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Objectives: Describe two 2009-H1N1 influenza outbreaks in university-based summer camps and the implementation of an infection control program. Participants: 7,906 campers across 73 residential camps from May 21–August 2, 2009. Methods: Influenza-like-illness (ILI) was defined as fever with cough and/or sore throat. Influenza A was identified using PCR or rapid-antigen testing. We implemented an infection control program consisting of education, hand hygiene, disinfection, symptom screening, and ILI case management. Results: An initial ILI cluster involved 60 cases across 3 camps from June 17–July 2. Academic Camp-1 had the most cases (n = 45, 14.9% attack rate); influenza A was identified in 84% of those tested. Despite implementation of an infection control program, a second ILI cluster began on July 12 in Academic Camp-2 (n = 47, 15.0% attack rate). Conclusions: ILI can spread rapidly in a university-based residential camp. Infection control is an important aspect of the medical response but i...

BACKGROUND: Bloodstream infections are a major cause of morbidity and mortality in adults. Bloodstream infections should be reassessed periodically because of increased antibiotic resistance, more patients receiving immunomodulatory therapy, improved antiretroviral therapy, and acquisition of infection in health care settings other than hospitals. METHODS: We conducted retrospective assessment by infectious disease physicians of hospitalized adults with positive blood cultures at 3 academic medical centers. RESULTS: Two thousand two hundred seventy positive blood culture episodes occurred in 1706 patients. Of 2669 isolates, 51% represented true infection, 41% contamination, and 8% unknown clinical significance. Although coagulase-negative staphylococci were most common, only 10% were clinically significant. Among 1225 true bloodstream infections, the most frequent isolates were Staphylococcus aureus, Escherichia coli, Enterococcus spp., Klebsiella pneumoniae, coagulase-negative staphylococci, Pseudomonas aeruginosa, Candida albicans, Enterobacter cloacae, and Serratia marcescens. Intravenous catheters were the most common primary source of bloodstream infection (23% of episodes). Most (81%) bloodstream infections were acquired in the hospital or other health care settings. Crude and attributable in-hospital case-fatality ratios were 20% and 12%, respectively, lower than in previous studies. Increasing age, hypotension, absence of fever, hospital acquisition, extreme white blood cell count values, and the presence of the acquired immunodeficiency syndrome, malignancy, or renal disease were significantly associated with an increased risk of in-hospital attributable death in multivariable analysis. CONCLUSIONS: The proportion of bloodstream infections due to intravenous catheters is continuing to increase. Most episodes were acquired in the hospital or other health care setting. In-hospital case-fatality ratios have decreased compared with previous studies. Several previously identified factors associated with an increased mortality remain statistically significant.

The performance of 4 laboratory methods for diagnosis of viral respiratory tract infections (RTI) in older adults was evaluated. Seventy-four nasopharyngeal (NP) swab specimens were obtained from 60 patients with RTI at a long-term care facility over 2 respiratory seasons. Sixteen specimens were positive for a respiratory virus by at least 1 method. Multiplex reverse transcriptase polymerase chain reaction (RT-PCR) by the Luminex xTAG® Respiratory Viral Panel (RVP) detected 16 (100%) of the positive specimens, RVP of 24-h culture supernatant detected 8 (50%), direct fluorescent antibody testing detected 4 (25%), rapid culture detected 2 (12.5%), and rapid antigen testing detected none. For a comparison group, RVP was performed on NP swabs from 20 outpatient children with RTI. The mean fluorescence intensity by RVP was significantly lower for positive adult patients than pediatric patients (P = 0.0373). Our data suggest that older adult patients shed lower titers of viruses, necessitating a highly sensitive assay such as RT-PCR to reliably detect respiratory viral pathogens.

There is increasing recognition of the importance of community-associated Clostridium difficile infection (CA-CDI) despite little being known about its epidemiology. We performed routine, active laboratory surveillance for CDI at the Durham Veterans Affairs Medical Center between January and December 2005 and extracted data from the electronic medical record for this investigation. Bivariable analyses were performed using the chi-square test, and continuous variables were compared using two sample t test and Wilcoxon rank sums. We identified 108 CDI cases during the study period; 38 (35%) had onset of disease in the community and, of these, 31 (82%) met the definition for CA-CDI. A comparison of CA- versus healthcare facility-associated (HCFA)-CDI revealed that CA-CDI patients were younger (median age 58 vs. 69 years, respectively; p = 0.01), with the majority being

Background Dengue is a leading cause of fever and mimics other acute febrile illnesses (AFI). In 2009, the World Health Organization (WHO) revised criteria for clinical diagnosis of dengue. Methodology/Principal findings The new WHO 2009 classification of dengue divides suspected cases into three categories: dengue without warning signs, dengue with warning signs and severe dengue. We evaluated the WHO 2009 classification vs physicians’ subjective clinical diagnosis (gestalt clinical impression) in a large cohort of patients presenting to a tertiary care center in southern Sri Lanka hospitalized with acute febrile illness. We confirmed acute dengue in 388 patients (305 adults ≥ 18 years and 83 children), including 103 primary and 245 secondary cases, of 976 patients prospectively enrolled with AFI. At presentation, both adults and children with acute dengue were more likely than those with other AFI to have leukopenia and thrombocytopenia. Additionally, adults were more likely than those with other AFI to have joint pain, higher temperatures, and absence of crackles on examination whereas children with dengue were more likely than others to have sore throat, fatigue, oliguria, and elevated hematocrit and transaminases. Similarly, presence of joint pain, thrombocytopenia, and absence of cough were independently associated with secondary vs primary dengue in adults whereas no variables were different in children. The 2009 WHO dengue classification was more sensitive than physicians’ clinical diagnosis for identification of acute dengue (71.5% vs 67.1%), but was less specific. However, despite the absence of on-site diagnostic confirmation of dengue, clinical diagnosis was more sensitive on discharge (75.2%). The 2009 WHO criteria classified almost 75% as having warning signs, even though only 9 (2.3%) patients had evidence of plasma leakage and 16 (4.1%) had evidence of bleeding Conclusions/Significance In a large cohort with AFI, we identified features predictive of dengue vs other AFI and secondary vs primary dengue in adults versus children. The 2009 WHO dengue classification criteria had high sensitivity but low specificity compared to physicians’ gestaldt diagnosis. Large cohort studies will be needed to validate the diagnostic yield of clinical impression and specific features for dengue relative to the 2009 WHO classification criteria., Author summary Dengue is an important cause of acute fever in the tropics that is difficult to distinguish from other common etiologies of fever. The World Health Organization (WHO) revised criteria for the clinical diagnosis and classification of acute dengue in 2009. The performance of these criteria has not been widely evaluated in countries where dengue is endemic. We confirmed acute dengue in 388 of 976 patients presenting with acute febrile illness (AFI) to the largest tertiary care center in the Southern Province of Sri Lanka. We found specific clinical features and laboratory investigations to be predictive of acute dengue versus other AFI. The new WHO 2009 classification was more sensitive than physicians’ clinical diagnosis for identification of acute dengue on admission to hospital, but also over-estimated the severity of illness. Further large cohort studies are warranted to validate the performance of the 2009 WHO criteria for diagnosis and prognosis of dengue in regions where the disease burden is high.

