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1.  Severe influenza cases in paediatric intensive care units in Germany during the pre-pandemic seasons 2005 to 2008 
BMC Infectious Diseases  2011;11:233.
Background
Data on complications in children with seasonal influenza virus infection are limited. We initiated a nation-wide three-year surveillance of children who were admitted to a paediatric intensive care unit (PICU) with severe seasonal influenza.
Methods
From October 2005 to July 2008, active surveillance was performed using an established reporting system for rare diseases (ESPED) including all paediatric hospitals in Germany. Cases to be reported were hospitalized children < 17 years of age with laboratory-confirmed influenza treated in a PICU or dying in hospital.
Results
Twenty severe influenza-associated cases were reported from 14 PICUs during three pre-pandemic influenza seasons (2005-2008). The median age of the patients (12 males/8 females) was 7.5 years (range 0.1-15 years). None had received vaccination against influenza. In 14 (70%) patients, the infection had been caused by influenza A and in five (25%) by influenza B; in one child (5%) the influenza type was not reported. Patients spent a median of 19 (IQR 12-38) days in the hospital and a median of 11 days (IQR 6-18 days) in the PICU; 10 (50%) needed mechanical ventilation. Most frequent diagnoses were influenza-associated pneumonia (60%), bronchitis/bronchiolitis (30%), encephalitis/encephalopathy (25%), secondary bacterial pneumonia (25%), and ARDS (25%). Eleven (55%) children had chronic underlying medical conditions, including 8 (40%) with chronic pulmonary diseases. Two influenza A- associated deaths were reported: i) an 8-year old boy with pneumococcal encephalopathy following influenza infection died from cerebral edema, ii) a 14-year-old boy with asthma bronchiale, cardiac malformation and Addison's disease died from cardiac and respiratory failure. For nine (45%) patients, possibly permanent sequelae were reported (3 neurological, 3 pulmonary, 3 other sequelae).
Conclusions
Influenza-associated pneumonia and secondary bacterial infections are relevant complications of seasonal influenza in Germany. The incidence of severe influenza cases in PICUs was relatively low. This may be either due to the weak to moderate seasonal influenza activity during the years 2005 to 2008 or due to under-diagnosis of influenza by physicians. Fifty% of the observed severe cases might have been prevented by following the recommendations for vaccination of risk groups in Germany.
doi:10.1186/1471-2334-11-233
PMCID: PMC3175218  PMID: 21880125
2.  Antimicrobial resistance predicts death in Tanzanian children with bloodstream infections: a prospective cohort study 
Background
Bloodstream infection is a common cause of hospitalization, morbidity and death in children. The impact of antimicrobial resistance and HIV infection on outcome is not firmly established.
Methods
We assessed the incidence of bloodstream infection and risk factors for fatal outcome in a prospective cohort study of 1828 consecutive admissions of children aged zero to seven years with signs of systemic infection. Blood was obtained for culture, malaria microscopy, HIV antibody test and, when necessary, HIV PCR. We recorded data on clinical features, underlying diseases, antimicrobial drug use and patients' outcome.
Results
The incidence of laboratory-confirmed bloodstream infection was 13.9% (255/1828) of admissions, despite two thirds of the study population having received antimicrobial therapy prior to blood culture. The most frequent isolates were klebsiella, salmonellae, Escherichia coli, enterococci and Staphylococcus aureus. Furthermore, 21.6% had malaria and 16.8% HIV infection. One third (34.9%) of the children with laboratory-confirmed bloodstream infection died. The mortality rate from Gram-negative bloodstream infection (43.5%) was more than double that of malaria (20.2%) and Gram-positive bloodstream infection (16.7%). Significant risk factors for death by logistic regression modeling were inappropriate treatment due to antimicrobial resistance, HIV infection, other underlying infectious diseases, malnutrition and bloodstream infection caused by Enterobacteriaceae, other Gram-negatives and candida.
Conclusion
Bloodstream infection was less common than malaria, but caused more deaths. The frequent use of antimicrobials prior to blood culture may have hampered the detection of organisms susceptible to commonly used antimicrobials, including pneumococci, and thus the study probably underestimates the incidence of bloodstream infection. The finding that antimicrobial resistance, HIV-infection and malnutrition predict fatal outcome calls for renewed efforts to curb the further emergence of resistance, improve HIV care and nutrition for children.
doi:10.1186/1471-2334-7-43
PMCID: PMC1891109  PMID: 17519011
3.  Predictors of mortality among TB-HIV Co-infected patients being treated for tuberculosis in Northwest Ethiopia: a retrospective cohort study 
BMC Infectious Diseases  2013;13:297.
Background
Tuberculosis (TB) is the leading cause of mortality in high HIV-prevalence populations. HIV is driving the TB epidemic in many countries, especially those in sub-Saharan Africa. The aim of this study was to assess predictors of mortality among TB-HIV co-infected patients being treated for TB in Northwest Ethiopia.
Methods
An institution-based retrospective cohort study was conducted between April, 2009 and January, 2012. Based on TB, antiretroviral therapy (ART), and pre-ART registration records, TB-HIV co-infected patients were categorized into “On ART” and “Non-ART” cohorts. A Chi-square test and a T-test were used to compare categorical and continuous variables between the two groups, respectively. A Kaplan-Meier test was used to estimate the probability of death after TB diagnosis. A log-rank test was used to compare overall mortality between the two groups. A Cox proportional hazard model was used to determine factors associated with death after TB diagnosis.
Results
A total of 422 TB-HIV co-infected patients (i.e., 272 On ART and 150 Non-ART patients) were included for a median of 197 days. The inter-quartile range (IQR) for On ART patients was 140 to 221 days and the IQR for Non-ART patients was 65.5 to 209.5 days. In the Non-ART cohort, more TB-HIV co-infected patients died during TB treatment: 44 (29.3%) Non-ART patients died, as compared to 49 (18%) On ART patients died. Independent predictors of mortality during TB treatment included: receiving ART (Adjusted Hazard Ratio (AHR) =0.35 [0.19-0.64]); not having initiated cotrimoxazole prophylactic therapy (CPT) (AHR = 3.03 [1.58-5.79]); being ambulatory (AHR = 2.10 [1.22-3.62]); CD4 counts category being 0-75cells/micro liter, 75-150cells/micro liter, or 150-250cells/micro liter (AHR = 4.83 [1.98-11.77], 3.57 [1.48-8.61], and 3.07 [1.33-7.07], respectively); and treatment in a hospital (AHR = 2.64 [1.51-4.62]).
