Molecular investigation of bacterial communities on intravascular catheters: no longer just Staphylococcus

Comparison of microbial colonization rates between central venous catheters and peripherally inserted central catheters

BACKGROUND

Central venous catheters (CVCs) and peripherally inserted central catheters (PICCs), have been widely used as intravascular devices in critically ill patients. However, they might evoke complications, such as catheter colonization that has been considered as predisposing factor for central line-associated bloodstream infections (CLABSIs). Although numerous studies have compared the risk of bloodstream infections between PICCs and CVCs, comparative studies on their colonization rates are limited.

OBJECTIVES

The episodes of catheter colonization in critically ill patients with CVCs or PICCs were retrospectively analysed during a two-year period in a Greek tertiary care hospital and colonization rates, microbial profiles and antimicrobial susceptibility patterns were compared.

METHODS

Clinical and laboratory data of consecutive hospitalized critically-ill patients who underwent PICC and CVC placement between May 2017-May 2019 were analysed. All catheters were examined by the semiquantitative culture technique for bacterial pathogens, either as a routine process after catheter removal or after suspicion of infection. Species identification and antimicrobial resistance patterns were determined by the Vitek2 automated system.

RESULTS

During the survey period a total of 122/1187 (10.28%) catheter colonization cases were identified among CVCs and 19/639 (2.97%) cases among PICCs (p = 0.001). The colonization rate was 12.48/1000 catheter-days for the CVC group and 1.71/1000 catheter-days for the PICC group (p < 0.001). The colonization rate per 1000 catheter-days due to multidrug-resistant organisms (MDROs) was 3.85 in all study cases, 7.26 (71/122) in the CVC group and 0.63 (7/19) in the PICC group (p < 0.001). Within the CVC group, the most common microorganism isolated was MDR Acinetobacter baumannii (n = 38, 31.1%) followed by MDR Klebsiella pneumoniae (n = 20, 16.4%). In the PICC group, the predominant microorganism isolated was Candida spp. (n = 5, 23.8%) followed by MDR K. pneumoniae and MDR A. baumannii in equal numbers (n = 3, 14.2%).

CONCLUSION

PICC lines were associated with significantly lower colonization rates comparing to the CVC ones. In addition, patterns of microbial colonization revealed a trend over the predominance of MDR gram-negatives in CVCs suggesting that PICCs might be a safer alternative for prolonged inpatient intravascular access. Prevention programs directed by local microbial ecology may diminish catheter colonization rates and CLABSIs.

A Journey into Animal Models of Human Osteomyelitis: A Review

Osteomyelitis is an infection of the bone characterized by progressive inflammatory destruction and apposition of new bone that can spread via the hematogenous route (hematogenous osteomyelitis (HO)), contiguous spread (contiguous osteomyelitis (CO)), and direct inoculation (osteomyelitis associated with peripheral vascular insufficiency (PVI)). Given the significant financial burden posed by osteomyelitis patient management, the development of new preventive and treatment methods is warranted. To achieve this objective, implementing animal models (AMs) of infection such as rats, mice, rabbits, avians, dogs, sheep, goats, and pigs might be of the essence. This review provides a literature analysis of the AMs developed and used to study osteomyelitis. Historical relevance and clinical applicability were taken into account to choose the best AMs, and some study methods are briefly described. Furthermore, the most significant strengths and limitations of each species as AM are discussed, as no single model incorporates all features of osteomyelitis. HO’s clinical manifestation results in extreme variability between patients due to multiple variables (e.g., age, sex, route of infection, anatomical location, and concomitant diseases) that could alter clinical studies. However, these variables can be controlled and tested through different animal models.

Composition and Diversity of the Ocular Surface Microbiota in Patients With Blepharitis in Northwestern China

Purpose: To investigate the composition and diversity of the microbiota on the ocular surface of patients with blepharitis in northwestern China via 16S rDNA amplicon sequencing.