We determined estimated incidence of and risk factors for community-associated Clostridium difficile infection (CA-CDI) among patients treated at 6 North Carolina hospitals. CA-CDI case-patients were defined as adults (>18 years of age) with a positive stool test result for C. difficile toxin and no hospitalization within the prior 8 weeks. CA-CDI incidence was 21 and 46 per 100,000 person-years in Veterans Affairs (VA) outpatients and Durham County populations, respectively. VA case-patients were more likely than controls to have received antimicrobial drugs (adjusted odds ratio [aOR] 17.8, 95% confidence interval [CI] 6.6–48] and to have had a recent outpatient visit (aOR 5.1, 95% CI 1.5–17.9). County case-patients were more likely than controls to have received antimicrobial drugs (aOR 9.1, 95% CI 2.9–28.9), to have gastroesophageal reflux disease (aOR 11.2, 95% CI 1.9–64.2), and to have cardiac failure (aOR 3.8, 95% CI 1.1–13.7). Risk factors for CA-CDI overlap with those for healthcare-associated infection.

We determined estimated incidence of and risk factors for community-associated Clostridium difficile infection (CA-CDI) among patients treated at 6 North Carolina hospitals. CA-CDI case-patients were defined as adults (>18 years of age) with a positive stool test result for C. difficile toxin and no hospitalization within the prior 8 weeks. CA-CDI incidence was 21 and 46 per 100,000 person-years in Veterans Affairs (VA) outpatients and Durham County populations, respectively. VA case-patients were more likely than controls to have received antimicrobial drugs (adjusted odds ratio [aOR] 17.8, 95% confidence interval [CI] 6.6-48] and to have had a recent outpatient visit (aOR 5.1, 95% CI 1.5-17.9). County case-patients were more likely than controls to have received antimicrobial drugs (aOR 9.1, 95% CI 2.9-28.9), to have gastroesophageal reflux disease (aOR 11.2, 95% CI 1.9-64.2), and to have cardiac failure (aOR 3.8, 95% CI 1.1-13.7). Risk factors for CA-CDI overlap with those for healthcare-associated infection.

Hemophagocytic lymphohistiocytosis (HLH) is a rare disease resulting from an abnormal proliferation of histiocytes within the body's tissues leading to an ineffective immune response. Typically, HLH is characterized by fever, hepatosplenomegaly, cytopenia, hypertriglyceridemia, hypofibrinogenemia, and hemophagocytosis. However, the premature infant with HLH may present differently making diagnosis of the disease cumbersome. If an infant is born with ascites, cytopenias, hypofibrinogenemia, and hepatosplenomegaly, a diagnosis of HLH cannot be ruled out. In addition, premature infants oftentimes will not present with fever because they are kept normothermic from ambient sources. Reports of premature infants with HLH in the literature are rare. This is a case presentation of a 27-week-gestation female with a family history of HLH.

A large norovirus outbreak affecting hospital patients and staff occurred during the winter of 2007. We administered a survey to affected staff to evaluate adherence to social distancing recommendations. Of the 102 survey respondents, 74 (73%) completed self-quarantine. Staff adherence was similar regardless of job responsibility. Incomplete adherence to recommendations could potentially accelerate and prolong infectious disease outbreaks.

Author(s): Caram, L Brett; Chen, Jodi; Taggart, E William; Hillyard, David R; She, Rosemary; Polage, Christopher R; Twersky, Jack; Schmader, Kenneth; Petti, Cathy A; Woods, Christopher W | Abstract: ObjectivesTo report an outbreak of respiratory synctyial virus (RSV) in a long-term care facility (LTCF) during ongoing routine respiratory illness surveillance.DesignRapid antigen testing, viral culture, direct fluorescent antibody (DFA) testing, and reverse transcriptase polymerase chain reaction (RT-PCR) testing for up to 15 viruses in symptomatic residents and chart review.SettingA 120-bed LTCF.MeasurementsComparison of rapid antigen testing, respiratory viral cultures, and DFA testing and RT-PCR in residents with symptoms of a respiratory tract infection.ResultsTwenty-two of 52 residents developed symptoms of a respiratory tract infection between January 29, 2008, and February 26, 2008. RSV was detected using RT-PCR in seven (32%) of the 22 cases. None of the seven cases had positive RSV rapid antigen testing, and only two had positive culture or DFA results. This outbreak occurred during a time when state wide RSV rates were rapidly declining. One patient was admitted to the hospital during the infection and subsequently died.ConclusionRSV may cause outbreaks in LTCFs that traditional diagnostic methods do not detect. RT-PCR can provide a more timely and accurate diagnosis of outbreaks, which allows for early symptomatic treatment, rational use of antibiotics, and improved infection control.

Sepsis is a common and severe medical condition with substantial associated morbidity, mortality and cost. Furthermore, the incidence of sepsis has been rising annually over the past three decades, and morbidity and mortality remain high. The management of sepsis is further complicated by its very heterogeneous nature. This extends not only to the offending pathogens, but also to the nature and severity of the host response as well as its clinical manifestations. Efforts to identify surrogate markers for sepsis have therefore been an ongoing struggle. In this article we present some insights into various sepsis markers through history, presenting advantages and caveats associated with their use and interpretation. We also discuss the state of functional genomics, a relatively recent technological advancement that has already begun to change our understanding of sepsis pathophysiology, and offer new directions in the development of a more sensitive and specific sepsis biomarker.

Murine typhus was diagnosed by PCR in 50 (7%) of 756 adults with febrile illness seeking treatment at Patan Hospital in Kathmandu, Nepal. Of patients with murine typhus, 64% were women, 86% were residents of Kathmandu, and 90% were unwell during the winter. No characteristics clearly distinguished typhus patients from those with blood culture-positive enteric fever.

Objective: Sri Lanka’s human, physical, social, and economic resources suffered a massive impact after the tsunami of December 26, 2004. To assist in preparing for future disasters, the authors sought to characterize the pattern of hospitalizations from the main impact zone in the Southern Province. Design: Retrospective chart review. Setting: Patients admitted to Teaching Hospital, Karapitiya, the only tertiary care hospital in the Southern Province. Patients, Participants: All hospital admissions on the day of and week following the tsunami, and a random sample (5 percent) of admissions from the month preceding, and the 3 months following the tsunami were coded according to the International Classification of Diseases, 10th Edition, analyzed, and geomapped. Intervention: N/A. Main Outcome Measure(s): The overall daily number of hospitalizations increased by 50 percent on the day of the tsunami and decreased in the following week. Results: Before the tsunami, injuries typically accounted for 20 percent of hospital admissions. However, injuries were markedly higher (89 percent of the total) on the day of the tsunami and remained elevated (35 percent) during the following week. After the initial peak in injuries (including near drownings), there was no increase in the frequency of infectious, cardiac, or psychiatric admissions. Conclusions: Injuries (including near drownings) were the most common cause of admissions immediately after the tsunami.The distribution of specific diagnoses differed from that seen after other natural disasters such as earthquakes and hurricanes. A central aspect of disaster relief operations and planning includes a thorough understanding of the postdisaster health effects and changes in disease patterns.

