Disclaimer: Early release articles are not considered as final versions. Any changes will be reflected in the online version in the month the article is officially released.
Volume 26, Number 11—November 2020
The Problem of Microbial Dark Matter in Neonatal Sepsis
Neonatal sepsis (NS) kills 750,000 infants every year. Effectively treating NS requires timely diagnosis and antimicrobial therapy matched to the causative pathogens, but most blood cultures for suspected NS do not recover a causative pathogen. We refer to these suspected but unidentified pathogens as microbial dark matter. Given these low culture recovery rates, many non–culture-based technologies are being explored to diagnose NS, including PCR, 16S amplicon sequencing, and whole metagenomic sequencing. However, few of these newer technologies are scalable or sustainable globally. To reduce worldwide deaths from NS, one possibility may be performing population-wide pathogen discovery. Because pathogen transmission patterns can vary across space and time, computational models can be built to predict the pathogens responsible for NS by region and season. This approach could help to optimally treat patients, decreasing deaths from NS and increasing antimicrobial stewardship until effective diagnostics that are scalable become available globally.
Two Pandemics, One Challenge—Leveraging Molecular Test Capacity of Tuberculosis Laboratories for Rapid COVID-19 Case-Finding
In many settings, the ongoing coronavirus disease (COVID-19) pandemic coincides with other major public health threats, in particular tuberculosis. Using tuberculosis (TB) molecular diagnostic infrastructure, which has substantially expanded worldwide in recent years, for COVID-19 case-finding might be warranted. We analyze the potential of using TB diagnostic and research infrastructures for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) testing. We focused on quality control by adapting the 12 Quality System Essentials framework to the COVID-19 and TB context. We conclude that diagnostic infrastructures for TB can in principle be leveraged to scale-up SARS-CoV-2 testing, in particular in resource-poor settings. TB research infrastructures also can support sequencing of SARS-CoV-2 to study virus evolution and diversity globally. However, fundamental principles of quality management must be followed for both TB and SARS-CoV-2 testing to ensure valid results and to minimize biosafety hazards, and the continuity of TB diagnostic services must be guaranteed at all times.
Measuring Timeliness of Outbreak Response in the World Health Organization African Region, 2017–2019
Large-scale protracted outbreaks can be prevented through early detection, notification, and rapid control. We assessed trends in timeliness of detecting and responding to outbreaks in the African Region reported to the World Health Organization during 2017–2019. We computed the median time to each outbreak milestone and assessed the rates of change over time using univariable and multivariable Cox proportional hazard regression analyses. We selected 296 outbreaks from 348 public reported health events and evaluated 184 for time to detection, 232 for time to notification, and 201 for time to end. Time to detection and end decreased over time, whereas time to notification increased. Multiple factors can account for these findings, including scaling up support to member states after the World Health Organization established its Health Emergencies Programme and support given to countries from donors and partners to strengthen their core capacities for meeting International Health Regulations.
Challenges to Achieving Measles Elimination, Georgia, 2013–2018
Controlling measles outbreaks in the country of Georgia and throughout Europe is crucial for achieving the measles elimination goal for the World Health Organization’s European Region. However, large-scale measles outbreaks occurred in Georgia during 2013–2015 and 2017–2018. The epidemiology of these outbreaks indicates widespread circulation and genetic diversity of measles viruses and reveals persistent gaps in population immunity across a wide age range that have not been sufficiently addressed thus far. Historic problems and recent challenges with the immunization program contributed to outbreaks. Addressing population susceptibility across all age groups is needed urgently. However, conducting large-scale mass immunization campaigns under the current health system is not feasible, so more selective response strategies are being implemented. Lessons from the measles outbreaks in Georgia could be useful for other countries that have immunization programs facing challenges related to health-system transitions and the presence of age cohorts with historically low immunization coverage.
Three Patients with COVID-19 and Pulmonary Tuberculosis, Wuhan, China, January–February 2020
During January–February 2020, coronavirus disease (COVID-19) and tuberculosis were diagnosed for 3 patients in Wuhan, China. All 3 patients had COVID-19 pneumonia. One severely ill patient died after acute respiratory distress syndrome developed. Clinicians and public health officials should be aware of underlying chronic infections such as tuberculosis in COVID-19 patients.
Validated Methods for Removing Select Agent Samples from Biosafety Level 3 Laboratories
The Federal Select Agent Program dictates that all research entities in the United States must rigorously assess laboratory protocols to sterilize samples being removed from containment areas. We validated procedures using sterile filtration and methanol to remove the following select agents: Francisella tularensis, Burkholderia pseudomallei, B. mallei, Yersinia pestis, and Bacillus anthracis. We validated methanol treatment for B. pseudomallei. These validations reaffirm safety protocols that enable researchers to keep samples sufficiently intact when samples are transferred between laboratories.
Epidemiology of COVID-19 Outbreak on Cruise Ship Quarantined at Yokohama, Japan, February 2020
To improve understanding of coronavirus disease (COVID-19), we assessed the epidemiology of an outbreak on a cruise ship, February 5–24, 2020. The study population included persons on board on February 3 (2,666 passengers, 1,045 crew). Passengers had a mean age of 66.1 years and were 55% female; crew had a mean age of 36.6 years and were 81% male. Of passengers, 544 (20.4%) were infected, 314 (57.7%) asymptomatic. Attack rates were highest in 4-person cabins (30.0%; n = 18). Of crew, 143 (13.7%) were infected, 64 (44.8%) asymptomatic. Passenger cases peaked February 7, and 35 had onset before quarantine. Crew cases peaked on February 11 and 13. The median serial interval between cases in the same cabin was 2 days. This study shows that severe acute respiratory syndrome coronavirus 2 is infectious in closed settings, that subclinical infection is common, and that close contact is key for transmission.
