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1.  Rapid Bacterial Whole-Genome Sequencing to Enhance Diagnostic and Public Health Microbiology 
JAMA internal medicine  2013;173(15):1397-1404.
IMPORTANCE
The latest generation of benchtop DNA sequencing platforms can provide an accurate whole-genome sequence (WGS) for a broad range of bacteria in less than a day. These could be used to more effectively contain the spread of multidrug-resistant pathogens.
OBJECTIVE
To compare WGS with standard clinical microbiology practice for the investigation of nosocomial outbreaks caused by multidrug-resistant bacteria, the identification of genetic determinants of antimicrobial resistance, and typing of other clinically important pathogens.
DESIGN, SETTING, AND PARTICIPANTS
A laboratory-based study of hospital inpatients with a range of bacterial infections at Cambridge University Hospitals NHS Foundation Trust, a secondary and tertiary referral center in England, comparing WGS with standard diagnostic microbiology using stored bacterial isolates and clinical information.
MAIN OUTCOMES AND MEASURES
Specimens were taken and processed as part of routine clinical care, and cultured isolates stored and referred for additional reference laboratory testing as necessary. Isolates underwent DNA extraction and library preparation prior to sequencing on the Illumina MiSeq platform. Bioinformatic analyses were performed by persons blinded to the clinical, epidemiologic, and antimicrobial susceptibility data.
RESULTS
We investigated 2 putative nosocomial outbreaks, one caused by vancomycin-resistant Enterococcus faecium and the other by carbapenem-resistant Enterobacter cloacae; WGS accurately discriminated between outbreak and nonoutbreak isolates and was superior to conventional typing methods. We compared WGS with standard methods for the identification of the mechanism of carbapenem resistance in a range of gram-negative bacteria (Acinetobacter baumannii, E cloacae, Escherichia coli, and Klebsiella pneumoniae). This demonstrated concordance between phenotypic and genotypic results, and the ability to determine whether resistance was attributable to the presence of carbapenemases or other resistance mechanisms. Whole-genome sequencing was used to recapitulate reference laboratory typing of clinical isolates of Neisseria meningitidis and to provide extended phylogenetic analyses of these.
CONCLUSIONS AND RELEVANCE
The speed, accuracy, and depth of information provided by WGS platforms to confirm or refute outbreaks in hospitals and the community, and to accurately define transmission of multidrug-resistant and other organisms, represents an important advance.
doi:10.1001/jamainternmed.2013.7734
PMCID: PMC4001082  PMID: 23857503
3.  Clinical Definitions of Melioidosis 
Clinical definitions of melioidosis and inhalation-acquired melioidosis (Burkholderia pseudomallei infection) are described together with the evidence used to develop these definitions. Such definitions support accurate public health reporting, preparedness planning for deliberate B. pseudomallei release, design of experimental models, and categorization of naturally acquired melioidosis.
doi:10.4269/ajtmh.12-0555
PMCID: PMC3592517  PMID: 23468355
4.  Whole-genome sequencing for analysis of an outbreak of meticillin-resistant Staphylococcus aureus: a descriptive study 
The Lancet Infectious Diseases  2013;13(2):130-136.
Summary
Background
The emergence of meticillin-resistant Staphylococcus aureus (MRSA) that can persist in the community and replace existing hospital-adapted lineages of MRSA means that it is necessary to understand transmission dynamics in terms of hospitals and the community as one entity. We assessed the use of whole-genome sequencing to enhance detection of MRSA transmission between these settings.
Methods
We studied a putative MRSA outbreak on a special care baby unit (SCBU) at a National Health Service Foundation Trust in Cambridge, UK. We used whole-genome sequencing to validate and expand findings from an infection-control team who assessed the outbreak through conventional analysis of epidemiological data and antibiogram profiles. We sequenced isolates from all colonised patients in the SCBU, and sequenced MRSA isolates from patients in the hospital or community with the same antibiotic susceptibility profile as the outbreak strain.
