Characteristics of nursing home residents and healthcare personnel with repeated severe acute respiratory coronavirus virus 2 (SARS-CoV-2) tests positive ≥90 days after initial infection: Four US jurisdictions, July 2020-March 2021.

One in six nursing home residents and staff with positive SARS-CoV-2 tests ≥90 days after initial infection had specimen cycle thresholds (Ct) <30. Individuals with specimen Ct<30 were more likely to report symptoms but were not different from individuals with high Ct value specimens by other clinical and testing data.

Outbreak of SARS-CoV-2 B.1.617.2 (Delta Variant) in a Youth Camp Associated With Community Spread, Nebraska, June-July 2021.

OBJECTIVES: During June-July 2021, an outbreak of SARS-CoV-2 occurred among attendees of a summer youth camp in Nebraska. We assessed the factors that contributed to onward transmission of disease. METHODS: The Four Corners Health Department conducted an outbreak investigation and recorded both laboratory-confirmed and self-reported cases of SARS-CoV-2 and mitigation measures employed. We generated sequences on positive specimens, created an epidemic curve to assist with outbreak visualization, and examined epidemiologic, genomic, and laboratory outcomes. RESULTS: Evaluation of 3 index cases led to the identification of 25 people with COVID-19 who interacted directly with the camp. Contact tracing revealed an additional 18 cases consistent with onward community transmission. Most (24 of 35, 68.5%) vaccine-eligible community cases were not vaccinated. We sequenced 8 positive specimens; all were identified as the Delta variant. Precamp planning incorporated local health officials who recommended wearing face masks, practicing social distancing, and using attendee cohorts to limit mixing of people involved in various activities. CONCLUSION: Low vaccination levels and poor face mask-wearing habits among attendees resulted in secondary and tertiary spread of SARS-CoV-2 and severe outcomes among young adults. This outbreak of COVID-19 at a youth camp highlights the importance of vaccination and use of other measures to interrupt opportunities for SARS-CoV-2 spread in the community and shows that vaccinated people remain vulnerable to infection when in an environment of high exposure to SARS-CoV-2. Proactive case identification and interruption of chains of transmission can help decrease the number of cases and avoid further severe outcomes.

Nosocomial outbreak of SARS-CoV-2 delta variant among vaccinated healthcare workers and immunocompromised patients on a solid-organ transplant unit: Complexities of an epidemiologic and genomic investigation.

In September 2021, a cluster of 6 patients with nosocomial coronavirus disease 2019 (COVID-19) were identified in a transplant unit. A visitor and 11 healthcare workers also tested positive for severe acute respiratory coronavirus virus 2 (SARS-CoV-2). Genomic sequencing identified 3 separate introductions of SARS-CoV-2 with related transmission among the identified patients and healthcare workers.

Investigation of a SARS-CoV-2 B.1.1.529 (Omicron) Variant Cluster - Nebraska, November-December 2021.

The B.1.1.529 (Omicron) variant of SARS-CoV-2 (the virus that causes COVID-19) was first detected in specimens collected on November 11, 2021, in Botswana and on November 14 in South Africa;* the first confirmed case of Omicron in the United States was identified in California on December 1, 2021 (1). On November 29, the Nebraska Department of Health and Human Services was notified of six probable cases† of COVID-19 in one household, including one case in a man aged 48 years (the index patient) who had recently returned from Nigeria. Given the patient's travel history, Omicron infection was suspected. Specimens from all six persons in the household tested positive for SARS-CoV-2 by reverse transcription-polymerase chain reaction (RT-PCR) testing on December 1, and the following day genomic sequencing by the Nebraska Public Health Laboratory identified an identical Omicron genotype from each specimen (Figure). Phylogenetic analysis was conducted to determine if this cluster represented an independent introduction of Omicron into the United States, and a detailed epidemiologic investigation was conducted. This activity was reviewed by CDC and was conducted consistent with applicable federal law and CDC policy.§.

Whole-Genome Sequences of Staphylococcus aureus Isolates from Positive Blood Cultures.

Staphylococcus aureus is a major cause of skin and soft tissue infections as well as bloodstream infections worldwide. Here, we report the draft genome sequences of 18 deidentified S. aureus clinical strains collected from positive blood cultures.