High Dengue Burden and Circulation of 4 Virus Serotypes among Children with Undifferentiated Fever, Kenya, 2014–2017
Little is known about the extent and serotypes of dengue viruses circulating in Africa. We evaluated the presence of dengue viremia during 4 years of surveillance (2014–2017) among children with febrile illness in Kenya. Acutely ill febrile children were recruited from 4 clinical sites in western and coastal Kenya, and 1,022 participant samples were tested by using a highly sensitive real-time reverse transcription PCR. A complete case analysis with genomic sequencing and phylogenetic analyses was conducted to characterize the presence of dengue viremia among participants during 2014–2017. Dengue viremia was detected in 41.9% (361/862) of outpatient children who had undifferentiated febrile illness in Kenya. Of children with confirmed dengue viremia, 51.5% (150/291) had malaria parasitemia. All 4 dengue virus serotypes were detected, and phylogenetic analyses showed several viruses from novel lineages. Our results suggests high levels of dengue virus infection among children with undifferentiated febrile illness in Kenya.
Systematic Review and Meta-Analyses of Incidence for Group B Streptococcus Disease in Infants and Antimicrobial Resistance, China
We performed a systematic review and meta-analysis of the incidence, case-fatality rate (CFR), isolate antimicrobial resistance patterns, and serotype and sequence type distributions for invasive group B Streptococcus (GBS) disease in infants <1–89 days of age in China. We searched the PubMed/Medline, Embase, Wanfang, and China National Knowledge Infrastructure databases for research published during January 1, 2000–March 16, 2018, and identified 64 studies. Quality of included studies was assessed by using Cochrane tools. Incidence and CFR were estimated by using random-effects meta-analyses. Overall incidence was 0.55 (95% CI 0.35–0.74) cases/1,000 live births, and the CFR was 5% (95% CI 3%–6%). Incidence of GBS in young infants in China was higher than the estimated global incidence (0.49 cases/1,000 live births) and higher than previous estimates for Asia (0.3 cases/1,000 live births). Our findings suggest that implementation of additional GBS prevention efforts in China, including maternal vaccination, could be beneficial.
Analysis of SARS-CoV-2 Transmission in Different Settings, Brunei
We report the transmission dynamics of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) across different settings in Brunei. An initial cluster of SARS-CoV-2 cases arose from 19 persons who had attended the Tablighi Jama’at gathering in Malaysia, resulting in 52 locally transmitted cases. The highest nonprimary attack rates (14.8%) were observed from a subsequent religious gathering in Brunei and in households of attendees (10.6%). Household attack rates from symptomatic case-patients were higher (14.4%) than from asymptomatic (4.4%) or presymptomatic (6.1%) case-patients. Workplace and social settings had attack rates of <1%. Our analyses highlight that transmission of SARS-CoV-2 varies depending on environmental, behavioral, and host factors. We identify red flags for potential superspreading events, specifically densely populated gatherings with prolonged exposure in enclosed settings, persons with recent travel history to areas with active SARS-CoV-2 infections, and group behaviors. We propose differentiated testing strategies to account for differing transmission risk.
Modeling Treatment Strategies to Inform Yaws Eradication
Yaws is a neglected tropical disease targeted for eradication by 2030. To achieve eradication, finding and treating asymptomatic infections as well as clinical cases is crucial. The proposed plan, the Morges strategy, involves rounds of total community treatment (i.e., treating the whole population) and total targeted treatment (TTT) (i.e., treating clinical cases and contacts). However, modeling and empirical work suggests asymptomatic infections often are not found in the same households as clinical cases, reducing the utility of household-based contact tracing for a TTT strategy. We use a model fitted to data from the Solomon Islands to predict the likelihood of elimination of transmission under different intervention schemes and levels of systematic nontreatment resulting from the intervention. Our results indicate that implementing additional treatment rounds through total community treatment is more effective than conducting additional rounds of treatment of at-risk persons through TTT.
Streptococcus pneumoniae Serotype 12F-CC4846 and Invasive Pneumococcal Disease after Introduction of 13-Valent Pneumococcal Conjugate Vaccine, Japan, 2015–2017
To prevent invasive pneumococcal disease (IPD), pneumococcal conjugate vaccines (PCVs) have been implemented in many countries; however, many cases of IPD still occur and can be attributable to nonvaccine serotypes of Streptococcus pneumoniae. In Japan, the number of IPD cases attributable to serotype 12F increased from 4.4% in 2015 to 24.6% in 2017 after 13-valent PCV was introduced. To clarify the associated genetic characteristics, we conducted whole-genome sequencing of 75 serotype 12F isolates. We identified 2 sequence types (STs) among the isolates: ST4846, which was the major type, and ST6945. Bayesian analysis suggested that these types diverged in »1942. Among serotype 12F-ST4846, we identified a major cluster, PC-JP12F, whose time of most recent common ancestor was estimated to be »2012. A phylogeographic analysis demonstrated that PC-JP12F isolates spread from the Kanto region, the most populated region in Japan, to other local regions.
Azithromycin to Prevent Pertussis in Household Contacts, Catalonia and Navarre, Spain, 2012–2013
We retrospectively assessed the effectiveness of azithromycin in preventing transmission of pertussis to a patient’s household contacts. We also considered the duration between symptom onset in the primary patient and azithromycin administration. We categorized contacts into 4 groups: those treated within <7 days, 8–14 days, 15–21 days, and >21 days after illness onset in the primary patient. We studied 476 primary index patients and their 1,975 household contacts, of whom 4.5% were later identified as having pertussis. When contacts started chemoprophylaxis within <21 days after the primary patient’s symptom onset, the treatment was 43.9% effective. Chemoprophylaxis started >14 days after primary patient’s symptom onset was less effective. We recommend that contacts of persons with pertussis begin chemoprophylaxis within <14 days after primary patient’s symptom onset.