Conclusions
Despite the availability of free ART from health institutions in Northwest Ethiopia, mortality was high among TB-HIV co-infected patients, and strongly associated with the absence of ART during TB treatment. In addition cotrimoxazol prophylactic therapy remained important factor in reduction of mortality during TB treatment. The study also noted importance of early ART even at higher CD4 counts.
doi:10.1186/1471-2334-13-297
PMCID: PMC3703293  PMID: 23815342
Predictors; Mortality; TB-HIV; Co-infection
4.  Childhood TB epidemiology and treatment outcomes in Thailand: a TB active surveillance network, 2004 to 2006 
Background
Of the 9.2 million new TB cases occurring each year, about 10% are in children. Because childhood TB is usually non-infectious and non-fatal, national programs do not prioritize childhood TB diagnosis and treatment. We reviewed data from a demonstration project to learn more about the epidemiology of childhood TB in Thailand.
Methods
In four Thai provinces and one national hospital, we contacted healthcare facilities monthly to record data about persons diagnosed with TB, assist with patient care, provide HIV counseling and testing, and obtain sputum for culture and susceptibility testing. We analyzed clinical and treatment outcome data for patients age < 15 years old registered in 2005 and 2006.
Results
Only 279 (2%) of 14,487 total cases occurred in children. The median age of children was 8 years (range: 4 months, 14 years). Of 197 children with pulmonary TB, 63 (32%) were bacteriologically-confirmed: 56 (28%) were smear-positive and 7 (4%) were smear-negative, but culture-positive. One was diagnosed with multi-drug resistant TB. HIV infection was documented in 75 (27%). Thirteen (17%) of 75 HIV-infected children died during TB treatment compared with 4 (2%) of 204 not known to be HIV-infected (p < 0.01).
Conclusion
Childhood TB is infrequently diagnosed in Thailand. Understanding whether this is due to absence of disease or diagnostic effort requires further research. HIV contributes substantially to the childhood TB burden in Thailand and is associated with high mortality.
doi:10.1186/1471-2334-8-94
PMCID: PMC2483984  PMID: 18637205
6.  Arcanobacterium haemolyticum associated with pyothorax: case report 
Arcanobacterium haemolyticum has an established role in the etiology of human pharyngitis. There are increasing reports of systemic infections caused by this organism. From India, we report the first case of Arcanobacterium haemolyticum causing pyothorax in an immunocompetent adolescent male patient. The probable mode of infection is also discussed. The role of A. hemolyticum as an animal pathogen needs further study.
doi:10.1186/1471-2334-5-68
PMCID: PMC1236925  PMID: 16144543
7.  Virulence difference between the prototypic Schu S4 strain (A1a) and Francisella tularensis A1a, A1b, A2 and type B strains in a murine model of infection 
Background
The use of prototypic strains is common among laboratories studying infectious agents as it promotes consistency for data comparability among and between laboratories. Schu S4 is the prototypic virulent strain of Francisella tularensis and has been used extensively as such over the past six decades. Studies have demonstrated virulence differences among the two clinically relevant subspecies of F. tularensis, tularensis (type A) and holarctica (type B) and more recently between type A subpopulations (A1a, A1b and A2). Schu S4 belongs to the most virulent subspecies of F. tularensis, subspecies tularensis.
Methods
In this study, we investigated the relative virulence of Schu S4 in comparison to A1a, A1b, A2 and type B strains using a temperature-based murine model of infection. Mice were inoculated intradermally and a hypothermic drop point was used as a surrogate for death. Survival curves and the length of temperature phases were compared for all infections. Bacterial burdens were also compared between the most virulent type A subpopulation, A1b, and Schu S4 at drop point.
Results
Survival curve comparisons demonstrate that the Schu S4 strain used in this study resembles the virulence of type B strains, and is significantly less virulent than all other type A (A1a, A1b and A2) strains tested. Additionally, when bacterial burdens were compared between mice infected with Schu S4 or MA00-2987 (A1b) significantly higher burdens were present in the blood and spleen of mice infected with MA00-2987.
Conclusions
The knowledge gained from using Schu S4 as a prototypic virulent strain has unquestionably advanced the field of tularemia research. The findings of this study, however, indicate that careful consideration of F. tularensis strain selection must occur when the overall virulence of the strain used could impact the outcome and interpretation of results.
doi:10.1186/1471-2334-14-67
PMCID: PMC3923427  PMID: 24502661
Prototypic strains; Murine model; Fever; Francisella tularensis; Tularemia; Schu S4; A1a
8.  Factors associated with seasonal influenza vaccine uptake among children in Japan 
Background
Seasonal influenza vaccine was once part of the routine immunization schedule that is routinely offered to all children in Japan, but it is now excluded from the schedule. This study aimed to investigate factors influential to parents’ decision to have their children receive seasonal influenza vaccine, as well as types of seasonal influenza vaccine information that is given to parents.
Methods
We conducted a cross-sectional online survey of 555 participants who have at least one child younger than 13 years of age. Respondents were asked to categorize the history of influenza vaccination of their youngest child as either ‘annual’ , ‘sometimes’ , or ‘never’. Participants were also asked about potentially influential factors in their decision to have their children receive a seasonal influenza vaccine.
Results
A total of 75% of respondents answered that their youngest child had received a seasonal influenza vaccine, and 57% of respondents answered that their child receives the vaccine every year. The higher income group was more likely than the lowest income group to have a history of influenza vaccine uptake. A recommendation from a pediatrician or school/nursery to have their child vaccinated was also positively associated with a history of influenza vaccine uptake. The most common reason for a pediatrician’s recommendation was ‘it leads to milder symptoms if infected’.