Methods: Thirty-seven patients with blepharitis divided into groups of anterior, posterior and mixed blepharitis and twenty healthy controls from northwestern China were enrolled in the study. Samples were collected from the eyelid margin and conjunctival sac of each participant. The V3–V4 region of bacterial 16S rDNA in each sample was amplified and sequenced on the Illumina HiSeq 2500 sequencing platform, and the differences in taxonomy and diversity among different groups were compared.

Results: The composition of the ocular surface microbiota of patients with blepharitis was similar to that of healthy subjects, but there were differences in the relative abundance of each bacterium. At the phylum level, the abundances of Actinobacteria, Cyanobacteria, Verrucomicrobia, Acidobacteria, Chloroflexi, and Atribacteria were significantly higher in the blepharitis group than in the healthy control group, while the relative abundance of Firmicutes was significantly lower (p < 0.05, Mann-Whitney U). At the genus level, the abundances of Lactobacillus, Ralstonia, Bacteroides, Akkermansia, Bifidobacterium, Escherichia-Shigella, Faecalibacterium, and Brevibacterium were significantly higher in the blepharitis group than in the healthy control group, while the relative abundances of Bacillus, Staphylococcus, Streptococcus, and Acinetobacter were significantly lower in the blepharitis group (p < 0.05, Mann-Whitney U). The microbiota of anterior blepharitis was similar to that of mixed blepharitis but different from that of posterior blepharitis. Lactobacillus and Bifidobacterium are biomarkers of posterior blepharitis, and Ralstonia is a biomarker of mixed blepharitis. There was no significant difference in the ocular surface microbiota between the eyelid margin and conjunctival sac with or without blepharitis.

Conclusion: The ocular surface microbiota of patients with blepharitis varied among different study groups, according to 16S rDNA amplicon sequencing analysis. The reason might be due to the participants being from different environments and having different lifestyles. Lactobacillus, Bifidobacterium, Akkermansia, Ralstonia, and Bacteroides may play important roles in the pathogenesis of blepharitis.

Wireless, Skin-Interfaced Devices for Pediatric Critical Care: Application to Continuous, Noninvasive Blood Pressure Monitoring

Indwelling arterial lines, the clinical gold standard for continuous blood pressure (BP) monitoring in the pediatric intensive care unit (PICU), have significant drawbacks due to their invasive nature, ischemic risk, and impediment to natural body movement. A noninvasive, wireless, and accurate alternative would greatly improve the quality of patient care. Recently introduced classes of wireless, skin-interfaced devices offer capabilities in continuous, precise monitoring of physiologic waveforms and vital signs in pediatric and neonatal patients, but have not yet been employed for continuous tracking of systolic and diastolic BP-critical for guiding clinical decision-making in the PICU. The results presented here focus on materials and mechanics that optimize the system-level properties of these devices to enhance their reliable use in this context, achieving full compatibility with the range of body sizes, skin types, and sterilization schemes typically encountered in the PICU. Systematic analysis of the data from these devices on 23 pediatric patients, yields derived, noninvasive BP values that can be quantitatively validated against direct recordings from arterial lines. The results from this diverse cohort, including those under pharmacological protocols, suggest that wireless, skin-interfaced devices can, in certain circumstances of practical utility, accurately and continuously monitor BP in the PICU patient population.

Skin colonization at peripheral intravenous catheter insertion sites increases the risk of catheter colonization and infection

BACKGROUND

Peripheral intravenous catheters (PIVCs) break the skin barrier, and preinsertion antiseptic disinfection and sterile dressings are used to reduce risk of catheter-related bloodstream infection (CRBSI). In this study, the impact of PIVC skin site colonization on tip colonization and the development of CRBSI was investigated.

METHODS

A total of 137 patients' PIVC skin site swabs and paired PIVC tips were collected at catheter removal, cultured, and bacterial species and clonality were identified.

RESULTS

Of 137 patients, 45 (33%) had colonized skin sites and/or PIVC tips. Of 16 patients with paired colonization of both the skin site and PIVC tips, 11 (69%) were colonized with the same bacterial species. Of these, 77% were clonally related, including 1 identical clone of Pseudomonas aeruginosa in a patient with systemic infection and the same organism identified in blood culture.

