48 Background. Nucleic acid amplification tests (NAATs) are the primary means of 49 identifying acute infections caused by severe acute respiratory syndrome coronavirus 2 50 (SARS-CoV-2). Accurate and fast test results may permit more efficient use of protective and 51 isolation resources and allow for rapid therapeutic interventions. 52 Methods. We evaluated the analytical and clinical performance characteristics of the Xpert ® 53 Xpress SARS-CoV-2 (Xpert) test, a rapid, automated molecular test for SARS-CoV-2. 54 Analytical sensitivity and specificity/interference were assessed with infectious SARS-CoV-2, 55 other infectious coronavirus species including SARS-CoV, and 85 nasopharyngeal swab 56 specimens positive for other respiratory viruses including endemic human coronaviruses 57 (hCoVs). Clinical performance was assessed using 483 remnant upper and lower respiratory 58 specimens previously analyzed by standard of care (SOC) NAATs. 59 Results. The limit of detection of the Xpert test was 0.01 plaque forming units (PFU)/mL. 60 Other hCoVs, including Middle East Respiratory Syndrome coronavirus, were not detected by 61 the Xpert test. SARS-CoV, a closely related species in the Sarbecovirus subgenus, was 62 detected by a broad-range target (E) but was distinguished from SARS-CoV-2 (SARS-CoV-2-63 specific N2 target). Compared to SOC NAATs, the positive agreement of the Xpert test was 64 219/220 (99.5%) and the negative agreement was 250/261 (95.8%). A third tie-breaker 65 NAAT resolved all but three of the discordant results in favor the Xpert test. 66 Conclusions. The Xpert test provided sensitive and accurate detection of SARS-CoV-2 in a 67 variety of upper and lower respiratory tract specimens. The high sensitivity and fast time to 68 results of approximately 45 minutes may impact patient management. 69 70 Laboratory diagnosis of infections caused by severe acute respiratory syndrome coronavirus 2 72 (SARS-CoV-2) is usually accomplished by performing nucleic acid amplification tests 73 (NAATs) on respiratory tract specimens. An antibody response is often not detected in the 74 first week to ten days of symptoms and antibody testing is therefore generally unhelpful for 75 acute diagnosis(1-3), with virus isolation in culture presenting significant biosafety risks. 76 Upper respiratory tract (URT) specimens such as nasopharyngeal swabs (NPS) and 77 oropharyngeal swabs (OPS) generally have high SARS-CoV-2 viral loads upon symptom 78 onset.(2, 4-6) URT specimens may also have detectable RNA during the pre-symptomatic 79 period(7), and pediatric patients who remain asymptomatic through the entire course of 80 on June 9, 2020 by guest http://jcm.asm.org/ Downloaded from 4 infection can persistently shed RNA in URT specimens for two weeks or longer.(4, 8) 81 Importantly, NPS may have higher viral loads than OPS.(6) Lower respiratory tract (LRT) 82 specimens including sputum(7, 9) and tracheal aspirates(10) (TA) are often positive for RNA 83 early in disease and remain positive longer than URT sources.(5) 84 NAATs are...

Carbapenem-resistant (CRE) represent a health threat, but effective control interventions remain unclear. Hospital wastewater sites are increasingly being highlighted as important potential reservoirs. We investigated a large carbapenemase (KPC)-producing outbreak and wider CRE incidence trends in the Central Manchester University Hospital NHS Foundation Trust (CMFT) (United Kingdom) over 8 years, to determine the impact of infection prevention and control measures. Bacteriology and patient administration data (2009 to 2017) were linked, and a subset of CMFT or regional hospital KPC-producing isolates ( = 268) were sequenced. Control interventions followed international guidelines and included cohorting, rectal screening ( = 184,539 screens), environmental sampling, enhanced cleaning, and ward closure and plumbing replacement. Segmented regression of time trends for CRE detections was used to evaluate the impact of interventions on CRE incidence. Genomic analysis ( = 268 isolates) identified the spread of a KPC-producing outbreak clone (strain A, sequence type 216 [ST216]; = 125) among patients and in the environment, particularly on 2 cardiac wards (wards 3 and 4), despite control measures. ST216 strain A had caused an antecedent outbreak and shared its KPC plasmids with other lineages and species. CRE acquisition incidence declined after closure of wards 3 and 4 and plumbing replacement, suggesting an environmental contribution. However, ward 3/ward 4 wastewater sites were rapidly recolonized with CRE and patient CRE acquisitions recurred, albeit at lower rates. Patient relocation and plumbing replacement were associated with control of a clonal KPC-producing outbreak; however, environmental contamination with CRE and patient CRE acquisitions recurred rapidly following this intervention. The large numbers of cases and the persistence of in, including pathogenic lineages, are of concern.

Rapid identification of patients who are colonized with carbapenemase-producing organisms (CPO) is included in multiple national guidelines for containment of these organisms. In a multisite study, we evaluated the performance of the Cepheid Xpert Carba-R assay, a qualitative diagnostic test that was designed for the rapid detection and differentiation of the blaKPC, blaNDM, blaVIM, blaOXA-48, and blaIMP-1 genes from rectal swab specimens. A double rectal swab set was collected from 383 patients admitted at four institutions (2 in the United States, 1 in the United Kingdom, 1 in Spain). One swab was used for reference culture (MacConkey broth containing 1 mg/liter of meropenem and subcultured to a MacConkey agar plate with a 10-μg meropenem disk) and for sequencing of DNA obtained from carbapenem-nonsusceptible isolates for carbapenemase identification. The other swab was used for the Xpert Carba-R assay. In addition to the clinical rectal swabs, 250 contrived specimens (108 well-characterized CPO and 142 negative controls spiked onto negative rectal swabs) were tested. Overall, 149/633 (23.5%) samples were positive by the Xpert Carba-R assay. In 6 samples, multiple targets were detected (4 VIM/OXA-48, 1 IMP-1/NDM, and 1 NDM/KPC). The Xpert Carba-R assay detected 155 targets (26 IMP-1, 30 VIM, 27 NDM, 33 KPC, 39 OXA-48) within a time range of 32 to 48 min. The sensitivity, specificity, and positive and negative predictive values of the Xpert Carba-R assay compared to those of the reference culture and sequencing results were 96.6% (95% confidence interval [CI], 92.2% to 98.9%), 98.6% (95% CI, 97.1% to 99.4%), 95.3%, and 99.0%, respectively. The Cepheid Xpert Carba-R assay is an accurate and rapid test to identify rectal colonization with CPO, which can guide infection control programs to limit the spread of these organisms.

Conclusion: Slow drainage rates and sink designs with the drain directly underneath the tap increase the risk of CRE present in waste traps and drains contaminating the ward environment.

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