A s we enter the second quarter of the COVID-19 pandemic, with testing for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) increasingly available (though still limited and/or slow in some areas), we are faced with new questions and challenges regarding this novel virus. When to test? Whom to test? What to test? How often to test? And, what to do with test results? Since SARS-CoV-2 is a new virus, there is little evidence to fall back on for test utilization and diagnostic stewardship (1). Several points need to be considered to begin answering of these questions; specifically, what types of tests are available and under which circumstances are they useful? This understanding can help guide the use of testing at the local, regional, state, and national levels and inform those assessing the supply chain to ensure that needed testing is and continues to be available. Here, we explain the types of tests available and how they might be useful in the face of a rapidly changing and never-beforeexperienced situation. There are two broad categories of SARS-CoV-2 tests: those that detect the virus itself and those that detect the host's response to the virus. Each will be considered separately.We must recognize that we are dealing with (i) a new virus, (ii) an unprecedented pandemic in modern times, and (iii) uncharted territory. With this in mind, in the absence of either proven effective therapy or a vaccine, diagnostic testing, which we have, becomes an especially important tool, informing patient management and potentially helping to save lives by limiting the spread of SARS-CoV-2. What is the most appropriate test, and for whom and when?Hypothetically, if the entire world's population could be tested all at once, with a test providing 100% specificity and sensitivity (unrealistic, obviously), we might be able to identify all infected individuals and sort people into those who at that moment in time were asymptomatic, minimally/moderately symptomatic, and severely symptomatic. The asymptomatic and minimally/moderately symptomatic could be quarantined to avoid the spread of the virus, with the severely symptomatic managed and isolated in health care settings. Contract tracing could be carried out to find those at risk of being in the incubation period by virtue of their exposure. Alternatively, testing for a host response, if, again, the test were hypothetically 100% sensitive and specific, could identify those previously exposed to the virus and (if we knew this to be true, which we do not) label those who are immune to the virus, who could be tapped to work in

SUMMARYRespiratory viral infections are associated with a wide range of acute syndromes and infectious disease processes in children and adults worldwide. Many viruses are implicated in these infections, and these viruses are spread largely via respiratory means between humans but also occasionally from animals to humans. This article is an American Society for Microbiology (ASM)-sponsored Practical Guidance for Clinical Microbiology (PGCM) document identifying best practices for diagnosis and characterization of viruses that cause acute respiratory infections and replaces the most recent prior version of the ASM-sponsored Cumitech 21 document,Laboratory Diagnosis of Viral Respiratory Disease, published in 1986. The scope of the original document was quite broad, with an emphasis on clinical diagnosis of a wide variety of infectious agents and laboratory focus on antigen detection and viral culture. The new PGCM document is designed to be used by laboratorians in a wide variety of diagnostic and public health microbiology/virology laboratory settings worldwide. The article provides guidance to a rapidly changing field of diagnostics and outlines the epidemiology and clinical impact of acute respiratory viral infections, including preferred methods of specimen collection and current methods for diagnosis and characterization of viral pathogens causing acute respiratory tract infections. Compared to the case in 1986, molecular techniques are now the preferred diagnostic approaches for the detection of acute respiratory viruses, and they allow for automation, high-throughput workflows, and near-patient testing. These changes require quality assurance programs to prevent laboratory contamination as well as strong preanalytical screening approaches to utilize laboratory resources appropriately. Appropriate guidance from laboratorians to stakeholders will allow for appropriate specimen collection, as well as correct test ordering that will quickly identify highly transmissible emerging pathogens.

OBJECTIVE To determine the role of unit-based transmission that accounts for cases of early Clostridium difficile infection (CDI) during hospitalization for allogeneic stem cell transplant. SETTING Stem cell transplant unit at a tertiary care cancer center. METHODS Serially collected stool from patients admitted for transplant was screened for toxigenic C. difficile through the hospital stay and genotyping was performed by multilocus sequence typing. In addition, isolates retrieved from cases of CDI that occurred in other patients hospitalized on the same unit were similarly characterized. Transmission links were established by time-space clustering of cases and carriers of shared toxigenic C. difficile strains. RESULTS During the 27-month period, 1,099 samples from 264 patients were screened, 69 of which had evidence of toxigenic C. difficile; 52 patients developed CDI and 17 were nonsymptomatic carriers. For the 52 cases, 41 had evidence of toxigenic C. difficile on the first study sample obtained within a week of admission, among which 22 were positive within the first 48 hours. A total of 24 sequence types were isolated from this group; 1 patient had infection with the NAP1 strain. A total of 11 patients had microbiologic evidence of acquisition; donor source could be established in half of these cases. CONCLUSIONS Most cases of CDI after stem cell transplant represent delayed onset disease in nonsymptomatic carriers. Transmission on stem cell transplant unit was confirmed in 19% of early CDI cases in our cohort with a probable donor source established in half of the cases.