CONCLUSIONS

The results demonstrate that opportunistic pathogen colonization at the skin site poses a significant risk for PIVC colonization and CRBSI. Further research is needed to improve current preinsertion antiseptic disinfection of PIVC skin site and the sterile insertion procedure to potentially reduce PIVC colonization and infection risk.

Retrospective Analysis of Microbial Colonization Patterns in Central Venous Catheters, 2013-2017

Objectives

This study was performed to provide epidemiological information on microbial colonization in central venous catheters (CVCs).

Methods

CVCs submitted to Medical Microbiology Laboratory from January 1, 2013, through October 1, 2017, which met our criteria would be included for analysis. Quantitative culture was used for CVCs. The results of culture and related information on CVCs were collected and recorded in detail. The prevalence was calculated, and related factors were analyzed statistically.

Results

A total of 2020 CVCs were submitted for culture and eligible for analysis. Positive microbial culture occurred in 379 catheters with 18.7% (379 of 2020) prevalence of colonization. There were 23 microbial genera and 45 organisms detected. Among the isolated organisms, there were 39 kinds of isolated bacteria and 6 kinds of isolated fungi. Acinetobacter (19.8%) predominated in total isolated microorganisms, followed by Staphylococcus epidermidis (11.3%) and Candida albicans (10.3%). There were no significant differences in isolated organisms and fungal species between different sexes (X² = 2.365, P = 0.50). Conversely, there were significant differences in isolated bacterial and fungal species between different wards and years (X² = 124.046, P = 0.000; X² = 77.064, P = 0.000). A total of 107 (5.3%, 107/2020) CVCs were associated with a diagnosis of central line-associated bloodstream infection (CLABSI). The most common organisms in causing CLABSI were Acinetobacter (23.4%), S. aureus (13.1%), and Candida albicans (12.1%).

Conclusion

The prevalence of microbial colonization in CVCs is still significant and even has gradually changed over time. The study provides a new view of microbial colonization pattern in CVCs and a prevalence of CLABSI, which will facilitate catheter-related infection prevention and control in clinic.

Anti-quorum sensing and antibiofilm activities of Blastobotrys parvus PPR3 against Pseudomonas aeruginosa PAO1

The bacterial cell communication also termed as Quorum sensing (QS) system was involved in the expression of several virulence traits during Pseudomonas infection. The attenuating of this bacterial cell communication system is an attractive approach for the management of bacterial infections without the complication of resistance development. In this respect, the marine environment has gained significant attention due to its biodiversity and as a source of novel bioactive compounds. The present study aimed to screening effective QS inhibitors from marine associated fungal species for QS inhibitors. Twelve morphologically distinct fungal isolates were isolated from the wood of Avicennia marina from marine ecosystem. The anti-QS potential of fungal crude extract from was investigated in biosensor strain and test bacterium, Chromobacterium violaceum and Pseudomonas aeruginosa PAO1, respectively. Promising anti-QS activity was observed in the crude extract of one of the fungal isolate and identified by molecular characterization using internal transcribed spacer (ITS) region as Blastobotrys parvus PPR3. The anti-virulence and antibiofilm effects of ethyl acetate fractions from PPR3 against P. aeruginosa PAO1 were evaluated. The fungal metabolites responsible for the anti-QS activity of fungal crude extract was identified using gas chromatography-mass spectrometry (GC-MS). Furthermore, molecular docking studies were performed to understand the interaction of bioactive compounds with as receptors of P. aeruginosa PAO1. The crude extract of PPR3 showed reduction in different virulence traits of P. aeruginosa PAO1 such as production of pyocyanin, elastase, protease, chitinase, swimming and swarming motility, biofilm formation, exopolysaccharide production and alginate production at different sub-MIC concentrations. Interaction of bioactive metabolites with LasR and RhlR receptors of P. aeruginosa PAO1 was reported. The findings of the present study suggested that metabolites of B. parvus PPR3 interfere with QS system of P. aeruginosa PAO1 and alters the production of virulence factors.