Conclusions
The main finding of the study is a significant association between household income and influenza vaccination of the youngest child in the household. We also found that cost could be a barrier to vaccinating children in low income households and that information from pediatricians and schools/nurseries could motivate parents to have their children vaccinated.
doi:10.1186/s12879-015-0821-3
PMCID: PMC4335773
Seasonal influenza vaccine; Self-paid vaccine; Voluntary vaccination; Children
9.  Stability of the pneumococcal population structure in Massachusetts as PCV13 was introduced 
Background
The success of 7-valent pneumococcal conjugate vaccination (PCV-7) introduced to the US childhood immunization schedule in 2000 was partially offset by increases in invasive pneumococcal disease (IPD) and pneumococcal carriage due to non-vaccine serotypes, in particular 19A, in the years that followed. A 13-valent conjugate vaccine (PCV-13) was introduced in 2010. As part of an ongoing study of the response of the Massachusetts pneumococcal population to conjugate vaccination, we report the findings from the samples collected in 2011, as PCV-13 was introduced.
Methods
We used multilocus sequence typing (MLST) to analyze 367 pneumococcal isolates carried by Massachusetts children (aged 3 months-7 years) collected during the winter of 2010–11 and used eBURST software to compare the pneumococcal population structure with that found in previous years.
Results
One hundred and four distinct sequence types (STs) were found, including 24 that had not been previously recorded. Comparison with a similar sample collected in 2009 revealed no significant overall difference in the ST composition (p = 0.39, classification index). However, we describe clonal dynamics within the important replacement serotypes 19A, 15B/C, and 6C, and clonal expansion of ST 433 and ST 432, which are respectively serotype 22F and 21 clones.
Conclusions
While little overall change in serotypes or STs was evident, multiple changes in the frequency of individual STs and or serotypes may plausibly be ascribed to the introduction of PCV-13. This 2011 sample documents the initial impact of PCV-13 and will be important for comparison with future studies of the evolution of the pneumococcal population in Massachusetts.
Electronic supplementary material
The online version of this article (doi:10.1186/s12879-015-0797-z) contains supplementary material, which is available to authorized users.
doi:10.1186/s12879-015-0797-z
PMCID: PMC4336693
Pneumococcal conjugate vaccine; Streptococcus pneumoniae; Colonization; Molecular epidemiology; MLST
10.  Stenotrophomonas maltophilia bloodstream infection in patients with hematologic malignancies: a retrospective study and in vitro activities of antimicrobial combinations 
Background
Stenotrophomonas maltophilia causes serious infections in immunocompromised hosts. Here, we analyzed the clinical characteristics of S. maltophilia bloodstream infection (BSI) in patients with hematologic malignancies and evaluated in vitro synergistic effects of antimicrobial combinations.
Methods
We retrospectively reviewed all consecutive episodes of S. maltophilia BSIs in adult hematologic patients from June 2009 to May 2014, with in vitro susceptibility and synergy tests using high-throughput bioluminescence assay performed for available clinical isolates.
Results
Among 11,004 admissions during 5-year period, 31 cases were identified as S. maltophilia BSIs. The incidence rate of S. maltophilia BSI was 0.134 cases/1,000 patient-days. Overall and attributable mortality of S. maltophilia BSI was 64.5% and 38.7%, respectively. Severe neutropenia (adjusted hazard ratio [HR] 5.24, p =0.013), shock at the onset of BSI (adjusted HR 6.05, p <0.001), and pneumonia (adjusted HR 3.15, p =0.017) were independent risk factors for mortality. In vitro susceptibilities to ceftazidime, levofloxacin, ticarcillin-clavulanic acid (TIM) and trimethoprim-sulfamethoxazole (SXT) were 11.1%, 44.0%, 40.7%, and 88.9%, respectively. MIC50/MIC90 for moxifloxacin and tigecycline were 1/4 mg/L and 4/8 mg/L. The 50% and 90% fractional inhibitory concentrations (FIC50/FIC90) of clinical isolates against a combination of SXT and TIM were 0.500/0.750. For SXT plus levofloxacin or moxifloxacin, FIC50/FIC90 were 0.625/1.000 and 0.625/0.625, respectively.
Conclusion
S. maltophilia BSIs show high mortality, which is related to severe neutropenia, shock, and S. maltophilia pneumonia. Based upon drug susceptibility testing, the primary treatment of choice for S. maltophilia BSIs should be SXT in hematologic patients, rather than quinolones, with combination therapies including SXT serving as a feasible treatment option.
doi:10.1186/s12879-015-0801-7
PMCID: PMC4336707
Bacteremia; Drug combinations; Hematologic diseases; Mortality; Stenotrophomonas maltophilia
11.  Molecular characterization of influenza viruses collected from young children in Uberlandia, Brazil - from 2001 to 2010 
Background
Influenza remains a major health problem due to the seasonal epidemics that occur every year caused by the emergence of new influenza virus strains. Hemagglutinin (HA) and neuraminidase (NA) glycoproteins are under selective pressure and subjected to frequent changes by antigenic drift. Therefore, our main objective was to investigate the influenza cases in Uberlândia city, Midwestern Brazil, in order to monitor the appearance of new viral strains, despite the availability of a prophylactic vaccine.
Methods
Nasopharyngeal samples were collected from 605 children less than five years of age presenting with acute respiratory disease and tested by immunofluorescence assay (IFA) for detection of adenovirus, respiratory syncytial virus, parainfluenza virus types 1, 2, and 3 and influenza virus types A and B. A reverse transcription-PCR (RT-PCR) for influenza viruses A and B was carried out to amplify partial segments of the HA and NA genes. The nucleotide sequences were analyzed and compared with sequences of the virus strains of the vaccine available in the same year of sample collection.
Results
Forty samples (6.6%) were tested positive for influenza virus by IFA and RT-PCR, with 39 samples containing virus of type A and one of type B. By RT-PCR, the type A viruses were further characterized in subtypes H3N2, H1N2 and H1N1 (41.0%, 17.9%, and 2.6%, respectively). Deduced amino acid sequence analysis of the partial hemagglutinin sequence compared to sequences from vaccine strains, revealed that all strains found in Uberlândia had variations in the antigenic sites. The sequences of the receptor binding sites were preserved, although substitutions with similar amino acids were observed in few cases. The neuraminidase sequences did not show significant changes. All the H3 isolates detected in the 2001-2003 period had drifted from vaccine strain, unlike the isolates of the 2004-2007 period.
