Screening Swabs Research Articles

DNA Methylation Analysis on Anal Swabs for Anal Cancer Screening in People Living With Human Immunodeficiency Virus

Abstract Background High-resolution anoscopy (HRA) to prevent anal cancer is complex and screening capacity is limited. Previously, DNA methylation analysis of anal high-grade squamous intraepithelial lesion (HSIL) biopsies was shown to distinguish between HSIL with an increased and a low cancer risk, supporting personalized treatment. Here, methylation analysis on anal swabs was assessed to detect underlying HSIL with an increased cancer risk. Methods A cross-sectional series of paired anal swabs and biopsies of 215 persons with human immunodeficiency virus and swabs of 19 cancer patients were tested for 6 methylation markers. Data were analyzed by logistic regression analysis. The primary endpoint was methylation-positive biopsy HSIL (M+ HSIL), indicating increased cancer risk. Test performance of methylation markers, human papillomavirus (HPV), and/or cytology, and cancer detection and HRA referral, were calculated. Results Anal cancer swabs showed highest methylation. ZNF582 and panels ASCL1/ZNF582 and LHX8/ZNF582 yielded an area under the curve of 0.68–0.70 to detect underlying M+ HSIL. Methylation at 80% sensitivity corresponded to 43% fewer patients requiring HRA, without missing any cancers and detecting 79% of HPV-16–positive HSIL-AIN3. Methylation/HPV and cytology/HPV co-testing performed similarly. Conclusions Methylation levels in anal swabs reflect underlying anal disease. Methylation analysis could reduce HRA referrals substantially, while maintaining a high sensitivity for M+ HSIL and detecting all cancers. These results encourage screening on anal swabs to preselect patients needing HRA.

Minimizing infectious complications following transrectal prostate biopsy: a proposal for a risk-adapted antibiotic treatment strategy with Ceftriaxone and Ertapenem as key components.

To investigate the effect of pre-biopsy rectal swab and urine screening combined with a risk-adapted antibiotic treatment strategy on reducing post-biopsy infections (PBIs) following multiparametric magnetic resonance imaging (mpMRI)/ transrectal ultrasound (TRUS) fusion-targeted transrectal prostate biopsy (TRPBx). 1119 Patients undergoing mpMRI-TRUS fusion TRPBx between June 2017 and February 2024 were included. Patients were screened for rectal extended-spectrum beta-lactamase (ESBL)/multi-resistant gram-negative (MRGN) and urinary pathogens. Standard-risk patients (rectal non-ESBL/MRGN-carriers) either received Cefuroxime (2017-2020) or Ceftriaxone (2020-2024) intravenously before biopsy. For high-risk patients (rectal ESBL/MRGN-carriers) intravenous Ertapenem was used. Patients with positive urine cultures received oral targeted prophylaxis. PBIs were the primary outcome of the study. We used uni- and multivariable logistic regression analysis (MLRA) to reveal predictors for the main outcome. Rectal ESBL/MRGN prevalence was 5.5%. For standard-risk patients, PBI-rates were 8.1% and 0.24% for Cefuroxime and Ceftriaxone (p < 0.0001), respectively. Only 1.7% of high-risk patients treated with Ertapenem developed PBI. On MLRA, Cefuroxime (OR 38.7, 95%-CI: 10.9-246), oral Ciprofloxacin (OR 103, 95%-CI: 10.8-994), other oral targeted antibiotics (OR 42.7, 95%-CI: 1.86-496) (reference Ceftriaxone, all p < 0.005) were significant predictors for PBI whereas Ertapenem (OR 7.30 95%-CI: 0.34-77.4, p = 0.11) was not. By integrating rectal swab ESBL/MRGN and urine screening, we developed a tailored antibiotic treatment strategy, resulting in low PBI-rates following TRPBx. Carbapenem-based treatment of high-risk patients is crucial. Ceftriaxone should be considered for routine use in standard-risk patients as it offers very low PBI-rates.

Is intestinal colonization with multidrug-resistant Enterobacterales associated with higher rates of nosocomial Enterobacterales bloodstream infections?