Objective.To determine the timing of community-onset Clostridium difficile–associated disease (CDAD) relative to the patient's last healthcare facility discharge, the association of postdischarge cases with healthcare facility–onset cases, and the influence of postdischarge cases on overall rates and interhospital comparison of rates of CDAD.Design.Retrospective cohort study for the period January 1, 2005, through December 31, 2005.Setting.Catchment areas of 6 acute care hospitals in North Carolina.Methods.We reviewed medical and laboratory records to determine the date of symptom onset, the dates of hospitalization, and stool C. difficile toxin assay results for patients with CDAD who had diarrhea and positive toxin–assay results. Cases were classified as healthcare facility–onset if they were diagnosed more than 48 hours after admission. Cases were defined as community-onset if they were diagnosed in the community or within 48 hours after admission, and were also classified on the basis of the time since the last discharge: if within 4 weeks, community-onset, healthcare facility–associated (CO-HCFA); if 4-12 weeks, indeterminate exposure; and if more than 12 weeks, community-associated. Pearson's correlation coefficient was used to assess the association between monthly rates of healthcare facility–onset, healthcare facility–associated (HO-HCFA) cases and CO-HCFA cases. We performed interhospital rate comparisons using HO-HCFA cases only and using both HO-HCFA and CO-HCFA cases.Results.Of 1046 CDAD cases, 442 (42%) were HO-HCFA cases and 604 (58%) were community-onset cases. Of the 604 community-onset cases, 94 (15%) were CO-HCFA, 40 (7%) were of indeterminate exposure, and 208 (34%) community-associated. A modest correlation was found between monthly rates of HO-HCFA cases and CO-HCFA cases across the 6 hospitals (r = 0.63, PConclusions.A substantial proportion of community-onset cases of CDAD occur less than 4 weeks after discharge from a healthcare facility, and inclusion of CO-HCFA cases influences interhospital comparisons. Our findings support the use of a proposed definition of healthcare facility–associated CDAD that includes cases that occur within 4 weeks after discharge.

Using 42 isolates contributed by laboratories in Canada, The Netherlands, the United Kingdom, and the United States, we compared the results of analyses done with seven Clostridium difficile typing techniques: multilocus variable-number tandem-repeat analysis (MLVA), amplified fragment length polymorphism (AFLP), surface layer protein A gene sequence typing ( slpA ST), PCR-ribotyping, restriction endonuclease analysis (REA), multilocus sequence typing (MLST), and pulsed-field gel electrophoresis (PFGE). We assessed the discriminating ability and typeability of each technique as well as the agreement among techniques in grouping isolates by allele profile A (AP-A) through AP-F, which are defined by toxinotype, the presence of the binary toxin gene, and deletion in the tcdC gene. We found that all isolates were typeable by all techniques and that discrimination index scores for the techniques tested ranged from 0.964 to 0.631 in the following order: MLVA, REA, PFGE, slpA ST, PCR-ribotyping, MLST, and AFLP. All the techniques were able to distinguish the current epidemic strain of C. difficile (BI/027/NAP1) from other strains. All of the techniques showed multiple types for AP-A (toxinotype 0, binary toxin negative, and no tcdC gene deletion). REA, slpA ST, MLST, and PCR-ribotyping all included AP-B (toxinotype III, binary toxin positive, and an 18-bp deletion in tcdC ) in a single group that excluded other APs. PFGE, AFLP, and MLVA grouped two, one, and two different non-AP-B isolates, respectively, with their AP-B isolates. All techniques appear to be capable of detecting outbreak strains, but only REA and MLVA showed sufficient discrimination to distinguish strains from different outbreaks.

Despite isolation precautions and enhanced hand hygiene product use, the transmission of healthcare-associated pathogens remains a major problem. Recent studies have confirmed that microbial contamination of the environment in intensive care units (ICUs) can lead to colonisation and infection of patients. Although environmental disinfectants have been used to minimise the spread of microbial pathogens, suboptimal cleaning may limit the effectiveness of such activities. In order to evaluate the thoroughness of cleaning near-patient surfaces, a transparent, easily cleanable and environmentally stable solution was developed that fluoresces when exposed to UV light. The solution was used to mark a standardised group of frequently touched objects in ICU patient rooms following discharge cleaning. These sites were then evaluated after at least two patients had occupied the room and at least two terminal cleanings had been completed. Evaluation of 2320 objects in 197 patient areas disclosed that 57.1% of the standardised sites were cleaned following discharge of the room's occupant in the 16 ICUs studied. Although high rates of cleaning (>80%) were found for toilet seats, sinks and tray tables, consistently low rates of cleaning (

New treatment modalities are needed for the treatment of infections due to multidrug-resistant Staphylococcus aureus. S. aureus capsular polysaccharide immune globulin (Altastaph) is a polyclonal immune globulin preparation that is being developed as adjunctive therapy for persons with S. aureus infections complicated by bacteremia. In a phase II, multicenter, randomized, double-blind, placebo-controlled trial, 40 subjects with documented S. aureus bacteremia received standard therapy plus either Altastaph at 200 mg/kg of body weight in each of two infusions 24 h apart or placebo. During the 42-day observation period, antibody pharmacokinetics and safety were the primary characteristics studied. Information regarding the resolution of bacteremia and fever was also analyzed. Anti-type-5 and anti-type-8 capsular antibody levels peaked after the second infusion at 550 μg/ml and 419 μg/ml, respectively, and remained above 100 μg/ml at day 28. A total of 316 adverse events were noted in 39 of 40 subjects. Infusion-related adverse events in Altastaph recipients were infrequent and similar to those among recipients of commercial intravenously administered immunoglobulin G products. Five of 21 (23%) subjects in the Altastaph group died, whereas 2 of 18 (11%) subjects in the placebo group died ( P = 0.42). Compared to the control patients, the Altastaph recipients had a shorter median time to the resolution of fever (2 days and 7 days, respectively; P = 0.09) and a shorter length of hospital stay (9 days and 14 days, respectively; P = 0.03). However, these findings are exploratory, and there were few differences in the other variables measured. High levels of opsonizing antibodies were maintained for the initial 4 weeks. Although the study was not powered to show efficacy, these preliminary findings and safety profile suggest that Altastaph may be an effective adjunct to antibiotics and warrants further investigation (ClinicalTrials.gov number NCT00063089).