Conclusions
These results suggest that the seasonal influenza vaccine effectiveness could be reduced because of A H3N2 variants that circulated in 2001-2003 years. Thus, an early monitoring of variants circulating in the country or in a region may provide important information about the probable efficacy of the vaccine that will be administered in an influenza season.
Electronic supplementary material
The online version of this article (doi:10.1186/s12879-015-0817-z) contains supplementary material, which is available to authorized users.
doi:10.1186/s12879-015-0817-z
PMCID: PMC4336712
Influenza virus; Children; RT-PCR; Sequencing; Hemagglutinin; Neuraminidase
12.  Predictors and outcomes of mycobacteremia among HIV-infected smear- negative presumptive tuberculosis patients in Uganda 
Background
Sputum smear microscopy for tuberculosis (TB) diagnosis lacks sensitivity in HIV-infected symptomatic patients and increases the likelihood that mycobacterial infections particularly disseminated TB will be missed; delays in diagnosis can be fatal. Given the duration for MTB growth in blood culture, clinical predictors of MTB bacteremia may improve early diagnosis of mycobacteremia. We describe the predictors and mortality outcome of mycobacteremia among HIV-infected sputum smear-negative presumptive TB patients in a high prevalence HIV/TB setting.
Methods
Between January and November 2011, all consenting HIV-infected adults suspected to have TB (presumptive TB) were consecutively enrolled. Diagnostic assessment included sputum smear microscopy, urine Determine TB lipoarabinomannan (LAM) antigen test, mycobacterial sputum and blood cultures, chest X-ray, and CD4 cell counts in addition to clinical and socio-demographic data. Patients were followed for 12 months post-enrolment.
Results
Of 394 sputum smear-negative participants [female, 63.7%; median age (IQR) 32 (28–39) years], 41/394 (10.4%) had positive mycobacterial blood cultures (mycobacteremia); all isolates were M. tuberculosis (MTB). The median CD4 cell count was significantly lower among patients with mycobacteremia when compared with those without (CD4 31 versus 122 cells/μL, p < 0.001). In a multivariate analysis, male gender [OR 3.4, 95%CI (1.4-7.6), p = 0.005], CD4 count <100 cells/μL [OR 3.1, 95% CI (1.1-8.6), p = 0.030] and a positive lateral flow urine TB LAM antigen test [OR 15.3, 95%CI (5.7-41.1), p < 0.001] were significantly associated with mycobacteremia. At 12 months of follow-up, a trend towards increased mortality was observed in patients that were MTB blood culture positive (35.3%) compared with those that were MTB blood culture negative (23.3%) (p = 0.065).
Conclusions
Mycobacteremia occurred in 10% of smear-negative patients and was associated with higher mortality compared with smear-negative patients without mycobacteremia. Advanced HIV disease (CD4 < 100 cells/mm3), male gender and positive lateral flow urine TB LAM test predicted mycobacteremia in HIV-infected smear-negative presumptive TB patients in this high prevalence TB/HIV setting.
doi:10.1186/s12879-015-0812-4
PMCID: PMC4332438
Predictors; Mortality; Mycobacterial infections; Bacteremia; Smear- negative; HIV; LAM; Sub-Saharan Africa
13.  Etiology of community-acquired pneumonia and diagnostic yields of microbiological methods: a 3-year prospective study in Norway 
Background
Despite recent advances in microbiological techniques, the etiology of community-acquired pneumonia (CAP) is still not well described. We applied polymerase chain reaction (PCR) and conventional methods to describe etiology of CAP in hospitalized adults and evaluated their respective diagnostic yields.
Methods
267 CAP patients were enrolled consecutively over our 3-year prospective study. Conventional methods (i.e., bacterial cultures, urinary antigen assays, serology) were combined with nasopharyngeal (NP) and oropharyngeal (OP) swab samples analyzed by real-time quantitative PCR (qPCR) for Streptococcus pneumoniae, and by real-time PCR for Mycoplasma pneumoniae, Chlamydophila pneumoniae, Bordetella pertussis and 12 types of respiratory viruses.
Results
Etiology was established in 167 (63%) patients with 69 (26%) patients having ≥1 copathogen. There were 75 (28%) pure bacterial and 41 (15%) pure viral infections, and 51 (19%) viral–bacterial coinfections, resulting in 126 (47%) patients with bacterial and 92 (34%) patients with viral etiology. S. pneumoniae (30%), influenza (15%) and rhinovirus (12%) were most commonly identified, typically with ≥1 copathogen. During winter and spring, viruses were detected more frequently (45%, P=.01) and usually in combination with bacteria (39%). PCR improved diagnostic yield by 8% in 64 cases with complete sampling (and by 15% in all patients); 5% for detection of bacteria; 19% for viruses (P=.04); and 16% for detection of ≥1 copathogen. Etiology was established in 79% of 43 antibiotic-naive patients with complete sampling. S. pneumoniae qPCR positive rate was significantly higher for OP swab compared to NP swab (P<.001). Positive rates for serology were significantly higher than for real-time PCR in detecting B. pertussis (P=.001) and influenza viruses (P<.001).
Conclusions
Etiology could be established in 4 out of 5 CAP patients with the aid of PCR, particularly in diagnosing viral infections. S. pneumoniae and viruses were most frequently identified, usually with copathogens. Viral–bacterial coinfections were more common than pure infections during winter and spring; a finding we consider important in the proper management of CAP. When swabbing for qPCR detection of S. pneumoniae in adult CAP, OP appeared superior to NP, but this finding needs further confirmation.
Trial registration
ClinicalTrials.gov Identifier: NCT01563315.
Electronic supplementary material
The online version of this article (doi:10.1186/s12879-015-0803-5) contains supplementary material, which is available to authorized users.
doi:10.1186/s12879-015-0803-5
PMCID: PMC4334764
Community-acquired pneumonia; Etiology; Microbiology; Virology; Diagnosis
14.  Microbiological characteristics of sepsis in a University hospital 
Background
Microbiological characteristics of sepsis and antimicrobial resistance are well studied, although in State University of Campinas, no data has been published yet.
Methods
The main agents related to sepsis and antimicrobial resistance were analyzed. The blood culture records requested from 4,793 hospitalized patients were analyzed. The samples were processed using the Bact/Alert® system for agent identification and antimicrobial susceptibility.