ObjectiveIntestinal colonization with multidrug-resistant Enterobacterales (MDRE-IC) increases the risk of MDRE bloodstream infection (MDRE-BSI). However, its impact on the overall risk of nosocomial Enterobacterales bloodstream infections (nE-BSI) remains unclear. This study aimed to determine this risk and identify associated factors in hospitalized patients. Design and methodsThis retrospective cohort study at a 3200-bed tertiary institution included patients hospitalized in 2019 who underwent MDRE rectal swab (RS) screening. Inclusion criteria were age ≥18 years, first RS in 2019, follow-up ≥7 days, and E-BSIs >48 hours post-RS. The primary outcome was the first nE-BSI during follow-up period, analysed using a Cox model. ResultsAmong 7006 patients, 817 (11.9%) had MDRE-IC. Most were male and primarily hospitalized in acute wards. nE-BSIs occurred in 433 (6.1%) patients and was more frequent in MDRE-IC patients compared to non-colonized group (aHR = 1.78, 95%CI: 1.40-2.26). Intestinal colonization with ESBL-producing and carbapenemase-resistant Enterobacterales showed similar risks for E-BSI onset: aHR = 1.73 (95%CI: 1.33-2.24) and aHR = 2.02 (95%CI: 1.27-3.22), respectively. ConclusionIn hospitalized patients, MDRE-IC is associated with a higher rate of nE-BSI compared to those without MDRE-IC, underscoring the urgent need for improved infection prevention and control measures, as well as optimized antibiotic use to mitigate this risk.

Investigation and successful control of a Candida auris outbreak at a tertiary health care facility in Kenya

ObjectivesThis study aimed to conduct an epidemiological and genomic investigation of a hospital outbreak of Candida auris, and implement measures for its control. MethodsWe collected demographic and clinical data from medical records of patients with C. auris from January 2017 to June 2019 after identifying increased cases in April 2019. Point-prevalence surveys for C. auris colonisation were conducted in the critical care units (CCU). Antifungal susceptibility testing and genomic sequencing of isolates were performed. A bundle of infection prevention and control measures was instituted. ResultsThirty-two patients with C. auris were identified. All patients had a history of CCU admission. A total of 283 screening swabs were obtained and 57 isolates of C. auris identified. Antifungal susceptibility testing was performed on 48 isolates. All but two isolates were resistant to fluconazole; one isolate was also resistant to amphotericin B. Forty-one of 46 isolate genomes were clonally related and formed a distinct genetic cluster in Clade III. C. auris colonisation reduced from 42% in June 2019 to 1% in August 2019, and no new hospital-acquired colonisation was identified in the subsequent 9 months. ConclusionsWe identified a new genetic subcluster of Clade III C. auris. We also show that strict implementation of infection prevention measures can lead to substantial reductions in C. auris transmission.

Do Post-debridement Cultures have a Role in Reduction of Infection in Open Fractures? Report of 166 Cases and Literature Review.

To evaluate the role of post-debridement cultures in the prevention of future infection following open fractures. Retrospective Cohort Study and Literature Review. Division of Orthopaedic Surgery, Sultan Qaboos University Hospital, Academic and tertiary health care, Muscat, Oman. A total of 166 patients from a cohort study and 539 patients from the literature review with open fractures. There were 640 cumulative patients fit the inclusion and exclusion criteria. Using predetermined inclusion and exclusion criteria, data on all open fractures were gathered from the electronic health system of a single institution between 2010 and 2019. PubMed and Embase electronic databases were also searched for relevant articles relating to post-surgical debridement culture and its correlation with future infection. Assessing the benefit, role of post-debridement cultures in the prevention of future infection following open fractures. Combining the results of this retrospective cohort study and previously published data, there were 640 Gustilo-Anderson grades II and III open fractures which had post-debridement screening. Eighty-eight patients (13.8%) developed an infection, out of which 16 had positive post- debridement cultures (18.2%). Only four grew similar organisms at screening and infection stages, two of which had different antibiotic resistance patterns at the infection stage. Seventy-two fractures had negative post-debridement screening swabs (81.8%). Of the 59 (9.2%) fractures with positive screening only four (6.8% of the infected fractures) developed later deep infection. All these 59 cases had culture-guided antibiotic treatment, with or without surgical debridement. Although the bacterial growth of post-debridement cultures is low, post-debridement screening as part of a comprehensive management protocol may have a role in reducing deep infection in open fractures. This is particularly the case in Gustilo and Anderson type 3 open fractures, the risk of infection is high. The poor association between organisms isolated from screening and those from subsequent deep infection may mean that the later infective organisms have been acquired from a secondary colonisation source after the debridement. III. Kindi NA, Abri FA, Yaseen A, et al. Do Post-debridement Cultures have a Role in Reduction of Infection in Open Fractures? Report of 166 Cases and Literature Review. Strategies Trauma Limb Reconstr 2024;19(2):94-98.