Findings
The hospital infection-control team identified 12 infants colonised with MRSA in a 6 month period in 2011, who were suspected of being linked, but a persistent outbreak could not be confirmed with conventional methods. With whole-genome sequencing, we identified 26 related cases of MRSA carriage, and showed transmission occurred within the SCBU, between mothers on a postnatal ward, and in the community. The outbreak MRSA type was a new sequence type (ST) 2371, which is closely related to ST22, but contains genes encoding Panton-Valentine leucocidin. Whole-genome sequencing data were used to propose and confirm that MRSA carriage by a staff member had allowed the outbreak to persist during periods without known infection on the SCBU and after a deep clean.
Interpretation
Whole-genome sequencing holds great promise for rapid, accurate, and comprehensive identification of bacterial transmission pathways in hospital and community settings, with concomitant reductions in infections, morbidity, and costs.
Funding
UK Clinical Research Collaboration Translational Infection Research Initiative, Wellcome Trust, Health Protection Agency, and the National Institute for Health Research Cambridge Biomedical Research Centre.
doi:10.1016/S1473-3099(12)70268-2
PMCID: PMC3556525  PMID: 23158674
5.  Short Report: Consensus Guidelines for Dosing of Amoxicillin-Clavulanate in Melioidosis 
Melioidosis is an infectious disease endemic to northern Australia and Southeast Asia. In response to clinical confusion regarding the appropriate dose of amoxicillin-clavulanate, we have developed guidelines for the appropriate dosing of this second-line agent. For eradication therapy for melioidosis, we recommend 20/5 mg/kg orally, three times daily.
PMCID: PMC3034162  PMID: 18256414
6.  Enhanced Determination of Streptococcus pneumoniae Serotypes Associated with Invasive Disease in Laos by Using a Real-Time Polymerase Chain Reaction Serotyping Assay with Cerebrospinal Fluid 
A prospective hospital-based study was undertaken to define the incidence of invasive pneumococcal disease (IPD) and circulating serotypes in Laos. Of 10,799 patients with hemocultures and 353 patients with cerebrospinal fluid samples, 0.21% and 5.4%, respectively, were positive for Streptococcus pneumoniae, giving a total of 35 IPD patients. We developed a real-time polymerase chain reaction to detect serotypes represented in the 13-valent pneumococcal vaccine. A blinded evaluation comparing serotype as defined by the Quellung reaction versus the polymerase chain reaction demonstrated 100% concordance. The most frequent serotype (n = 33 patients) was 1 (n = 6), followed by serotypes 5, 6A/B/C, 14, and 23F. Serotypes represented in the 7-valent polysaccharide-protein conjugate vaccine (PCV-7) infected 39% of patients, with 73% coverage for the PCV-10 and PCV-13 vaccines. Although the sample size is small, these data suggest that the PCV-7 vaccine may have relatively low efficacy in Laos. Further studies are urgently needed to guide pneumococcal vaccine policy in Laos.
doi:10.4269/ajtmh.2010.10-0225
PMCID: PMC2929034  PMID: 20810803
7.  Melioidosis Diagnostic Workshop, 20131 
Emerging Infectious Diseases  2015;21(2):e141045.
Melioidosis is a severe disease that can be difficult to diagnose because of its diverse clinical manifestations and a lack of adequate diagnostic capabilities for suspected cases. There is broad interest in improving detection and diagnosis of this disease not only in melioidosis-endemic regions but also outside these regions because melioidosis may be underreported and poses a potential bioterrorism challenge for public health authorities. Therefore, a workshop of academic, government, and private sector personnel from around the world was convened to discuss the current state of melioidosis diagnostics, diagnostic needs, and future directions.
doi:10.3201/eid2102.141045
PMCID: PMC4313648  PMID: 25626057
melioidosis; Burkholderia pseudomallei; diagnosis; bacteria
8.  Emergence of Pediatric Melioidosis in Siem Reap, Cambodia 
We describe the first cases of pediatric melioidosis in Cambodia. Thirty-nine cases were diagnosed at the Angkor Hospital for Children, Siem Reap, between October 2005 and December 2008 after the introduction of microbiology capabilities. Median age was 7.8 years (range = 1.6–16.2 years), 15 cases were male (38%), and 4 cases had pre-existing conditions that may have pre-disposed the patient to melioidosis. Infection was localized in 27 cases (69%) and disseminated in 12 cases (31%). Eleven cases (28%) were treated as outpatients, and 28 (72%) cases were admitted. Eight children (21%) died a median of 2 days after admission; seven deaths were attributable to melioidosis, all of which occurred in children receiving suboptimal antimicrobial therapy and before bacteriological culture results were available. Our findings indicate the need for heightened awareness of melioidosis in Cambodia, and they have led us to review microbiology procedures and antimicrobial prescribing of suspected and confirmed cases.
