR = 80.6, 95% CI 4.5−1458.6, p-value < 0.001). Factors associated with the risk of infection in colonized patients also included a higher Charlson comorbidity index, a longer length of stay in the ICU, a longer duration of mechanical ventilation, and a longer duration of treatment with carbapenem and vasopressors (not infected vs. infected: 0(0−4) vs. 1(0−3), p = 0.012; 24.82 ± 16.77 vs. 47 ± 28.51, p = 0.016; 13.54 ± 15.84 vs. 31.7 ± 16.22, p = 0.008; 1.09 ± 1.14 vs. 7.82 ± 9.15, p = 0.008). The adoption of MDR-GNB colonization prevention strategies in critically ill patients with severe trauma is required to improve the quality of care and reduce nosocomial infections, length of hospital stay and mortality.

Analysis of RNA virome in rectal swabs of healthy and diarrheic pigs of different age.

The porcine enteric virome comprises a wide range of eukaryotic and prokaryotic viruses in healthy and diarrheic pigs. As RNA viruses are considered to be important agents responsible for diarrhoea in pigs, this work was focused on the RNA virome. To identify viruses, a next generation sequencing technique and bioinformatics analysis was employed. A wide spectrum of viral genera with RNA genomes, such as Kobuvirus, Picobirnavirus, Teschovirus, Posavirus, Mamastovirus, Enterovirus and Rotavirus were identified in both diarrheic and healthy pigs. No clear differences in the virome composition were found between healthy and diarrheic pigs. The data visualisation using Non-Metric Multidimensional Scaling as well as by the Analysis of Similarities test suggested that the virome depended on the age of animals and differed in piglets when compared to weaned and fattening pigs.