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1.
J Infect ; 86(3): 227-232, 2023 03.
Article in English | MEDLINE | ID: mdl-36702308

ABSTRACT

AIM: This study investigated the compliance with a guideline-based antibiotic regimen on the outcome of patients surgically treated for a fracture-related infection (FRI). METHOD: In this international multicenter observational study, patients were included when diagnosed with an FRI between 2015 and 2019. FRI was defined according to the FRI consensus definition. All patients were followed for at least one year. The chosen antibiotic regimens were compared to the published guidelines from the FRI Consensus Group and correlated to outcome. Treatment success was defined as the eradication of infection with limb preservation. RESULTS: A total of 433 patients (mean age 49.7 ± 16.1 years) with FRIs of mostly the tibia (50.6%) and femur (21.7%) were included. Full compliance of the antibiotic regime to the published guidelines was observed in 107 (24.7%) cases. Non-compliance was mostly due to deviations from the recommended dosing, followed by the administration of an alternative antibiotic than the one recommended or an incorrect use or non-use of rifampin. Non-compliance was not associated with a worse outcome: treatment failure was 12.1% in compliant versus 13.2% in non-compliant cases (p = 0.87). CONCLUSIONS: We report good outcomes in the treatment of FRI and demonstrated that minor deviations from the FRI guideline are not associated with poorer outcomes.


Subject(s)
Fractures, Bone , Humans , Adult , Middle Aged , Aged , Fractures, Bone/complications , Fractures, Bone/drug therapy , Fractures, Bone/surgery , Anti-Bacterial Agents/therapeutic use , Treatment Outcome , Consensus , Treatment Failure
2.
Antibiotics (Basel) ; 11(10)2022 Sep 29.
Article in English | MEDLINE | ID: mdl-36289989

ABSTRACT

This international, multi-center study evaluated the effect of antibiotic-loaded carriers (ALCs) on outcome in patients with a fracture-related infection (FRI) and evaluated whether bacterial resistance to the implanted antibiotics influences their efficacy. All patients who were retrospectively diagnosed with FRI according to the FRI consensus definition, between January 2015 and December 2019, and who underwent surgical treatment for FRI at any time point after injury, were considered for inclusion. Patients were followed-up for at least 12 months. The primary outcome was the recurrence rate of FRI at follow-up. Inverse probability for treatment weighting (IPTW) modeling and multivariable regression analyses were used to assess the relationship between the application of ALCs and recurrence rate of FRI at 12 months and 24 months. Overall, 429 patients with 433 FRIs were included. A total of 251 (58.0%) cases were treated with ALCs. Gentamicin was the most frequently used antibiotic (247/251). Recurrence of infection after surgery occurred in 25/251 (10%) patients who received ALCs and in 34/182 (18.7%) patients who did not (unadjusted hazard ratio (uHR): 0.48, 95% CI: [0.29-0.81]). Resistance of cultured microorganisms to the implanted antibiotic was not associated with a higher risk of recurrence of FRI (uHR: 0.75, 95% CI: [0.32-1.74]). The application of ALCs in treatment of FRI is likely to reduce the risk of recurrence of infection. The high antibiotic concentrations of ALCs eradicate most pathogens regardless of susceptibility test results.

3.
Bone Joint J ; 104-B(9): 1095-1100, 2022 Sep.
Article in English | MEDLINE | ID: mdl-36047024

ABSTRACT

AIMS: Excision of chronic osteomyelitic bone creates a dead space which must be managed to avoid early recurrence of infection. Systemic antibiotics cannot penetrate this space in high concentrations, so local treatment has become an attractive adjunct to surgery. The aim of this study was to present the mid- to long-term results of local treatment with gentamicin in a bioabsorbable ceramic carrier. METHODS: A prospective series of 100 patients with Cierny-Mader Types III and IV chronic ostemyelitis, affecting 105 bones, were treated with a single-stage procedure including debridement, deep tissue sampling, local and systemic antibiotics, stabilization, and immediate skin closure. Chronic osteomyelitis was confirmed using strict diagnostic criteria. The mean follow-up was 6.05 years (4.2 to 8.4). RESULTS: At final follow-up, six patients (six bones) had recurrent infection; thus 94% were infection-free. Three infections recurred in the first year, two in the second year, and one 4.5 years postoperatively. Recurrence was not significantly related to the physiological class of the patient (1/20 Class A (5%) vs 5/80 Class B (6.25%); p = 0.833), nor was it significantly related to the aetiology of the infection, the organisms which were cultured or the presence of nonunion before surgery (1/10 with nonunion (10%) vs 5/90 without nonunion (5.6%); p = 0.570). Organisms with intermediate or high-grade resistance to gentamicin were significantly more likely in polymicrobial infections (9/21; 42.8%) compared with monobacterial osteomyelitis (7/79 (8.9%); p < 0.001). However, recurrence was not significantly more frequent when a resistant organism was present (1/16 for resistant cases (6.25%) vs 5/84 in those with a microbiologically sensitive infection (5.95%); p = 0.958). CONCLUSION: We found that a single-stage protocol, including the use of a high-delivery local antibiotic ceramic carrier, was effective over a period of several years. The method can be used in a wide range of patients, including those with significant comorbidities and an infected nonunion.Cite this article: Bone Joint J 2022;104-B(9):1095-1100.