doi:10.4269/ajtmh.2010.10-0030
PMCID: PMC2877419  PMID: 20519608
9.  Clinical, Environmental, and Serologic Surveillance Studies of Melioidosis in Gabon, 2012–2013 
Emerging Infectious Diseases  2015;21(1):40-47.
Burkholderia pseudomallei and B. thailandensis are in the soil; a novel B. pseudomallei sequence type causes lethal septic shock.
Burkholderia pseudomallei, an environmental gram-negative bacillus, is the causative agent of melioidosis and a bio-threat agent. Reports of B. pseudomallei isolation from soil and animals in East and West Africa suggest that melioidosis might be more widely distributed than previously thought. Because it has been found in equatorial areas with tropical climates, we hypothesized that B. pseudomallei could exist in Gabon. During 2012–2013, we conducted a seroprevalance study in which we set up microbiology facilities at a large clinical referral center and prospectively screened all febrile patients by conducting blood cultures and testing for B. pseudomallei and related species; we also determined whether B. pseudomallei could be isolated from soil. We discovered a novel B. pseudomallei sequence type that caused lethal septic shock and identified B. pseudomallei and B. thailandensis in the environment. Our data suggest that melioidosis is emerging in Central Africa but is unrecognized because of the lack of diagnostic microbiology facilities.
doi:10.3201/eid2101.140762
PMCID: PMC4285261  PMID: 25530077
Burkholderia pseudomallei; Burkholderia thailandensis; melioidosis; epidemiology; seroprevalance; Africa; Gabon; soil; sepsis; bacteria
10.  A Spaetzle-like role for Nerve Growth Factor β in vertebrate immunity to Staphylococcus aureus 
Science (New York, N.Y.)  2014;346(6209):641-646.
Many key components of innate immunity to infection are shared between Drosophila and humans. However, the fly Toll ligand Spaetzle is not thought to have a vertebrate equivalent. We have found that the structurally related cystine-knot protein, Nerve Growth Factor β (NGFβ), plays an unexpected Spaetzle-like role in immunity to Staphylococcus aureus infection in chordates. Deleterious mutations of either human NGFβ or its high-affinity receptor TRKA were associated with severe S. aureus infections. NGFβ was released by macrophages in response to S. aureus exoproteins through activation of NLRP3 and NLRP4, and enhanced phagocytosis and superoxide-dependent killing, stimulated pro-inflammatory cytokine production, and promoted calcium-dependent neutrophil recruitment. TrkA knockdown in zebrafish increased susceptibility to S. aureus infection, confirming an evolutionarily conserved role for NGFβ-TRKA signaling in pathogen-specific host immunity.
doi:10.1126/science.1258705
PMCID: PMC4255479  PMID: 25359976
11.  Microbial sequencing to improve individual and population health 
Genome Medicine  2014;6(11):103.
Editorial summary
Recent advances in sequencing technologies are changing the face of infectious disease investigation and control. Personalized anti-infective therapies and surveillance of emergent pathogen outbreaks are just two examples of the potential benefits of merging the fields of genomics and infectious diseases.
doi:10.1186/s13073-014-0103-5
PMCID: PMC4262389  PMID: 25505493
12.  Next-generation pathogen genomics 
Genome Biology  2014;15(11):528.
doi:10.1186/s13059-014-0528-6
PMCID: PMC4283783  PMID: 25417942
13.  Burkholderia pseudomallei in Water Supplies, Southern Thailand 
Emerging Infectious Diseases  2014;20(11):1947-1949.