Pilot postal birth cohort HCV Screening in UK primary care.

Birth cohort screening has been implemented in some countries to identify the potentially 'missed population' of undiagnosed chronic Hepatitis C Virus (HCV) in people who may not be found through targeted approaches. To determine uptake of HCV antibody testing using an oral swab screening method, overall yield, whether those testing positive had risk markers in their primary care record, and cost per case detected. Pilot screening study set in general practices in the Southwest, South London and Yorkshire and Humber. Participants consenting were sent an oral swab kit in the post and saliva samples were tested for antibody to HCV. 16,436/98,396 (16.7%) patients consented and were sent an oral swab kit. 12,216 (12.4%) returned a kit, with 31 participants (yield 0.03%) testing positive for HCV antibody. 45% of those positive had a risk marker for HCV on their primary care record. Two (yield 0.002%) were confirmed RNA positive and referred for treatment, both had HCV risk markers. Cost per case detected was £16,000 per HCV antibody and £247,997 per chronic HCV. Wide-scale screening could be delivered and identified people infected with HCV, however most of these individuals could have been detected through lower-cost targeted screening. Yield and cost per case found were substantially worse than model estimates and targeted screening studies. Birth cohort screening should not be rolled out in primary care in England.

Candida auris Screening of High-Risk Patients: A Descriptive Comparison of 2 Strategies.

Background: Candida auris infection is associated with high morbidity and mortality. C. auris can persist in the healthcare environment and is associated with outbreaks. We compare screening strategies for C. auris in two high-risk patient populations. Methods: Our center is a tertiary, 865-bed hospital. In the context of known regional outbreaks of C. auris in post-acute care (PAC) facilities, we experienced extended clusters of apparent C. auris acquisition across several hospital units. Hospital acquisition was defined as new C. auris in clinical cultures in patients with no known history of C. auris colonization/infection. We performed point prevalence surveys (PPS) on affected units weekly until all tests were negative for two consecutive weeks. We also initiated admission screening for C. auris for patients admitted from PAC. All screening swabs were collected per CDC’s procedure. Tests were performed either by RT-PCR or Chromagar C. auris media, depending on availability. We compared the overall positivity rates of exposure PPS versus PAC admission screenings using Z-test for two proportions with statistical significance set at p &lt; 0 .05 Results: From 2/2023-12/2023, a total of 533 tests on 367 unique patients were processed during PPS; 512 tests were negative and 21 were positive (3.9% positivity rate). Three additional samples were either unable to be processed or indeterminate. There were 68 patients who had repeat testing weekly for ≥2 weeks. Most remained negative, but 5 tested positive after variable amounts of negative-week intervals: 3 patients at week 2, 1 patient at week 4 and 1 patient at week 5. From 8/2023 to 12/2023, a total of 89 patients admitted from 35 different PAC facilities underwent admission screening for C. auris. Only three patients were positive (3.4%), each from a different facility. The difference in the positivity rates between PPS and PAC was not statistically significant (Z-score 0.25, p = 0.79). Discussion: Our C. auris screening strategies found similar positivity rates for patients admitted to the hospital from PACs compared to targeted PPS in the setting of apparent hospital acquisition events. These strategies may be considered as complementary. Facilities experiencing apparent acquisition events should consider screening high-risk admissions to identify and isolate colonized patients, particularly if standard infection prevention practices are being performed with high fidelity.

Longitudinal Follow Up of Patients Colonized with Clostridioides difficile: a Retrospective Cohort Study