Subject(s)
Gentamicins , Osteomyelitis , Absorbable Implants , Anti-Bacterial Agents/therapeutic use , Ceramics , Debridement/methods , Humans , Osteomyelitis/diagnosis , Osteomyelitis/drug therapy , Osteomyelitis/surgery , Treatment Outcome
4.
Antibiotics (Basel) ; 11(7)2022 Jul 14.
Article in English | MEDLINE | ID: mdl-35884197

ABSTRACT

Fracture-related infections (FRIs) are classically considered to be early (0−2 weeks), delayed (3−10 weeks) or late (>10 weeks) based on hypothesized differences in causative pathogens and biofilm formation. Treatment strategies often reflect this classification, with debridement, antimicrobial therapy and implant retention (DAIR) preferentially reserved for early FRI. This study examined pathogens isolated from FRI to confirm or refute these hypothesized differences in causative pathogens over time. Cases of FRI managed surgically at three centres between 2015−2019 and followed up for at least one year were included. Data were analysed regarding patient demographics, time from injury and pathogens isolated. Patients who underwent DAIR were also analysed separately. In total, 433 FRIs were studied, including 51 early cases (median time from injury of 2 weeks, interquartile range (IQR) of 1−2 weeks), 82 delayed cases (median time from injury of 5 weeks, IQR of 4−8 weeks) and 300 late cases (median time from injury of 112 weeks, IQR of 40−737 weeks). The type of infection was associated with time since injury; early or delayed FRI are most likely to be polymicrobial, whereas late FRIs are more likely to be culture-negative, or monomicrobial. Staphylococcus aureus was the most commonly isolated pathogen at all time points; however, we found no evidence that the type of pathogens isolated in early, delayed or late infections were different (p = 0.2). More specifically, we found no evidence for more virulent pathogens (S. aureus, Gram-negative aerobic bacilli) in early infections and less virulent pathogens (such as coagulase negative staphylococci) in late infections. In summary, decisions on FRI treatment should not assume microbiological differences related to time since injury. From a microbiological perspective, the relevance of classifying FRI by time since injury remains unclear.

5.
Antibiotics (Basel) ; 11(7)2022 Jul 14.
Article in English | MEDLINE | ID: mdl-35884200

ABSTRACT

This international, multi-center study investigated the effect of individual components of surgery on the clinical outcomes of patients treated for fracture-related infection (FRI). All patients with surgically treated FRIs, confirmed by the FRI consensus definition, were included. Data were collected on demographics, time from injury to FRI surgery, soft tissue reconstruction, stabilization and systemic and local anti-microbial therapy. Patients were followed up for a minimum of one year. In total, 433 patients were treated with a mean age of 49.7 years (17−84). The mean follow-up time was 26 months (range 12−72). The eradication of infection was successful in 86.4% of all cases and 86.0% of unhealed infected fractures were healed at the final review. In total, 3.3% required amputation. The outcome was not dependent on age, BMI, the presence of metalwork or time from injury (recurrence rate 16.5% in FRI treated at 1−10 weeks after injury; 13.1% at 11−52 weeks; 12.1% at >52 weeks: p = 0.52). The debridement and retention of a stable implant (DAIR) had a failure rate of 21.4%; implant exchange to a new internal fixation had a failure rate of 12.5%; and conversion to external fixation had a failure rate of 10.3% (adjusted hazard ratio (aHR) DAIR vs. Ext Fix 2.377; 95% C.I. 0.96−5.731). Tibial FRI treated with a free flap was successful in 92.1% of cases and in 80.4% of cases without a free flap (HR 0.38; 95% C.I. 0.14−1.0), while the use of NPWT was associated with higher recurrence rates (HR 3.473; 95% C.I. 1.852−6.512). The implantation of local antibiotics reduced the recurrence from 18.7% to 10.0% (HR 0.48; 95% C.I. 0.29−0.81). The successful treatment of FRI was multi-factorial. These data suggested that treatment decisions should not be based on time from injury alone, as other factors also affected the outcome. Further work to determine the best indications for DAIR, free flap reconstruction and local antibiotics is warranted.