doi:10.3201/eid2011.140832
PMCID: PMC4215545  PMID: 25340393
melioidosis; B. pseudomallei; water; Phangan; Thailand; bacteria; Koh Phangan
14.  CAUSES OF COMMUNITY-ACQUIRED BACTEREMIA AND PATTERNS OF ANTIMICROBIAL RESISTANCE IN VIENTIANE, LAOS 
There is no published information on the causes of bacteremia in the Lao PDR (Laos). Between 2000 and 2004, 4512 blood culture pairs were taken from patients admitted to Mahosot Hospital, Vientiane, Laos, with suspected community-acquired bacteremia; 483 (10.7%) cultures grew a clinically significant community-acquired organism, most commonly Salmonella enterica serovar typhi (50.9%), Staphylococcus aureus (19.0%), and Escherichia coli (12.4%). S. aureus bacteremia was common among infants (69.2%), while children 1–5 years had a high frequency of typhoid (44%). Multi–drug-resistant S. Typhi was rare (6%). On multiple logistic regression analysis, typhoid was associated with younger age, longer illness, diarrhea, higher admission temperature, and lower peripheral white blood cell count than non-typhoidal bacteremia. Empirical parenteral ampicillin and gentamicin would have some activity against ∼ 88% of clinically significant isolates at a cost of US $1.4/day, an important exception being B. pseudomallei. Bacteremic infants in this setting require an anti-staphylococcal antibiotic.
PMCID: PMC2213713  PMID: 17124000
15.  Increasing Incidence of Hospital-Acquired and Healthcare-Associated Bacteremia in Northeast Thailand: A Multicenter Surveillance Study 
PLoS ONE  2014;9(10):e109324.
Background
Little is known about the epidemiology of nosocomial bloodstream infections in public hospitals in developing countries. We evaluated trends in incidence of hospital-acquired bacteremia (HAB) and healthcare-associated bacteremia (HCAB) and associated mortality in a developing country using routinely available databases.
Methods
Information from the microbiology and hospital databases of 10 provincial hospitals in northeast Thailand was linked with the national death registry for 2004–2010. Bacteremia was considered hospital-acquired if detected after the first two days of hospital admission, and healthcare-associated if detected within two days of hospital admission with a prior inpatient episode in the preceding 30 days.
Results
A total of 3,424 patients out of 1,069,443 at risk developed HAB and 2,184 out of 119,286 at risk had HCAB. Of these 1,559 (45.5%) and 913 (41.8%) died within 30 days, respectively. Between 2004 and 2010, the incidence rate of HAB increased from 0.6 to 0.8 per 1,000 patient-days at risk (p<0.001), and the cumulative incidence of HCAB increased from 1.2 to 2.0 per 100 readmissions (p<0.001). The most common causes of HAB were Acinetobacter spp. (16.2%), Klebsiella pneumoniae (13.9%), and Staphylococcus aureus (13.9%), while those of HCAB were Escherichia coli (26.3%), S. aureus (14.0%), and K. pneumoniae (9.7%). There was an overall increase over time in the proportions of ESBL-producing E. coli causing HAB and HCAB.
Conclusions
This study demonstrates a high and increasing incidence of HAB and HCAB in provincial hospitals in northeast Thailand, increasing proportions of ESBL-producing isolates, and very high associated mortality.
doi:10.1371/journal.pone.0109324
PMCID: PMC4195656  PMID: 25310563
16.  NLRC4 and TLR5 Each Contribute to Host Defense in Respiratory Melioidosis 
Burkholderia pseudomallei causes the tropical infection melioidosis. Pneumonia is a common manifestation of melioidosis and is associated with high mortality. Understanding the key elements of host defense is essential to developing new therapeutics for melioidosis. As a flagellated bacterium encoding type III secretion systems, B. pseudomallei may trigger numerous host pathogen recognition receptors. TLR5 is a flagellin sensor located on the plasma membrane. NLRC4, along with NAIP proteins, assembles a canonical caspase-1-dependent inflammasome in the cytoplasm that responds to flagellin (in mice) and type III secretion system components (in mice and humans). In a murine model of respiratory melioidosis, Tlr5 and Nlrc4 each contributed to survival. Mice deficient in both Tlr5 and Nlrc4 were not more susceptible than single knockout animals. Deficiency of Casp1/Casp11 resulted in impaired bacterial control in the lung and spleen; in the lung much of this effect was attributable to Nlrc4, despite relative preservation of pulmonary IL-1β production in Nlrc4−/− mice. Histologically, deficiency of Casp1/Casp11 imparted more severe pulmonary inflammation than deficiency of Nlrc4. The human NLRC4 region polymorphism rs6757121 was associated with survival in melioidosis patients with pulmonary involvement. Co-inheritance of rs6757121 and a functional TLR5 polymorphism had an additive effect on survival. Our results show that NLRC4 and TLR5, key components of two flagellin sensing pathways, each contribute to host defense in respiratory melioidosis.
