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Volume 23, Number 9—September 2017

Perspective

  • Bioinformatic Analyses of Whole-Genome Sequence Data in a Public Health Laboratory
    K. F. Oakeson et al.
        View Abstract

    The ability to generate high-quality sequence data in a public health laboratory enables the identification of pathogenic strains, the determination of relatedness among outbreak strains, and the analysis of genetic information regarding virulence and antimicrobial-resistance genes. However, the analysis of whole-genome sequence data depends on bioinformatic analysis tools and processes. Many public health laboratories do not have the bioinformatic capabilities to analyze the data generated from sequencing and therefore are unable to take full advantage of the power of whole-genome sequencing. The goal of this perspective is to provide a guide for laboratories to understand the bioinformatic analyses that are needed to interpret whole-genome sequence data and how these in silico analyses can be implemented in a public health laboratory setting easily, affordably, and, in some cases, without the need for intensive computing resources and infrastructure.

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Research

  • Real-Time Whole-Genome Sequencing for Surveillance of Listeria monocytogenes, France
    A. Moura et al.
        View Abstract

    During 2015–2016, we evaluated the performance of whole-genome sequencing (WGS) as a routine typing tool. Its added value for microbiological and epidemiologic surveillance of listeriosis was compared with that for pulsed-field gel electrophoresis (PFGE), the current standard method. A total of 2,743 Listeria monocytogenes isolates collected as part of routine surveillance were characterized in parallel by PFGE and core genome multilocus sequence typing (cgMLST) extracted from WGS. We investigated PFGE and cgMLST clusters containing human isolates. Discrimination of isolates was significantly higher by cgMLST than by PFGE (p<0.001). cgMLST discriminated unrelated isolates that shared identical PFGE profiles and phylogenetically closely related isolates with distinct PFGE profiles. This procedure also refined epidemiologic investigations to include only phylogenetically closely related isolates, improved source identification, and facilitated epidemiologic investigations, enabling identification of more outbreaks at earlier stages. WGS-based typing should replace PFGE as the primary typing method for L. monocytogenes.

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  • Prevalence of Yersinia enterocolitica Bioserotype 3/O:3 among Children with Diarrhea, China, 2010–2015
    R. Duan et al.
        View Abstract

    Yersinia enterocolitica is thought to not significantly contribute to diarrheal disease in China, but evidence substantiating this claim is limited. We determined the prevalence of Y. enterocolitica infection and strain types present among children <5 years of age with diarrhea in China. The overall prevalence of pathogenic isolates was 0.59%. Prevalence of pathogenic bioserotype 3/O:3 varied geographically. In this population, the presence of fecal leukocytes was a characteristic of Y. enterocolitica infection and should be used as an indication for microbiological diagnostic testing, rather than for the diagnosis of bacillary dysentery. In contrast with Y. enterocolitica isolates from adults, which were primarily biotype 1A, isolates from children were primarily bioserotype 3/O:3. Most pathogenic isolates from children shared pulsed-field gel electrophoresis patterns with isolates from pigs and dogs, suggesting a possible link between isolates from animals and infections in children. Our findings underscore the need for improved diagnostics for this underestimated pathogen.

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  • Convergence of Humans, Bats, Trees, and Culture in Nipah Virus Transmission, Bangladesh
    E. S. Gurley et al.
        View Abstract

    Preventing emergence of new zoonotic viruses depends on understanding determinants for human risk. Nipah virus (NiV) is a lethal zoonotic pathogen that has spilled over from bats into human populations, with limited person-to-person transmission. We examined ecologic and human behavioral drivers of geographic variation for risk of NiV infection in Bangladesh. We visited 60 villages during 2011–2013 where cases of infection with NiV were identified and 147 control villages. We compared case villages with control villages for most likely drivers for risk of infection, including number of bats, persons, and date palm sap trees, and human date palm sap consumption behavior. Case villages were similar to control villages in many ways, including number of bats, persons, and date palm sap trees, but had a higher proportion of households in which someone drank sap. Reducing human consumption of sap could reduce virus transmission and risk for emergence of a more highly transmissible NiV strain.