Using PCR in conjunction with pre-enrichment culture, we detected Bartonella henselae and B. vinsonii subspecies berkhoffii in the blood of 14 immunocompetent persons who had frequent animal contact and arthropod exposure.

Objectives To evaluate pneumococcal immunization in older adults living in retirement communities and to measure nasopharyngeal carriage of Streptococcus pneumoniae to better assess the potential for herd protection from the 13-valent pneumococcal conjugate vaccine (PCV-13) in these settings. Design Cross-sectional observational study of adults aged 65 and older living in retirement communities to determine coverage with 23-valent pneumococcal vaccine (PPSV-23), coverage with PCV-13 in immuncompromised individuals according to 2012 Advisory Committee on Immunization Practices (ACIP) guidelines, and nasopharyngeal carriage of S. pneumoniae. Setting Two retirement communities in North Carolina. Participants Older adults recruited between December 2013 and April 2014 (N = 21, 64.8% female, mean age 81.4). Measurements A survey was used to assess chronic illnesses, immunization history, and potential risk factors for pneumococcal carriage; a chart review was used to confirm immunization history and abstract chronic conditions; and a nasopharyngeal swab was collected and cultured for S. pneumoniae. Results Eighty-seven percent of participants reported receiving PPSV-23 since age 65. Of the 16.2% of participants with an immunocompromising condition, only one had received PCV-13. Nasopharyngeal carriage with S. pneumoniae was detected in 1.9% (95% confidence interval = 0.0–3.8%) of participants. Conclusion In this select sample, PPSV-23 coverage was high, but adherence to the ACIP recommendation for PCV-13 in immunocompromised groups was low. Nasopharyngeal carriage of S. pneumoniae was present, although infrequent, suggesting that immunization with PCV-13 could provide an individual benefit and a small degree of herd protection.

Phenol-soluble modulins (PSMs) are amphipathic, pro-inflammatory proteins secreted by most Staphylococcus aureus isolates. This study tested the hypothesis that in vitro PSM production levels are associated with specific clinical phenotypes.177 methicillin-resistant S. aureus (MRSA) isolates from infective endocarditis (IE), skin and soft tissue infection (SSTI), and hospital-acquired/ventilator-associated pneumonia (HAP) were matched by geographic origin, then genotyped using spa-typing. In vitro PSM production was measured by high performance liquid chromatography/mass spectrometry. Statistical analysis was performed using Chi-squared or Kruskal-Wallis tests as appropriate.Spa type 1 was significantly more common in SSTI isolates (62.7% SSTI; 1.7% IE; 16.9% HAP; p 0.0001) while HAP and IE isolates were more commonly spa type 2 (0% SSTI; 37.3% IE; 40.7% HAP; p 0.0001). USA300 isolates produced the highest levels of PSMs in vitro. SSTI isolates produced significantly higher quantities of PSMα1-4, PSMβ1, and δ-toxin than other isolates (p 0.001). These findings persisted when USA300 isolates were excluded from analysis.Increased in vitro production of PSMs is associated with an SSTI clinical source. This significant association persisted after exclusion of USA300 genotype isolates from analysis, suggesting that PSMs play a particularly important role in the pathogenesis of SSTI as compared to other infection types.

In Kenya, more than 10 million episodes of acute febrile illness are treated annually among children under 5 years. Most are clinically managed as malaria without parasitological confirmation. There is an unmet need to describe pathogen-specific etiologies of fever. We enrolled 370 febrile children and 184 healthy controls. We report demographic and clinical characteristics of patients with Plasmodium falciparum, group A streptococcal (GAS) pharyngitis, and respiratory viruses (influenza A and B, respiratory syncytial virus [RSV], parainfluenza [PIV] types 1-3, adenovirus, human metapneumovirus [hMPV]), as well as those with undifferentiated fever. Of febrile children, 79.7% were treated for malaria. However, P. falciparum was detected infrequently in both cases and controls (14/268 [5.2%] versus 3/133 [2.3%], P = 0.165), whereas 41% (117/282) of febrile children had a respiratory viral infection, compared with 24.8% (29/117) of controls (P = 0.002). Only 9/515 (1.7%) children had streptococcal infection. Of febrile children, 22/269 (8.2%) were infected with > 1 pathogen, and 102/275 (37.1%) had fevers of unknown etiology. Respiratory viruses were common in both groups, but only influenza or parainfluenza was more likely to be associated with symptomatic disease (attributable fraction [AF] 67.5% and 59%, respectively). Malaria was overdiagnosed and overtreated. Few children presented to the hospital with GAS pharyngitis. An enhanced understanding of carriage of common pathogens, improved diagnostic capacity, and better-informed clinical algorithms for febrile illness are needed.

The field of infectious diseases is witnessing the rapid evolution of molecular diagnostics, mostly focused on pathogen detection. However, targeting the host response for diagnostic and prognostic purposes has been described as a paradigm shift ( Ramilo & Mejias, 2009 ). The concept of host response is not new. The erythrocyte sedimentation rate described in 1917 and C-reactive protein in 1930 are still used today albeit with limitations. More contemporary biomarkers based on known biology include procalcitonin, cytokines, and lactate. However, completion of the Human Genome Project in 2003 triggered the rapid pace of discovery we see today. This has set the stage for various ‘omic technologies to identify new biomarkers from these unbiased systems biology approaches. The massive streams of data associated with omics impose their own challenges, spurring developments in statistics, bioinformatics, and computing. Fortunately, the availability of data and the means to process it have converged, creating the right environment for host-based molecular diagnostics in infectious diseases to flourish. Transcriptomics, metabolomics, and proteomics constitute the major tools to identify host-response biomarkers of infectious diseases. Specifically, research generated by these approaches has led to the development of bacterial, viral, fungal, and parasite pathogen class diagnostic and prognostic biomarkers.

The development of sensitive and selective techniques for multiplex detection of DNA biomarkers is paramount for clinical diagnosis. Various multiplex DNA detection techniques have been reported. However, most of these techniques require multiple incubation and/or washing steps or target sequence labeling. In this work, we demonstrated a unique multiplex DNA biosensor for viral infection diagnosis using the surface-enhanced Raman scattering (SERS) “Molecular Sentinel-on-Chip” (MSC) technique. The sensing mechanism is based upon the change of SERS intensity when Raman labels tagged at 3′-ends of molecular sentinel nanoprobes are physically displaced from the Nanowave chip’s surface upon target DNA hybridization. SERS measurements were performed immediately following a single hybridization reaction between the target single-stranded DNA (ssDNA) sequences and the complementary molecular sentinel nanoprobes immobilized on the Nanowave chip without requiring target labeling (i.e., label-free assay), secondary hybridization, or post-hybridization washing, thus reducing the assay time and lowering cost. Two nucleic acid transcripts, interferon alpha-inducible protein 27 (IFI27) and interferon-induced protein 44-like (IFI44L), are used as model systems for the multiplex detection concept demonstration. These two genes are well known for their critical role in host immune response to viral infections and can be used as molecular signature for viral infection diagnosis. The results indicate the effectiveness and potential of the MSC technology for multiplex DNA detection for point-of-care diagnostics and global health applications.