Case-Control Study of Use of Personal Protective Measures and Risk for SARS-CoV 2 Infection, Thailand
We evaluated effectiveness of personal protective measures against severe acute respiratory disease coronavirus 2 (SARS-CoV-2) infection. Our case-control study included 211 cases of coronavirus disease (COVID-19) and 839 controls in Thailand. Cases were defined as asymptomatic contacts of COVID-19 patients who later tested positive for SARS-CoV-2; controls were asymptomatic contacts who never tested positive. Wearing masks all the time during contact was independently associated with lower risk for SARS-CoV-2 infection compared with not wearing masks; wearing a mask sometimes during contact did not lower infection risk. We found the type of mask worn was not independently associated with infection and that contacts who always wore masks were more likely to practice social distancing. Maintaining >1 m distance from a person with COVID-19, having close contact for <15 minutes, and frequent handwashing were independently associated with lower risk for infection. Our findings support consistent wearing of masks, handwashing, and social distancing to protect against COVID-19.
Transmission of SARS-CoV 2 During Long-Haul Flight
To assess the role of in-flight transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), we investigated a cluster of cases among passengers on a 10-hour commercial flight. Affected persons were passengers, crew, and their close contacts. We traced 217 passengers and crew to their final destinations and interviewed, tested, and quarantined them. Among the 16 persons in whom SARS-CoV-2 infection was detected, 12 (75%) were passengers seated in business class along with the only symptomatic person (attack rate 62%). Seating proximity was strongly associated with increased infection risk (risk ratio 7.3, 95% CI 1.2–46.2). We found no strong evidence supporting alternative transmission scenarios. In-flight transmission that probably originated from 1 symptomatic passenger caused a large cluster of cases during a long flight. Guidelines for preventing SARS-CoV-2 infection among air passengers should consider individual passengers’ risk for infection, the number of passengers traveling, and flight duration.
Endotheliopathy and Platelet Dysfunction as Hallmarks of Fatal Lassa Fever
Lassa fever (LF) causes multisystem disease and has a fatality rate <70%. Severe cases exhibit abnormal coagulation, endothelial barrier disruption, and dysfunctional platelet aggregation but the underlying mechanisms remain poorly understood. In Sierra Leone during 2015–2018, we assessed LF patients’ day-of-admission plasma samples for levels of proteins necessary for coagulation, fibrinolysis, and platelet function. P-selectin, soluble endothelial protein C receptor, soluble thrombomodulin, plasminogen activator inhibitor 1, ADAMTS-13, von Willebrand factor, tissue factor, soluble intercellular adhesion molecule 1, and vascular cell adhesion molecule 1 were more elevated in LF patients than in controls. Endothelial protein C receptor, thrombomodulin, intercellular adhesion molecule 1, plasminogen activator inhibitor 1, D-dimer, and hepatocyte growth factor were higher in fatal than nonfatal LF cases. Platelet disaggregation occurred only in samples from fatal LF cases. The impaired homeostasis and platelet dysfunction implicate alterations in the protein C pathway, which might contribute to the loss of endothelial barrier function in fatal infections.
Medscape CME Activity
Phage-Mediated Immune Evasion and Transmission of Livestock-Associated Methicillin-Resistant Staphylococcus aureus in Humans
Livestock-associated methicillin-resistant Staphylococcus aureus (LA-MRSA) can acquire phage-encoded immune modulators, such as the immune evasion cluster (IEC), which protects bacteria from components of the human innate immune system, and the enzyme TarP, which protects against antibody-mediated immune recognition. We used whole-genome sequencing and epidemiologic investigations to study the effects of IEC- and tarP-harboring phages on household transmission of LA-MRSA in North Denmark Region during 2004–2011. We reviewed information about all patients throughout Denmark who experienced LA-MRSA infection during 2007–2018 to determine whether IEC is associated with increased spread into the general population. Horizontal acquisition of IEC in the human host was associated with increased household transmission of LA-MRSA and spillover into the community and healthcare settings, whereas we found no evidence to suggest that IEC-positive LA-MRSA isolates have become self-sustainable in the general population. By contrast, TarP did not seem to influence household transmission of LA-MRSA.
Nowcasting (Short-Term Forecasting) of Influenza Epidemics in Local Settings, Sweden, 2008–2019
The timing of influenza case incidence during epidemics can differ between regions within nations and states. We conducted a prospective 10-year evaluation (January 2008–February 2019) of a local influenza nowcasting (short-term forecasting) method in 3 urban counties in Sweden with independent public health administrations by using routine health information system data. Detection-of-epidemic-start (detection), peak timing, and peak intensity were nowcasted. Detection displayed satisfactory performance in 2 of the 3 counties for all nonpandemic influenza seasons and in 6 of 9 seasons for the third county. Peak-timing prediction showed satisfactory performance from the influenza season 2011–12 onward. Peak-intensity prediction also was satisfactory for influenza seasons in 2 of the counties but poor in 1 county. Local influenza nowcasting was satisfactory for seasonal influenza in 2 of 3 counties. The less satisfactory performance in 1 of the study counties might be attributable to population mixing with a neighboring metropolitan area.
Multidrug-Resistant Candida auris Infections in Critically Ill Coronavirus Disease Patients, India, April–July 2020
In New Delhi, India, candidemia affected 15 critically ill coronavirus disease patients admitted to an intensive care unit during April–July 2020. Candida auris accounted for two thirds of cases; case-fatality rate was high (60%). Hospital-acquired C. auris infections in coronavirus disease patients may lead to adverse outcomes and additional strain on healthcare resources.
Multiple Introductions of Salmonella enterica Serovar Typhi H58 with Reduced Fluoroquinolone Susceptibility into Chile
Salmonella enterica serovar Typhi H58, an antimicrobial-resistant lineage, is globally disseminated but has not been reported in Latin America. Genomic analysis revealed 3 independent introductions of Salmonella Typhi H58 with reduced fluoroquinolone susceptibility into Chile. Our findings highlight the utility of enhanced genomic surveillance for typhoid fever in this region.
SARS-CoV-2 Virus Culture and Subgenomic RNA for Respiratory Specimens from Patients with Mild Coronavirus Disease
We investigated 68 respiratory specimens from 35 coronavirus disease patients in Hong Kong, of whom 32 had mild disease. We found that severe acute respiratory syndrome coronavirus 2 and subgenomic RNA were rarely detectable beyond 8 days after onset of illness. However, virus RNA was detectable for many weeks by reverse transcription PCR.