6.
J Clin Microbiol ; 60(4): e0215621, 2022 04 20.
Article in English | MEDLINE | ID: mdl-35354286

ABSTRACT

Diagnosis of orthopedic device-related infection is challenging, and causative pathogens may be difficult to culture. Metagenomic sequencing can diagnose infections without culture, but attempts to detect antimicrobial resistance (AMR) determinants using metagenomic data have been less successful. Human DNA depletion may maximize the amount of microbial DNA sequence data available for analysis. Human DNA depletion by saponin was tested in 115 sonication fluid samples generated following revision arthroplasty surgery, comprising 67 where pathogens were detected by culture and 48 culture-negative samples. Metagenomic sequencing was performed on the Oxford Nanopore Technologies GridION platform. Filtering thresholds for detection of true species versus contamination or taxonomic misclassification were determined. Mobile and chromosomal genetic AMR determinants were identified in Staphylococcus aureus-positive samples. Of 114 samples generating sequence data, species-level positive percent agreement between metagenomic sequencing and culture was 50/65 (77%; 95% confidence interval [CI], 65 to 86%) and negative percent agreement was 103/114 (90%; 95% CI, 83 to 95%). Saponin treatment reduced the proportion of human bases sequenced in comparison to 5-µm filtration from a median (interquartile range [IQR]) of 98.1% (87.0% to 99.9%) to 11.9% (0.4% to 67.0%), improving reference genome coverage at a 10-fold depth from 18.7% (0.30% to 85.7%) to 84.3% (12.9% to 93.8%). Metagenomic sequencing predicted 13/15 (87%) resistant and 74/74 (100%) susceptible phenotypes where sufficient data were available for analysis. Metagenomic nanopore sequencing coupled with human DNA depletion has the potential to detect AMR in addition to species detection in orthopedic device-related infection. Further work is required to develop pathogen-agnostic human DNA depletion methods, improving AMR determinant detection and allowing its application to other infection types.


Subject(s)
Anti-Bacterial Agents , Saponins , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/therapeutic use , Drug Resistance, Bacterial , High-Throughput Nucleotide Sequencing/methods , Humans , Metagenome , Metagenomics/methods
7.
Antibiotics (Basel) ; 12(1)2022 Dec 22.
Article in English | MEDLINE | ID: mdl-36671214

ABSTRACT

Background: It remains unclear how accurately patients' previous microbiology correlates with that ascertained from deep sampling in long bone infection. This study assessed the quality of microbiology referral information and compared it to the gold standard of intra-operative deep tissue sampling. Methods: All patients referred to a single specialist centre within the UK between January 2019 and March 2020 who received surgery for long bone infection were eligible for inclusion. Data on microbiological testing that was performed prior to referral was collected prospectively at the time of clinic appointment and prior to surgery. Pre-referral microbiology was compared to microbiology from deep tissue samples taken during surgery. Results: 141 patients met the diagnostic criteria for long bone infection and were included for analysis. Of these, 72 patients had microbiological information available at referral from 88 samples, obtained from either sinus swab (n = 40), previous surgical sampling (n = 25), biopsy (n = 19) or blood cultures (n = 4). In 65.9% of samples, pre-referral microbiology was deemed to be a non-match when compared to intra-operative samples. Factors that increased risk of a non-match included presence of a sinus (odd's ratio (OR) 11.3 [95% CI 2.84−56.6], p = 0.001), increased duration of time from sampling (OR 2.29, [95% CI 1.23−5.90], p = 0.030) and results from prior surgical sampling (OR 23.0 [95% CI 2.80−525.6], p = 0.011). Furthermore, previous surgical debridement gave an increased risk of multi-, extensively or pan-resistant isolates cultured from intra-operative sampling (OR 3.6 [95% CI 1.5−8.7], p < 0.01). Conclusions: We have demonstrated that presence of a sinus, a long time from the sample being taken and results from prior surgical sampling are more likely to give inaccurate representation of current microbiology. Importantly, in cases with previous debridement surgery, there was an increased risk of multi drug resistant isolates which should be planned for in future treatments.