International audience; Background - The impact of early valve surgery (EVS) on the outcome of Staphylococcus aureus (SA) prosthetic valve infective endocarditis (PVIE) is unresolved. The objective of this study was to evaluate the association between EVS, performed within the first 60 days of hospitalization, and outcome of SA PVIE within the International Collaboration on Endocarditis-Prospective Cohort Study. Methods - Participants were enrolled between June 2000 and December 2006. Cox proportional hazards modeling that included surgery as a time-dependent covariate and propensity adjustment for likelihood to receive cardiac surgery was used to evaluate the impact of EVS and 1-year all-cause mortality on patients with definite left-sided S. aureus PVIE and no history of injection drug use. Results - EVS was performed in 74 of the 168 (44.3%) patients. One-year mortality was significantly higher among patients with S. aureus PVIE than in patients with non-S. aureus PVIE (48.2% vs 32.9%; P = .003). Staphylococcus aureus PVIE patients who underwent EVS had a significantly lower 1-year mortality rate (33.8% vs 59.1%; P = .001). In multivariate, propensity-adjusted models, EVS was not associated with 1-year mortality (risk ratio, 0.67 [95% confidence interval, .39-1.15]; P = .15). Conclusions - In this prospective, multinational cohort of patients with S. aureus PVIE, EVS was not associated with reduced 1-year mortality. The decision to pursue EVS should be individualized for each patient, based upon infection-specific characteristics rather than solely upon the microbiology of the infection causing PVIE.

A systems biology approach was used to comprehensively examine the impact of renal disease and hemodialysis (HD) on patient response during critical illness. To achieve this, we examined the metabolome, proteome, and transcriptome of 150 patients with critical illness, stratified by renal function. Quantification of plasma metabolites indicated greater change as renal function declined, with the greatest derangements in patients receiving chronic HD. Specifically, 6 uremic retention molecules, 17 other protein catabolites, 7 modified nucleosides, and 7 pentose phosphate sugars increased as renal function declined, consistent with decreased excretion or increased catabolism of amino acids and ribonucleotides. Similarly, the proteome showed increased levels of low-molecular-weight proteins and acute-phase reactants. The transcriptome revealed a broad-based decrease in mRNA levels among patients on HD. Systems integration revealed an unrecognized association between plasma RNASE1 and several RNA catabolites and modified nucleosides. Further, allantoin, N1-methyl-4-pyridone-3-carboxamide, and N-acetylaspartate were inversely correlated with the majority of significantly downregulated genes. Thus, renal function broadly affected the plasma metabolome, proteome, and peripheral blood transcriptome during critical illness; changes were not effectively mitigated by hemodialysis. These studies allude to several novel mechanisms whereby renal dysfunction contributes to critical illness.

Background. Outbreaks of meningococcal disease are infrequent but important public health events. We characterize outbreak-associated cases in the United States and compare them with sporadic disease. Methods. Outbreaks of meningococcal disease that occurred during the period of 1 July 1994 through 30 June 2002 were identified through state health departments, Centers for Disease Control and Prevention records, and a review of newspapers and the medical literature. Cases associated with outbreaks were compared with sporadic cases identified through population-based surveillance. Results. We identified 69 outbreaks of Neisseria meningitidis infection (median, 9.5 outbreaks per year; range, 3-14 outbreaks per year), which involved 229 patients from 30 states. Forty-three (62%) of the outbreaks involved N. meningitidis serogroup C, 17 (25%) involved serogroup B, and 9 (13%) involved serogroup Y. Twenty-five outbreaks (36%) occurred in communities, and 44 (64%) were organization based, including 12 that occurred in colleges and universities, 19 that occurred in primary and secondary schools, and 8 that occurred in nursing homes. Vaccination campaigns (with the A/C/Y/W-135 meningococcal polysaccharide vaccine) were conducted for 31 outbreaks (28 involving serogroup C and 3 involving serogroup Y). After controlling for age, serogroup, and clinical presentation, outbreak-associated cases were associated with a higher case-fatality rate than were sporadic cases (21% vs. 11%; odds ratio, 3.3; 95% confidence interval, 2.0-5.5). Conclusions. Outbreaks remain an important but infrequent public health issue, representing

With the persistent threat of emerging infectious diseases and bioterrorism, it has become increasingly important that clinicians be able to identify the diseases that might signal the occurrence of these unusual events. Essential to a thoughtful diagnostic approach is understanding when to initiate a public health investigation and how to appropriately use commonly performed microbiology procedures in the sentinel laboratory to evaluate potential pathogens. Although diagnostic test development is evolving rapidly, recognizing many of these pathogens continues to challenge the capabilities of most sentinel laboratories. Therefore, effective, ongoing communication and education among clinicians, infection control personnel, sentinel laboratorians, public health authorities, and Laboratory Response Network reference laboratorians is the key to preparedness.

In Georgia, most individuals reported with West Nile virus (WNV) disease have been diagnosed with West Nile neuroinvasive disease (WNND). Relatively few cases of West Nile Fever (WNF) are reported, and the burden of illness due to WNV is likely underestimated. From July through October 2003, WNV serologic testing was performed on enrolled patients>or=18 years of age with fever admitted to a large, urban hospital in Atlanta, Georgia through the emergency department (ED). Patients' history, clinical, and laboratory data were recorded. Residual blood drawn in the ED was tested to determine the presence of WNV IgG and IgM antibodies. Of 254 patients tested for WNV, four (1.6%) patients were positive for WNV IgM and IgG antibodies, and had a clinical illness compatible with WNV. None of the four positive patients were clinically suspected of having WNV infection; discharge diagnoses included pneumonia, migraine, stroke, and gout. These four patients accounted for 80% of all WNV diagnosed in this hospital, 44% of all cases in Fulton County, and 7% of all cases reported in Georgia in 2003. The occurrence of WNV disease may be substantially greater than currently reflected in disease statistics in Georgia and many other states. When indicators of WNV activity are present and patients are likely to have had intensive mosquito exposure, WNV should be considered in the differential diagnosis of seriously ill, febrile patients.