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  • Estimated Annual Numbers of Foodborne Pathogen–Associated Illnesses, Hospitalizations, and Deaths, France, 2008–2013
    D. Van Cauteren et al.
        View Abstract

    Estimates of the annual numbers of foodborne illnesses and associated hospitalizations and deaths are needed to set priorities for surveillance, prevention, and control strategies. The objective of this study was to determine such estimates for 2008–2013 in France. We considered 15 major foodborne pathogens (10 bacteria, 3 viruses, and 2 parasites) and estimated that each year, the pathogens accounted for 1.28–2.23 million illnesses, 16,500–20,800 hospitalizations, and 250 deaths. Campylobacter spp., nontyphoidal Salmonella spp., and norovirus accounted for >70% of all foodborne pathogen–associated illnesses and hospitalizations; nontyphoidal Salmonella spp. and Listeria monocytogenes were the main causes of foodborne pathogen–associated deaths; and hepatitis E virus appeared to be a previously unrecognized foodborne pathogen causing ≈68,000 illnesses in France every year. The substantial annual numbers of foodborne illnesses and associated hospitalizations and deaths in France highlight the need for food-safety policymakers to prioritize foodborne disease prevention and control strategies.

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  • Medscape CME Activity
    Epidemiology of Salmonella enterica Serotype Dublin Infections among Humans, United States, 1968–2013
    R. Harvey et al.
    View Summary

    Infection incidence and antimicrobial drug resistance are increasing.

        View Abstract

    Salmonella enterica serotype Dublin is a cattle-adapted bacterium that typically causes bloodstream infections in humans. To summarize demographic, clinical, and antimicrobial drug resistance characteristics of human infections with this organism in the United States, we analyzed data for 1968–2013 from 5 US surveillance systems. During this period, the incidence rate for infection with Salmonella Dublin increased more than that for infection with other Salmonella. Data from 1 system (FoodNet) showed that a higher percentage of persons with Salmonella Dublin infection were hospitalized and died during 2005−2013 (78% hospitalized, 4.2% died) than during 1996–2004 (68% hospitalized, 2.7% died). Susceptibility data showed that a higher percentage of isolates were resistant to >7 classes of antimicrobial drugs during 2005–2013 (50.8%) than during 1996–2004 (2.4%).

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  • Processes Underlying Rabies Virus Incursions across US–Canada Border as Revealed by Whole-Genome Phylogeography
    H. Trewby et al.
        View Abstract

    Disease control programs aim to constrain and reduce the spread of infection. Human disease interventions such as wildlife vaccination play a major role in determining the limits of a pathogen’s spatial distribution. Over the past few decades, a raccoon-specific variant of rabies virus (RRV) has invaded large areas of eastern North America. Although expansion into Canada has been largely prevented through vaccination along the US border, several outbreaks have occurred in Canada. Applying phylogeographic approaches to 289 RRV whole-genome sequences derived from isolates collected in Canada and adjacent US states, we examined the processes underlying these outbreaks. RRV incursions were attributable predominantly to systematic virus leakage of local strains across areas along the border where vaccination has been conducted but also to single stochastic events such as long-distance translocations. These results demonstrate the utility of phylogeographic analysis of pathogen genomes for understanding transboundary outbreaks.

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  • Role of Food Insecurity in Outbreak of Anthrax Infections among Humans and Hippopotamuses Living in a Game Reserve Area, Rural Zambia
    M. W. Lehman et al.
        View Abstract

    In September 2011, a total of 511 human cases of anthrax (Bacillus anthracis) infection and 5 deaths were reported in a game management area in the district of Chama, Zambia, near where 85 hippopotamuses (Hippopotamus amphibious) had recently died of suspected anthrax. The human infections generally responded to antibiotics. To clarify transmission, we conducted a cross-sectional, interviewer-administered household survey in villages where human anthrax cases and hippopotamus deaths were reported. Among 284 respondents, 84% ate hippopotamus meat before the outbreak. Eating, carrying, and preparing meat were associated with anthrax infection. Despite the risk, 23% of respondents reported they would eat meat from hippopotamuses found dead again because of food shortage (73%), lack of meat (12%), hunger (7%), and protein shortage (5%). Chronic food insecurity can lead to consumption of unsafe foods, leaving communities susceptible to zoonotic infection. Interagency cooperation is necessary to prevent outbreaks by addressing the root cause of exposure, such as food insecurity.

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  • Patterns of Human Plague in Uganda, 2008–2016
    J. D. Forrester et al.
        View Abstract

    Plague is a highly virulent fleaborne zoonosis that occurs throughout many parts of the world; most suspected human cases are reported from resource-poor settings in sub-Saharan Africa. During 2008–2016, a combination of active surveillance and laboratory testing in the plague-endemic West Nile region of Uganda yielded 255 suspected human plague cases; approximately one third were laboratory confirmed by bacterial culture or serology. Although the mortality rate was 7% among suspected cases, it was 26% among persons with laboratory-confirmed plague. Reports of an unusual number of dead rats in a patient’s village around the time of illness onset was significantly associated with laboratory confirmation of plague. This descriptive summary of human plague in Uganda highlights the episodic nature of the disease, as well as the potential that, even in endemic areas, illnesses of other etiologies might be being mistaken for plague.