Synthesis and antimicrobial photodynamic effect of methylene blue conjugated carbon nanotubes on E. coli and S. aureus

The methylene blue and CNT nanoconjugate effectively produced singlet oxygen via photoactivation using a diode laser. It was employed for aPDT against pathogenic bacteria.

Tetrasodium EDTA Is Effective at Eradicating Biofilms Formed by Clinically Relevant Microorganisms from Patients' Central Venous Catheters

The colonization of catheters by microorganisms often precludes their long-term use, which can be a problem for human patients that have few body sites available for new catheters. The colonizing organisms often form biofilms, and increasingly these organisms are resistant to multiple antibiotics, making them difficult to treat. In this article, we have taken microorganisms that are associated with biofilm formation in catheters from two Canadian hospitals and tested them with tetrasodium EDTA, a new antimicrobial catheter lock solution. Tetrasodium EDTA was effective at eliminating Gram-positive, Gram-negative, and fungal species and represents a promising alternative to antibiotic treatment with less chance of the organisms developing resistance. We expect that our results will be of interest to researchers and clinicians and will lead to improved patient care.

Central venous access devices (CVADs) are an essential component of modern health care. However, their prolonged use commonly results in microbial colonization, which carries the potential risk of hospital-acquired bloodstream infections. These infections complicate the treatment of already sick individuals and cost the existing health care systems around the world millions of dollars. The microbes that colonize CVADs typically form multicellular biofilms that are difficult to dislodge and are resistant to antimicrobial treatments. Clinicians are searching for better ways to extend the working life span of implanted CVADs, by preventing colonization and reducing the risk of bloodstream infections. In this study, we analyzed 210 bacterial and fungal isolates from colonized CVADs or human bloodstream infections from two hospitals geographically separated in the east and west of Canada and screened the isolates for biofilm formation in vitro. Twenty isolates, representing 12 common, biofilm-forming species, were exposed to 4% tetrasodium EDTA, an antimicrobial lock solution that was recently approved in Canada for use as a medical device. The EDTA solution was effective at eradicating surface-attached biofilms from each microbial species, indicating that it could likely be used to prevent biofilm growth within CVADs and to eliminate established biofilms. This new lock solution fits with antibiotic stewardship programs worldwide by sparing the use of important antibiotic agents, targeting prevention rather than the expensive treatment of hospital-acquired infections.

IMPORTANCE The colonization of catheters by microorganisms often precludes their long-term use, which can be a problem for human patients that have few body sites available for new catheters. The colonizing organisms often form biofilms, and increasingly these organisms are resistant to multiple antibiotics, making them difficult to treat. In this article, we have taken microorganisms that are associated with biofilm formation in catheters from two Canadian hospitals and tested them with tetrasodium EDTA, a new antimicrobial catheter lock solution. Tetrasodium EDTA was effective at eliminating Gram-positive, Gram-negative, and fungal species and represents a promising alternative to antibiotic treatment with less chance of the organisms developing resistance. We expect that our results will be of interest to researchers and clinicians and will lead to improved patient care.

Comparative Analysis of Bacterial Community Composition and Structure in Clinically Symptomatic and Asymptomatic Central Venous Catheters