Background Sepsis, a leading cause of morbidity and mortality, is not a homogeneous disease but rather a syndrome encompassing many heterogeneous pathophysiologies. Patient factors including genetics predispose to poor outcomes, though current clinical characterizations fail to identify those at greatest risk of progression and mortality. Methods The Community Acquired Pneumonia and Sepsis Outcome Diagnostic study enrolled 1,152 subjects with suspected sepsis. We sequenced peripheral blood RNA of 129 representative subjects with systemic inflammatory response syndrome (SIRS) or sepsis (SIRS due to infection), including 78 sepsis survivors and 28 sepsis non-survivors who had previously undergone plasma proteomic and metabolomic profiling. Gene expression differences were identified between sepsis survivors, sepsis non-survivors, and SIRS followed by gene enrichment pathway analysis. Expressed sequence variants were identified followed by testing for association with sepsis outcomes. Results The expression of 338 genes differed between subjects with SIRS and those with sepsis, primarily reflecting immune activation in sepsis. Expression of 1,238 genes differed with sepsis outcome: non-survivors had lower expression of many immune function-related genes. Functional genetic variants associated with sepsis mortality were sought based on a common disease-rare variant hypothesis. VPS9D1, whose expression was increased in sepsis survivors, had a higher burden of missense variants in sepsis survivors. The presence of variants was associated with altered expression of 3,799 genes, primarily reflecting Golgi and endosome biology. Conclusions The activation of immune response-related genes seen in sepsis survivors was muted in sepsis non-survivors. The association of sepsis survival with a robust immune response and the presence of missense variants in VPS9D1 warrants replication and further functional studies. Trial registration ClinicalTrials.gov NCT00258869. Registered on 23 November 2005. Electronic supplementary material The online version of this article (doi:10.1186/s13073-014-0111-5) contains supplementary material, which is available to authorized users.

A retrospective cohort analysis was conducted in Kazakhstan to define modifiable risk factors during seven outbreaks of human anthrax. Fifty-three cases and 255 non-ill persons with an epidemiologic link to an infected animal were enrolled. Cases were 58% male and had a median age of 35 years (range = 5–71). Nearly all cases had cutaneous disease (96%). Two patients (4%) were diagnosed with gastrointestinal disease. Although all cases had some contact with an infected animal other than consumption, in multivariable analysis the act of butchering an animal (relative risk [RR] = 3.6, 95% confidence interval [CI] = 1.5–9.6) and the presence of visible cuts on the hands were associated with anthrax (RR = 3.0, 95% CI = 0.9–9.6). Contact with infected livestock, in particular butchering, is associated with developing anthrax. The risk may be exacerbated by the presence of cuts on the hands at the time of contact with the animal or animal products.

In Nepal, many infections remain poorly characterized, partly due to limited diagnostic facilities. We studied consecutive febrile adults presenting to a general hospital in Kathmandu, Nepal. Of the 876 patients enrolled, enteric fever and pneumonia were the most common clinical diagnoses. Putative pathogens were identified in 323 (37%) patients, the most common being Salmonella enterica serotype Typhi and S. enterica serotype Paratyphi A (117), Rickettsia typhi (97), Streptococcus pneumoniae (53), Leptospira spp. (36), and Orientia tsutsugamushi (28). Approximately half of the Salmonella isolates were resistant to nalidixic acid. No clinical predictors were identified to reliably distinguish between the different infections. These findings confirm the heavy burden of enteric fever and pneumonia in Kathmandu, and highlight the importance of murine typhus, scrub typhus, and leptospirosis. Given the lack of reliable clinical predictors, the development of cheap and accurate diagnostic tests are likely to be of great clinical utility in this setting.

The Burkholderia cepacia complex includes 9 genomovars. The relative virulence of each is unknown. Host and pathogen features associated with mortality were evaluated among patients with B. cepacia complex bacteremia. Cases were ascertained through review of blood culture results for the period of May 1996 through May 2002. Isolates were identified to species level with 16S rDNA and recA-based species-specific polymerase chain reaction analyses and recA restriction fragment-length polymorphism. Strain typing was performed with pulsed-field gel electrophoresis. Fifty-three patients with B. cepacia complex bacteremia were identified; only 9 (17%) had cystic fibrosis. Twenty-five patients (47%) died within 14 days of bacteremia. After controlling for comorbid conditions and therapeutic interventions, 2 outbreak-related strains of Burkholderia cenocepacia (genomovar III) were associated with 14-day mortality (odds ratio, 5.5; 95% confidence interval, 1.20-25.02). B. cenocepacia is an emerging nosocomial pathogen. Certain strains are associated with an enhanced capacity for interpatient spread and poor outcome.

Standard aerobic media are widely used for culturing blood with the BacT/ALERT (BioMérieux, Inc., Durham, N.C.) (BM) and BACTEC 9240 (BD Diagnostic Systems, Sparks, Md.) (BD) automated continuously monitoring instrument systems. Although similarly composed of soybean-casein digest broths, the formulations of the standard aerobic media available for these instruments differ from each other in supplements and in sodium polyanetholesulfonate concentration. Therefore, we compared the standard aerobic media available for these systems at two university hospitals. Blood samples from adult patients with suspected bloodstream infection were inoculated at the bedside into nonvented BM and BD standard aerobic blood culture bottles and incubated in their respective instruments. The laboratories received 6,743 pairs of bottles that were each filled with 8 to 12 ml of blood. A total of 523 isolates representing true infections were recovered from 257 patients; of these isolates, 348 were recovered from both the BD and the BM bottles, 108 were recovered from the BM bottles only, and 67 were recovered from the BD bottles only ( P < 0.005). More staphylococci ( P < 0.05), especially coagulase-negative staphylococci ( P < 0.05), and yeasts ( P < 0.01) were recovered from BM bottles than from BD bottles. Of 291 unimicrobial episodes of bloodstream infection, 220 were detected with both bottles, 41 were detected with the BM bottles only, and 30 were detected with the BD bottles only (difference not significant). Among 335 cultures that were positive in both bottles within the first 72 h of incubation, the median times to detection were 14 h for BM bottles and 13 h for BD bottles. Rates for false-positive results were 0.5% for BM bottles and 0.1% for BD bottles. One BM bottle and seven BD bottles yielded false-negative results. We conclude that the BM medium provides improved recovery of microorganisms, especially staphylococci and yeasts, compared with that provided by the BD medium.

Four rapid tests for the serologic diagnosis of leptospirosis were evaluated, and the performance of each was compared with that of the current standard, the microscopic agglutination test (MAT). The four rapid tests were a microplate immunoglobulin M (IgM)-enzyme-linked immunosorbent assay (ELISA), an indirect hemagglutination assay (IHA), an IgM dipstick assay (LDS), and an IgM dot-ELISA dipstick test (DST). A panel of 276 sera from 133 cases of leptospirosis from four different geographic locations was tested as well as 642 sera from normal individuals or individuals with other infectious or autoimmune diseases. Acute-phase sera from cases ( n = 148) were collected ≤14 days (median = 6.0) after the onset of symptoms, and convalescent-phase sera ( n = 128) were collected ≥15 days after onset (median = 29.1). By a traditional method (two-by-two contingency table), the sensitivities for detection of leptospirosis cases were 93.2% by LDS, 92.5% by DST, 86.5% by ELISA, and 79.0% by IHA. Specificity was 98.8% by DST, 97% by ELISA and MAT, 95.8% by IHA, and 89.6% by LDS. With a latent class analysis (LCA) model that included all the rapid tests and the clinical case definition, sensitivity was 95.5% by DST, 94.5% by LDS, 89.9% by ELISA, and 81.1% by IHA. The sensitivity and specificity estimated by the traditional methods were quite close to the LCA estimates. However, LCA allowed estimation of the sensitivity of the MAT (98.2%), which traditional methods do not allow. For acute-phase sera, sensitivity was 52.7% by LDS, 50.0% by DST, 48.7% by MAT and ELISA, and 38.5% by IHA. The sensitivity for convalescent-phase sera was 93.8% by MAT, 84.4% by DST, 83.6% by LDS, 75.0% by ELISA, and 67.2% by IHA. A good overall correlation with the MAT was obtained for each of the assays, with the highest concordance being with the DST (kappa value, 0.85; 95% confidence interval [CI], 0.8 to 0.90). The best correlation was between ELISA and DST (kappa value, 0.86; 95% CI, 0.81 to 0.91). False-positive LDS results were frequent (≥20%) in sera from individuals with Epstein-Barr virus, human immunodeficiency virus, and periodontal disease and from healthy volunteers. The ease of use and significantly high sensitivity and specificity of DST and ELISA make these good choices for diagnostic testing.

