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Background. Community-acquired pneumonia (CAP) is the major manifestation of Q fever, an emerging disease in French Guiana. Consequently, the empirical antibiotherapy used for the treatment of CAP combines doxycycline and the recommended amoxicillin. Our objectives were to estimate the prevalence of Q fever pneumonia and to build a prediction rule to identify patients with Q fever pneumonia for empirical antibiotic guidance. Methods. A retrospective case-control study was conducted on inpatients admitted with CAP in the Department of Infectious Diseases of Cayenne Hospital from 2004 to 2007. Serodiagnosis for Coxiella burnetii was performed for all patients. Risk factor analysis was performed using multivariate logistic regression, and a prognostic score was computed using bootstrap procedures. The score performance characteristics were used to choose the best prediction rule to identify patients with Q fever pneumonia. Results. One hundred thirty-one patients with CAP were included and the Q fever pneumonia prevalence was 24.4% (95% confidence interval [CI], 17.1-31.9). In multivariate analysis, male sex, middle age (age, 30-60 years), headache, leukocyte count <10 × 10 9 /L and C-reactive protein level >185 mg/L were independently associated with Q fever pneumonia. Patients with a predictive score ≤3 had a low risk of Q fever pneumonia with a negative predictive value of 0.97 (95% CI, 90-1) and a sensitivity of 0.97 (95% CI, .89-1). Conclusions. The prediction rule described here accurately identifies patients with low risk of Q fever pneumonia and may help physicians to make more rational decisions about the empirical use of antibiotherapy. Further prospective studies should be performed to validate this score.

Methicillin-resistant Staphylococcus aureus (MRSA) is one of the most successful modern pathogens. The same organism that lives as a commensal and is transmitted in both health-care and community settings is also a leading cause of bacteraemia, endocarditis, skin and soft tissue infections, bone and joint infections and hospital-acquired infections. Genetically diverse, the epidemiology of MRSA is primarily characterized by the serial emergence of epidemic strains. Although its incidence has recently declined in some regions, MRSA still poses a formidable clinical threat, with persistently high morbidity and mortality. Successful treatment remains challenging and requires the evaluation of both novel antimicrobials and adjunctive aspects of care, such as infectious disease consultation, echocardiography and source control. In this Review, we provide an overview of basic and clinical MRSA research and summarize the expansive body of literature on the epidemiology, transmission, genetic diversity, evolution, surveillance and treatment of MRSA.Methicillin-resistant Staphylococcus aureus (MRSA) is a major pathogen both within hospitals and in the community. In this Review, Fowler and colleagues provide an overview of basic and clinical MRSA research and explore the epidemiology, transmission, genetic diversity, evolution, surveillance and treatment of MRSA.

10 days after the first reported case of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) infection in the Netherlands (on Feb 27, 2020), 55 (4%) of 1497 health-care workers in nine hospitals located in the south of the Netherlands had tested positive for SARS-CoV-2 RNA. We aimed to gain insight in possible sources of infection in health-care workers. We did a cross-sectional study at three of the nine hospitals located in the south of the Netherlands. We screened health-care workers at the participating hospitals for SARS-CoV-2 infection, based on clinical symptoms (fever or mild respiratory symptoms) in the 10 days before screening. We obtained epidemiological data through structured interviews with health-care workers and combined this information with data from whole-genome sequencing of SARS-CoV-2 in clinical samples taken from health-care workers and patients. We did an in-depth analysis of sources and modes of transmission of SARS-CoV-2 in health-care workers and patients. Between March 2 and March 12, 2020, 1796 (15%) of 12 022 health-care workers were screened, of whom 96 (5%) tested positive for SARS-CoV-2. We obtained complete and near-complete genome sequences from 50 health-care workers and ten patients. Most sequences were grouped in three clusters, with two clusters showing local circulation within the region. The noted patterns were consistent with multiple introductions into the hospitals through community-acquired infections and local amplification in the community. Although direct transmission in the hospitals cannot be ruled out, our data do not support widespread nosocomial transmission as the source of infection in patients or health-care workers. EU Horizon 2020 (RECoVer, VEO, and the European Joint Programme One Health METASTAVA), and the National Institute of Allergy and Infectious Diseases, National Institutes of Health.

Clostridioides difficile infection is a major cause of nosocomial and community illness. In this report from the Emerging Infections Program, associated with the U.S. CDC, the national burden of C. difficile infection is estimated from 2011 through 2017. In 2017, an estimated 462,100 cases of C. difficile infection occurred.