8.
Clin Infect Pract ; 12: 100095, 2021 Nov.
Article in English | MEDLINE | ID: mdl-36338177

ABSTRACT

Infection expertise in the NHS has historically been provided predominantly by hospital-based medical microbiologists responsible for provision of diagnostic services and advice to front-line clinicians. While most hospitals had consultant-led microbiology departments, infectious iiseases departments were based in a small number of specialist centres. The demand for infection expertise is growing in the NHS, driven by advances in medical care, increasing awareness of the impact of antibiotic resistant and healthcare associated infections and threats from emerging infectious diseases. At the same time diagnostic services are being reorganised into pathology networks. The Combined Infection Training (CIT) is delivering a consultant workforce with expertise both in laboratory diagnostic practice and delivery of direct patient care. These changes create challenges for delivery of high quality infection expertise equitably across the NHS. They also offer an opportunity to shape infection services to meet clinical and laboratory demands. To date there has not been an attempt to bring together a single set of best practice guidelines for the requirements of an infection service. This document sets out seven standards. These are written to be practical and flexible according to the diverse ways in which infection expertise may be required across the NHS. It has been prepared by the Clinical Services Committee of the British Infection Association drawing on published evidence and guidance where they exist and on the group's extensive experience of delivering infection services in hospitals across the NHS. It was then refined with input from the RCP Joint Specialist committee (JSC) and the RCPath Specialist Advisory Committee (SAC) and through consultation with the RCPath membership. It has been endorsed by the Royal College of Pathologists and the Royal College of Physicians. It will be reviewed annually by the CSC and updated as additional evidence becomes available.

10.
J Orthop Trauma ; 34(1): 8-17, 2020 Jan.
Article in English | MEDLINE | ID: mdl-31855973

ABSTRACT

Fracture-related infection (FRI) is a severe complication after bone injury and can pose a serious diagnostic challenge. Overall, there is a limited amount of scientific evidence regarding diagnostic criteria for FRI. For this reason, the AO Foundation and the European Bone and Joint Infection Society proposed a consensus definition for FRI to standardize the diagnostic criteria and improve the quality of patient care and applicability of future studies regarding this condition. The aim of this article was to summarize the available evidence and provide recommendations for the diagnosis of FRI. For this purpose, the FRI consensus definition will be discussed together with a proposal for an update based on the available evidence relating to the diagnostic value of clinical parameters, serum inflammatory markers, imaging modalities, tissue and sonication fluid sampling, molecular biology techniques, and histopathological examination. Second, recommendations on microbiology specimen sampling and laboratory operating procedures relevant to FRI will be provided. LEVEL OF EVIDENCE:: Diagnostic Level V. See Instructions for Authors for a complete description of levels of evidence.


Subject(s)
Fractures, Bone , Surgical Wound Infection , Biomarkers , Consensus , Fractures, Bone/complications , Fractures, Bone/diagnosis , Humans , Specimen Handling
11.
J Orthop Trauma ; 34(1): 30-41, 2020 Jan.
Article in English | MEDLINE | ID: mdl-31567902

ABSTRACT

Fracture-related infection (FRI) is a major complication in musculoskeletal trauma and one of the leading causes of morbidity. Standardization of general treatment strategies for FRI has been poor. One of the reasons is the heterogeneity in this patient population, including various anatomical locations, multiple fracture patterns, different degrees of soft-tissue injury, and different patient conditions. This variability makes treatment complex and hard to standardize. As these infections are biofilm-related, surgery remains the cornerstone of treatment, and this entails multiple key aspects (eg, fracture fixation, tissue sampling, debridement, and soft-tissue management). Another important aspect, which is sometimes less familiar to the orthopaedic trauma surgeon, is systemic antimicrobial therapy. The aim of this article is to summarize the available evidence and provide recommendations for systemic antimicrobial therapy with respect to FRI, based on the most recent literature combined with expert opinion. LEVEL OF EVIDENCE:: Therapeutic Level V. See Instructions for Authors for a complete description of levels of evidence.


