Evaluation of the contribution of shotgun metagenomics in the microbiological diagnosis of liver abscesses.

BACKGROUND: Shotgun metagenomics (SMg) sequencing has gained a considerable interest, as it enables the detection of any microorganisms through a single analysis. Due to the limitations of standard microbiological approaches, the microbial documentation of liver abscesses (LA), which is crucial for their medical management, can be difficult. Here we aimed to compare the performance of SMg with standard approaches for the microbiological documentation of LA. METHODS: In this retrospective study conducted at two centers, we compared the results of standard microbiology with metagenomics analysis of consecutive LA samples. For samples tested positive for Klebsiella pneumoniae, we compared the analysis of virulence and resistance genes using metagenomics data to whole-genome sequencing of corresponding isolates obtained in culture. RESULTS: Out of the 62 samples included, standard approaches and SMg yielded documentation in 80.6% and 96.8%, respectively. In 37.1% (23/62) of cases, both methods showed identical results, whereas in 43.5% (27/62) of cases, the samples were positive by both methods, but SMg found additional species in 88.9% (24/27), mostly anaerobes. When the standard approaches were negative, the SMg was able to detect microorganisms in 80.0% of cases (8/10). Overall, SMg identified significantly more microorganisms than culture (414 vs.105; p<0.05). K. pneumoniae genome analysis was able to detect resistance and virulence genes with a level of sensitivity depending on the depth of sequencing. DISCUSSION: Overall, we showed that SMg had better performance in detecting and identifying microorganisms from LA samples and could help characterizing strain's resistome and virulome. Although still costly and requiring specific skills and expensive equipment, MGs methods are set to expand in the future.

First case of bloodstream infection due to Caulobacter spp. associated with a postoperative meningitis.

Caulobacter species are aerobic Gram-negative bacilli initially isolated from aquatic environments and are an uncommon cause of human infection. We report a case of bloodstream infection and postoperative meningitis caused by Caulobacter spp. that occurred in a 53-year old woman two weeks after surgery for a breast carcinoma cerebral metastasis. Polymerase chain reaction (PCR) amplification and sequencing of the 16 S ribosomal DNA identified Caulobacter spp. in three blood cultures and two cerebrospinal fluid (CSF) cultures. Based on our susceptibility results, the patient was successfully treated by a 2-week course of iv imipenem followed by a 4-week course of oral trimethoprim-sulfamethoxazole.

Pyogenic liver abscess in liver transplant recipient: A warning signal for the risk of recurrence and retransplantation.

BACKGROUND: Pyogenic liver abscesses in liver transplant recipients (PLA-LTR) are a rare disease whose specificities compared with PLA in non-transplanted patients (PLA-C) are unknown. METHODS: A retrospective case-control study was conducted in a French academic hospital from January 1, 2010, to December 31, 2014. RESULTS: Among 176 patients diagnosed with PLA, 14 were LTR; each case was matched with 3 PLA-C controls by date of PLA diagnosis and pathophysiological mechanism of PLA. Median time from liver transplantation to PLA diagnosis was 34.5 months. Among 14 PLA-LTR, 8/14 (57.1%) had bacteremia and 10/14 (71.4%) had positive PLA cultures. Most commonly isolated bacteria were Enterobacteriaceae (9/14; 64.3%), Enterococcus spp. (4/14; 28.6%), and anaerobic bacteria (3/14; 21.4%). Clinical, radiological, and microbiological characteristics did not significantly differ between PLA-LTR and PLA-C but there was a tendency toward more diabetic patients and a less acute presentation. All but one PLA-LTR were associated with ischemic cholangitis, whereas this was a rare cause among PLA-C (13/14 vs 3/42, respectively, P < .001) among patients with PLA-LTR. In contrast, hepatobiliary neoplasia was rare in PLA-LTR but frequent in PLA-C (1/14 vs 24/42, P = .001). No significant difference was found between PLA-LTR and PLA-C in terms of duration of antibiotic therapy (6.5 and 6 weeks, respectively), PLA drainage rates (10/14 and 26/42, respectively), or mortality at 12 months after PLA diagnosis (2/14 and 5/42, respectively). Recurrence rates within the first year were observed in 6/14 patients (42.9%), and retransplantation was needed in 5/14 (35.7%). CONCLUSIONS: Occurrence of PLA in LTR is a severe event leading to high risk of recurrence and retransplantation.