Background: Patients colonized with Clostridioides difficile are at risk of transmitting C. difficile to other patients, and of developing C. difficile infection (CDI). Known risk factors for carriage include previous hospitalization, gastric acid suppression and previous CDI. Data regarding duration of carriage and its predictors are lacking but could be useful to better understand the natural evolution of carriage and better estimate the likelihood of transmission or progression to CDI. Methods: We performed a retrospective cohort study of C. difficile colonized patients with &gt; = 1 admission to a tertiary academic institution between November 2013 and January 2017. Colonization status was determined upon hospital admission by detection of TcdB gene by polymerase chain reaction on a rectal screening swab, as part of a systematic screening program. Overall duration of carriage and predictors of prolonged carriage were explored using Kaplan-Meier methods and Cox regression. Results: There were 134 patients, who after having a positive initial screening test (and therefore identified as colonized with C. difficile), had subsequent testing. The median age was 77 years (IQR, 66 to 85), and 53.6% of the patients were female. After hospital discharge, 26 (19.4%) colonized patients progressed to CDI. Mean duration of follow up was 269 days, with a median of 179 days. Median duration of carriage was 211 days, (95% confidence interval (CI) [157, 264]). Predictors associated with decreased duration of C. difficile colonization included younger age (HR per unit decrease (year), 1.013; 95% CI, 1.025 to 1.001; p=0.03), and receipt of antibiotics in the 3 months prior to first admission (mean days to clearance of patients with and without recent antibiotic use, 252 days vs 372 days, respectively; HR, 1.55; 95% CI, 1.01 to 2.36; p &lt; 0 .04). By contrast, the presence of comorbidities (e.g. heart failure, diabetes, cancer, and chronic kidney disease), the use of proton-pump inhibitors (PPIs), the receipt of antibiotics during the first admission, and the duration of first hospitalization were not associated with significant differences in duration of carriage. Conclusion: This study is the largest cohort of C. difficile carriers with longitudinal follow up of their colonization status. It highlights the extended duration of carrier status especially in older patients and identifies predictors of prolonged carriage. Further studies are needed to understand the underlying relationship with the predictors identified in this study.

Risk Factors and Outcomes of Patients Colonized with KPC and NDM Carbapenemase-Producing Enterobacterales.

Carbapenemase-producing enterobacterales (CPE) poses an increasing threat in hospitals worldwide. Recently, the prevalence of different carbapenemases conferring carbapenem resistance in enterobacterales changed in our country, including an increase in New Delhi Metallo-beta-lactamase (NDM)-CPE. We conducted a comparative historical study of adult patients colonized with Klebsiella pneumoniae carbapenemase (KPC)-CPE (July 2016 to June 2018, a historical cohort) vs. NDM-CPE (July 2016 to January 2023). We identified patients retrospectively through the microbiology laboratory and reviewed their files, extracting demographics, underlying diseases, Charlson Comorbidity Index (CCI) scores, treatments, and outcomes. This study included 228 consecutive patients from whom a CPE rectal swab screening was obtained: 136 NDM-CPE positive and 92 KPC-CPE positive. NDM-CPE-colonized patients had a shorter hospitalization length and a significantly lower 30-day post-discharge mortality rate (p = 0.002) than KPC-CPE-colonized patients. Based on multivariate regression, independent risk factors predicting CPE-NDM colonization included admission from home and CCI < 4 (p < 0.001, p = 0.037, respectively). The increase in NDM-CPE prevalence necessitates a modified CPE screening strategy upon hospital admission tailored to the changing local CPE epidemiology. In our region, the screening of younger patients residing at home with fewer comorbidities should be considered, regardless of a prior community healthcare contact or hospital admission.

Significance of colonization by antibiotic-resistant organisms prior to congenital heart disease surgery in children from low- to middle-income countries sent by non-governmental organizations to Switzerland.

Children with congenital heart disease (CHD) from low- to middle-income countries (LMIC) are suspected to have a high prevalence of antibiotic-resistant microorganisms (ARMOs) carriage, but data are currently lacking. Carriage of ARMOs could impact the post-operative course in pediatric intensive care unit (PICU). The aim of the study was to assess the prevalence of ARMOs carriage in children with CHD from LMIC and its impact on post-operative outcomes. This was a retrospective monocentric study from 01/2019 to 12/2022. Included patients were children (0-18 years) from a LMIC admitted after CHD surgery and with AMRO screening performed the week before. Infections and post-operative evolution were compared based on ARMOs carriage status. Among 224 surgeries (median age 38.5 months (IQR 22-85.5)), ARMOs carriage was evidenced in 95 cases (42.4%). Main organisms isolated were Extended Spectrum Beta-Lactamase (ESBL) producing E. coli (75/224) 33.5%)) and ESBL-K. pneumoniae (30/224) 13.4%)). Median mechanical ventilation duration was 1 day (IQR 0-1), PICU stay 3 days (IQR 2-4) and hospital stay 6.5 days (IQR 5-10). A total of 17 infectious episodes occurred in 15 patients, mostly consisting in hospital-acquired pneumonia (HAP) (12/17). Only two infections were caused by a colonizing ARMO. Occurrence of infections and patients' outcome were similar between ARMO carriers and non-carriers. Higher use of carbapenems (6 (6.3%) vs 1 (0.8%), p = 0.04) and a trend to a higher use of vancomycin (14 (13.7%) vs 9 (6.9%), p = 0.04) in case of ARMOs carriage. Applying current guidelines, negative swab screening could have led to sparing most of empirical vancomycin therapy (11/12) for HAP based on current guidelines. Prevalence of AMROs carriage is high in children from LMIC and has a limited impact on patients' outcome. However, ARMOs carriage leads to higher consumption of antibiotics. Screening may help saving use of broad-spectrum antibiotic in non-carrier patients.