This article provides U.S. national estimates for six common nosocomial pathogens. The incidence of infection decreased for four (MRSA, vancomycin-resistant enterococcus, carbapenem-resistant acinetobacter species, and multidrug-resistant P. aeruginosa ), was constant for one (carbapenem-resistant Enterobacteriaceae), and increased for one (ESBL-producing Enterobacteriaceae).

Understanding the burden of community-acquired pneumonia (CAP) is critical to allocate resources for prevention, management, and research. The objectives of this study were to define incidence, epidemiology, and mortality of adult patients hospitalized with CAP in the city of Louisville, and to estimate burden of CAP in the US adult population. This was a prospective population-based cohort study of adult residents in Louisville, Kentucky, from 1 June 2014 to 31 May 2016. Consecutive hospitalized patients with CAP were enrolled at all adult hospitals in Louisville. The annual population-based CAP incidence was calculated. Geospatial epidemiology was used to define ecological associations among CAP and income level, race, and age. Mortality was evaluated during hospitalization and at 30 days, 6 months, and 1 year after hospitalization. During the 2-year study, from a Louisville population of 587499 adults, 186384 hospitalizations occurred. A total of 7449 unique patients hospitalized with CAP were documented. The annual age-adjusted incidence was 649 patients hospitalized with CAP per 100000 adults (95% confidence interval, 628.2-669.8), corresponding to 1591825 annual adult CAP hospitalizations in the United States. Clusters of CAP cases were found in areas with low-income and black/African American populations. Mortality during hospitalization was 6.5%, corresponding to 102821 annual deaths in the United States. Mortality at 30 days, 6 months, and 1 year was 13.0%, 23.4%, and 30.6%, respectively. The estimated US burden of CAP is substantial, with >1.5 million unique adults being hospitalized annually, 100000 deaths occurring during hospitalization, and approximately 1 of 3 patients hospitalized with CAP dying within 1 year.

Key Points Clostridium difficile infection (CDI) is a continually evolving global health-care problem Community-onset CDI is increasing and multiple potential reservoirs of infection exist including environmental sources, animals, asymptomatic patients and symptomatic patients Highly discriminatory typing techniques such as whole-genome sequencing and multi-locus variable-number tandem-repeat analysis offer the potential for illuminating previously under-recognized routes of C. difficile transmission The optimal approach to sampling and testing for CDI remains a contentious issue Multi-step algorithms are recommended to improve diagnostic sensitivity and specificity Clostridium difficile infection (CDI) is a global health-care problem and represents an important infection in both health-care facilities and the wider community. Here, the authors describe advances in understanding of CDI epidemiology, transmission and diagnosis, which are all key factors in the management of CDI. Clostridium difficile infection (CDI) continues to affect patients in hospitals and communities worldwide. The spectrum of clinical disease ranges from mild diarrhoea to toxic megacolon, colonic perforation and death. However, this bacterium might also be carried asymptomatically in the gut, potentially leading to 'silent' onward transmission. Modern technologies, such as whole-genome sequencing and multi-locus variable-number tandem-repeat analysis, are helping to track C. difficile transmission across health-care facilities, countries and continents, offering the potential to illuminate previously under-recognized sources of infection. These typing strategies have also demonstrated heterogeneity in terms of CDI incidence and strain types reflecting different stages of epidemic spread. However, comparison of CDI epidemiology, particularly between countries, is challenging due to wide-ranging approaches to sampling and testing. Diagnostic strategies for C. difficile are complicated both by the wide range of bacterial targets and tests available and the need to differentiate between toxin-producing and non-toxigenic strains. Multistep diagnostic algorithms have been recommended to improve sensitivity and specificity. In this Review, we describe the latest advances in the understanding of C. difficile epidemiology, transmission and diagnosis, and discuss the effect of these developments on the clinical management of CDI.