Population-based surveillance for unexplained death and critical illness possibly due to infectious causes (UNEX) was conducted in four U.S. Emerging Infections Program sites (population 7.7 million) from May 1, 1995, to December 31, 1998, to define the incidence, epidemiologic features, and etiology of this syndrome. A case was defined as death or critical illness in a hospitalized, previously healthy person, 1 to 49 years of age, with infection hallmarks but no cause identified after routine testing. A total of 137 cases were identified (incidence rate 0.5 per 100,000 per year). Patients’ median age was 20 years, 72 (53%) were female, 112 (82%) were white, and 41 (30%) died. The most common clinical presentations were neurologic (29%), respiratory (27%), and cardiac (21%). Infectious causes were identified for 34 cases (28% of the 122 cases with clinical specimens); 23 (68%) were diagnosed by reference serologic tests, and 11 (32%) by polymerase chain reaction-based methods. The UNEX network model would improve U.S. diagnostic capacities and preparedness for emerging infections.

Acute respiratory infection (ARI) is a common diagnosis in outpatient and emergent care settings. Currently available diagnostics are limited, creating uncertainty in the use of antibacterial, antiviral, or supportive care. Up to 72% of ambulatory care patients with ARI are treated with an antibacterial, despite only a small fraction actually needing one. Antibiotic overuse is not restricted to ambulatory care: ARI accounts for approximately 5 million emergency department (ED) visits annually in the USA, where 52–61% of such patients receive antibiotics. Thus, an accurate test for the presence or absence of viral or bacterial infection is needed. In this review, we focus on recent research showing that the host-response (genomic, proteomic, or miRNA) can accomplish this task.

This chapter focuses on two clinically important gram-positive genera, Staphylococcus and Streptococcus, and the complications and persistent infections caused by these bacteria. Many streptococci are part of the normal flora of the mouth, skin, intestine, and upper respiratory tract. In the clinical laboratory, streptococci are differentiated based on their hemolytic properties on blood agar plates. Beta-hemolytic streptococci fully break down red blood cells, leaving a clear zone of true hemolysis around colonies. Beta-hemolytic streptococci are further divided into separate groups based on their Lancefield antigens. As with other streptococci, peptidoglycan and teichoic acid are the principal constituents of the pneumococcal cell wall. Non-dextran-producing streptococci may produce infective endocarditis (IE) in humans and adhere to artificial fibrinplatelet surfaces in vitro, which suggests that other characteristics are required. Ubiquitous colonizers of the skin and mucosa of most animals, the staphylococci are gram-positive cocci found singly, in pairs, or in grape-like clusters. Persistent infection is heavily mediated by the ability to elaborate biofilm. Biofilm-producing staphylococci are described primarily as coagulase-negative staphylococci (CoNS), and they are implicated in colonization and persistence on catheters and other prosthetic materials. Prosthetic devices can become contaminated with staphylococci at the time of insertion or due to contiguous spread of infection or through hematogenous seeding at the time of S. aureus bacteremia. The most important predictors of complicated S. aureus infection include persistent fever or bacteremia.

Affinity maturation of the antibody response is a fundamental process in adaptive immunity during which B cells activated by infection or vaccination undergo rapid proliferation accompanied by the acquisition of point mutations in their rearranged immunoglobulin (Ig) genes and selection for increased affinity for the eliciting antigen. The rate of somatic hypermutation at any position within an Ig gene is known to depend strongly on the local base sequence, and Ig genes have region-specific codon biases that influence the local mutation rate within the gene resulting in increased differential mutability in the regions that encode the antigen-binding domains. We have isolated a set of clonally related natural immunoglobulin heavy chain-light chain pairs from an experimentally infected influenza patient, inferred the unmutated ancestral rearrangements and the maturation intermediates, and synthesized all of the antibodies using recombinant methods. The lineage exhibits a remarkably uniform rate of improvement of the effective affinity to influenza hemagglutinin (HA) over evolutionary time, increasing 1000-fold overall from the unmutated ancestor to the best of the observed antibodies. Furthermore, analysis of selection reveals that selection and mutation bias were concordant even at the level of maturation to a single antigen. Substantial improvement in affinity to HA occurred along mutationally-preferred paths in sequence space and was thus strongly facilitated by the underlying local codon biases.

In this article, we review recent progress in using high-dimensional longitudinal genomic data collected from virus challenge studies, per- formed with healthy human volun- teers. The focus of the article is on statistical signal processing, but we also show how the results may be used to yield biological insights.

In 2010, Nicaragua became the first developing nation to add 13-valent pneumococcal conjugate vaccine (PCV-13) to its national immunization schedule, using a "3+0" dosing schedule. We assessed changes in incidence rates of health facility visits for childhood pneumonia and infant mortality after PCV-13 introduction in the Department of León, Nicaragua.We collected visit diagnoses from all 107 public health facilities in León between 2008 and 2012. We compared rates of pneumonia hospitalizations, ambulatory visits for pneumonia and infant mortality during the prevaccine (2008-2010) and vaccine (2011-2012) periods among different age groups of children using generalized estimating equations, accounting for clustering by municipality. Exposure time was estimated by official municipality population estimates.The adjusted incidence rate ratio for pneumonia hospitalization in the vaccine versus prevaccine period was 0.67 (0.59-0.75) among infants and 0.74 (0.67-0.81) among 1-year olds. The adjusted incidence rate ratio for ambulatory visits for pneumonia was 0.87 (0.75-1.01) among infants, and 0.84 (0.74, 0.95) among 1-year olds. The adjusted incidence rate ratio for infant mortality was 0.67 (0.57-0.80). We also observed lower rates of health facility visits for pneumonia among age groups (2- to 4-year old and 5- to 14-year old) not eligible to receive PCV-13.Within the first 2 years of a PCV-13 immunization program in Nicaragua, we observed lower rates of hospitalizations and ambulatory visits for pneumonia among children of all ages and a lower infant mortality rate. Lower rates of pneumonia among age groups not eligible to receive PCV-13 suggest an indirect effect of the vaccine.