Results
A total of 1,017 patients met the inclusion criteria for a sepsis diagnosis, with 2,309 samples tested (2.27 samples/patient). There were 489 positive samples (21% positive) isolated from 337 patients (33.13%), but more rigorous criteria excluding potential contaminants resulted in analysis being restricted to 266 patients (315 agents). The prevalent microorganisms were coagulase negative Staphylococcus (CNS) (15.87%), Escherichia coli (13.0%), Staphylococcus aureus (11.7%), Klebsiella pneumoniae (9.8%), Enterobacter sp (9.5%), Acinetobacter baumannii (9.2%), Pseudomonas aeruginosa (5.7%) and Candida sp (5.1%). Examining antimicrobial resistance in the agents revealed that 51% of the S. aureus isolates were methicillin-resistant S. aureus (MRSA) and 80% of the CNS isolates were oxacillin-resistant. For A. baumannii, the ideal profile drugs were ampicillin sulbactam and piperacillin/tazobactam, and for P. aeruginosa, they were piperacillin/tazobactam and ceftazidime. Enterobacteria showed on average 32.5% and 35.7% resistance to beta-lactams and ciprofloxacin, respectively. When all Gram-negative bacteria were considered, the resistance to beta-lactams rose to 40.5%, and the resistance to ciprofloxacin rose to 42.3%.
Conclusions
Eighty percent of the agents identified in blood cultures from patients with sepsis belonged to a group of eight different agents. For empirical treatment, carbapenems and vancomycin unfortunately still remain the best therapeutic choice, except for A. baumannii and P. aeruginosa, for which piperacillin/tazobactan is the best option.
doi:10.1186/s12879-015-0798-y
PMCID: PMC4334605
Sepsis; Antimicrobial resistance; Blood cultures; Etiological agent
15.  Pneumococcal meningitis and vaccine effects in the era of conjugate vaccination: results of 20 years of nationwide surveillance in Germany 
Background
Long-term complications and a case mortality rate of 7.5% make meningitis caused by Streptococcus pneumoniae a serious clinical threat. In 2006, a general pneumococcal conjugate vaccination (PCV) recommendation was issued for all children under 2 years in Germany. Here, we investigate serotype changes in meningitis cases after this vaccine recommendation.
Methods
The German National Reference Center for Streptococci (NRCS) has conducted surveillance for invasive pneumococcal disease (IPD) in Germany since 1992. Pneumococcal isolates were serotyped by the Neufeld’s Quellung reaction and antibiotic susceptibility was tested using the broth microdilution method.
Results
Of 22,204 IPD isolates sent to the NRCS from July 1992 to June 2013, 3,086 were meningitis cases. Microbiological and statistical investigations were performed to characterize and quantify all meningitis cases, focusing on changes reflecting implementation of the national PCV recommendation. 1,766 isolates (57.2% of meningitis cases) were from adults (≥16 years) and 1,320 isolates (42.8%) originated from children (<16 years). Overall, the leading serotypes were 14 (9.7%), 7F (7.8%), 3 (6.9%), 19F (5.7%) and 23F (5.0%). Among children, serotypes 14 (16.2%), 7F (8.9%) and 19F (7.1%) were most common, whereas among adults, serotypes 3 (9.6%), 7F (6.9%), 22F (5.0%), 23F (4.9%) and 14 (4.8%) were most prevalent. After the introduction of general PCV7/10/13 vaccination a significant decrease for most vaccine serotypes was observed. Generally, the differences in antibiotic nonsusceptibility between children <16 years and adults ≥16 were low. For macrolides in the pre-PCV7 period, a significantly higher proportion of resistant isolates was found in children (25.1%), compared to the post-vaccination period (9.7%; p<0.0001).
Conclusions
Implementation of the pneumococcal conjugate vaccines broadly reduced vaccine-type meningitis cases. Changes in serotype prevalence must be continuously monitored to observe future trends concerning pneumococcal meningitis.
doi:10.1186/s12879-015-0787-1
PMCID: PMC4335684
Streptococcus pneumoniae; Meningitis; Serotypes; Vaccine coverage; Antibiotic susceptibility; Age
16.  Prevalence of Mycoplasma genitalium and Mycoplasma hominis in urogenital tract of Brazilian women 
Background
The role of Mycoplasma hominis and M. genitalium in urogenital tract infections remains unknown. Furthermore these mollicutes present a complex relationship with the host immune response. The role of inflammatory cytokines in infections also makes them good candidates to investigate bacterial vaginosis and mycoplasma genital infections. Therefore, the aim of this study was to detect the above-mentioned mollicutes by quantitative Polymerase Chain Reaction (qPCR) methodologies in vaginal swabs and dosage of cytokines.
Methods
Vaginal swabs and peripheral blood were collected from 302 women, including healthy individuals. The molecular findings were correlated with some individual behavioral variables, clinical and demographic characteristics, presence of other important microorganisms in vaginal swabs, and levels of interleukin (IL)-1β and IL-6.
Results
M. hominis and M. genitalium were detected in 31.8% and 28.1% of samples, respectively. The qPCR results were associated with clinical signs and symptoms of the infections studied. The frequency of Trichomonas vaginalis, Gardnerella vaginalis, Neisseria gonorrhoeae and Chlamydia trachomatis was 3.0%, 21.5%, 42.4%, and 1.7% respectively. Increased levels of IL-1β were associated with the presence of M. hominis and signs and/or symptoms of the genital infection of women studied.
Conclusion
IL-1β production was associated with the detection of M. hominis by qPCR. The sexual behavior of women studied was associated with the detection of mycoplasma and other agents of genital infections.
Electronic supplementary material
The online version of this article (doi:10.1186/s12879-015-0792-4) contains supplementary material, which is available to authorized users.
doi:10.1186/s12879-015-0792-4
PMCID: PMC4336719
Mycoplasma genitalium; Mycoplasma hominis; urogenital infection
17.  Spatial, temporal and genetic dynamics of highly pathogenic avian influenza A (H5N1) virus in China 
Background
The spatial spread of H5N1 avian influenza, significant ongoing mutations, and long-term persistence of the virus in some geographic regions has had an enormous impact on the poultry industry and presents a serious threat to human health.
Methods
We applied phylogenetic analysis, geospatial techniques, and time series models to investigate the spatiotemporal pattern of H5N1 outbreaks in China and the effect of vaccination on virus evolution.