Subject(s)
Anti-Infective Agents , Fractures, Bone , Anti-Bacterial Agents/therapeutic use , Consensus , Fractures, Bone/complications , Fractures, Bone/drug therapy , Humans , Surgical Wound Infection/drug therapy
12.
J Infect ; 79(3): 189-198, 2019 09.
Article in English | MEDLINE | ID: mdl-31319142

ABSTRACT

AIM: This study quantified changes in the microbiology of osteomyelitis over a ten year period from a single centre within the UK with regard to infection with multi-drug resistant (MDR) bacteria and susceptibility of antimicrobial regimens. METHOD: Patients with chronic osteomyelitis undergoing definitive surgery from 2013-2017 were inluded (n = 223). Microbiology was compared to patients in a cohort from 2001-2004, using the same diagnostic criteria, and same deep tissue sampling technique (n = 157). Clinical features associated with MDR bacterial infection were analysed using logistic regression. RESULTS: Both cohorts had similar baseline characteristics. Despite a similar proportion of Staphylococcus aureus in both cohorts, the rate of methicillin resistant Staphylococcus aureus (MRSA) infection was lower in 2013-2017 compared to 2001-2004 (11.4% vs 30.8% of Staphylococcus aureus, p = 0.007). However, the proportion of MDR infections was similar in both cohorts (15.2% versus 17.2%). Metalwork was associated with MDR infection (unadjusted OR 5.0; 95% CI: 1.15 to 22.0). There was no change in resistance to glycopeptide / meropenem combination treatment (2.2% vs 2.5%, p > 0.9). CONCLUSIONS: In this centre, rates of MRSA osteomyelitis have fallen by two thirds, over the past 10 years, in line with the reducing rate of MRSA bacteraemia nationally. A history of metalwork may predict MDR infection. A glycopeptide with an anti-pseudomonal carbapenem remains the post-operative empiric systemic regimen of choice. Resistance patterns support the use of a glycopeptide with an aminoglycoside in local antibiotic therapy.


Subject(s)
Bacterial Infections/microbiology , Osteomyelitis/microbiology , Adolescent , Adult , Aged , Aged, 80 and over , Anti-Bacterial Agents/pharmacology , Anti-Bacterial Agents/therapeutic use , Bacterial Infections/diagnosis , Bacterial Infections/drug therapy , Bacterial Typing Techniques , Chronic Disease , Cohort Studies , Combined Modality Therapy , Disease Management , Disease Susceptibility , Drug Resistance, Multiple, Bacterial , Female , Humans , Male , Microbial Sensitivity Tests , Middle Aged , Osteomyelitis/diagnosis , Osteomyelitis/therapy , Risk Factors , Symptom Assessment , Treatment Outcome , Young Adult
13.
N Engl J Med ; 380(5): 425-436, 2019 01 31.
Article in English | MEDLINE | ID: mdl-30699315

ABSTRACT

BACKGROUND: The management of complex orthopedic infections usually includes a prolonged course of intravenous antibiotic agents. We investigated whether oral antibiotic therapy is noninferior to intravenous antibiotic therapy for this indication. METHODS: We enrolled adults who were being treated for bone or joint infection at 26 U.K. centers. Within 7 days after surgery (or, if the infection was being managed without surgery, within 7 days after the start of antibiotic treatment), participants were randomly assigned to receive either intravenous or oral antibiotics to complete the first 6 weeks of therapy. Follow-on oral antibiotics were permitted in both groups. The primary end point was definitive treatment failure within 1 year after randomization. In the analysis of the risk of the primary end point, the noninferiority margin was 7.5 percentage points. RESULTS: Among the 1054 participants (527 in each group), end-point data were available for 1015 (96.3%). Treatment failure occurred in 74 of 506 participants (14.6%) in the intravenous group and 67 of 509 participants (13.2%) in the oral group. Missing end-point data (39 participants, 3.7%) were imputed. The intention-to-treat analysis showed a difference in the risk of definitive treatment failure (oral group vs. intravenous group) of -1.4 percentage points (90% confidence interval [CI], -4.9 to 2.2; 95% CI, -5.6 to 2.9), indicating noninferiority. Complete-case, per-protocol, and sensitivity analyses supported this result. The between-group difference in the incidence of serious adverse events was not significant (146 of 527 participants [27.7%] in the intravenous group and 138 of 527 [26.2%] in the oral group; P=0.58). Catheter complications, analyzed as a secondary end point, were more common in the intravenous group (9.4% vs. 1.0%). CONCLUSIONS: Oral antibiotic therapy was noninferior to intravenous antibiotic therapy when used during the first 6 weeks for complex orthopedic infection, as assessed by treatment failure at 1 year. (Funded by the National Institute for Health Research; OVIVA Current Controlled Trials number, ISRCTN91566927 .).