More complications in cervical than in non-cervical spine tuberculosis.

Purpose: Cervical spine tuberculosis (CST) is a rare disease that may lead to severe neurological complications. The goal of the study was to compare the characteristics of patients with CST with those of patients with non-cervical spine tuberculosis (NCST).Methods: Between 1997 and 2016, we reviewed all cases of proven tuberculosis from a cohort of spine infections in a tertiary care hospital. Clinical, biological, and imaging data were collected at baseline and after treatment.Results: Fifty-one cases of spine tuberculosis were included: 14 with CST on imaging (27%) and 37 with no cervical localization. Median age was 39 y. Demographic characteristics, duration of symptoms and neurological findings of spine compression were similarly present at presentation in CST and NCST patients. On imaging, lesions were more often multifocal in CST than in NCST patients (9/14 [64%] versus 10/37 [27%], p = .014). Spinal surgery was required in 32/51 (63%) patients. At the end of follow-up (median: 20 months), cure rates were similar in CST and NCST patients but motor and/or sensitive functional sequel were more frequent in CST than NCST patients (6/14 [43%] versus 2/37 [5%], p = .003).Conclusions: Cervical involvement is present in more than a quarter of patients with spinal tuberculosis. Patients with CST had more frequent neurological sequelae than patients with NCST. This was mainly due to a more multifocal disease at presentation. Screening for cervical localization should be systematic in patients with spinal tuberculosis even in the absence of cervical symptoms.

Surgery is safe and effective when indicated in the acute phase of hematogenous pyogenic vertebral osteomyelitis.

BACKGROUND: The overall benefit of surgical management in the acute phase of hematogenous pyogenic vertebral osteomyelitis remains difficult to evaluate because of the balance between potential functional benefit versus complications of surgery. METHODS: Between 2000 and 2013, in a tertiary care hospital, we analyzed a cohort of patients with hematogenous pyogenic vertebral osteomyelitis treated surgically and compared them to those treated medically. Neurologic deficit (using the ASIA impairment scale) and pain (using the analgesic level required) 4 months later, recurrences and infection-related deaths 12 months later were evaluated. A propensity score was developed to adjust for nonrandomized allocation to surgery. RESULTS: Ninety patients were included (mean age 64 years, 63% male); 28 (31%) were treated surgically. After adjustment for the propensity score, the improvement in neurological deficit at 4 months did not differ between surgical and medical treatment (p = .82), but the reduction of pain tended to be greater in surgical versus medical treatment (p = .051). Recurrences of infection (5%) and infection-related deaths (12%) occurred at similar rates in both groups at 12 months (p = 1.00 for both). CONCLUSIONS: Patients with hematogenous pyogenic vertebral osteomyelitis requiring surgery improved equally as non-surgical patients in terms of neurological deficit and residual pain. This result was not hampered by increased complications related to surgery. When indicated, surgery is safe and effective in patients suffering from hematogenous pyogenic vertebral osteomyelitis.

Chlorhexidine-impregnated sponges and less frequent dressing changes for prevention of catheter-related infections in critically ill adults: a randomized controlled trial.