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  • Protective Effect of Val-PrP against Bovine Spongiform Encephalopathy but not Variant Creutzfeldt-Jakob Disease
    N. Fernández-Borges et al.
    View Summary

    The severely restricted transmission of BSE to human Val129 polymorphic variant can be overcome by adaptation of the agent to the human Met129 PrP variant, resulting in a prion with different strain features when compared to vCJD.

        View Abstract

    Bovine spongiform encephalopathy (BSE) is the only known zoonotic prion that causes variant Creutzfeldt-Jakob disease (vCJD) in humans. The major risk determinant for this disease is the polymorphic codon 129 of the human prion protein (Hu-PrP), where either methionine (Met129) or valine (Val129) can be encoded. To date, all clinical and neuropathologically confirmed vCJD cases have been Met129 homozygous, with the exception of 1 recently reported Met/Val heterozygous case. Here, we found that transgenic mice homozygous for Val129 Hu-PrP show severely restricted propagation of the BSE prion strain, but this constraint can be partially overcome by adaptation of the BSE agent to the Met129 Hu-PrP. In addition, the transmission of vCJD to transgenic mice homozygous for Val129 Hu-PrP resulted in a prion with distinct strain features. These observations may indicate increased risk for vCJD secondary transmission in Val129 Hu-PrP–positive humans with the emergence of new strain features.

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  • Risk for Low Pathogenicity Avian Influenza Virus on Poultry Farms, the Netherlands, 2007–2013
    R. Bouwstra et al.
        View Abstract

    Using annual serologic surveillance data from all poultry farms in the Netherlands during 2007–2013, we quantified the risk for the introduction of low pathogenicity avian influenza virus (LPAIV) in different types of poultry production farms and putative spatial-environmental risk factors: distance from poultry farms to clay soil, waterways, and wild waterfowl areas. Outdoor-layer, turkey (meat and breeder), and duck (meat and breeder) farms had a significantly higher risk for LPAIV introduction than did indoor-layer farms. Except for outdoor-layer, all poultry types (i.e., broilers, chicken breeders, ducks, and turkeys) are kept indoors. For all production types, LPAIV risk decreased significantly with increasing distance to medium-sized waterways and with increasing distance to areas with defined wild waterfowl, but only for outdoor-layer and turkey farms. Future research should focus not only on production types but also on distance to waterways and wild bird areas. In addition, settlement of new poultry farms in high-risk areas should be discouraged.

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  • Molecular Antimicrobial Resistance Surveillance for Neisseria gonorrhoeae, Northern Territory, Australia
    D. M. Whiley et al.
        View Abstract

    Neisseria gonorrhoeae antimicrobial resistance (AMR) is a globally recognized health threat; new strategies are needed to enhance AMR surveillance. The Northern Territory of Australia is unique in that 2 different first-line therapies, based primarily on geographic location, are used for gonorrhea treatment. We tested 1,629 N. gonorrhoeae nucleic acid amplification test–positive clinical samples, collected from regions where ceftriaxone plus azithromycin or amoxicillin plus azithromycin are recommended first-line treatments, by using 8 N. gonorrhoeae AMR PCR assays. We compared results with those from routine culture-based surveillance data. PCR data confirmed an absence of ceftriaxone resistance and a low level of azithromycin resistance (0.2%), and that penicillin resistance was <5% in amoxicillin plus azithromycin regions. Rates of ciprofloxacin resistance and penicillinase-producing N. gonorrhoeae were lower when molecular methods were used. Molecular methods to detect N. gonorrhoeae AMR can increase the evidence base for treatment guidelines, particularly in settings where culture-based surveillance is limited.

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Dispatches

Research Letters

About the Cover

Etymologia

Volume 23, Number 10—October 2017

Synopsis

  • Fatal Rocky Mountain Spotted Fever along the United States–Mexico border, 2013–2016
    N. A. Drexler et al.
    View Summary

    Although these cases are uncommon, early recognition and prompt initiation of appropriate treatment are vital for averting severe illness and death.