Subject(s)
Administration, Oral , Anti-Bacterial Agents/administration & dosage , Bone Diseases, Infectious/drug therapy , Joint Diseases/drug therapy , Administration, Intravenous , Adolescent , Adult , Aged , Aged, 80 and over , Anti-Bacterial Agents/adverse effects , Anti-Bacterial Agents/pharmacokinetics , Female , Humans , Intention to Treat Analysis , Male , Medication Adherence , Middle Aged , Treatment Outcome , Young Adult
14.
Wellcome Open Res ; 4: 108, 2019.
Article in English | MEDLINE | ID: mdl-31930174

ABSTRACT

Background: Bone and joint infections are becoming increasingly common and are usually treated with surgery and a course of intravenous antibiotics. However, there is no evidence to support the superiority of intravenous therapy and there is a growing body of literature showing that oral therapy is effective in treating these infections.Given this lack of evidence the clinical trial 'Oral Versus Intravenous Antibiotics' (OVIVA) was designed to assess the clinical and cost-effectiveness of intravenous versus oral antibiotics for the treatment of bone and joint infections, using a non-inferiority design. Clinical results from the trial indicate that oral antibiotics are non-inferior to intravenous antibiotics. The aim of this paper is to evaluate the cost-effectiveness of intravenous compared to oral antibiotics for treating bone and joint infections, using data from OVIVA. Methods: A cost-utility analysis was carried out, the main economic outcome measure was the quality adjusted life-year, measured using the EQ-5D-3L questionnaire, combined with costs to estimate cost-effectiveness over 12-months follow-up. Results: Results show that costs were significantly lower in the oral arm compared to the intravenous arm, a difference of £2,740 (95% confidence interval £1,488 to £3,992). Results of four sensitivity analyses were consistent with the base-case results. QALYs were marginally higher in the oral arm, however this difference was not statistically significant; -0.007 (95% confidence interval -0.045 to 0.031). Conclusions: Treating patients with bone and joint infections for the first six weeks of therapy with oral antibiotics is both less costly and does not result in detectable differences in quality of life compared to treatment with intravenous antibiotics. Adopting a practice of treating bone and joint infections with oral antibiotics early in the course of therapy could potentially save the UK National Health Service over £17 million annually.

15.
BMC Genomics ; 19(1): 714, 2018 Sep 27.
Article in English | MEDLINE | ID: mdl-30261842

ABSTRACT

BACKGROUND: Prosthetic joint infections are clinically difficult to diagnose and treat. Previously, we demonstrated metagenomic sequencing on an Illumina MiSeq replicates the findings of current gold standard microbiological diagnostic techniques. Nanopore sequencing offers advantages in speed of detection over MiSeq. Here, we report a real-time analytical pathway for Nanopore sequence data, designed for detecting bacterial composition of prosthetic joint infections but potentially useful for any microbial sequencing, and compare detection by direct-from-clinical-sample metagenomic nanopore sequencing with Illumina sequencing and standard microbiological diagnostic techniques. RESULTS: DNA was extracted from the sonication fluids of seven explanted orthopaedic devices, and additionally from two culture negative controls, and was sequenced on the Oxford Nanopore Technologies MinION platform. A specific analysis pipeline was assembled to overcome the challenges of identifying the true infecting pathogen, given high levels of host contamination and unavoidable background lab and kit contamination. The majority of DNA classified (> 90%) was host contamination and discarded. Using negative control filtering thresholds, the species identified corresponded with both routine microbiological diagnosis and MiSeq results. By analysing sequences in real time, causes of infection were robustly detected within minutes from initiation of sequencing. CONCLUSIONS: We demonstrate a novel, scalable pipeline for real-time analysis of MinION sequence data and use of this pipeline to show initial proof of concept that metagenomic MinION sequencing can provide rapid, accurate diagnosis for prosthetic joint infections. The high proportion of human DNA in prosthetic joint infection extracts prevents full genome analysis from complete coverage, and methods to reduce this could increase genome depth and allow antimicrobial resistance profiling. The nine samples sequenced in this pilot study have shown a proof of concept for sequencing and analysis that will enable us to investigate further sequencing to improve specificity and sensitivity.