Using molecular diagnostic methods, the prevalence of Mycoplasma pneumoniae was the highest among hospitalized children aged 10-17 years admitted with community-acquired pneumonia; 12% required intensive care. Macrolide resistance was infrequent. Clinical presentations could not differentiate M. pneumoniae from other etiologies. Abstract Background The epidemiology of Mycoplasma pneumoniae (Mp) among US children (<18 years) hospitalized with community-acquired pneumonia (CAP) is poorly understood. Methods In the Etiology of Pneumonia in the Community study, we prospectively enrolled 2254 children hospitalized with radiographically confirmed pneumonia from January 2010-June 2012 and tested nasopharyngeal/oropharyngeal swabs for Mp using real-time polymerase chain reaction (PCR). Clinical and epidemiological features of Mp PCR-positive and -negative children were compared using logistic regression. Macrolide susceptibility was assessed by genotyping isolates. Results One hundred and eighty two (8%) children were Mp PCR-positive (median age, 7 years); 12% required intensive care and 26% had pleural effusion. No in-hospital deaths occurred. Macrolide resistance was found in 4% (6/169) isolates. Of 178 (98%) Mp PCR-positive children tested for copathogens, 50 (28%) had ≥1 copathogen detected. Variables significantly associated with higher odds of Mp detection included age (10-17 years: adjusted odds ratio [aOR], 10.7 [95% confidence interval {CI}, 5.4-21.1] and 5-9 years: aOR, 6.4 [95% CI, 3.4-12.1] vs 2-4 years), outpatient antibiotics ≤5 days preadmission (aOR, 2.3 [95% CI, 1.5-3.5]), and copathogen detection (aOR, 2.1 [95% CI, 1.3-3.3]). Clinical characteristics were non-specific. Conclusions Usually considered as a mild respiratory infection, Mp was the most commonly detected bacteria among children aged ≥5 years hospitalized with CAP, one-quarter of whom had codetections. Although associated with clinically nonspecific symptoms, there was a need for intensive care in some cases. Mycoplasma pneumoniae should be included in the differential diagnosis for school-aged children hospitalized with CAP.

Pneumonia is a major cause of severe illness in children. In a study of community-acquired pneumonia requiring hospitalization among U.S. children, those younger than 2 years of age were most affected, and viruses were most commonly found. Pneumonia is a leading cause of hospitalization among children in the United States, 1 – 3 with medical costs estimated at almost $1 billion in 2009. 4 Despite this large burden of disease, critical gaps remain in our knowledge about pneumonia in children. 5 Contemporary estimates of the incidence and microbiologic causes of hospitalization for community-acquired pneumonia among children in the United States would be of value. 5 Most recent published estimates of the incidence of pneumonia have used administrative data, which are limited because a strict clinical and radiographic definition of community-acquired pneumonia is difficult to apply to such data and because diagnostic testing . . .

More than 500 000 neonatal deaths per year result from possible serious bacterial infections (pSBIs), but the causes are largely unknown. We investigated the incidence of community-acquired infections caused by specific organisms among neonates in south Asia. From 2011 to 2014, we identified babies through population-based pregnancy surveillance at five sites in Bangladesh, India, and Pakistan. Babies were visited at home by community health workers up to ten times from age 0 to 59 days. Illness meeting the WHO definition of pSBI and randomly selected healthy babies were referred to study physicians. The primary objective was to estimate proportions of specific infectious causes by blood culture and Custom TaqMan Array Cards molecular assay (Thermo Fisher, Bartlesville, OK, USA) of blood and respiratory samples. 6022 pSBI episodes were identified among 63 114 babies (95·4 per 1000 livebirths). Causes were attributed in 28% of episodes (16% bacterial and 12% viral). Mean incidence of bacterial infections was 13·2 (95% credible interval [CrI] 11·2–15·6) per 1000 livebirths and of viral infections was 10·1 (9·4–11·6) per 1000 livebirths. The leading pathogen was respiratory syncytial virus (5·4, 95% CrI 4·8–6·3 episodes per 1000 livebirths), followed by Ureaplasma spp (2·4, 1·6–3·2 episodes per 1000 livebirths). Among babies who died, causes were attributed to 46% of pSBI episodes, among which 92% were bacterial. 85 (83%) of 102 blood culture isolates were susceptible to penicillin, ampicillin, gentamicin, or a combination of these drugs. Non-attribution of a cause in a high proportion of patients suggests that a substantial proportion of pSBI episodes might not have been due to infection. The predominance of bacterial causes among babies who died, however, indicates that appropriate prevention measures and management could substantially affect neonatal mortality. Susceptibility of bacterial isolates to first-line antibiotics emphasises the need for prudent and limited use of newer-generation antibiotics. Furthermore, the predominance of atypical bacteria we found and high incidence of respiratory syncytial virus indicated that changes in management strategies for treatment and prevention are needed. Given the burden of disease, prevention of respiratory syncytial virus would have a notable effect on the overall health system and achievement of Sustainable Development Goal. Bill & Melinda Gates Foundation