Rapid Diagnostic Testing for Response to the Monkeypox Outbreak - Laboratory Response Network, United States, May 17-June 30, 2022.

As part of public health preparedness for infectious disease threats, CDC collaborates with other U.S. public health officials to ensure that the Laboratory Response Network (LRN) has diagnostic tools to detect Orthopoxviruses, the genus that includes Variola virus, the causative agent of smallpox. LRN is a network of state and local public health, federal, U.S. Department of Defense (DOD), veterinary, food, and environmental testing laboratories. CDC developed, and the Food and Drug Administration (FDA) granted 510(k) clearance* for the Non-variola Orthopoxvirus Real-time PCR Primer and Probe Set (non-variola Orthopoxvirus [NVO] assay), a polymerase chain reaction (PCR) diagnostic test to detect NVO. On May 17, 2022, CDC was contacted by the Massachusetts Department of Public Health (DPH) regarding a suspected case of monkeypox, a disease caused by the Orthopoxvirus Monkeypox virus. Specimens were collected and tested by the Massachusetts DPH public health laboratory with LRN testing capability using the NVO assay. Nationwide, 68 LRN laboratories had capacity to test approximately 8,000 NVO tests per week during June. During May 17-June 30, LRN laboratories tested 2,009 specimens from suspected monkeypox cases. Among those, 730 (36.3%) specimens from 395 patients were positive for NVO. NVO-positive specimens from 159 persons were confirmed by CDC to be monkeypox; final characterization is pending for 236. Prompt identification of persons with infection allowed rapid response to the outbreak, including isolation and treatment of patients, administration of vaccines, and other public health action. To further facilitate access to testing and increase convenience for providers and patients by using existing provider-laboratory relationships, CDC and LRN are supporting five large commercial laboratories with a national footprint (Aegis Science, LabCorp, Mayo Clinic Laboratories, Quest Diagnostics, and Sonic Healthcare) to establish NVO testing capacity of 10,000 specimens per week per laboratory. On July 6, 2022, the first commercial laboratory began accepting specimens for NVO testing based on clinician orders.

Genotyping and Subtyping Cryptosporidium To Identify Risk Factors and Transmission Patterns - Nebraska, 2015-2017.

Cryptosporidium is an enteric pathogen that is transmitted through animal-to-person or person-to-person contact or through ingestion of contaminated water or food. In the United States, Cryptosporidium affects an estimated 750,000 persons each year; however, only approximately 11,000 cases are reported nationally (1,2). Persons infected with Cryptosporidium typically develop symptoms within 2 to 10 days after exposure. Common symptoms include watery diarrhea, abdominal cramps, nausea, vomiting, or fever, which can last 1 to 2 weeks. Cryptosporidiosis is a nationally notifiable disease in the United States. Nebraska presents a unique setting for the evaluation of this pathogen because, compared with other states, Nebraska has a greater reliance on agriculture and a higher proportion of the population residing and working in rural communities. Cryptosporidium species and subtypes are generally indistinguishable using conventional diagnostic methods. Using molecular characterization, Nebraska evaluated the genetic diversity of Cryptosporidium and found a dichotomy in the distribution of cases of cryptosporidiosis caused by Cryptosporidium parvum and Cryptosporidium hominis among rural and urban settings. Characterizing clusters of C. hominis cases revealed that several child care facilities were affected by the same subtype, suggesting community-wide transmission and indicating a need for effective exclusion policies. Several cases of cryptosporidiosis caused by non-C. parvum or non-C. hominis species and genotypes indicated unique animal exposures that were previously unidentified. This study enhanced epidemiologic data by validating known Cryptosporidium sources, confirming outbreaks, and, through repeat interviews, providing additional information to inform cryptosporidiosis prevention and control efforts.

A Public Health Laboratory Information System in Support of Health Emergencies: The Nebraska Public Health Laboratory COVID-19 Experience.

OBJECTIVES: Public health laboratories (PHLs) are essential components of US Public Health Service operations. The health information technology that supports PHLs is central to effective and efficient laboratory operations and overall public health response to infectious disease management. This analysis presents key information on how the Nebraska Public Health Laboratory (NPHL) information technology system evolved to meet the demands of the COVID-19 pandemic. MATERIALS AND METHODS: COVID-19 presented numerous, unforeseen information technology system challenges. The most notable challenges requiring changes to NPHL software systems and capability were improving efficiency of the laboratory operation due to high-volume testing, responding daily to demands for timely data for analysis by partner systems, interfacing with multiple testing (equipment) platforms, and supporting community-based specimen collection programs. RESULTS: Improvements to the NPHL information technology system enabled NPHL to perform >121 000 SARS-CoV-2 polymerase chain reaction tests from March 2020 through January 2022 at a sustainable rate of 2000 SARS-CoV-2 tests per day, with no increase in laboratory staffing. Electronic reporting of 62 000 rapid antigen tests eliminated paper reporting and extended testing services throughout the state. Collection of COVID-19 symptom data before specimen collection enabled NPHL to make data-driven decisions to perform pool testing and conserve testing kits when supplies were low. PRACTICE IMPLICATIONS: NPHL information technology applications proved essential for managing health care provider workload, prioritizing the use of scarce testing supplies, and managing Nebraska's overall pandemic response. The NPHL experience provides useful examples of a highly capable information technology system and suggests areas for additional attention in the PHL environment, including a focus on end users, collaboration with various partners, and investment in information technology.

Fatal Primary Amebic Meningoencephalitis in Nebraska: Case Report and Environmental Investigation, August 2022.