Totally implanted venous access ports (TIVAPs) are commonly used catheters for the management of acute or chronic pathologies. Although these devices improve health care, repeated use of this type of device for venous access over long periods of time is also associated with risk of colonization and infection by pathogenic bacteria, often originating from skin. However, although the skin microbiota is composed of both pathogenic and nonpathogenic bacteria, the extent and the consequences of TIVAP colonization by nonpathogenic bacteria have rarely been studied. Here, we used culture-dependent and 16S rRNA gene-based culture-independent approaches to identify differences in bacterial colonization of TIVAPs obtained from two French hospitals. To explore the relationships between nonpathogenic organisms colonizing TIVAPs and the potential risk of infection, we analyzed the bacterial community parameters between TIVAPs suspected (symptomatic) or not (asymptomatic) of infection. Although we did not find a particular species assemblage or community marker to distinguish infection risk on an individual sample level, we identified differences in bacterial community composition, diversity, and structure between clinically symptomatic and asymptomatic TIVAPs that could be explored further. This study therefore provides a new view of bacterial communities and colonization patterns in intravascular TIVAPs and suggests that microbial ecology approaches could improve our understanding of device-associated infections and could be a prognostic tool to monitor the evolution of bacterial communities in implants and their potential susceptibility to infections. IMPORTANCE Totally implanted venous access ports (TIVAPs) are commonly used implants for the management of acute or chronic pathologies. Although their use improves the patient's health care and quality of life, they are associated with a risk of infection and subsequent clinical complications, often leading to implant removal. While all TIVAPs appear to be colonized, only a fraction become infected, and the relationship between nonpathogenic organisms colonizing TIVAPs and the potential risk of infection is unknown. We explored bacteria present on TIVAPs implanted in patients with or without signs of TIVAP infection and identified differences in phylum composition and community structure. Our data suggest that the microbial ecology of intravascular devices could be predictive of TIVAP infection status and that ultimately a microbial ecological signature could be identified as a tool to predict TIVAP infection susceptibility and improve clinical management.

Ralstonia mannitolilytica infections in an oncologic day ward: description of a cluster among high-risk patients

BACKGROUND

Ralstonia spp, an environmental microorganism, has been occasionally associated with healthcare infections. The aim of this study was to investigate an outbreak caused by Ralstonia mannitolilytica in oncology patients.

METHODS

Case definition: Oncology outpatients attending a day ward, with positive blood and/or central venous catheter (CVC) culture for Ralstonia spp from September 2013 - June 2014. We analysed medical records, procedures and environmental samples. R. mannitolilytica was identified by 16S rRNA sequencing, and typed by Pulsed Field Gel Electrophoresis (PFGE); resistance to carbapenemes was investigated by phenotypic and molecular methods.

RESULTS

The patients (N = 22) had different malignancies and received different therapy; all had a CVC and 16 patients presented chills and/or fever. R. mannitolilytica was isolated from both blood and CVC (n = 12) or only blood (n = 6) or CVC tips (n = 4). The isolates had indistinguishable PFGE profile, and showed resistance to carbapenems. All the isolates were negative for carbapenemase genes while phenotypic tests suggests the presence of an AmpC β-lactamase activity,responsible for carbapenem resistance. All patients had had CVC flushed with saline to keep the venous access pervious or before receiving chemotherapy at various times before the onset of symptoms. After the first four cases occurred, the multi-dose saline bottles used for CVC flushing were replaced with single-dose vials; environmental samples were negative for R. mannitolilytica.

CONCLUSIONS

Although the source of R. mannitolilytica remains unidentified, CVC flushing with contaminated saline solution seems to be the most likely origin of R. mannitolilytica CVC colonization and subsequent infections. In order to prevent similar outbreaks we recommend removal of any CVC that is no longer necessary and the use of single-dose solutions for any parenteral treatment of oncology patients.

Non-culture based diagnostics for intravascular catheter related bloodstream infections

INTRODUCTION

intravascular catheter related bloodstream infection (IVC-BSI) is a leading cause of nosocomial infections and associated with significant morbidity and mortality. Early detection and adequate treatment of causative pathogens is critical for a favourable outcome. However, it takes significant time to receive microbiological results due to the current reference diagnostic method's reliance on microbial growth. Areas covered: This review discusses culture and non-culture based techniques for the diagnosis of non IVC-BSI and IVC-BSI, including molecular methods and biomarkers. Different diagnostic strategies are evaluated and the potential of new generation of diagnostic assays highlighted. Expert commentary: The development of additional diagnostic methods has potential to beneficially supplement conventional culture diagnosis, and molecular techniques have particular potential to fulfil this need. They would also contribute significant new knowledge on the bacterial species present on catheters that are generally missed by diagnosis using traditionally culture-dependent methods. Advances in molecular strategies, together with new biomarkers, might lead to the development of faster, more sensitive and cheaper technologies and instruments. This review aims to provide a platform for the further development of IVCBSI diagnostic techniques.