Results
Results showed obvious spatial and temporal clusters of H5N1 outbreaks on different scales, which may have been associated with poultry and wild-bird transmission modes of H5N1 viruses. Lead–lag relationships were found among poultry and wild-bird outbreaks and human cases. Human cases were preceded by poultry outbreaks, and wild-bird outbreaks were led by human cases. Each clade has gained its own unique spatiotemporal and genetic dominance. Genetic diversity of the H5N1 virus decreased significantly between 1996 and 2011; presumably under strong selective pressure of vaccination. Mean evolutionary rates of H5N1 virus increased after vaccination was adopted in China. A clear signature of positively selected sites in the clade 2.3.2 virus was discovered and this may have resulted in the emergence of clade 2.3.2.1.
Conclusions
Our study revealed two different transmission modes of H5N1 viruses in China, and indicated a significant role of poultry in virus dissemination. Furthermore, selective pressure posed by vaccination was found in virus evolution in the country.
Electronic supplementary material
The online version of this article (doi:10.1186/s12879-015-0770-x) contains supplementary material, which is available to authorized users.
doi:10.1186/s12879-015-0770-x
PMCID: PMC4329208
18.  Detection and serotyping of pneumococci in community acquired pneumonia patients without culture using blood and urine samples 
Background
Treatment of community acquired pneumonia (CAP) patients with antibiotics before laboratory-confirmed diagnosis leads to loss of knowledge on the causative bacterial pathogen. Therefore, an increasing number of pneumococcal infections is identified using non-culture based techniques. However, methods for serotyping directly on the clinical specimen remain scarce. Here we present three approaches for detection and serotyping of pneumococci using samples from patients with CAP.
Methods
The first approach is quantitative PCR (qPCR) analysis on blood samples (n = 211) followed by capsular sequence typing (CST) to identify the serotype. The second approach, a urinary antigen assay (n = 223), designated as inhibition multiplex immunoassay (IMIA), is based on Luminex technology targeting 14 serotypes. The third approach is a multiplex immunoassay (MIA) (n = 171) also based on Luminex technology which detects serologic antibody responses against 14 serotypes. The three alternative assays were performed on samples obtained from 309 adult hospitalized CAP patients in 2007–2010 and the results were compared with those obtained from conventional laboratory methods to detect pneumococcal CAP, i.e. blood cultures, sputum cultures and BinaxNOW® urinary antigen tests.
Results
Using qPCR, MIA and IMIA, we were able to detect the pneumococcus in samples of 56% more patients compared to conventional methods. Furthermore, we were able to assign a serotype to the infecting pneumococcus from samples of 25% of all CAP patients, using any of the three serotyping methods (CST, IMIA and MIA).
Conclusion
This study indicates the usefulness of additional molecular methods to conventional laboratory methods for the detection of pneumococcal pneumonia. Direct detection and subsequent serotyping on clinical samples will improve the accuracy of pneumococcal surveillance to monitor vaccine effectiveness.
doi:10.1186/s12879-015-0788-0
PMCID: PMC4330648
Streptococcus pneumoniae; Pneumococcus; Community acquired pneumonia; Detection; Serotype; Blood; Urine
19.  Measurement of serum procalcitonin levels for the early diagnosis of spontaneous bacterial peritonitis in patients with decompensated liver cirrhosis 
Background
It is difficult to diagnose spontaneous bacterial peritonitis (SBP) early in decompensated liver cirrhotic ascites patients (DCPs). The aim of the study was to measure serum procalcitonin (PCT) levels and peripheral blood leukocyte/platelet (WBC/PLT) ratios to obtain an early diagnostic indication of SBP in DCPs.
Methods
Our cohort of 129 patients included 112 DCPs (94 of whom had infections) and 17 cases with compensated cirrhosis as controls. Bacterial cultures, ascitic fluid (AF) leukocyte and peripheral WBC/PLT counts, and serum PCT measurements at admission were carried out prior to the use of antibiotics. Receiver operating characteristic (ROC) curves were generated to test the accuracies and cut-off values for different inflammatory markers.
Results
Among the 94 infected patients, 66 tested positive by bacterial culture, for which the positivity of blood, ascites and other secretions were 25.8%, 30.3% and 43.9%, respectively. Lung infection, SBP and unknown sites of infection accounted for 8.5%, 64.9% and 26.6% of the cases, respectively. Serum PCT levels (3.02 ± 3.30 ng/mL) in DCPs with infections were significantly higher than those in control patients (0.15 ± 0.08 ng/mL); p < 0.05. We used PCT ≥0.5 ng/mL as a cut-off value to diagnose infections, for which the sensitivity and specificity was 92.5% and 77.1%. The area under the curve (AUC) was 0.89 (95% confidence interval: 0.84–0.91). The sensitivity and specificity were 62.8% and 94.2% for the diagnosis of infections, and were 68.8% and 94.2% for the diagnosis of SBP in DCPs when PCT ≥2 ng/mL was used as a cut-off value. For the combined PCT and WBC/PLT measurements, the sensitivity was 76.8% and 83.6% for the diagnosis of infections or SBP in DCPs, respectively.
Conclusion
Serum PCT levels alone or in combination with WBC/PLT measurements seem to provide a satisfactory early diagnostic biomarker in DCPs with infections, especially for patients with SBP.
doi:10.1186/s12879-015-0776-4
PMCID: PMC4332920
Cirrhosis; Infection; Spontaneous bacterial peritonitis; Procalcitonin; Early diagnosis
20.  MicroRNA-29 family expression and its relation to antiviral immune response and viro-immunological markers in HIV-1-infected patients 
Background
Several in vitro studies suggested the microRNA-29 (miRNA-29) family is involved in regulating HIV-1 and modulating the expression of interleukin (IL)-32, an anti-HIV-1 cytokine.
Methods
To investigate the contribution of the miRNA-29 family to HIV-1 infection in vivo, we compared miRNA-29 expression in PBMC collected from 58 HIV-1-infected patients, naïve for antiretroviral therapy, and 21 gender- and age-matched HIV-1 seronegative healthy donors, using RT-Taqman assays. The relation between miRNA-29 levels and HIV-1 viro-immunological markers and the activation rate of antiviral immune response were also evaluated. In addition, we profiled miRNA-29 expression in CD4+ T lymphocytes and CD14+ monocytes collected from 5 antiretroviral treated HIV-1 infected patients.