           

Research

  • Enteric Infections Circulating during Hajj Seasons, 2011–2013
    M. El Ghany et al.
           
  • Economic Assessment of Waterborne Outbreak of Cryptosporidiosis
    A. Chyzheuskaya et al.
           
  • Disease Burden of Clostridium difficile Infections in Adults, Hong Kong, China, 2006–2014
    J. Ho et al.
           
  • Investigation of Outbreaks of Salmonella enterica Serovar Typhimurium and Its Monophasic Variants Using Whole-Genome Sequencing, Denmark
    P. Gymoese et al.
           

Dispatches

  • Molecular Tracing to Find Source of Protracted Invasive Listeriosis Outbreak, Southern Germany, 2012–2016
    S. Kleta et al.
           
  • Off-Label Use of Bedaquiline in Children and Adolescents with Multidrug-Resistant Tuberculosis
    J. Achar et al.
        View Abstract

    We describe 27 children and adolescents <18 years of age who received bedaquiline during treatment for multidrug-resistant tuberculosis. We report good treatment responses and no cessation attributable to adverse effects. Bedaquiline could be considered for use with this age group for multidrug-resistant tuberculosis when treatment options are limited.

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  • Bedaquiline and Delamanid Combination Treatment of 5 Patients with Pulmonary Extensively Drug-Resistant Tuberculosis
    A. Maryandyshev et al.
        View Abstract

    We report the experiences of 5 patients taking bedaquiline with delamanid in combination: 1 patient was cured; 3 culture converted, with 2 continuing and 1 changing therapy; and 1 died from respiratory insufficiency. For 2 patients, QT-interval prolongation but no arrhythmias occurred. Use of this therapy is justified for patients with limited options.

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  • Mild Illness and Absence of Hemolytic Uremic Syndrome during Shiga Toxin−Producing Escherichia coli O157 Outbreak Associated with Agricultural Show, Australia, 2013
    B. R. Vasant et al.
           
  • Enterovirus D68–Associated Acute Flaccid Myelitis in Immunocompromised Woman, Italy
    E. Giombini et al.
        View Abstract

    In Italy in 2016, acute flaccid myelitis developed in a woman who had received a hematopoietic stem cell transplant. Enterovirus D68 viral genome was detected in respiratory and cerebrospinal fluid samples, and the viral protein 1 sequence clustered with lineage B3. Immunocompromised adults may be at risk for enterovirus D68–associated neurologic complications.

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  • Hantavirus Pulmonary Syndrome Caused by Maripa Virus in French Guiana, 2008–2016
    S. Matheus et al.
           
  • Usutu Virus RNA in Mosquitoes, Israel, 2014–2015
    B. Mannasse et al.
        View Abstract

    We identified Usutu virus (USUV) RNA in 6 pools of mosquitoes trapped in northern Israel during 2014–2015. These strains Israel were most similar to strains identified in Senegal and Germany, which further elucidates common ancestry and evolutionary dynamics of USUV. Our findings suggest that human infection with USUV might occur in Israel.

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  • Macrolide-Resistant Mycoplasma pneumoniae Infection, Japan, 2008–2015
    T. Tanaka et al.
        View Abstract

    We evaluated isolates obtained from children with Mycoplasma pneumoniae infection throughout Japan during 2008–2015. The highest prevalence of macrolide-resistant M. pneumoniae was 81.6% in 2012, followed by 59.3% in 2014 and 43.6% in 2015. The prevalence of macrolide-resistant M. pneumoniae among children in Japan has decreased.

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  • Monitoring Avian Influenza Viruses from Chicken Carcasses Sold at Markets, China, 2016
    X. Mao et al.
        View Abstract

    During 2016 in Guangzhou, China, we detected infectious avian influenza viruses (AIVs) in 39.8% of samples from chicken carcasses slaughtered at live poultry markets but none from carcasses supplied to supermarkets by facilities bypassing live poultry markets. Promoting supply chains with high biosecurity may reduce the risk for zoonotic AIV transmission.

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  • Berlin Squirrelpox Virus, a New Poxvirus in Red Squirrels, Berlin, Germany
    G. Wibbelt et al.
        View Abstract

    Near Berlin, Germany, several juvenile red squirrels (Sciurus vulgaris) were found with moist, crusty skin lesions. Histology, electron microscopy, and cell culture isolation revealed an orthopoxvirus-like infection. Subsequent PCR and genome analysis identified a new poxvirus (Berlin squirrelpox virus) that could not be assigned to any known poxvirus genera.