Objective To identify metabolomic biomarkers predictive of Intensive Care Unit (ICU) mortality in adults. Rationale Comprehensive metabolomic profiling of plasma at ICU admission to identify biomarkers associated with mortality has recently become feasible. Methods We performed metabolomic profiling of plasma from 90 ICU subjects enrolled in the BWH Registry of Critical Illness (RoCI). We tested individual metabolites and a Bayesian Network of metabolites for association with 28-day mortality, using logistic regression in R, and the CGBayesNets Package in MATLAB. Both individual metabolites and the network were tested for replication in an independent cohort of 149 adults enrolled in the Community Acquired Pneumonia and Sepsis Outcome Diagnostics (CAPSOD) study. Results We tested variable metabolites for association with 28-day mortality. In RoCI, nearly one third of metabolites differed among ICU survivors versus those who died by day 28 (N = 57 metabolites, p

A Bayesian statistical model is developed for analysis of the time-evolving properties of infectious disease, with a particular focus on viruses. The model employs a latent semi-Markovian state process, and the state-transition statistics are driven by three terms: (i) a general time-evolving trend of the overall population, (ii) a semi-periodic term that accounts for effects caused by the days of the week, and (iii) a regression term that relates the probability of infection to covariates (here, specifically, to the Google Flu Trends data). Computations are performed using Markov Chain Monte Carlo sampling. Results are presented using a novel data set: daily self-reported symptom scores from hundreds of Duke University undergraduate students, collected over three academic years. The illnesses associated with these students are (imperfectly) labeled using real-time (RT) polymerase chain reaction (PCR) testing for several viruses, and gene-expression data were also analyzed. The statistical analysis is performed on the daily, self-reported symptom scores, and the RT PCR and gene-expression data are employed for analysis and interpretation of the model results.

Pneumococcal pneumonia is a leading cause of bacterial infection and death worldwide. Current diagnostic tests for detecting Streptococcus pneumoniae can be unreliable and can mislead clinical decision-making and treatment. To address this concern, we developed a preclinical model of pneumococcal pneumonia in nonhuman primates useful for identifying novel biomarkers, diagnostic tests, and therapies for human S. pneumoniae infection. Adult colony-bred baboons (n = 15) were infected with escalating doses of S. pneumoniae (Serotype 19A-7). We characterized the pathophysiological and serological profiles of healthy and infected animals over 7 days. Pneumonia was prospectively defined by the presence of three criteria: (1) change in white blood cell count, (2) isolation of S. pneumoniae from bronchoalveolar lavage fluid (BALF) or blood, and (3) concurrent signs/symptoms of infection. Animals given 10(9) CFU consistently met our definition and developed a phenotype of tachypnea, tachycardia, fever, hypoxemia, and radiographic lobar infiltrates at 48 hours. BALF and plasma cytokines, including granulocyte colony-stimulating factor, IL-6, IL-10, and IL-1ra, peaked at 24 to 48 hours. At necropsy, there was lobar consolidation with frequent pleural involvement. Lung histopathology showed alveolar edema and macrophage influx in areas of organizing pneumonia. Hierarchical clustering of peripheral blood RNA data at 48 hours correctly identified animals with and without pneumonia. Dose-dependent inoculation of baboons with S. pneumoniae produces a host response ranging from spontaneous clearance (10(6) CFU) to severe pneumonia (10(9) CFU). Selected BALF and plasma cytokine levels and RNA profiles were associated with severe pneumonia and may provide clinically useful parameters after validation.

Using A/J mice, which are susceptible to Staphylococcus aureus, we sought to identify genetic determinants of susceptibility to S. aureus, and evaluate their function with regard to S. aureus infection. One QTL region on chromosome 11 containing 422 genes was found to be significantly associated with susceptibility to S. aureus infection. Of these 422 genes, whole genome transcription profiling identified five genes (Dcaf7, Dusp3, Fam134c, Psme3, and Slc4a1) that were significantly differentially expressed in a) S. aureus –infected susceptible (A/J) vs. resistant (C57BL/6J) mice and b) humans with S. aureus blood stream infection vs. healthy subjects. Three of these genes (Dcaf7, Dusp3, and Psme3) were down-regulated in susceptible vs. resistant mice at both pre- and post-infection time points by qPCR. siRNA-mediated knockdown of Dusp3 and Psme3 induced significant increases of cytokine production in S. aureus-challenged RAW264.7 macrophages and bone marrow derived macrophages (BMDMs) through enhancing NF-κB signaling activity. Similar increases in cytokine production and NF-κB activity were also seen in BMDMs from CSS11 (C57BL/6J background with chromosome 11 from A/J), but not C57BL/6J. These findings suggest that Dusp3 and Psme3 contribute to S. aureus infection susceptibility in A/J mice and play a role in human S. aureus infection., Author Summary Staphylococcus aureus causes life-threatening infections in humans. Host genetic determinants influence the outcome of S. aureus infection, yet are poorly understood. Susceptible A/J and resistant C57BL/6J mice provide a unique platform to study the genetic difference responsible for variable host response to S. aureus infection. We showed that chromosome 11 in A/J was responsible for susceptibility to S. aureus. We further identified a QTL locus on Chromosome 11 significantly associated with S. aureus susceptibility. Five genes in the QTL (Dcaf7, Dusp3, Fam134c, Psme3, and Slc4a1) were significantly differently expressed in a) susceptible vs. resistant mice, and b) humans with S. aureus blood stream infection vs. healthy human subjects. Three genes (Dusp3, Psme3, and Dcaf7) were down-regulated in susceptible A/J mice. siRNA-mediated knockdown of Dusp3 and Psme3 in bone marrow derived macrophage (BMDMs) significantly enhanced cytokine responses through NF-κB activity upon S. aureus challenge in a pattern that was also present in S. aureus-challenged BMDMs from susceptible CSS11 (chr. 11 from A/J but otherwise C57BL/6J) mice, but not resistant C57BL/6J mice. These findings suggest that Dusp3 and Psme3 contribute to S. aureus infection susceptibility in A/J mice and play a role in human S. aureus infection.

Extended-spectrum-β-lactamase (ESBL)-producing organisms are increasingly prevalent. We determined the characteristics of 66 consecutive ESBL-producing isolates from six community hospitals in North Carolina and Virginia from 2010 to 2012. Fifty-three (80%) ESBL-producing isolates contained CTX-M enzymes; CTX-M-15 was found in 68% of Escherichia coli and 73% of Klebsiella isolates. Sequence type 131 (ST131) was the commonest type of E. coli , accounting for 48% of CTX-M-15-producing and 66% of CTX-M-14-producing isolates. In conclusion, the CTX-M genotype and ST131 E. coli were common among ESBL isolates from U.S. community hospitals.