Evidence of transmission of New Delhi metallo-β-lactamase-producing Klebsiella pneumoniae through a gastrointestinal endoscope without an elevator channel.

To investigate the source and transmission dynamics of an endoscope-associated New Delhi metallo-β-lactamase-producing Klebsiella pneumonia (NDM-KP) outbreak. Epidemiological and genomic investigation. Academic acute care hospital in New Jersey. Five patients with active NDM-KP infection identified on clinical isolates, and four NDM-KP colonized patients identified via rectal swab screening. Over a twelve-month period, nine patients were identified with NDM-KP infection or colonization. Whole-genome sequencing (WGS) revealed that all of the identified cases were related by 25 mutational events or less. Seven of the cases were linked to gastrointestinal endoscopic procedures (four clinical cases and three positive screens among patients exposed to endoscopes suspected of transmission). Two cases demonstrated delayed transmission that occurred five months after the initial outbreak, likely through shared usage of a non-therapeutic gastroscope without an elevator channel. Although all endoscope cultures in our investigation were negative, the epidemiological link to gastrointestinal endoscopes, the high degree of relatedness via WGS, and the identification of asymptomatic NDM-KP colonization among patients exposed to shared endoscopes make the endoscopic mode of transmission most likely. This investigation highlights the probable transmission of NDM-KP via a gastroscope without an elevator channel, observed several months after an initial outbreak. We hypothesize that persistent mechanical defects may have contributed to the delayed device-related transmission of NDM-KP.

Addition of vancomycin to cefazolin is often unnecessary for preoperative antibiotic prophylaxis during total joint arthroplasties

PurposeThe gold standard to decrease total joint arthroplasty (TJA) periprosthetic joint infection (PJI) is preoperative antibiotic prophylaxis. Despite substantial prevention efforts, rates of PJIs are increasing. While cefazolin is the drug of choice for preoperative prophylaxis, adjunctive vancomycin therapy has been used in methicillin-resistant Staphylococcus aureus (MRSA) endemic areas. However, studies examining these combinations are lacking. Therefore, we sought to examine complications among vancomycin plus cefazolin and cefazolin-only recipients prior to primary TJA in a single institutional sample and specifically assessed: (1) microbiological aspects, including periprosthetic joint and surgical site infections, microbes cultured from the infection, and frequency of microbes cultured from nasal swab screening; (2) 30-day emergency department (ED) visits and re-admissions; as well as (3) associated risk factors for infection.MethodsA total of 2,907 patients (1,437 receiving both cefazolin and vancomycin and 1,470 given cefazolin only) who underwent primary TJA between 1 January 2014 and 31 May 2021 were identified. SSI and PJI as well as rates of cultured microbes rates were obtained through one year, those with prior nasal swab screening and 30-day re-admission were identified. Subsequently, multiple regression analyses were performed to investigate potential independent risk factors for PJIs.ResultsThere was no significant difference in the rates of SSI (P = 0.089) and PJI (P = 0.279) between the groups at one year after operation. Commonly identified organisms included Staphylococcus and Streptococcus species. The VC cohort did have a greater reduction of MRSA in the previously nasal swab-screened subset of patients. Multiple regression analyses demonstrated emergency as well as inpatient admissions as risk factors for PJI.ConclusionsAdjunctive vancomycin therapy offers increased protection against MRSA in previously screened individuals. However, those negative for MRSA screening do not require vancomycin and have similar protection to infection compared to recipients of cefazolin only in a high-powered single institution analysis in an MRSA endemic area.