Results
miRNA-29b levels were higher in HIV-1-infected patients than in the control group (p < 0.001). There were no correlations with either HIV-1 RNA levels or CD4+ T count, whereas a significant correlation was found between miRNA-29-a/c levels and integrated HIV-1 DNA (miRNA-29a: p = 0.009, r = −0.448; miRNA-29c: p = 0.029; r = −0.381). When the HIV-1-infected patients were grouped on the basis of their plasma HIV-1 RNA and CD4+ T cell count, we also found that patients expressing the lowest levels of miRNA-29c showed high viraemia, low CD4+ T cell count and high levels of integrated HIV-1 DNA. Moreover, miRNA-29b levels were correlated with those of IL-32nonα (p = 0.028; r = −0.298). Patients expressing higher levels of miRNA-29b showed lower levels of MxA, an interferon-stimulated gene, also induced by IL-32 (p = 0.006 r = −0.397). Lastly, we found that CD4+ T lymphocytes and CD14+ monocytes shared similar miRNA-29a/b/c expression patterns but the amount of miRNA-29a/b/c, IL-32 isoforms and MxA were highly variable in these two cellular subsets.
Conclusions
The miRNA-29 family could influence the clinical progression of HIV-1 infection, the HIV-1 proviral load and the innate immune response against HIV-1.
doi:10.1186/s12879-015-0768-4
PMCID: PMC4336718
miRNA-29; HIV-1; IL-32; MxA
21.  Concurrent peritonsillar abscess and poststreptococcal reactive arthritis complicating acute streptococcal tonsillitis in a young healthy adult: a case report 
Background
Streptococcus pyogenes is responsible for 5-15% and 20-30% of acute pharyngitis/tonsillitis in adults and children, respectively. It not only causes acute illness but also can give rise to local suppurative complications such as peritonsillar abscess as well as trigger the postinfectious syndromes of glomerulonephritis, acute rheumatic fever and poststreptococcal reactive arthritis. Here, we report a case of a young healthy adult in whom both peritonsillar abscess and poststreptococcal reactive arthritis developed as a complication of acute streptococcal tonsillitis. To the best of our knowledge, such a coincidence of poststreptococcal sequelae has not been reported previously.
Case presentation
A 32-year-old previously healthy woman was diagnosed with acute tonsillitis by her family doctor and treated empirically with amoxicillin/clavulanic acid (875/125 mg) twice daily for 5 days. Four days after completing antibiotic therapy, peritonsillar abscess of left tonsil developed. Needle aspiration followed by incision and drainage were performed by otolaryngologist at the Emergency Department. Next, the patient was discharged home on a 10-day course of cefuroxime and metronidazole. The symptoms of peritonsillar abscess were subsiding during treatment, however on the last day of antibiotic therapy, swelling and pain of the left ankle appeared. Five days later the patient was consulted by rheumatologist. Cultures of throat swabs and abscess aspirate collected 2 weeks before revealed the presence of Streptococcus pyogenes. Antistreptolysin O (ASO) titer was evaluated and proved to be 412 IU/ml (normal 0–200 IU/ml). The level of C-reactive protein was 13,0 mg/L (normal <5,0 mg/L). There was no known cardiac involvement. Poststreptococcal reactive arthritis was diagnosed. Left ankle arthralgia persisted for about 5–6 weeks. Six months after the presentation at the Emergency Department, the patient was well, with ASO titer reaching 262 IU/ml.
Conclusions
Clinicians should be aware that appropriate choice of antibiotic, proper dose as well as duration of therapy of acute GAS pharyngitis/tonsillitis are crucial to prevent poststreptococcal sequelae.
doi:10.1186/s12879-015-0780-8
PMCID: PMC4327960
Streptococcus pyogenes; Tonsillitis; Peritonsillar abscess; Poststreptococcal reactive arthritis; Antibiotic therapy
22.  Delays, interruptions, and losses from prevention of mother-to-child transmission of HIV services during antenatal care in Johannesburg, South Africa: a cohort analysis 
Background
Between 2010–2013, South Africa implemented WHO ‘Option A’ for prevention of mother to child transmission (PMTCT), where all HIV-infected pregnant women (from 14 weeks gestation) received zidovudine (AZT) as ARV prophylaxis and initiated CD4 testing at their first antenatal care (ANC) visit. After returning for a second visit to collect CD4 results, women with CD4 counts ≤ 350 were referred to the ART clinic and fast-tracked for initiation on lifelong ART while continuing to visit the ANC clinic every four weeks. Women with CD4 counts >350 were dispensed daily AZT prophylaxis at monthly follow up visits (every 4 weeks). The primary objective of this study was to evaluate adherence of HIV-infected pregnant women to recommended PMTCT services at and after their first antenatal care (ANC) visit.
Methods
We conducted an observational cohort study from August 2012 to February 2013 at two primary health care clinics in Johannesburg, South Africa using routinely collected clinic data from first ANC visit for up to 60 days.
Results
Of the 158 patients newly diagnosed with HIV at their first ANC visit, records indicated that 139 women initiated CD4 testing during their first ANC visit. 52 patients (33% of 158) did not return again to the clinic within 60 days. Of the 118 (84% of 139) women with known gestational age > 13 weeks and known Hb ≥ 8 g/dl who should have received a 4-week supply of daily AZT at first ANC visit, 81 women (69% of 118) had a record of AZT being dispensed. Among the 139 women with CD4 results, 72 (52%) were eligible for lifelong ART (CD4 count ≤350); however, only 2 initiated ART within 30 days.
Conclusions
Loss to initiation of both single and triple ARV therapy, loss to follow-up, and treatment interruptions were common during ANC care for pregnant women with HIV after their first ANC visit.
doi:10.1186/s12879-015-0778-2
PMCID: PMC4322445  PMID: 25656597
Patient adherence; HIV prevention; Antiretroviral therapy; Pregnant women; South Africa
23.  Retrospective analysis of 14 cases of disseminated Penicillium marneffei infection with osteolytic lesions 
Background
Penicillium marneffei disseminates hematogenously and can infect most organs, though infection leading to osteolysis is extremely rare. We describe the clinical and laboratory features, management, and outcomes of patients with penicilliosis marneffei (PSM) with osteolytic lesions.