Diagnostic deficiencies of C. difficile infection among patients in a tertiary hospital in Saudi Arabia: A laboratory-based case series.

Clostridioides difficile infection (CDI) has become a threatening public health problem in the developed world. In the kingdom of Saudi Arabia, prevalence of CDI is still unknown due to limited surveillance protocols and diagnostic resources. We used a two-step procedure to study and confirm C. difficile cases. We also studied toxin profiles of these isolates. Stool samples were collected from symptomatic patients and clinically suspected of CDI for almost 12 months. Isolates were confirmed by culture method followed by 16S rRNA sequencing. Multiplex PCR was performed for the identification of toxin A, toxin B and binary toxin genes and compared to Gene Expert results. Out of the 47 collected samples, 27 were successfully grown on culture media. 18 samples were confirmed as C. difficile by both culture and 16S rRNA sequencing. Interestingly, the rest of the isolates (9 species) belonged to different genera. Our results showed 95% of samples were positive for both toxin A and B (tcdA, tcdB) and all samples exhibited the toxin gene regulator tcdC. All samples were confirmed negative for the binary toxin gene ctdB and 11% of the isolates were positive for ctdA gene. Interestingly, one isolate harbored the binary toxin gene (cdtA +) and tested negative for both toxins A and B. We believe that combining the standard culture method with molecular techniques can make the detection of C. difficile more accurate.

Genotypic Characterization of Multidrug-Resistant Pseudomonas aeruginosa Using Whole-Genome Sequencing.

Multidrug-resistant Pseudomonas aeruginosa is a serious threat worldwide causing health care-acquired infections and is associated with significant morbidity and mortality. This report describes the draft genome sequences of five multidrug-resistant Pseudomonas aeruginosa strains isolated from human infections.

Identification of an mcr-9-Carrying Salmonella enterica Serotype Heidelberg Strain Isolated from Blood.

Salmonella enterica, represented by a large number of serotypes, can cause a broad variety of diseases that range from mild gastroenteritis to severe systemic infections. This report provides a draft genome sequence of an mcr-9-carrying Salmonella enterica serotype Heidelberg strain isolated from blood.

mCIM test as a reliable assay for the detection of CRE in the Gulf region.

Introduction. Carbapenem resistant Enterobacterales (CRE) are one of the leading causes of systemic and nosocomial infections and are multidrug-resistant organisms producing different carbapenemases. There are many genotypic and phenotypic methods for detecting the carbapenemases; however, there is a limitation for each. Modified carbapenem inactivation method (mCIM) assay is a recent phenotypic method which has been published by the Clinical and Laboratory Standards Institute.Hypothesis / Gap Statement. mCIM assay could provide a reliable method for the detection of carbapenemases in CRE.Aim. Evaluation of the mCIM assay performance for the detection of carbapenemases in Enterobacterales and the identification of the common carbapenemase genes at Eastern Province of Saudi Arabia and Kingdom of Bahrain.Methodology. A collection of 197 non-duplicate carbapenem resistant Enterobacterales clinical isolates, were evaluated with the mCIM test comparing its performance to multiplex PCR. The minimum inhibitory concentration susceptibility testing was done by the Etest method for imipenem, meropenem, and ertapenem.Results. The sensitivity of the mCIM assay was 94 % (95 % CI, (89.3-97.1)). In Saudi Arabia and Bahrain, OXA-48 was the most prevalent carbapenemase gene followed by NDM. Coexistence of multiple carbapenemase genes is reported in eleven cases.Conclusion. These findings indicate that the mCIM test is a reliable and simple assay for detecting the activity of carbapenemase in Enterobacterales, especially in resource-limited laboratories.

Characterization of Carbapenem-Resistant Acinetobacter baumannii Isolates from Clinical Specimens.

Carbapenem-resistant Acinetobacter baumannii is an urgent threat worldwide. This bacterium is associated with high morbidity and mortality, with limited available treatment options. Here, we report the draft genome sequences of five carbapenem-resistant Acinetobacter baumannii isolates from human samples.

Differences in Blood-derived Francisella tularensis Type B Strains from Clinical Cases of Tularemia.