Key microbial monitoring and clinical analysis of bloodstream infections and CRO colonization after hematopoietic stem cell transplantation in hematological patients

Objective: To investigate the distribution and clinical characteristics of pathogenic bacteria following hematopoietic stem cell transplantation (HSCT), as well as to provide a preliminary research foundation for key microbial monitoring, and clinical diagnosis and treatment of infections after HSCT in hematological patients. Methods: We retrospectively analyzed the clinical data of 190 patients who tested positive for microbial testing [G-bacteria blood culture and/or carbapenem-resistant organism (CRO) screening of perianal swabs] at our center from January 2018 to December 2022. Patients were divided into blood culture positive, perianal swab positive, and double positive groups based on the testing results. The three patient groups underwent statistical analysis and comparison. Results: The top four pathogenic bacteria isolated from sixty-three patients with G-bacteria bloodstream infection (BSI) were Escherichia coli (28 strains, 43.75% ), Klebsiella pneumonia (26 strains, 40.63% ), Pseudomonas aeruginosa (3 strains, 4.69% ), and Enterobacter cloacae (3 strains, 4.69% ). The top three pathogenic bacteria isolated from 147 patients with CRO perianal colonization were carbapenem-resistant Klebsiella pneumoniae (58 strains, 32.58% ), carbapenem-resistant Escherichia coli (49 strains, 27.53% ), and carbapenem-resistant Enterobacter cloacae (20 strains, 11.24% ). The 3-year disease-free survival (DFS ) and overall survival (OS) of double positive group patients were significantly lower compared to those in the blood culture and perianal swab positive groups (DFS: 35.6% vs 53.7% vs 68.6%, P=0.001; OS: 44.4% vs 62.4% vs 76.9%, P<0.001), while non-relapse mortality (NRM) was significantly higher (50.0% vs 34.9% vs 10.6%, P<0.001). Failed engraftment of platelets and BSI are independent risk factors for NRM (P<0.001). Using polymyxin and/or ceftazidime-avibactam for more than 7 days is an independent protective factor for NRM (P=0.035) . Conclusion: This study suggests that the occurrence of BSI significantly increases the NRM after HSCT in patients with hematological diseases; CRO colonization into the bloodstream has a significant impact on the DFS and OS of HSCT patients.

Optimization of the STARlet workflow for semi-automatic SARS-CoV-2 screening of swabs and deep respiratory materials using the RealAccurate Quadruplex SARS-CoV-2 PCR kit and Allplex SARS-CoV-2 PCR kit.

The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic triggered the implementation of large-scale screenings in the health care and in the general population. Consequently, medical laboratories have to apply lean laboratory management to design workflows that are able to process large batches within short turnaround times while maintaining flexibility to use different SARS-CoV-2 reverse transcription polymerase chain reactions (RT-PCRs) and to be able to process a variety of clinical samples. We validated two SARS-CoV-2 PCR assays on the STARlet workflow: Allplex SARS-CoV-2 PCR kit and RealAccurate Quadruplex SARS-CoV-2 PCR kit. Furthermore, we optimized and validated the STARlet workflow for semi-automatic screening for SARS-CoV-2 in upper respiratory swabs and deep respiratory materials (sputa, bronchoalveolar lavage, and aspirate). Strikingly, guanidine-containing lysis buffers allow for easy processing and can enhance sensitivity of SARS-COV-2 screening since sampling in these buffers may preserve viral transcripts as evident by the higher copy numbers of the SARS-CoV-2 N gene. Moreover, using the principles of lean laboratory management, several bottlenecks that are typical for medical laboratories were addressed. We show that lean laboratory management resulted in significant reduction of the turnaround times of the SARS-CoV-2 PCR in our laboratory. This report thus describes a useful framework for laboratories to implement similar semi-automated workflows.IMPORTANCEThe SARS-CoV-2 pandemic triggered the implementation of large-scale screenings in the health care and in the general population. Consequently, medical laboratories had to adapt and evolve workflows that are able to process large batches within short turnaround times while maintaining flexibility to use different assays and to be able to process a variety of clinical samples. We describe how the need for increased outputs and greater flexibility was addressed with respect to clinical samples and assays (Allplex SARS-CoV-2 PCR and RealAccurate Quadruplex SARS-CoV-2 PCR). Strikingly, we found that upper respiratory swabs collected in guanidine-containing lysis buffers both improved the ease of processing as well as enhanced the sensitivity of the SARS-CoV-2 screening. This report thus describes a useful framework for laboratories to implement and optimize similar semi-automated workflows.

Evaluation of methicillin-resistant Staphylococcus aureus nasal swab screening at a large comprehensive cancer center.