Asymptomatic Transmission of SARS-CoV-2 on Evacuation Flight
We conducted a cohort study in a controlled environment to measure asymptomatic transmission of severe acute respiratory syndrome coronavirus 2 on a flight from Italy to South Korea. Our results suggest that stringent global regulations are necessary for the prevention of transmission of this virus on aircraft.
Worldwide Effects of Coronavirus Disease Pandemic on Tuberculosis Services, January–April 2020
Coronavirus disease has disrupted tuberculosis services globally. Data from 33 centers in 16 countries on 5 continents showed that attendance at tuberculosis centers was lower during the first 4 months of the pandemic in 2020 than for the same period in 2019. Resources are needed to ensure tuberculosis care continuity during the pandemic.
Potential Role of Social Distancing in Mitigating Spread of Coronavirus Disease, South Korea
In South Korea, the coronavirus disease outbreak peaked at the end of February and subsided in mid-March. We analyzed the likely roles of social distancing in reducing transmission. Our analysis indicated that although transmission might persist in some regions, epidemics can be suppressed with less extreme measures than those taken by China.
Preventing Vector-Borne Transmission of Zika Virus Infection During Pregnancy, Puerto Rico, USA, 2016–2017
We examined pregnant women’s use of personal protective measures to prevent mosquito bites during the 2016–2017 Zika outbreak in Puerto Rico. Healthcare provider counseling on recommended measures was associated with increased use of insect repellent among pregnant women but not with wearing protective clothing.
Multidrug-Resistant Hypervirulent Group B Streptococcus in Neonatal Invasive Infections, France, 2007–2019
We analyzed group B Streptococcus (GBS) neonatal invasive infections reported during 2007–2019 in France. The hypervirulent clonal complex (CC) 17 GBS was responsible for 66% (827/1,262) of cases. The role of CC17 GBS increased over time (p for trend = 0.0001), together with the emergence of a multidrug-resistant CC17 GBS sublineage.
Epileptic Seizure after Use of Moxifloxacin in Man with Legionella longbeachae Pneumonia
Legionellosis caused by Legionella longbeachae is diagnosed mainly by PCR. We report a case of L. longbeachae infection in mainland China, which was diagnosed by metagenomic next-generation sequencing, in a man who developed an epileptic seizure after using moxifloxacin. Metagenomic next-generation sequencing may be a useful tool to detect Legionella spp.
Two New Cases of Pulmonary Infection by Mycobacterium shigaense, Japan
We report 2 case-patients in Japan with Mycobacterium shigaense pulmonary infections. One patient was given aggressive treatment and the other conservative treatment, according to distinctive radiologic evidence. A close phylogenetic relationship based on whole-genome sequencing was found between strain from the conservatively treated patient and a reference strain of cutaneous origin.
Thresholds versus Anomaly Detection for Surveillance of Pneumonia and Influenza Mortality
Computational surveillance of pneumonia and influenza mortality in the United States using FluView uses epidemic thresholds to identify high mortality rates but is limited by statistical issues such as seasonality and autocorrelation. We used time series anomaly detection to improve recognition of high mortality rates. Results suggest that anomaly detection can complement mortality reporting.
In-Flight Transmission of SARS-CoV-2
Four persons with severe acute respiratory syndrome coronavirus 2 infection had traveled on the same flight from Boston, Massachusetts, USA, to Hong Kong, China. Their virus genetic sequences are identical, unique, and belong to a clade not previously identified in Hong Kong, which strongly suggests that the virus can be transmitted during air travel.
Chikungunya Virus Infection in Blood Donors and Patients During Outbreak, Mandalay, Myanmar, 2019
In 2019, an outbreak of chikungunya virus infection occurred in Mandalay, Myanmar, and 3.2% of blood donors and 20.5% of patients who were children were confirmed as being infected. The prevalence rate was up to 6.3% among blood donors. The East Central/South African genotype was predominantly circulating during this outbreak.
KPC-3–Producing Serratia marcescens Outbreak between Acute and Long-Term Care Facilities, Florida, USA
We describe an outbreak caused by Serratia marcescens carrying blaKPC-3 that was sourced to a long-term care facility in Florida, USA. Whole-genome sequencing and plasmid profiling showed involvement of 3 clonal lineages of S. marcescens and 2 blaKPC-3-carrying plasmids. Determining the resistance mechanism is critical for timely implementation of infection control measures.
Abrupt Subsidence of Seasonal Influenza after COVID-19 Outbreak, Hong Kong, China
The onset of the 2019–20 winter influenza season in Hong Kong coincided with the emergence of the coronavirus disease epidemic in neighboring mainland China. After widespread adoption of large-scale social distancing interventions in response to the impending coronavirus disease outbreak, the influenza season ended abruptly with a decrease to a low trough.
Seroprevalence of SARS-CoV-2–Specific Antibodies, Faroe Islands
We conducted a nationwide study of the prevalence of severe acute respiratory syndrome coronavirus 2 infection in the Faroe Islands. Of 1,075 randomly selected participants, 6 (0.6%) tested seropositive for antibodies to the virus. Adjustment for test sensitivity and specificity yielded a 0.7% prevalence. Our findings will help us evaluate our public health response.
Detection of SARS-CoV-2 in Hemodialysis Effluent of Patient with COVID-19 Pneumonia, Japan
We report detection of severe acute respiratory syndrome coronavirus 2 RNA in hemodialysis effluent from a patient in Japan with coronavirus disease and prolonged inflammation. Healthcare workers should observe strict standard and contact precautions and use appropriate personal protective equipment when handling hemodialysis circuitry from patients with diagnosed coronavirus disease.
Four Patients with COVID-19 and Tuberculosis, Singapore, April–May 2020
Coronavirus disease (COVID-19) and tuberculosis (TB) developed in 4 foreign workers living in dormitories in Singapore during April–May 2020. Clinical manifestations and atypical radiographic features of COVID-19 led to the diagnosis of TB through positive interferon-gamma release assay and culture results. During the COVID-19 pandemic, TB should not be overlooked.