Francisella tularensis can cause the zoonotic disease tularemia and is partitioned into subspecies due to differences in chromosomal organization and virulence. The subspecies holarctica (type B) is generally considered more clonal than the other subpopulations with moderate virulence compared to the hypervirulent A.I clade. We performed whole genome sequencing (WGS) on six type B strains isolated from the blood of patients with tularemia within a one-year period from the same United States region, to better understand the associated pathogenicity. The WGS data were compared to the prototype strain for this subspecies, specifically FSC200, which was isolated from a patient with tularemia in Europe. These findings revealed 520-528 single nucleotide polymorphisms (SNPs) between the six United States type B strains compared to FSC200, with slightly higher A+T content in the latter strain. In contrast, comparisons between the six type B isolates showed that five of the six type B isolates had only 4-22 SNPs, while one of the strains had 47-53 SNPs. Analysis of SNPs in the core genome for the six United States type B isolates and the FSC200 strain gave similar results, suggesting that some of these mutations may have been nonsynonymous, resulting in altered protein function and pathogenicity.

Assessment of Specimen Pooling to Conserve SARS CoV-2 Testing Resources.

Objectives To establish the optimal parameters for group testing of pooled specimens for the detection of SARS-CoV-2. Methods The most efficient pool size was determined to be 5 specimens using a web-based application. From this analysis, 25 experimental pools were created using 50 microliter from one SARS-CoV-2 positive nasopharyngeal specimen mixed with 4 negative patient specimens (50 microliter each) for a total volume of 250 microliter l. Viral RNA was subsequently extracted from each pool and tested using the CDC SARS-CoV-2 RT-PCR assay. Positive pools were consequently split into individual specimens and tested by extraction and PCR. This method was also tested on an unselected group of 60 nasopharyngeal specimens grouped into 12-pools. Results All 25 pools were positive with Cycle threshold (Ct) values within 0 and 5.03 Ct of the original individual specimens. The analysis of 60 specimens determined that two pools were positive followed by identification of two individual specimens among the 60 tested. This testing was accomplished while using 22 extractions/PCR tests, a savings of 38 reactions. Conclusions When the incidence rate of SARS-CoV-2 infection is 10% or less, group testing will result in the saving of reagents and personnel time with an overall increase in testing capability of at least 69%.

Tests in short supply? Try group testing.

Christopher R. Bilder, Peter C. Iwen, Baha Abdalhamid, Joshua M. Tebbs and Christopher S. McMahan explain how, by pooling specimens, testing capacity for SARS-CoV-2 can be increased.

Assessment of Specimen Pooling to Conserve SARS CoV-2 Testing Resources.

OBJECTIVES: To establish the optimal parameters for group testing of pooled specimens for the detection of SARS-CoV-2. METHODS: The most efficient pool size was determined to be five specimens using a web-based application. From this analysis, 25 experimental pools were created using 50 µL from one SARS-CoV-2 positive nasopharyngeal specimen mixed with 4 negative patient specimens (50 µL each) for a total volume of 250 µL. Viral RNA was subsequently extracted from each pool and tested using the CDC SARS-CoV-2 RT-PCR assay. Positive pools were consequently split into individual specimens and tested by extraction and PCR. This method was also tested on an unselected group of 60 nasopharyngeal specimens grouped into 12 pools. RESULTS: All 25 pools were positive with cycle threshold (Ct) values within 0 and 5.03 Ct of the original individual specimens. The analysis of 60 specimens determined that 2 pools were positive followed by identification of 2 individual specimens among the 60 tested. This testing was accomplished while using 22 extractions/PCR tests, a savings of 38 reactions. CONCLUSIONS: When the incidence rate of SARS-CoV-2 infection is 10% or less, group testing will result in the saving of reagents and personnel time with an overall increase in testing capability of at least 69%.

Genome Sequences of Uncommon Shiga Toxin-Producing Escherichia coli Serotypes.

Shiga toxin-producing Escherichia coli (STEC) is a foodborne disease with worldwide outbreaks. STEC serotypes O157, O26, O45, O103, O111, O121, and O145 cause the most outbreaks. There is little published information regarding the other serotypes. We report the draft genome sequences for 11 uncommon STEC serotypes from Nebraska.