The aim of this study is to determine the predictive values of MRSA swab screenings in patients with cancer. This is a retrospective cohort observational study of adult patients admitted to The University of Texas MD Anderson Cancer Center between January 2019 and October 2022. Data collected from patients with documented MRSA nasal swab screenings and clinical cultures taken within 7 days were collected. The first documented MRSA swab screening and culture results from unique patients were included for analysis to calculate sensitivity, specificity, positive predictive value, and NPV. A total of 6475 patients with MRSA nasal swab cultures had 13129 clinical cultures from different anatomical sites. Of the patients included, 57% had a solid tumor and 37% had a hematological malignancy, with 82% of patients receiving an anti-MRSA antibiotic prior to MRSA nasal swab. There were 167 documented positive MRSA cultures, most commonly from a wound (41.3%) or respiratory source (24%). Overall sensitivity and specificity for all culture sites were 50.9% and 98.4%, respectively, with an overall NPV of 99.4%. The NPV was 99.8% for bloodstream infections, 98.5% for respiratory infections, 92.6% for wound infections, and greater than 99% for other culture sites. The specificity and negative predictive value of MRSA swab screenings in patients with cancer was high overall and consistent with the literature in immunocompetent patients. These results may aid in antimicrobial stewardship activities that can help guide the discontinuation of empiric antibiotics in patients with cancer.

Emergence of carbapenemase-producing Enterobacterales (CPE) in patients with severe COVID-19 infection and successful control in intensive care.

We aim to highlight therisks of acquiring carbapenemase-producing Enterobacterales (CPE) resistance genes in patients with severe coronavirus disease 2019 (COVID-19) in intensive care. Outbreak analysis to assess for a transmission risk area (TRA) conducted after identification ofpotential CPE outbreak within shared room spaces in intensive care. Analysis conducted within a24-bed single-room model intensive-care department within a level-3 tertiary center public hospital in regional Victoria, Australia. 3 patients, with severe COVID-19 admitted to intensive care over a3-month period with shared room spaces requiring prolonged mechanical ventilation and broad-spectrum antimicrobials, identified and were managed for CPE isolated from sputum. Overlap carbapenemase genes were identified among different organisms raising suspicion of transmitted resistance genes. A subsequent case managed for severe community-acquired pneumonia isolated CPE 3 months beyond these cases. Outbreak analysis via weekly cross-sectional point prevalence screening of fecal samples or rectal swabs for CPE from patients admitted to the intensive-care department over a4-week period. 34 patients were included in the analysis with 51 tests for CPE screening conducted. No further cases of CPE were identified. Statewide Infection Surveillance team and theDepartment of Health and Human Services did not find the cases to derive from a TRA. No further action including environmental screening was indicated. These cases highlight theindependent acquisition of CPE genes in patients with severe COVID-19 and antimicrobial selective pressures resulting in significant morbidity and mortality. Increasing awareness, robust antimicrobial stewardship, and infection prevention measures could reduce pressures driving CPE resistance mutations and therisk of CPE transmission.

A novel characterized multi-drug-resistant Pseudocitrobacter sp. isolated from a patient colonized while admitted to a tertiary teaching hospital

Reports of nosocomial infections typically describe recognised microorganisms. In this study, a novel bacterial species was isolated, based on rectal swab screening for carbapenemases post-admission, then phenotypically and genetically characterised. Determined to be a possible Enterobacterales, whole genome sequencing and phylogenetic analysis confirmed identification as Pseudocitrobacter, a relatively new genus (2013) with three known species. This isolate was found to be distinct from these, with 99.7% 16s rRNA identity to Pseudocitrobacter corydidari; an Asian cockroach-associated species. Given the highly conserved/low variability of 16S rRNA genes in Enterobacteriaceae, average nucleotide identity (ANI) analysis compared the new isolate's genome with those of 18 Enterobacteriaceae species, including confirmed species of Pseudocitrobacter and unnamed Pseudocitrobacter species in the SILVA database. Of these, Pseudocitrobacter corydidari had the highest ANI at 0.9562. The published genome of the only known isolate of P. corydidari is stated to not include Antimicrobial Resistance Genes (ARGs), with exception of potential drug efflux transporters. In contrast, our clinical isolate bears recognised antimicrobial resistance genes, including Klebsiella pneumoniae carbapenemase. The associated genome suggests resistance to carbapenems, β-lactams, sulfonamides, fluoroquinolones, macrolides, aminoglycosides and cephalosporins. Phenotypic antimicrobial resistances were confirmed. In addition to evident variations in ARG profiles, human colonisation and origin in a clinically-relevant niche that is geographically, physically and chemically disparate, lend credibility for divergent evolution or, less likely, parallel evolution with P. corydidari. Genome data for this new species have been submitted to GENBANK using proposed nomenclature Pseudocitrobacter limerickensis. The patient was colonised only and did not require antimicrobial treatment.