Seroprevalence of SARS-CoV-2 and Infection Fatality Ratio, Orleans and Jefferson Parishes, Louisiana, USA, May 2020
Using a novel recruitment method and paired molecular and antibody testing for severe acute respiratory syndrome coronavirus 2 infection, we determined seroprevalence in a racially diverse municipality in Louisiana, USA. Infections were highly variable by ZIP code and differed by race/ethnicity. Overall census-weighted seroprevalence was 6.9%, and the calculated infection fatality ratio was 1.63%.
Saliva Alternative to Upper Respiratory Swabs for SARS-CoV-2 Diagnosis
PCR of upper respiratory specimens is the diagnostic standard for severe acute respiratory syndrome coronavirus 2 infection. However, saliva sampling is an easy alternative to nasal and throat swabbing. We found similar viral loads in saliva samples and in nasal and throat swab samples from 110 patients with coronavirus disease.
Burkholderia pseudomallei in Soil, US Virgin Islands, 2019
The distribution of Burkholderia pseudomallei in the Caribbean is poorly understood. We isolated B. pseudomallei from US Virgin Islands soil. The soil isolate was genetically similar to other isolates from the Caribbean, suggesting that B. pseudomallei might have been introduced to the islands multiple times through severe weather events.
Nontuberculous Mycobacterial Pulmonary Disease from Mycobacterium hassiacum, Austria
The clinical relevance of newly described nontuberculous mycobacteria is often unclear. We report a case of pulmonary infection caused by Mycobacterium hassiacum in an immunocompetent patient in Austria who had chronic obstructive pulmonary disease. Antimicrobial drug susceptibility testing showed low MICs for macrolides, aminoglycosides, fluoroquinolones, tetracyclines, imipenem, and linezolid.
Large Outbreak of Guillain-Barré Syndrome, Peru, 2019
Outbreaks of Guillain-Barré syndrome (GBS) are uncommon. In May 2019, national surveillance in Peru detected an increase in GBS cases in excess of the expected incidence of 1.2 cases/100,000 population. Several clinical and epidemiologic findings call into question the suggested association between this GBS outbreak and Campylobacter.
Osteomyelitis Due to Mycobacterium goodii in an Adolescent, United States
Osteomyelitis is a rare clinical manifestation of infection with nontuberculous mycobacteria (NTM). We report an adolescent with femoral osteomyelitis associated with prosthetic material due to an emerging pathogen, Mycobacterium goodii. Application of secA1 and 16S ribosomal RNA gene sequencing reliably determined the NTM species, enabling targeted antimicrobial therapy.
Sporotrichosis Cases in Commercial Insurance Data, United States, 2012–2018
The geographic distribution of sporotrichosis in the United States is largely unknown. In a large commercial health insurance database, sporotrichosis was rare but most frequently occurred in southern and south-central states. Knowledge about where sporotrichosis is most likely to occur is essential for increasing clinician awareness of this rare fungal disease.
COVID-19 Outbreak, Senegal, 2020
The spread of severe acute respiratory syndrome coronavirus 2 began later in Africa than in Asia and Europe. Senegal confirmed its first case of coronavirus disease on March 2, 2020. By March 4, a total of 4 cases had been confirmed, all in patients who traveled from Europe.
Sociodemographic Predictors of SARS-CoV-2 Infection in Obstetric Patients, Georgia, USA
We conducted a cohort study to determine sociodemographic risk factors for severe acute respiratory syndrome coronavirus 2 infection among obstetric patients in 2 urban hospitals in Atlanta, Georgia, USA. Prevalence of infection was highest among women who were Hispanic, were uninsured, or lived in high-density neighborhoods.
- Nocardia ignorata Infection in Heart Transplant Patient
- COVID-19 Outbreak Associated with Air Conditioning in Restaurant, Guangzhou, China, 2020
- COVID-19 Outbreak Associated with Air Conditioning in Restaurant, Guangzhou, China, 2020
About the Cover
Early Insights from Statistical and Mathematical Modeling of Key Epidemiologic Parameters of COVID-19
We report key epidemiologic parameter estimates for coronavirus disease identified in peer-reviewed publications, preprint articles, and online reports. Range estimates for incubation period were 1.8–6.9 days, serial interval 4.0–7.5 days, and doubling time 2.3–7.4 days. The effective reproductive number varied widely, with reductions attributable to interventions. Case burden and infection fatality ratios increased with patient age. Implementation of combined interventions could reduce cases and delay epidemic peak up to 1 month. These parameters for transmission, disease severity, and intervention effectiveness are critical for guiding policy decisions. Estimates will likely change as new information becomes available.
Volume 26, Number 12—December 2020
- Outbreak of Anthrax Associated with Handling and Eating Meat from a Cow, Uganda, 2018
- Animal Rabies Surveillance, China, 2004–2018
- Outbreak of Mycoplasma bovis Infections in Free-Ranging Pronghorn (Antilocapra americana), Wyoming, USA
- Control and Prevention of Anthrax, Texas, USA, 2019
Small Particle Aerosol Exposure of African Green Monkeys to MERS-CoV as a Model for Highly Pathogenic Coronavirus Infection
Emerging coronaviruses are a global public health threat because of the potential for person-to-person transmission and high mortality rates. Middle East respiratory syndrome coronavirus (MERS-CoV) emerged in 2012, causing lethal respiratory disease in »35% of cases. Primate models of coronavirus disease are needed to support development of therapeutics, but few models exist that recapitulate severe disease. For initial development of a MERS-CoV primate model, 12 African green monkeys were exposed to 103, 104, or 105 PFU target doses of aerosolized MERS-CoV. We observed a dose-dependent increase of respiratory disease signs, although all 12 monkeys survived for the 28-day duration of the study. This study describes dose-dependent effects of MERS-CoV infection of primates and uses a route of infection with potential relevance to MERS-CoV transmission. Aerosol exposure of African green monkeys might provide a platform approach for the development of primate models of novel coronavirus diseases.