The study was undertaken to determine if microsatellite instability (MSI) status influences the composition of the tumor microbiome in primary colon carcinoma. 426 unique primary, stage I-III colon biopsy or resection specimens (234 right-sided, 192 left-sided) were sequenced by MSK-IMPACT, a large panel next generation sequencing (NGS) assay. MSI status [150 MSI-H; 276 microsatellite stable (MSS)] was determined using the MSISensor algorithm, which is clinically validated to detect MSI status from NGS data. We have developed a technique for identifying the presence of microbial species in tumor tissue being tested with NGS by analysis of non-human DNA read sequences. The method has been validated and determined to have comparable accuracy to reference microbial tests for both viruses and bacteria. We identified 13 bacterial species that are enriched in MSI-H colon carcinoma compared to MSS (odds ratio, 95% confidence interval greater than 1 with Bonferonni adjustment) (Table 1). We also observed that MSI-H is more common in right-sided tumors compared to left-sided tumors (53% vs. 13%, p=1.0E-4). To understand if sidedness of the tumor was a significant confounder, we performed stratified analysis of bacteria enrichment for right and left sided colon carcinoma. 8 of the 13 species remained significantly enriched in MSI-H tumors independent of sidedness; 9 of 13 in right-sided tumors; and 12 of 13 in left-sided tumors. Non-significant confidence intervals are underlined in Table 1. While Fusobacterium nucleatum has previously been reported to be enriched in MSI-H colon cancer, the broader spectrum of species enriched in MSI-H colon carcinoma we observed in our study has not been reported. The different microbiome suggests that either these bacteria play a role in development of MSI-H tumors or a unique immune environment exists in MSI-H tumors. The relationship between this unique microbiome and MSI status is the focus of further investigation. Table 1:Bacteria enriched in MSI-H colon cancerMSI-HMSI-HMSI-HMSSMSSMSSBacteria speciesLocationPositiveNegativeTotalPositiveNegativeTotalOdds ratioBonferroni adjusted 95% confidence intervalFusobacterium nucleatumTotal/right/left54/44/1096/81/15150/125/2538/20/18238/89/149276/109/1673.5/2.4/5.5(1.6-7.7)/(1.3-4.4)/(2.2-14.1)Bacteroides fragilisTotal/right/left47/35/12103/90/13150/125/2537/16/21239/93/146276/109/1672.9/2.3/6.4(1.3-6.5)/(1.2-4.4)/(2.6-15.9)Prevotella intermediaTotal/right/left27/22/5123/103/20150/125/2514/10/4262/99/163276/109/1674.1/2.1/10.2(1.4-12.5)/(1.01-4.7)/(2.5-41.1)Prevotella melaninogenicaTotal/right/left20/18/2130/107/23150/125/256/3/3270/106/164276/109/1676.9/5.9/4.8(1.5-31.9)/(1.7-20.8)/(0.8-30.0)Odoribacter splanchnicusTotal/right/left26/20/6124/105/19150/125/2513/5/8263/104/159276/109/1674.2/4.0/6.3(1.4-13.3)/(1.4-11.0)/(2.0-20.0)Selenomonas sputigenaTotal/right/left33/31/2117/94/23150/125/2522/15/7254/94/160276/109/1673.3/2.1/2.0(1.3-8.4)/(1.04-4.1)/(0.4-10.2)Bacteroides xylanisolvensTotal/right/left32/25/7118/100/18150/125/2521/8/13255/101/154276/109/1673.3/3.2/4.6(1.3-8.6)/(1.4-7.3)/(1.6-13.0)Prevotella denticolaTotal/right/left20/16/4130/109/21150/125/259/3/6267/106/161276/109/1674.6/5.2/5.1(1.2-17.2)/(1.5-18.3)/(1.3-19.6)Leptotrichia buccalisTotal/right/left17/13/4133/112/21150/125/256/5/1270/104/166276/109/1675.8/2.4/31.6(1.2-27.2)/(0.8-7.0)/(3.4-296.4)Prevotella sp. oral taxon 299Total/right/left14/12/2136/113/23150/125/252/1/1274/108/166276/109/16714.1/11.5/14.4(1.2-161.7)/(1.5-89.7)/(1.3-165.6)Porphyromonas gingivalisTotal/right/left13/10/3137/115/22150/125/252/0/2274/109/165276/109/16713.0/19.9/11.3(1.1-150.8)/(1.1-343.0)/(1.8-71.1)Streptococcus anginosusTotal/right/left19/16/3131/109/22150/125/2510/4/6266/105/161276/109/1673.9/3.9/3.7(1.1-14.1)/(1.2-11.9)/(0.9-15.7)Fretibacterium fastidiosumTotal/right/left15/13/2135/112/23150/125/256/3/3270/106/164276/109/1675.0/4.1/4.8(1.03-24.3)/(1.1-14.8)/(0.8-30.0) Citation Format: Chad Michael Vanderbilt, Ajaratu Keshinro, Chin-Tung Chen, Esther Babady, Michael F. Berger, Ahmet Zehir, Marc Ladanyi, Jaclyn F. Hechtman, Zsofia K. Stadler, Jinru Shia, Martin R. Weiser. Unique tumor microbiome in microsatellite instability high (MSI-H) colon carcinoma [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 6095.

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