Comparison of cultures and 16S rRNA sequencing for identification of bacteria in two-stage revision arthroplasties: preliminary report

BACKGROUND

The use of a prefabricated spacer in two-stage revision arthroplasty remains one of the few surgery strategies for infected-joint arthroplasty treatment, despite the many unidentified microorganisms in the infected joint replacements reported in some recent studies. The aim of this prospective survey was to investigate if the sonication followed by polymerase chain reaction (PCR) can improve bacterial identification on the surfaces of prefabricated spacers and if the systemic laboratory mediators of infection and positive microbiological results can take a role of predictive factors of infection and clinical failures in 2-years follow-up.

METHODS

Thirteen patients with prosthetic joint infection were investigated. Bacterial culture and deoxyribonucleic acid (DNA) sequencing were used to detect bacteria on the surface of prefabricated spacers removed during the second stage of revision arthroplasty. The results of pre- and intraoperative culture and DNA sequencing were compared. Minimum follow-up was 2 years.

RESULTS

The result of tissue cultures in second-stage revision arthroplasties revealed positive results in 15 % of patients with Coagulase-negative Staphylococci (CNS) growth. Bacterial DNA was found in over 90 % of patients with negative synovial fluid culture. Positive PCR results revealed potential pathogenic bacteria and species of human and environmental microflora with low virulence. Clinical failures at final follow-up were recorded in 2 (16.6 %) patients.

CONCLUSION

The lack of clinical signs of infection, negative culture of preoperative joint aspirate, and intraoperative specimens do not exclude the presence of bacteria on the surfaces of spacers. The positive results of sonication and molecular tests should be interpreted as real pathogenicity factors in the light of the clinical and laboratory data, especially for patients with immunodeficiency. We confirmed our previous results that sonication followed by PCR and sequencing improved bacterial identification.

Molecular Comparison of Bacterial Communities on Peripheral Intravenous Catheters and Matched Skin Swabs

Skin bacteria at peripheral intravenous catheter (PIVC) insertion sites pose a serious risk of microbial migration and subsequent colonisation of PIVCs, and the development of catheter related bloodstream infections (CRBSIs). Common skin bacteria are often associated with CRBSIs, therefore the bacterial communities at PIVC skin sites are likely to have major implications for PIVC colonisation. This study aimed to determine the bacterial community structures on skin at PIVC insertion sites and to compare the diversity with associated PIVCs. A total of 10 PIVC skin site swabs and matching PIVC tips were collected by a research nurse from 10 hospitalised medical/surgical patients at catheter removal. All swabs and PIVCs underwent traditional culture and high-throughput sequencing. The bacterial communities on PIVC skin swabs and matching PIVCs were diverse and significantly associated (correlation coefficient = 0.7, p<0.001). Methylobacterium spp. was the dominant genus in all PIVC tip samples, but not so for skin swabs. Sixty-one percent of all reads from the PIVC tips and 36% of all reads from the skin swabs belonged to this genus. Staphylococcus spp., (26%), Pseudomonas spp., (10%) and Acinetobacter spp. (10%) were detected from skin swabs but not from PIVC tips. Most skin associated bacteria commonly associated with CRBSIs were observed on skin sites, but not on PIVCs. Diverse bacterial communities were observed at skin sites despite skin decolonization at PIVC insertion. The positive association of skin and PIVC tip communities provides further evidence that skin is a major source of PIVC colonisation via bacterial migration but microbes present may be different to those traditionally identified via culture methods. The results provide new insights into the colonisation of catheters and potential pathogenesis of bacteria associated with CRBSI, and may assist in developing new strategies designed to reduce the risk of CRBSI.