- Equine-Like H3 Avian Influenza Viruses in Wild Birds, Chile
- Trends in Population Dynamics of Escherichia coli Sequence Type 131, 2006–2016
- Risk for Hepatitis E Virus Transmission by Solvent/Detergent–Treated Plasma
SARS-CoV-2 Seroprevalence among Healthcare, First Response, and Public Safety Personnel, Detroit Metropolitan Area, Michigan, USA, May–June 2020
To estimate seroprevalence of severe acute respiratory syndrome 2 (SARS-CoV-2) among healthcare, first response, and public safety personnel, antibody testing was conducted in emergency medical service agencies and 27 hospitals in the Detroit, Michigan, USA, metropolitan area during May–June 2020. Of 16,403 participants, 6.9% had SARS-CoV-2 antibodies. In adjusted analyses, seropositivity was associated with exposure to SARS-CoV-2–positive household members (adjusted odds ratio [aOR] 6.18, 95% CI 4.81–7.93) and working within 15 km of Detroit (aOR 5.60, 95% CI 3.98–7.89). Nurse assistants (aOR 1.88, 95% CI 1.24–2.83) and nurses (aOR 1.52, 95% CI 1.18–1.95) had higher likelihood of seropositivity than physicians. Working in a hospital emergency department increased the likelihood of seropositivity (aOR 1.16, 95% CI 1.002–1.35). Consistently using N95 respirators (aOR 0.83, 95% CI 0.72–0.95) and surgical facemasks (aOR 0.86, 95% CI 0.75–0.98) decreased the likelihood of seropositivity.
- HIV-Associated Tuberculosis Among Children and Adolescents in High HIV/TB Settings
- Game Animal Density, Climate, and Tick-borne Encephalitis in Finland, 2007–2017
Flight-Associated Transmission of Severe Acute Respiratory Syndrome Coronavirus 2 Corroborated by Whole-Genome Sequencing
To investigate potential transmission of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) during a domestic flight within Australia, we performed epidemiologic analyses with whole-genome sequencing. Eleven passengers with PCR-confirmed SARS-CoV-2 infection and symptom onset within 48 hours of the flight were considered infectious during travel; 9 had recently disembarked from a cruise ship with a retrospectively identified SARS-CoV-2 outbreak. The virus strain of those on the cruise and the flight was linked (A2-RP) and had not been previously identified in Australia. For 11 passengers, none of whom had traveled on the cruise ship, PCR-confirmed SARS-CoV-2 illness developed between 48 hours and 14 days after the flight. Eight cases were considered flight associated with the distinct SARS-CoV-2 A2-RP strain; the remaining 3 cases (1 with A2-RP) were possibly flight associated. All 11 passengers had been in the same cabin with symptomatic persons who had primary, culture-positive, A2-RP cases. This investigation provides evidence of flight-associated SARS-CoV-2 transmission.
Coronavirus Disease Model to Inform Transmission Reducing Measures and Health System Preparedness, Australia
The ability of health systems to cope with coronavirus disease (COVID-19) cases is of major concern. In preparation, we used clinical pathway models to estimate healthcare requirements for COVID-19 patients in the context of broader public health measures in Australia. An age- and risk-stratified transmission model of COVID-19 demonstrated that an unmitigated epidemic would dramatically exceed the capacity of the health system of Australia over a prolonged period. Case isolation and contact quarantine alone are insufficient to constrain healthcare needs within feasible levels of expansion of health sector capacity. Overlaid social restrictions must be applied over the course of the epidemic to ensure systems do not become overwhelmed and essential health sector functions, including care of COVID-19 patients, can be maintained. Attention to the full pathway of clinical care is needed, along with ongoing strengthening of capacity.
- Genomic Epidemiology of Severe Acute Respiratory Syndrome Coronavirus 2, Colombia
- Clinical and Multimodal Imaging Findings and Risk Factors for Ocular Involvement in a Presumed Waterborne Toxoplasmosis Outbreak, Brazil
- Outbreak of Haff Disease along the Yangtze River, Anhui, China, 2016
- Human-Pathogenic Kasokero Virus in Field-Collected Ticks
- Coyotes as Reservoirs for Onchocerca lupi, United States, 2015–2018
- Direct Transmission of Severe Fever with Thrombocytopenia Syndrome Virus from Domestic Cat to Veterinary Personnel
Differential Tropism of SARS-CoV and SARS-CoV-2 in Bat Cells
Severe acute respiratory syndrome coronavirus 2 did not replicate efficiently in 13 bat cell lines, whereas severe acute respiratory syndrome coronavirus replicated efficiently in kidney cells of its ancestral host, the Rhinolophus sinicus bat, suggesting different evolutionary origins. Structural modeling showed that RBD/RsACE2 binding may contribute to the differential cellular tropism.
- Novel Rickettsia Species Infecting Dogs, United States
- Zoonotic Pathogens in Ticks from Migratory Birds, Italy
- Lymphocytic Choriomeningitis Virus Infections and Seroprevalence, Southern Iraq
Characterization and Source Investigation of Multidrug-Resistant Salmonella Anatum from a Sustained Outbreak, Taiwan
An ongoing outbreak of multidrug-resistant Salmonella enterica serovar Anatum began in Taiwan in 2015. Pork and poultry were identified as vehicles for transmission. Contaminated meat contributed to the high rate of infections among children. Nearly identical Salmonella Anatum strains have been identified in the United Kingdom, the United States, and the Philippines.
- Shedding of Marburg Virus in Naturally Infected Egyptian Rousette Bats, South Africa, 2017
Highly Pathogenic Avian Influenza A(H7N3) Virus in Poultry, United States, 2020
An outbreak of low-pathogenicity avian influenza A(H7N3) virus of North American wild bird lineage occurred on commercial turkey farms in North Carolina and South Carolina, USA, during March–April 2020. The virus mutated to the highly pathogenic form in 1 house on 1 farm via recombination with host 28S rRNA.