Rectal culture could predict carbapenem-resistant organism bloodstream infection and reduce the mortality in haematological patients: A retrospective cohort study

The objective is to explore the correlation between rectal swab culture and the overall 30-d survival of hematologic patients diagnosed with carbapenem-resistant organism (CRO) bloodstream infection. A total of 434 haematological patients who were complicated with Gram-negative bacilli (GNB) bloodstream infections (BSIs) caused by Gram-negative bacteria between January 2020 and December 2021 were included in our retrospective study. Based on their drug susceptibility results, we classified patients into CRO BSIs and non-CRO BSIs cases. Through group comparison, to uncover the correlation between the positive screening of rectal swabs and reducing the mortality of CRO BSI in patients with haematological diseases. Among the 434 cases of Gram-negative bacteria bloodstream infection, 96 were identified as carbapenem-resistant bloodstream infection, which consisted of 57 cases of carbapenem-resistant Klebsiella pneumoniae (CR-KP), 19 cases of carbapenem-resistant Pseudomonas aeruginosa (CR-PA), 11 cases of carbapenem-resistant Escherichia coli (CR-CO), 5 cases of carbapenem-resistant Acinetobacter baumannii (CR-AB), and 4 cases of other Enterobacteriaceae. Before the onset of CRO bloodstream infection, rectal swab cultures were conducted on 36 patients, and the positive result rate was 75.0% (27/36), with 20 cases of CR-KP, 6 cases of CR-CO, and one case of carbapenem-resistant Enterobacter cloacae. It was observed that the rectal and blood cultures had matching outcomes in 75.0% of cases. The mortality rate within 30 d for CRO BSIs was 53.1% (51/96), while for carbapenem-resistant Enterobacteriaceae (CRE) BSIs it was 62.5% (45/72). Univariate analysis showed that 30-d mortality was significantly reduced when there were positive rectal culture results preceding bloodstream infection (P < 0.001), as well as preemptive anti-infection treatment (P < 0.001). Multivariate analysis demonstrated that preemptive adjustment to an effective antibiotic regimen, guided by positive rectal culture results, had a significant effect on decreasing 30-d mortality following CRO BSIs (P= 0.002). Furthermore, for the management of CRE BSIs, antibiotic treatments utilising ceftazidime/avibactam (CAV/AVI) may be more beneficial compared to those that use tigecycline (TGC) or polymyxin (PMB). CRO BSI, especially CRE BSI, can be life-threatening for those with haematological diseases. Utilising rectal culture can effectively identify CRO strains with high sensitivity and specificity. Adjusting antibiotic treatment based on the preemptive positive rectal culture results may significantly decrease 30-d mortality rates for haematological patients with CRO BSIs.

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

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. 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. 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. 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.

Vancomycin resistant enterococcus risk factors for hospital colonization in hematological patients: a matched case-control study

BackgroundVancomycin-resistant enterococcus (VRE) was the fastest growing pathogen in Europe in 2022 (+ 21%) but its clinical relevance is still unclear. We aim to identify risk factors for acquired VRE rectal colonization in hematological patients and evaluate the clinical impact of VRE colonization on subsequent infection, and 30- and 90-day overall mortality rates, compared to a matched control group.MethodsA retrospective, single center, case–control matched study (ratio 1:1) was conducted in a hematological department from January 2017 to December 2020. Case patients with nosocomial isolation of VRE from rectal swab screening (≥ 48 h) were matched to controls by age, sex, ethnicity, and hematologic disease. Univariate and multivariate logistic regression compared risk factors for colonization.ResultsA total of 83 cases were matched with 83 controls. Risk factors for VRE colonization were febrile neutropenia, bone marrow transplant, central venous catheter, bedsores, reduced mobility, altered bowel habits, cachexia, previous hospitalization and antibiotic treatments before and during hospitalization. VRE bacteraemia and Clostridioides difficile infection (CDI) occurred more frequently among cases without any impact on 30 and 90-days overall mortality. Vancomycin administration and altered bowel habits were the only independent risk factors for VRE colonization at multivariate analysis (OR: 3.53 and 3.1; respectively).ConclusionsAntimicrobial stewardship strategies to reduce inappropriate Gram-positive coverage in hematological patients is urgently required, as independent risk factors for VRE nosocomial colonization identified in this study include any use of vancomycin and altered bowel habits. VRE colonization and infection did not influence 30- and 90-day mortality. There was a strong correlation between CDI and VRE, which deserves further investigation to target new therapeutic approaches.