Microbial biofilms associated with intravascular catheter-related bloodstream infections in adult intensive care patients

Catheter-related bloodstream infection (CRBSI) is one of the most serious complications in hospitalised patients, leading to increased hospitalisation, intensive care admissions, extensive antibiotic treatment and mortality. A greater understanding of these bacterial infections is needed to improve the prevention and the management of CRBSIs. We describe here the systematic culture-independent evaluation of intravascular catheter (IVC) bacteriology. Twelve IVCs (6 central venous catheters and 6 arterial catheters) were collected from 6 patients. By using traditional culture methods, 3 patients were diagnosed with catheter colonisation including 1 patient who also had CRBSI, and 3 had no colonisation. From a total of 839,539 high-quality sequence reads from high-throughput sequencing, 8 microbial phyla and 76 diverse microbial genera were detected. All IVCs examined in this study were colonised with complex microbial communities including "non-colonised IVCs," as defined using traditional culture methods. Two main community types were observed: Enterobacteriaceae spp., dominant in patients without colonisation or CRBSI; and Staphylococcus spp., dominant in patients with colonisation and CRBSI. More diverse pathogens and a higher microbial diversity were present in patients with IVC colonisation and CRBSI. Community composition did not appear to be affected by patients' antibiotic treatment or IVC type. Characterisation of these communities is the first step in elucidating roles of these pathogens in disease progression, and to ultimately facilitate the improved prevention, refined diagnosis and management of CRBSI.

Microbial diversity on intravascular catheters from paediatric patients

Microorganisms play important roles in intravascular catheter (IVC)-related infections, which are the most serious complications in children with IVCs, leading to increased hospitalisation, intensive care admissions, extensive antibiotic treatment and mortality. A greater understanding of bacterial communities is needed in order to improve the management of infections. We describe here the systematic culture-independent evaluation of IVC bacteriology in IVC biofilms. Twenty-four IVC samples (six peripherally inserted central catheters, eight central venous catheters and ten arterial catheters) were collected from 24 paediatric patients aged 0 to 14 years old. Barcoded amplicon libraries produced from genes coding 16S rRNA and roll-plate culture methods were used to determine the microbial composition of these samples. From a total of 1,043,406 high-quality sequence reads, eight microbial phyla and 136 diverse microbial genera were detected, separated into 12,224 operational taxonomic units (OTUs). Three phyla (Actinobacteria, Firmicutes and Proteobacteria) predominate the microorganism on the IVC surfaces, with Firmicutes representing nearly half of the OTUs found. Among the Firmicutes, Staphylococcus (15.0% of 16S rRNA reads), Streptococcus (9.6%) and Bacillus (6.1%) were the most common. Community composition did not appear to be affected by patients' age, gender, antibiotic treatment or IVC type. Differences in IVC microbiota were more likely associated with events arising from catheter dwell time, rather than the type of IVC used.

The development and application of a molecular community profiling strategy to identify polymicrobial bacterial DNA in the whole blood of septic patients

Background

The application of molecular based diagnostics in sepsis has had limited success to date. Molecular community profiling methods have indicated that polymicrobial infections are more common than suggested by standard clinical culture. A molecular profiling approach was developed to investigate the propensity for polymicrobial infections in patients predicted to have bacterial sepsis.

Results

Disruption of blood cells with saponin and hypotonic shock enabled the recovery of microbial cells with no significant changes in microbial growth when compared to CFU/ml values immediately prior to the addition of saponin. DNA extraction included a cell-wall digestion step with both lysozyme and mutanolysin, which increased the recovery of terminal restriction fragments by 2.4 fold from diverse organisms. Efficiencies of recovery and limits of detection using Illumina sequencing of the 16S rRNA V3 region were determined for both viable cells and DNA using mock bacterial communities inoculated into whole blood. Bacteria from pre-defined communities could be recovered following lysis and removal of host cells with > 97 % recovery of total DNA present. Applying the molecular profiling methodology to three septic patients in the intensive care unit revealed microbial DNA from blood had consistent alignment with cultured organisms from the primary infection site providing evidence for a bloodstream infection in the absence of a clinical lab positive blood culture result in two of the three cases. In addition, the molecular profiling indicated greater diversity was present in the primary infection sample when compared to clinical diagnostic culture.

Conclusions

A method for analyzing bacterial DNA from whole blood was developed in order to characterize the bacterial DNA profile of sepsis infections. Preliminary results indicated that sepsis infections were polymicrobial in nature with the bacterial DNA recovered suggesting a more complex etiology when compared to blood culture data.