Author Summary
Melioidosis is an infection caused by Burkholderia pseudomallei, a bacterium that is found in tropical soil and water. Melioidosis can present in a variety of ways, but lung involvement is common and usually severe. The host response to infection governs outcome. In this study, we examined the role of two host sensors of bacterial components–TLR5 and NLRC4–to determine their necessity in respiratory melioidosis. Although both proteins are involved in detection of bacterial flagellin, in mice we defined specific and individual roles for TLR5 and NLRC4 in protecting against death from melioidosis. In humans with melioidosis involving the lung, genetic variation in these receptors also had independent associations with survival. These results underscore the importance of these elements of host defense in respiratory melioidosis and support further studies of the underlying mechanisms.
doi:10.1371/journal.pntd.0003178
PMCID: PMC4169243  PMID: 25232720
17.  Open-Label Randomized Trial of Oral Trimethoprim-Sulfamethoxazole, Doxycycline, and Chloramphenicol Compared with Trimethoprim-Sulfamethoxazole and Doxycycline for Maintenance Therapy of Melioidosis 
Antimicrobial Agents and Chemotherapy  2005;49(10):4020-4025.
Melioidosis (infection caused by Burkholderia pseudomallei) requires a prolonged course of oral antibiotics following initial intravenous therapy to reduce the risk of relapse after cessation of treatment. The current recommendation is a four-drug regimen (trimethoprim [TMP], sulfamethoxazole [SMX], doxycycline, and chloramphenicol) and a total treatment time of 12 to 20 weeks. Drug side effects are common; the aim of this study was to compare the efficacy and tolerance of the four-drug regimen with a three-drug regimen (TMP-SMX and doxycycline). An open-label, randomized trial was conducted in northeast Thailand. A total of 180 adult Thai patients were enrolled, of which 91 were allocated to the four-drug regimen and 89 to the three-drug regimen. The trial was terminated early due to poor drug tolerance, particularly of the four-drug regimen. The culture-confirmed relapse rates at 1 year were 6.6% and 5.6% for the four- and three-drug regimens, respectively (P = 0.79). The three-drug regimen was better tolerated than the four-drug regimen; 36% of patients receiving four drugs and 19% of patients receiving three drugs required a switch in therapy due to side effects (P = 0.01). The duration of oral therapy was significantly associated with relapse; after adjustment for confounders, patients receiving less than 12 weeks of oral therapy had a 5.7-fold increase of relapse or death. A combination of TMP-SMX and doxycycline is as effective as and better tolerated than the conventional four-drug regimen for the oral treatment phase of melioidosis.
doi:10.1128/AAC.49.10.4020-4025.2005
PMCID: PMC1251512  PMID: 16189075
18.  Screen of whole blood responses to flagellin identifies TLR5 variation associated with outcome in melioidosis 
Genes and immunity  2013;15(2):63-71.
Melioidosis is a severe infection caused by the flagellated bacterium Burkholderia pseudomallei. The nonsense polymorphism TLR51174C>T is associated with improved outcome in Thais with melioidosis. We hypothesized that other TLR5 variants may modulate the host response and determine outcome in melioidosis. We genotyped 12 TLR5 variants selected de novo from the HapMap database and examined the association of each with cytokines induced by flagellin stimulation of whole blood from healthy Thai subjects. We found a blunted cytokine response for three related markers that were in linkage disequilibrium with a non-synonymous variant, TLR51846T>C. Carriers of TLR51846T>C had broadly impaired cytokine responses induced by flagellin. TLR51846T>C was associated with protection against death in melioidosis patients (OR 0.62, 95% CI: 0.42-0.93, p=0.021). We observed no impairment in TLR51846C-dependent NF-κB activation, however, suggesting an alternative mechanism for the effect. We found that TLR51846T>C was in strong linkage disequilibrium with TLR51174C>T. Many of the blunted cytokine responses observed and the association of TLR51846T>C with survival in melioidosis patients may be attributable to TLR51174C>T, but we could not exclude an independent effect of TLR51846T>C. These data identify novel associations for TLR51846T>C, enhance our understanding of TLR5 genetic architecture in Thais, and provide future directions of study.