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  • Fatal Human Case of Mosquitoborne St. Louis Encephalitis Virus Infection Diagnosed by Metagenomic Sequencing, California, 2016
    C. Y. Chiu et al.
           
  • Epidemiology of Reemerging Scarlet Fever, Hong Kong, 2005–2015
    C. Lee et al.
           

Another Dimension

  • Summer dreams
    V. Liyanapathirana
           

Research Letters

  • Bedaquiline and Linezolid for Extensively Drug-Resistant Tuberculosis in Pregnant Woman
    M. Jaspard et al.
        View Abstract

    A woman with extremely drug-resistant tuberculosis treated with a drug regimen including linezolid and bedaquiline during her last 3 weeks of pregnancy gave birth to a child without abnormalities. No fetal toxicities were noted by 2 years after delivery. This drug combination might be safe during the late third trimester of pregnancy.

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  • Dengue Virus Exported from Côte d’Ivoire to Japan, June 2017
    T. Suzuki et al.
        View Abstract

    Since April 2017, a dengue fever outbreak has been ongoing in Côte d’Ivoire. We diagnosed dengue fever (type 2 virus) in a traveler returning to Japan from Côte d’Ivoire. Phylogenetic analysis revealed strain homology with the Burkina Faso 2016 strain. This case may serve as an alert to possible disease spread outside Africa.

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  • Autochthonous Transmission of East/Central/South African Genotype Chikungunya Virus, Brazil
    M. S. Cunha et al.
        View Abstract

    We isolated East/Central/South African genotype chikungunya virus during the 2016 epidemic in Rio de Janeiro, Brazil. Genome sequencing revealed unique mutations in the nonstructural protein 4 (NSP4-A481D) and envelope protein 1 (E1-K211T). Moreover, all Brazil East/Central/South isolates shared the exclusive mutations E1-M407L and E2-A103T.

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  • Six-Month Response to Delamanid Treatment in MDR TB Patients
    C. Hewison et al.
        View Abstract

    Delamanid, recently available for the treatment of multidrug-resistant tuberculosis (MDR TB), has had limited use outside clinical trials. We present the early treatment results for 53 patients from 7 countries who received a delamanid-containing treatment for MDR TB. Results show good tolerability and treatment response at 6 months.

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  • Carbapenemase VCC-1–Producing Vibrio cholerae in Coastal Waters of Germany
    J. A. Hammerl et al.
           
  • Mycobacterium orygis Lymphadenitis in New York, USA
    L. A. Marcos et al.
           
  • Unrecognized Subclinical Infection with Tick-Borne Encephalitis Virus, Japan
    K. Yoshii et al.
           
  • Angiostrongylus cantonensis Eosinophilic Meningitis in an Infant, Tennessee, USA
    T. Flerlage et al.
           
  • Familial Transmission of emm12 Group A Streptococcus
    C. Duployez et al.
           
  • Fluoroquinolone-resistant Alcaligenes faecalis Related to Chronic Suppurative Otitis Media, Angola
    M. Filipe et al.
           
  • Ross River Virus Seroprevalence, French Polynesia, 2014–2015
           

Letter

Books and Media

  • Media Lens on the 2015–2016 Zika Epidemic
    M. F. Boni
           

Volume 23, Number 11—November 2017

Research

  • Legionnaires’ Disease Outbreak Caused by Persistent Endemic Strain of Legionella sp., New York City, New York, USA, 2015
    P. Lapierre et al.
           

Dispatches

  • High-Level Fosfomycin Resistance in Vancomycin-Resistant Enterococcus faecium
    Y. Guo et al.
           
  • Long-Term Viruria in Zika-Infected Pregnant Women
    A. B. Terzian et al.
           

Research Letter

  • Paracoccidioidomycosis after Highway Construction, Rio de Janeiro, Brazil
    A. C. do Valle et al.
           

Books and Media

  • The Politics of Fear: Médecins Sans Frontières and the West African Ebola Epidemic
    K. Hamilton
           

Volume 23, Number 12—December 2017

Synopsis

  • Fatal Outbreak in Tonkean Macaques Caused by Possibly Novel Orthopoxvirus, January 2015
    G. Cardeti et al.
           

Historical Review

  • History of Taenia saginata Tapeworms in Northern Russia
    S. V. Konyaev et al.
           

Dispatch

  • Mycobacterium ulcerans DNA in Bandicoot Excreta in Buruli Ulcer–Endemic Area, Far Northern Queensland, Australia
    K. Röltgen et al.
           
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