- Endovascular Infection with Kingella kingae Complicated by Septic Arthritis in Immunocompromised Adult Patient
- Human Rickettsiosis Caused by Rickettsia parkeri Strain Atlantic Rainforest, Urabá, Colombia
- Unusual Outbreak of Rift Valley Fever in Sudan, 2019
Antibody Profiles According to Mild or Severe SARS-CoV-2 Infection, Atlanta, Georgia, USA, 2020
Among patients with coronavirus disease (COVID-19), IgM levels increased early after symptom onset for those with mild and severe disease, but IgG levels increased early only in those with severe disease. A similar pattern was observed in a separate serosurveillance cohort. Mild COVID-19 should be investigated separately from severe COVID-19.
Outbreaks of Highly Pathogenic Avian Influenza (H5N6) Virus Subclade 184.108.40.206h in Swans, Xinjiang, Western China, 2020
In January 2020, the subclade 220.127.116.11h of highly pathogenic avian influenza (H5N6) virus infected migratory whooper swans and mute swans in Xinjiang, western China. The virus is lethal to chickens and ducks but has low pathogenicity in mice. Antigenically, this subclade is similar to the H5N1 vaccine seed virus Re-11.
- Human Monocytic Ehrlichiosis, Mexico City, Mexico
Experimental Infection of Cattle with SARS-CoV-2
We inoculated 6 cattle with severe acute respiratory syndrome coronavirus 2 and kept them together with 3 in-contact, virus-naive cattle. We observed viral replication and specific seroreactivity in 2 inoculated animals, despite high levels of preexisting antibody titers against a bovine betacoronavirus. The in-contact animals did not become infected.
Sensitive Detection of SARS-CoV-2–Specific Antibodies in Dried Blood Spot Samples
Dried blood spot (DBS) samples can be used for the detection of severe acute respiratory syndrome coronavirus 2 spike antibodies. DBS sampling is comparable to matched serum samples with a relative 98.1% sensitivity and 100% specificity. Thus, DBS sampling offers an alternative for population-wide serologic testing in the coronavirus pandemic.
- Susceptibility of Raccoon Dogs for Experimental SARS-CoV-2 Infection
- Transmission of Multidrug-Resistant Salmonella enterica Subspecies enterica 4,,12:i:- Sequence Type 34 between Europe and United States
- Range Expansion of Bombali Virus in Mops condylurus Bats, Kenya
- Detection and Characterization of Bat Sarbecovirus Phylogenetically Related to SARS-CoV-2, Japan
- Hantavirus Cardiopulmonary Syndrome in Canada
- Hypervirulent Klebsiella pneumoniae as an Unexpected Cause of a Fatal Outbreak in Captive Marmosets in South America
- Identification of a Novel α-herpesvirus Associated with Ulcerative Stomatitis in Donkeys
- Lyssaviruses in Insectivorous Bats, South Africa, 2003–2018
- Pathogenic New World relapsing fever Borrelia in a Myotis bat, Eastern China, 2015
- One-Year Retrospective Review of Psychiatric Consultations in Lassa Fever, Southern Nigeria
SARS-CoV-2 Natural Transmission from Human to Cat, Belgium, March 2020
In March 2020, a severe respiratory syndrome developed in a cat, 1 week after its owner received positive test results for severe acute respiratory syndrome coronavirus 2. Viral RNA was detected in the cat’s nasopharyngeal swab samples and vomitus or feces; immunoglobulin against the virus was found in convalescent-phase serum. Human-to-cat transmission is suspected.
- Autochthonous Rat-Borne Seoul Virus Infection with Acute Kidney Injury, Germany, 2018
Effects of Cocooning on Coronavirus Disease Rates after Relaxing Social Distancing
As coronavirus disease spreads throughout the United States, policymakers are contemplating reinstatement and relaxation of shelter-in-place orders. By using a model capturing high-risk populations and transmission rates estimated from hospitalization data, we found that postponing relaxation will only delay future disease waves. Cocooning vulnerable populations can prevent overwhelming medical surges.
SARS-CoV-2 in Quarantined Domestic Cats from COVID-19 Households or Close Contacts, Hong Kong, China
We tested 50 cats from coronavirus disease households or close contacts in Hong Kong, China, for severe acute respiratory syndrome coronavirus 2 RNA in respiratory and fecal samples. We found 6 cases of apparent human-to-feline transmission involving healthy cats. Virus genomes sequenced from 1 cat and its owner were identical.