Primary amebic meningoencephalitis (PAM) is a rare and lethal infection caused by Naegleria fowleri. We report an epidemiological and environmental investigation relating to a case of PAM in a previously healthy boy age 8 years. An interview of the patient's family was conducted to determine the likely exposure site and to assess risk factors. Data from the United States Geological Survey site at Waterloo, NE, on the Elkhorn River were used to estimate water temperature and streamflow at the time and site of exposure. Data from the National Weather Service were used to estimate precipitation and ambient air temperature at the time and site of exposure. Despite conventional treatment, the patient died 2 days after hospital admission. The patient participated in recreational water activities in the Elkhorn River in northeastern Nebraska 5 days before symptom onset. In the week before exposure, water and ambient air high temperatures reached annual highs, averaging 32.4°C and 35.8°C, respectively. The day before infection, 2.2 cm of precipitation was reported. Streamflow was low (407 ft3/s). Infections in several northern states, including Nebraska, suggest an expanding geographic range of N. fowleri transmission, which may lead to increased incidence of PAM in the United States. Similar environmental investigations at suspected exposure sites of future cases will allow data aggregation, enabling investigators to correlate environmental factors with infection risk accurately.

Probable vertical transmission of Alpha variant of concern (B.1.1.7) with evidence of SARS-CoV-2 infection in the syncytiotrophoblast, a case report.

Introduction: Definitive vertical transmission of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) infection has been rarely reported. We present a case of a third trimester pregnancy with fetal distress necessitating cesarean section that demonstrated maternal, placental, and infant infection with the SARS-CoV-2 Alpha variant/B.1.1.7. Methods: CDC's Influenza SARS-CoV-2 Multiplex RT-PCR Assay was used to test for SARS-CoV-2 in a maternal NP swab, maternal plasma, infant NP swab, and formalin-fixed paraffin-embedded (FFPE) placental tissue specimens. Whole genome sequencing (WGS) was performed on maternal plasma, infant, and placental specimens to determine the SARS-CoV-2 genotype. Histopathological evaluation, SARS-CoV-2 immunohistochemistry testing (IHC), and electron microscopy (EM) analysis were performed on placenta, umbilical cord, and membrane FFPE blocks. Results: All specimens tested positive for SARS-CoV-2 by RT-PCR. WGS further revealed identical SARS-CoV-2 sequences from clade 20I/501Y.V1 (lineage Alpha/B.1.1.7) in maternal plasma, infant, and placental specimens. Histopathologic evaluation of the placenta showed histiocytic and neutrophilic intervillositis with fibrin deposition and trophoblast necrosis with positive SARS-CoV-2 immunostaining in the syncytiotrophoblast and electron microscopy evidence of coronavirus. Discussion: These findings suggest vertical transmission of SARS-CoV-2, supported by clinical course timing, identical SARS-CoV-2 genotypes from maternal, placental, and infant samples, and IHC and EM evidence of placental infection. However, determination of the timing or distinction between prepartum and peripartum SARS-CoV-2 transmission remains unclear.

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.

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%.

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%.

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.

Genome Sequences of Multidrug-Resistant Salmonella enterica Serovar Dublin Isolates.

Salmonella enterica serovar Dublin, which can cause enteritis and systemic infections in humans, has been associated with antimicrobial resistance. Here, we report draft genome sequences of seven multidrug-resistant S Dublin isolates from human samples. These sequences will contribute to an understanding of pathogenesis and resistance determinants in this serovar.

Whole genome sequencing to characterize shiga toxin-producing Escherichia coli O26 in a public health setting.

BACKGROUND: Shiga-toxin producing Escherichia coli (STEC) O26:H11 is the second most common cause of severe diarrhea and hemolytic uremic syndrome worldwide. The implementation of whole genome sequencing (WGS) enhances the detection and in-depth characterization of these non-O157 STEC strains. The aim of this study was to compare WGS to phenotypic serotyping and pulse field gel electrophoresis (PFGE) for characterization of STECO26 strains following a zoonotic outbreak from cattle to humans. METHODS AND RESULTS: This study evaluated seven E. coli strains; two strains isolated from two children with gastrointestinal symptoms and five strains from five calves suspected as the source of infection. Six of these isolates were serotyped phenotypically and by WGS as E. coli O26:H11 while one bovine isolate could be serotyped only by WGS as E. coli O182:H25. Stx1 was detected in two human- and two bovine-isolates using PCR and WGS. Using WGS, all four STECO26 isolates belong to sequence type (ST) 21 while the two stx1 negative E. coli O26 were ST29. All four STECO26 isolates were indistinguishable by PFGE. However, the data generated by WGS linked the two human STECO26 isolates to only one bovine STECO26 strain by having identical high-quality single nucleotide polymorphisms (hqSNPs) and identical virulence factor profiles while the remaining bovine STECO26 isolate differed by 7 hqSNPs and lacked virulence factor toxB. CONCLUSIONS: These data demonstrated that WGS provided significant information beyond traditional epidemiological tools allowing for comprehensive characterization of the STEC. Using this approach, WGS was able to identify the specific source of infection in this study.

Genome Sequence of a Salmonella enterica subsp. enterica Serovar Corvallis Strain Isolated from Human Blood.

Salmonella enterica subsp. enterica serovar Corvallis is commonly reported in avian populations and avian by-products. We report the draft genome sequence of a multidrug-resistant S. Corvallis strain (NPHL 15376). To our knowledge, this is the first reported case of this serovar isolated from human blood in the United States.