CONTEXT: Use of a chlorhexidine gluconate-impregnated sponge (CHGIS) in intravascular catheter dressings may reduce catheter-related infections (CRIs). Changing catheter dressings every 3 days may be more frequent than necessary. OBJECTIVE: To assess superiority of CHGIS dressings regarding the rate of major CRIs (clinical sepsis with or without bloodstream infection) and noninferiority (less than 3% colonization-rate increase) of 7-day vs 3-day dressing changes. DESIGN, SETTING, AND PATIENTS: Assessor-blind, 2 x 2 factorial, randomized controlled trial conducted from December 2006 through June 2008 and recruiting patients from 7 intensive care units in 3 university and 2 general hospitals in France. Patients were adults (>18 years) expected to require an arterial catheter, central-vein catheter, or both inserted for 48 hours or longer. INTERVENTIONS: Use of CHGIS vs standard dressings (controls). Scheduled change of unsoiled adherent dressings every 3 vs every 7 days, with immediate change of any soiled or leaking dressings. MAIN OUTCOME MEASURES: Major CRIs for comparison of CHGIS vs control dressings; colonization rate for comparison of 3- vs 7-day dressing changes. RESULTS: Of 2095 eligible patients, 1636 (3778 catheters, 28,931 catheter-days) could be evaluated. The median duration of catheter insertion was 6 (interquartile range [IQR], 4-10) days. There was no interaction between the interventions. Use of CHGIS dressings decreased the rates of major CRIs (10/1953 [0.5%], 0.6 per 1000 catheter-days vs 19/1825 [1.1%], 1.4 per 1000 catheter-days; hazard ratio [HR], 0.39 [95% confidence interval {CI}, 0.17-0.93]; P = .03) and catheter-related bloodstream infections (6/1953 catheters, 0.40 per 1000 catheter-days vs 17/1825 catheters, 1.3 per 1000 catheter-days; HR, 0.24 [95% CI, 0.09-0.65]). Use of CHGIS dressings was not associated with greater resistance of bacteria in skin samples at catheter removal. Severe CHGIS-associated contact dermatitis occurred in 8 patients (5.3 per 1000 catheters). Use of CHGIS dressings prevented 1 major CRI per 117 catheters. Catheter colonization rates were 142 of 1657 catheters (7.8%) in the 3-day group (10.4 per 1000 catheter-days) and 168 of 1828 catheters (8.6%) in the 7-day group (11.0 per 1000 catheter-days), a mean absolute difference of 0.8% (95% CI, -1.78% to 2.15%) (HR, 0.99; 95% CI, 0.77-1.28), indicating noninferiority of 7-day changes. The median number of dressing changes per catheter was 4 (IQR, 3-6) in the 3-day group and 3 (IQR, 2-5) in the 7-day group (P < .001). CONCLUSIONS: Use of CHGIS dressings with intravascular catheters in the intensive care unit reduced risk of infection even when background infection rates were low. Reducing the frequency of changing unsoiled adherent dressings from every 3 days to every 7 days modestly reduces the total number of dressing changes and appears safe. TRIAL REGISTRATION: clinicaltrials.gov Identifier: NCT00417235.

Optimization of bacterial diagnosis yield after needle aspiration in immunocompetent adults with brain abscesses.

OBJECTIVE: Brain abscesses (BA) are life threatening, even in immunocompetent patients, in part because microbiological diagnosis is often lacking and management is empirical. Recent epidemiological changes make it all the more important to have a precise microbiological diagnosis. Our purpose was to evaluate the efficacy of a strategy aimed at obtaining a microbiological diagnosis in immunocompetent patients presenting with suspected BAs. METHODS: We conducted a cohort study including all consecutive patients suspected of having BAs according to clinical, biological, and radiological findings. Severely immunocompromised patients were excluded. Aspiration was performed free-hand in patients with superficial abscesses (<1 cm depth from the cortical surface) and under stereotactic guidance in patients with deep-seated abscesses. Microbiological diagnosis was optimized, using the best aerobic and anaerobic growth conditions, blood culture bottles inoculated in the operating room, and molecular biology techniques if necessary. Antibiotic treatment was adapted according to the findings. RESULTS: Twenty-six patients were suspected of having BAs during the study period. Twenty-four patients benefited from aspiration (stereotactic puncture in 3 cases), which was safe, confirmed the diagnosis of BAs, and yielded microbiological diagnosis in all cases, even in those patients who had previously received antibiotics (n = 8; 33%). In 10 patients (42%), microbiological results led to a different choice in antibiotic therapy than the recommended empirical regimen. CONCLUSION: Microbiological diagnosis can be obtained in all cases of BA. This is achieved by the conjunction of rapid needle aspiration and the optimization of microbiological diagnosis resulting from fast management of the surgical specimen, good anaerobic culture conditions, and the use of blood culture bottles and molecular biology techniques when appropriate. Moreover, it is of clinical and therapeutic interest when BAs are suspected in immunocompetent patients.

Spread of a Klebsiella pneumoniae strain producing a plasmid-mediated ACC-1 AmpC beta-lactamase in a teaching hospital admitting disabled patients.

We describe a large outbreak involving a Klebsiella pneumoniae strain producing a plasmid-encoded ACC-1 type AmpC beta-lactamase in a hospital caring for patients with motor impairment. The epidemic strain was isolated from 57 patients in six wards between September 1999 and May 2003 and caused clinical infections in 19 patients.