doi:10.1038/gene.2013.60
PMCID: PMC3948086  PMID: 24285178
melioidosis; TLR5; innate immune response; flagellin; genetic variation
19.  Whole-genome sequencing to control antimicrobial resistance 
Trends in Genetics  2014;30(9):401-407.
Highlights
•Owing to improvements in sequencing technologies, microbial whole-genome sequencing (WGS) has emerged as a central tool to control antibiotic resistance.•WGS has been used to develop novel antibiotics and diagnostic tests.•WGS has been key to surveillance and the study of the emergence of antibiotic resistance.•Rapid WGS has the potential to be used as a tool for infection control in the clinic and, in some cases, as a primary diagnostic tool to detect resistance.
Following recent improvements in sequencing technologies, whole-genome sequencing (WGS) is positioned to become an essential tool in the control of antibiotic resistance, a major threat in modern healthcare. WGS has already found numerous applications in this area, ranging from the development of novel antibiotics and diagnostic tests through to antibiotic stewardship of currently available drugs via surveillance and the elucidation of the factors that allow the emergence and persistence of resistance. Numerous proof-of-principle studies have also highlighted the value of WGS as a tool for day-to-day infection control and, for some pathogens, as a primary diagnostic tool to detect antibiotic resistance. However, appropriate data analysis platforms will need to be developed before routine WGS can be introduced on a large scale.
doi:10.1016/j.tig.2014.07.003
PMCID: PMC4156311  PMID: 25096945
whole-genome sequencing; antibiotic resistance; surveillance; diagnostics
20.  Microevolution of Burkholderia pseudomallei during an Acute Infection 
Journal of Clinical Microbiology  2014;52(9):3418-3421.
We used whole-genome sequencing to evaluate 69 independent colonies of Burkholderia pseudomallei isolated from seven body sites of a patient with acute disseminated melioidosis. Fourteen closely related genotypes were found, providing evidence for the rapid in vivo diversification of B. pseudomallei after inoculation and systemic spread.
doi:10.1128/JCM.01219-14
PMCID: PMC4313173  PMID: 24966357
21.  Fatal Melioidosis in Goats in Bangkok, Thailand 
Bangkok, Thailand, is a city considered to be at low risk for melioidosis. We describe 10 goats that died of melioidosis in Bangkok. Half of them were born and reared in the city. Multilocus sequence typing ruled out an outbreak. This finding challenges the assumption that melioidosis is rarely acquired in central Thailand.
doi:10.4269/ajtmh.14-0115
PMCID: PMC4125250  PMID: 24891468
22.  The role of NOD2 in murine and human melioidosis 
Journal of immunology (Baltimore, Md. : 1950)  2013;192(1):10.4049/jimmunol.1301436.
NOD2 is a cytosolic pathogen recognition receptor that regulates susceptibility to a variety of infections and chronic diseases. Burkholderia pseudomallei, a facultative intracellular bacterium, causes the tropical infection melioidosis. We hypothesized that NOD2 may participate in host defense in melioidosis. We performed a series of in vitro assays and in vivo experiments, and analyzed the association of human genetic variation with infection to delineate the contribution of NOD2 to the host response to B. pseudomallei. We found that transfection with NOD2 mediated NF-κB activation induced by B. pseudomallei stimulation of HEK293 cells. After low dose inoculation with aerosolized B. pseudomallei, Nod2-deficient mice showed impaired clinical responses and permitted greater bacterial replication in the lung and dissemination to the spleen compared to wild type mice. IL-6 and KC levels were higher in the lungs of Nod2-deficient mice. In a cohort of 1,562 Thai subjects, a common genetic polymorphism in the NOD2 region, rs7194886, was associated with melioidosis and this effect was most pronounced in women. rs7194886 was not associated with differences in cytokine production induced by whole blood stimulation with the NOD2 ligand, MDP, or B. pseudomallei. These findings are the first to characterize the role of NOD2 in host defense in mammalian melioidosis.