Methods
This retrospective study was conducted between January 1, 2003 and May 1, 2014 at the First Affiliated Hospital of Guangxi Medical University. Patients who presented with culture and/or histopathologic proof of disseminated PSM within osteolytic lesions were included.
Results
P. marneffei infection was diagnosed in 100 patients (65 HIV-infected and 35 HIV-negative). Fourteen patients, all HIV-negative, (14/35, 40%) had osteolytic lesions. The most common comorbidity was diabetes mellitus, though previous glucocorticoid therapy, β-thalassemia, breast cancer, and Langerhans cell histiocytosis also occurred. Five patients had no comorbidity. Fever, malaise, ostealgia, weight loss, and anemia were the most common symptoms, followed by cutaneous lesions, lymphadenopathy, hepatosplenomegaly, cough, sputum, and stethalgia. Ostealgia, joint pain, and joint disorders were also recorded. White blood cell and neutrophil counts were increased (mean 22.3 ± 7.4 × 109 cells/L; mean 18.84 ± 4.5 × 109 cells/L, respectively). The most common sites were the vertebrae, skull and femur, ribs and ilium, though the clavicle, scapula, humerus, and tibia were also involved. Radiography and computed tomography (CT) showed multiple radiolucencies with moth-eaten bone destruction, periosteal proliferation, bone fracture, and surrounding soft-tissue swelling. Emission CT showed significantly increased uptake in many skeletal regions. Positron emission tomography/CT showed generalized lymphadenopathy, bone metabolic activity, and bone destruction. The 18 F-FDG standard uptake value was increased in the entire skeleton (mean 6.16). Twelve patients received antifungal therapy, four of whom died during treatment, and eight recovered, though four of these eight relapsed within 3–24 months. Two patients discontinued treatment because of severe multiple organ failure and died.
Conclusions
Osteolysis is often overlooked in HIV-negative individuals with disseminated P. marneffei infection. However, P. marneffei involving the bone and leading to osteolysis may indicate severe systemic disturbance, and is characterized by a poor prognosis, high recurrence rate, and the need for prolonged antifungal treatment.
doi:10.1186/s12879-015-0782-6
PMCID: PMC4322545  PMID: 25656710
HIV-negative; Penicilliosis marneffei; Ostealgia; Osteolytic lesion
24.  Pertussis outbreak in university students and evaluation of acellular pertussis vaccine effectiveness in Japan 
Background
Recent studies worldwide have reported increasing numbers of adults diagnosed with Bordetella pertussis despite receiving childhood vaccinations. This study describes a pertussis outbreak at a university medical faculty campus and examines the effectiveness of diphtheria, tetanus, and pertussis (DTaP) vaccination completed during infancy in Japan.
Methods
After the outbreak, self-administered questionnaires and serum samples were collected from students on campus to determine the incidence of pertussis and underlying diseases. Pertussis was diagnosed on the basis of clinical criteria and serum anti-pertussis toxin antibody levels. Using data collected from 248 first and second grade students who had submitted copies of their vaccination records, we evaluated the effectiveness of DTaP vaccination in infancy against adult pertussis.
Results
Questionnaire responses were obtained from 636 students (of 671 registered students; 95% response rate). Of 245 students who reported a continuous cough during the outbreak period, 84 (attack rate: 13.2%) were considered “probable” pertussis cases that met clinical criteria. The outbreak occurred mainly in first and second grade students in the Faculty of Medicine. Of 248 students who provided vaccination records, 225 had received 4 DTaP doses (coverage: 90.7%); the relative risk of the complete vaccination series compared to those with fewer than 4 doses or no doses for probable cases was 0.48 (95% confidence interval: 0.24-0.97).
Conclusions
Waning protection was suspected due to over time. Booster vaccination for teenagers and development of highly efficacious pertussis vaccines are needed.
Electronic supplementary material
The online version of this article (doi:10.1186/s12879-015-0777-3) contains supplementary material, which is available to authorized users.
doi:10.1186/s12879-015-0777-3
PMCID: PMC4323135  PMID: 25656486
Pertussis; Outbreak; Vaccine effectiveness
25.  Higher blood volumes improve the sensitivity of direct PCR diagnosis of blood stream tuberculosis among HIV-positive patients: an observation study 
Background
Blood stream tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB) is common among HIV-positive patients, turning rapidly fatal unless detected and treated promptly. Blood culture is currently the standard test for the detection of MTB in whole blood but results take weeks; patients deteriorate markedly and often die before a diagnosis of blood stream TB is made. Rapid molecular tests on whole blood, with potential for same day diagnosis of blood stream TB usually show low sensitivity due to the problem of insufficient MTB DNA template when extraction is performed directly on low blood volumes. This study assessed the influence of blood volume on the sensitivity of a HyBeacon PCR assay-the FluoroType® MTB (Hain Lifescience, Nehren, Germany) on direct detection of MTB in whole blood.
Methods
Prospective recruitment of HIV-positive patients with clinical suspicion of blood stream TB but not on anti-TB or HIV drug treatment was done. Venous blood samples were collected and DNA extracted using the MolYsis (Molzym, Bremen, Germany) methods; for study A, from duplicate 1 ml (42 patients) and for study B (31 patients) from 9 ml EDTA blood samples. The FluoroType® MTB PCR assay targeting an IS6110 sequence was performed and results compared with blood culture.
Results
The diagnostic sensitivity and specificity of the FluoroType® MTB PCR in study A was 33% and 97%, respectively. Corresponding values in study B were 71% and 96%, respectively. In both studies, one case each of blood culture-negative blood stream TB was detected with the FluoroType® MTB PCR assay. The median time to positivity of blood culture was 20.1 (range 12–32) for study A and 19.9 days (range 15–30) for study B.
Conclusion
Larger blood volumes (9 ml) improved and gave acceptable sensitivity of direct PCR diagnosis of blood stream TB.
doi:10.1186/s12879-015-0785-3
PMCID: PMC4326319  PMID: 25656799
Tuberculosis; Blood stream; Direct; Real time; PCR Diagnosis

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