- Pediatric Lyme Disease Biobank, United States, 2015–2020
- Serologic Responses in Healthy Adult with SARS-CoV-2 Reinfection, Hong Kong, August, 2020
- Lack of Susceptibility to SARS-CoV-2 and MERS-CoV in Poultry
- Brucella canis in Commercial Dog Breeding Kennels, Ontario, Canada
- Phylogenetic Analysis of MERS-CoV in a Camel Abattoir, Saudi Arabia, 2016–2018
- Low Pathogenicity Avian Influenza (H5N2) Viruses, Dominican Republic
- High Coxiella burnetii Seroconversion Rate in Veterinary Students, the Netherlands, 2006–2010
- Transmission Electron Microscopy Confirmation of Orientia tsutsugamushi in Human Bile
- Buruli Ulcer
- Proactive Case-Finding and Isolation Are Crucial for Preventing Large SARS-CoV-2 Outbreaks
- Interpreting Transmissibility of COVID-19 in Children
- Novel Serotype of Epizootic Hemorrhagic Disease Virus, China
- Role of Oral Rabies Vaccines in the Elimination of Dog-Mediated Human Rabies Deaths
Volume 27, Number 1—January 2021
- Aspergillosis Complicating Severe Viral Pneumonia in Persons with Coronavirus Disease
- Nosocomial COVID-19 Outbreak Containment, Hanoi, Vietnam, March–April 2020
- Comparative Omics Analysis of Historic and Recent Isolates of Bordetella pertussis and Effects of Genome Rearrangements on Evolution
- Estimate of Burden and Direct Healthcare Cost of Infectious Waterborne Disease in the United States
- Using Repeated Serosurveys to Estimate the Force of Dengue Virus Infection in Ouagadougou, Burkina Faso
- Performance of Nucleic Acid Amplification Tests for Detection of Severe Acute Respiratory Syndrome Coronavirus 2 in Prospectively Pooled Specimens
- Intrafamilial Exposure to SARS-CoV-2 Associated with Cellular Immune Response without Seroconversion
- Differential Yellow Fever Susceptibility in New World Nonhuman Primates, Comparison with Humans, and Implications for Surveillance
- Using Structured Expert Judgment for Attribution of Foodborne and Waterborne Illnesses to Comprehensive Transmission Pathways, United States
Cellular Immunity in COVID-19 Convalescents with PCR-Confirmed Infection but with Undetectable SARS-CoV-2–Specific IgG
We investigated immune responses against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) among a group of convalescent, potential blood donors in Germany who had PCR-confirmed SARS-CoV-2 infection. Sixty days after onset of symptoms, 13/78 (17%) study participants had borderline or negative results to an ELISA detecting IgG against the S1 protein of SARS-CoV-2. We analyzed participants with PCR-confirmed infection who had strong antibody responses (ratio >3) as positive controls and participants without symptoms of SARS-CoV-2 infection and without household contact with infected patients as negative controls. Using interferon-γ ELISpot, we observed that 78% of PCR-positive volunteers with undetectable antibodies showed T cell immunity against SARS-CoV-2. We observed a similar frequency (80%) of T-cell immunity in convalescent donors with strong antibody responses but did not detect immunity in negative controls. We concluded that, in convalescent patients with undetectable SARS-CoV-2 IgG, immunity may be mediated through T cells.
- Human Diversity of Killer Cell Immunoglobulin-Like Receptors and Human Leukocyte Antigen Class I Alleles, and Ebola Virus Disease Outcomes
- IgG Seroconversion and Pathophysiology in Severe Acute Respiratory Syndrome Coronavirus 2 Infection
- Hannibal’s Ophthalmia—A New Answer to An Ancient Question
- Primary Amebic Meningoencephalitis Associated with Recreational Aquatic Exposures, USA, 1978–2018
- In Vivo Observation of Cutaneous Larva Migrans by Fluorescence-Advanced Videodermatoscopy
- Ocular Filariasis in Human Caused by Breinlia (Johnstonema) annulipapillata, Australia
- Listeriosis Caused by Persistence of Listeria monocytogenes Serotype 4b Sequence Type 6 in Cheese Production Environment
- Fatal Case of Chronic Jamestown Canyon Virus Encephalitis Diagnosed by Metagenomic Sequencing in a Patient on Rituximab
- Prevalence of SARS-CoV-2, Verona, Italy, April–May 2020
- Severe Human Bocavirus-Associated Pneumonia in Adults at a Referral Hospital, Seoul, South Korea
- Large-Scale Testing of Asymptomatic Healthcare Personnel for Severe Acute Respiratory Syndrome Coronavirus 2
- Economic Burden of Legionnaires’ Disease, United States, 2014
Coronavirus Disease among Workers in Food Processing, Food Manufacturing, and Agriculture Workplaces
We describe coronavirus disease (COVID-19) among US food manufacturing and agriculture workers and provide updated information on meat and poultry processing workers. Among 742 food and agriculture workplaces in 30 states, 8,978 workers had confirmed COVID-19; 55 workers died. Racial and ethnic minority workers could be disproportionately affected by COVID-19.
Risk for SARS-CoV-2 Infection in Healthcare Workers, Turin, Italy
We measured severe acute respiratory syndrome coronavirus 2 spike protein subunits S1/S2 antibodies by using capillary electrophoresis and a chemiluminescence immunoassay for 5,444 active healthcare workers in Italy. Seroprevalence was 6.9% and higher among participants having contact with patients. Seroconversion was not observed in 37/213 previously infected participants.
Waning Antibody Responses in Asymptomatic and Symptomatic SARS-CoV-2 Infection
We investigated the kinetics of severe acute respiratory syndrome coronavirus 2 neutralizing antibodies in 7 asymptomatic persons and 11 patients with pneumonia. The geometric mean titer of neutralizing antibodies declined from 219.4 at 2 months to 143.7 at 5 months after infection, indicating a waning antibody response.
- Attitudes about COVID-19 Lockdown among General Population, France, March 2020
- Relative Bradycardia in Patients with Mild-to-Moderate Coronavirus Disease, Japan
- Etiology of Severe Acute Respiratory Infections, Bangladesh, 2017
SARS-CoV-2 Cluster in Nursery, Poland
We report a cluster of surprisingly high spread of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) associated with a single nursery in Poland. Our findings contrast with the presumed negligible role of children in driving the SARS-CoV-2 pandemic. Children 1–2 years of age might be effective SARS-CoV-2 spreaders.
- Nonpolio Enterovirus Activity during the COVID-19 Pandemic, Taiwan, 2020
Superspreading Event of SARS-CoV-2 Infection at a Bar, Ho Chi Minh City, Vietnam
We report a superspreading event of severe acute respiratory syndrome coronavirus 2 infection initiated at a bar in Vietnam with evidence of symptomatic and asymptomatic transmission, based on ministry of health reports, patient interviews, and whole-genome sequence analysis. Crowds in enclosed indoor settings with poor ventilation may be considered at high risk for transmission.
- Absence of SARS-CoV-2 Transmission from Children in Isolation to Guardians, South Korea
- Large-Scale Isolation Facilities and Potential for Secondary Infectious Disease Outbreak
Volume 27, Number 2—February 2021
- Addressing COVID-19 Misinformation on Social Media Preemptively and Responsively
- Murine Typhus in Canary Islands, Spain, 1999–2015
- Potential Association between Zika Infection and Microcephaly during 2007 Fever Outbreak, Gabon