Subject(s)
Bacteria/classification , Joint Prosthesis/microbiology , Metagenomics/methods , Sequence Analysis, DNA/methods , Bacteria/genetics , Bacteria/isolation & purification , DNA, Bacterial/analysis , High-Throughput Nucleotide Sequencing/methods , Humans , Nanopores , Pilot Projects , Reproducibility of Results
16.
J Clin Microbiol ; 55(8): 2334-2347, 2017 08.
Article in English | MEDLINE | ID: mdl-28490492

ABSTRACT

Culture of multiple periprosthetic tissue samples is the current gold standard for microbiological diagnosis of prosthetic joint infections (PJI). Additional diagnostic information may be obtained through culture of sonication fluid from explants. However, current techniques can have relatively low sensitivity, with prior antimicrobial therapy and infection by fastidious organisms influencing results. We assessed if metagenomic sequencing of total DNA extracts obtained direct from sonication fluid can provide an alternative rapid and sensitive tool for diagnosis of PJI. We compared metagenomic sequencing with standard aerobic and anaerobic culture in 97 sonication fluid samples from prosthetic joint and other orthopedic device infections. Reads from Illumina MiSeq sequencing were taxonomically classified using Kraken. Using 50 derivation samples, we determined optimal thresholds for the number and proportion of bacterial reads required to identify an infection and confirmed our findings in 47 independent validation samples. Compared to results from sonication fluid culture, the species-level sensitivity of metagenomic sequencing was 61/69 (88%; 95% confidence interval [CI], 77 to 94%; for derivation samples 35/38 [92%; 95% CI, 79 to 98%]; for validation samples, 26/31 [84%; 95% CI, 66 to 95%]), and genus-level sensitivity was 64/69 (93%; 95% CI, 84 to 98%). Species-level specificity, adjusting for plausible fastidious causes of infection, species found in concurrently obtained tissue samples, and prior antibiotics, was 85/97 (88%; 95% CI, 79 to 93%; for derivation samples, 43/50 [86%; 95% CI, 73 to 94%]; for validation samples, 42/47 [89%; 95% CI, 77 to 96%]). High levels of human DNA contamination were seen despite the use of laboratory methods to remove it. Rigorous laboratory good practice was required to minimize bacterial DNA contamination. We demonstrate that metagenomic sequencing can provide accurate diagnostic information in PJI. Our findings, combined with the increasing availability of portable, random-access sequencing technology, offer the potential to translate metagenomic sequencing into a rapid diagnostic tool in PJI.


Subject(s)
Bacteriological Techniques/methods , Metagenomics/methods , Molecular Diagnostic Techniques/methods , Prostheses and Implants/microbiology , Prosthesis-Related Infections/diagnosis , Sonication , Specimen Handling/methods , Humans , Sensitivity and Specificity , Time Factors
18.
BMC Infect Dis ; 14: 233, 2014 May 04.
Article in English | MEDLINE | ID: mdl-24885168

ABSTRACT

BACKGROUND: For the diagnosis of prosthetic joint infection (PJI) automated BACTEC™ blood culture bottle methods have comparable sensitivity, specificity and a shorter time to positivity than traditional cooked meat enrichment broth methods. We evaluate the culture incubation period required to maximise sensitivity and specificity of microbiological diagnosis, and the ability of BACTEC™ to detect slow growing Propionibacteria spp. METHODS: Multiple periprosthetic tissue samples taken by a standardised method from 332 patients undergoing prosthetic joint revision arthroplasty were cultured for 14 days, using a BD BACTEC™ instrumented blood culture system, in a prospective study from 1st January to 31st August 2012. The "gold standard" definition for PJI was the presence of at least one histological criterion, the presence of a sinus tract or purulence around the device. Cases where > =2 samples yielded indistinguishable isolates were considered culture-positive. 1000 BACTEC™ bottle cultures which were negative after 14 days incubation were sub-cultured for Propionibacteria spp. RESULTS: 79 patients fulfilled the definition for PJI, and 66 of these were culture-positive. All but 1 of these 66 culture-positive cases of PJI were detected within 3 days of incubation. Only one additional (clinically-insignificant) Propionibacterium spp. was identified on terminal subculture of 1000 bottles. CONCLUSIONS: Prolonged microbiological culture for 2 weeks is unnecessary when using BACTEC™ culture methods. The majority of clinically significant organisms grow within 3 days, and Propionibacteria spp. are identified without the need for terminal subculture. These findings should facilitate earlier decisions on final antimicrobial prescribing.