doi:10.4049/jimmunol.1301436
PMCID: PMC3872087  PMID: 24298015
Burkholderia pseudomallei; melioidosis; NOD2; innate immunity; genetic variation; animal model; pneumonia; sepsis
23.  The role of NOD2 in murine and human melioidosis 
NOD2 is a cytosolic pathogen recognition receptor that regulates susceptibility to a variety of infections and chronic diseases. Burkholderia pseudomallei, a facultative intracellular bacterium, causes the tropical infection melioidosis. We hypothesized that NOD2 may participate in host defense in melioidosis. We performed a series of in vitro assays and in vivo experiments, and analyzed the association of human genetic variation with infection to delineate the contribution of NOD2 to the host response to B. pseudomallei. We found that transfection with NOD2 mediated NF-κB activation induced by B. pseudomallei stimulation of HEK293 cells. After low dose inoculation with aerosolized B. pseudomallei, Nod2-deficient mice showed impaired clinical responses and permitted greater bacterial replication in the lung and dissemination to the spleen compared to wild type mice. IL-6 and KC levels were higher in the lungs of Nod2-deficient mice. In a cohort of 1,562 Thai subjects, a common genetic polymorphism in the NOD2 region, rs7194886, was associated with melioidosis and this effect was most pronounced in women. rs7194886 was not associated with differences in cytokine production induced by whole blood stimulation with the NOD2 ligand, MDP, or B. pseudomallei. These findings are the first to characterize the role of NOD2 in host defense in mammalian melioidosis.
doi:10.4049/jimmunol.1301436
PMCID: PMC3872087  PMID: 24298015
Burkholderia pseudomallei; melioidosis; NOD2; innate immunity; genetic variation; animal model; pneumonia; sepsis
24.  Genetic diversity within Mycobacterium tuberculosis complex impacts on the accuracy of genotypic pyrazinamide drug-susceptibility assay 
doi:10.1016/j.tube.2014.04.002
PMCID: PMC4075347  PMID: 24870943
Mycobacterium tuberculosis complex; Pyrazinamide resistance; Phylogenetic diversity
25.  Impact of infectious diseases consultation on the management of Staphylococcus aureus bacteraemia in children 
BMJ Open  2014;4(7):e004659.
Objectives
Infectious diseases consultation (IDC) in adults with Staphylococcus aureus bacteraemia (SAB) has been shown to improve management and outcome. The aim of this study was to evaluate the impact of IDC on the management of SAB in children.
Study design
Observational cohort study of children with SAB.
Setting
Cambridge University Hospitals National Health Service (NHS) Foundation Trust, a large acute NHS Trust in the UK.
Participants
All children with SAB admitted to the Cambridge University Hospitals NHS Foundation Trust between 16 July 2006 and 31 December 2012.
Methods
Children with SAB between 2006 and 31 October 2009 were managed by routine clinical care (pre-IDC group) and data were collected retrospectively by case notes review. An IDC service for SAB was introduced in November 2009. All children with SAB were reviewed regularly and data were collected prospectively (IDC group) until 31 December 2012. Baseline characteristics, quality metrics and outcome were compared between the pre-IDC group and IDC group.
Results
There were 66 episodes of SAB in 63 children—28 patients (30 episodes) in the pre-IDC group, and 35 patients (36 episodes) in the IDC group. The median age was 3.4 years (IQR 0.2–10.7 years). Patients in the IDC group were more likely to have echocardiography performed, a removable focus of infection identified and to receive a longer course of intravenous antimicrobial therapy. There were no differences in total duration of antibiotic therapy, duration of hospital admission or outcome at 30 or 90 days following onset of SAB.
Conclusions
IDC resulted in improvements in the investigation and management of SAB in children.
doi:10.1136/bmjopen-2013-004659
PMCID: PMC4091395  PMID: 24989617

Results 1-25 (172)