Subject(s)
Culture Techniques/instrumentation , Prosthesis-Related Infections/diagnosis , Aged , Female , Humans , Male , Propionibacterium/isolation & purification , Prospective Studies , Prosthesis-Related Infections/microbiology , Sensitivity and Specificity
19.
Curr Opin Infect Dis ; 27(2): 137-45, 2014 Apr.
Article in English | MEDLINE | ID: mdl-24464139

ABSTRACT

PURPOSE OF REVIEW: Skin and soft tissues infections (SSTIs) caused by nontuberculous mycobacteria (NTM) are underrecognized and difficult to treat. Controversies exist for optimal medical management and the role of surgery. Defining the epidemiology in the environment, in animals and in healthcare aids disease prevention. This review focuses on recent advances in epidemiology, risk factors, diagnostics and therapy. RECENT FINDINGS: The increasing consumer appetite for cosmetic and body-modifying procedures (e.g. tattooing, mesotherapy, liposuction) has been associated with rises in sporadic cases and outbreaks of NTM SSTIs. In mainstream healthcare, recent epidemiological studies have helped to quantify the increased risk of NTM infection related to anti-tumour necrosis factor-α monoclonal antibody therapy. Cervicofacial lymphadenitis in children poses management dilemmas, but recent studies and resultant algorithms have simplified decision-making. Molecular studies have led to a better understanding of the epidemiology, therapy and course of Mycobacterium ulcerans infection (Buruli ulcer) that remains prevalent in many areas including sub-Saharan Africa and southeastern Australia. Apart from molecular methods, the widespread adoption of matrix-assisted laser desorption ionization-time of flight mass spectrometry by routine laboratories has potential to simplify and expedite the laboratory identification of NTMs. SUMMARY: An improved understanding of the epidemiology of NTM SSTIs indicates a need to apply effective infection control and ensure regulation of cosmetic and related procedures associated with nonsterile fluids. Broader access to newer diagnostic methods will continue to improve recognition of NTM disease. Along with a paucity of therapeutic agents, there is need for more reliable methods to assess susceptibility and selection of effective combination therapy.


Subject(s)
Mycobacterium Infections, Nontuberculous , Skin Diseases, Bacterial/microbiology , Soft Tissue Infections/microbiology , Anti-Bacterial Agents/therapeutic use , Humans , Microbial Sensitivity Tests , Molecular Diagnostic Techniques/methods , Mycobacterium Infections, Nontuberculous/diagnosis , Mycobacterium Infections, Nontuberculous/drug therapy , Mycobacterium Infections, Nontuberculous/epidemiology , Risk Factors , Skin Diseases, Bacterial/diagnosis , Skin Diseases, Bacterial/drug therapy , Skin Diseases, Bacterial/epidemiology , Soft Tissue Infections/diagnosis , Soft Tissue Infections/drug therapy , Soft Tissue Infections/epidemiology
20.
J Antimicrob Chemother ; 66(7): 1590-3, 2011 Jul.
Article in English | MEDLINE | ID: mdl-21565806

ABSTRACT

OBJECTIVES: Prosthetic joint infection is usually treated using surgery and antibiotics. The response to the treatment regimen is often evaluated using serial monitoring of plasma C-reactive protein (CRP) concentrations. In order to examine how useful this monitoring is, we calculated the sensitivity and specificity of CRP concentrations for predicting treatment failure. PATIENTS AND METHODS: We examined 3732 CRP measurements from 260 patients who were treated by either two-stage revision or debridement and retention. We tested the association between CRP concentration and outcome using logistic regression models, and assessed sensitivity and specificity by using receiver operator curves. RESULTS: The areas under receiver operator curves for CRP concentrations predicting outcome ranged from 0.55 to 0.65. CONCLUSIONS: CRP concentrations did not accurately predict treatment failure. Serial monitoring may not be of benefit.


Subject(s)
C-Reactive Protein/analysis , Drug Monitoring/methods , Osteoarthritis/drug therapy , Osteoarthritis/surgery , Prosthesis-Related Infections/drug therapy , Prosthesis-Related Infections/surgery , Humans , Sensitivity and Specificity , Treatment Outcome
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