Rational Use of Microbiological Tests in the Diagnosis of Central Nervous System Infections Using Restrictive Criteria: a Retrospective Study

Microbiological testing in general and in the setting of central nervous system (CNS) infection in particular are often excessive, leading to superfluous laboratory work and costs. In this regard, restrictive criteria, named Reller criteria, have been developed to reduce unnecessary CSF herpes simplex virus 1 (HSV-1) PCR testing when suspecting encephalitis.

Comparison of the Copan WASPLab incorporating the BioRad expert system against the SIRscan 2000 automatic for routine antimicrobial disc diffusion susceptibility testing

OBJECTIVES

This study investigated the agreement at the categorical level between the Copan WASPLab incorporating the BioRad expert system against the SIRscan 2000 automatic for antimicrobial disc diffusion susceptibility testing.

METHODS

The 338 clinical strains (67 Pseudomonas aeruginosa, 19 methicillin-resistant Staphylococcus aureus, 75 methicillin-sensitive S. aureus and 177 Enterobacterales isolates) analysed in this study were non-duplicate isolates obtained from consecutive clinical samples referred to the clinical bacteriology laboratory at Geneva University Hospitals between June and August 2019. For the WASPLab the inoculum suspension was prepared in strict accordance with the manufacturer's instruction (Copan WASP srl, Brescia, Italy) by adding 2 mL of the 0.5 McFarland primary suspension used for the SIRscan analysis into a sterile tube filled with 4 mL of sterile saline (1:3 dilution). The inoculum (2 × 30 μL loop/spreader) was spread over the entire surface of Mueller-Hinton agar plates according to the AST streaking pattern defined by Copan. The antibiotic discs were dispensed by the WASP and inoculated media were loaded on conveyors for transfer to the automatic incubators. The plates were incubated for 16 h, and several digital images were acquired. Inhibition zone diameters were automatically read by the WASPLab and were adjusted manually whenever necessary. For the SIRscan 2000 automatic, the antimicrobial disc diffusion susceptibility testing was performed according to the EUCAST guidelines. The gradient strip method was used to resolve discrepancies.

RESULTS

The overall categorical agreement between the compared methods reached 99.1% (797/804; 95% CI 98.2%-99.6%), 99.5% (1029/1034; 95% CI 98.9%-99.8%), and 98.8% (2798/2832; 95% CI 98.3%-99.1%) for P. aeruginosa, S. aureus and the Enterobacterales, respectively.

CONCLUSIONS

WASPLab incorporating the BioRad expert system provides a fully automated solution for antimicrobial disc diffusion susceptibility testing with equal or better accuracy than other available phenotypic methods.

A molecular based diagnosis of positive blood culture in the context of viral haemorrhagic fever: proof of concept

OBJECTIVES

The aim of this study was to evaluate the possibility of using a PCR-based panel to identify bacterial and fungal bloodstream infections in the setting of suspected or confirmed viral haemorrhagic fever.

METHODS

The accuracy of the FilmArray® Blood Culture Identification Panel (BCID) assay was assessed to identify the common bacterial and fungal pathogens associated with bloodstream infections after positive blood culture inactivation using a guanidinium thiocyanate containing buffer lysis that is commonly used for viral haemorrhagic fever molecular diagnostics.

RESULTS

The FilmArray® BCID panel assay detected 95% (19/20) of the pathogens analysed in this study by using both protocols with and without inactivation. Absolute consistency (100%) was observed in all isolates with phenotypes compatible with the presence of the antibiotic resistance genes mecA, vanA, vanB and blaKPC.

CONCLUSIONS

The FilmArray® BCID panel assay coupled to inactivation using a guanidinium thiocyanate containing buffer lysis represents a convenient, sensitive and specific diagnostic tool to detect some of the most pathogens associated with bloodstream infections in the context of a suspected or confirmed viral haemorrhagic fever.

Copan WASPLab automation significantly reduces incubation times and allows earlier culture readings

OBJECTIVE

The aim was to evaluate whether laboratory automation (inoculation and automated incubation combined with timely defined high-resolution digital imaging) may help reduce the time required to obtain reliable culture analysis results.

METHODS

We compared the results obtained by WASPLab automation against WASP-based automated inoculation coupled to conventional incubation and manual diagnostic on 1294 clinical samples (483 for the derivation set and 811 for the independent validation set) that included urine, genital tract and non-sterile site specimens, as well as ESwabs for screening of methicillin-resistant Staphylococcus aureus (MRSA), methicillin-sensitive Staphylococcus aureus (MSSA), extended-spectrum beta-lactamases (ESBLs) and carbapenemase-producing Enterobacteriaceae (CPE). We used sequential routine specimens referred to the bacteriology laboratory at Geneva University Hospitals between October 2018 and March 2019.

RESULTS

The detection sensitivity of MRSA and MSSA at 18 hr on WASPLab was 100% (95% confidence interval [CI], 94.48-100.00%). The detection sensitivity of ESBL and CPE at 16 hr on WASPLab was 100% (95% confidence interval [CI], 94.87% to 100.00%). For urine specimens, the similarity was 79% (295/375) between 18 hr and 24 hr of incubation on WASPLab. For genital tract and non-sterile site specimens, the similarity between 16 hr and 28 hr of incubation on WASPLab were 26% (72/281) and 77% (123/159) respectively. Thus, 28 hr was defined as the final incubation time on WASPLab for genital tract and non-sterile site specimens.

CONCLUSIONS

The results of this study show that WASPLab automation enables a reduction of the culture reading time for all specimens tested without affecting performances. Implementing the established and duly validated incubation times will allow appropriate laboratory workflows for improved efficiency to be built.

In vivo selection of a multidrug-resistant Aeromonas salmonicida during medicinal leech therapy

We report the selection in a 15-year-old boy of a multidrug-resistant, extended-spectrum β-lactamase (ESBL)-producing Aeromonas salmonicida after medicinal leech therapy that required an antibiotic prophylaxis based on piperacillin/tazobactam and cotrimoxazole. Whole genome sequencing of the strain indeed revealed 13 antibiotic resistance genes, including the ESBL CTX-M-3 and the unusual β-lactamase SCO-1.

Imipenem heteroresistance in nontypeable Haemophilus influenzae is linked to a combination of altered PBP3, slow drug influx and direct efflux regulation

OBJECTIVE

To investigate the potential roles of PBPs, efflux pumps and slow drug influx for imipenem heteroresistance in nontypeable Haemophilus influenzae (NTHi).

METHODS

Fifty-nine NTHi clinical isolates examined in this study were collected at Geneva University Hospitals between 2009 and 2014. Alterations in PBPs were investigated by gene sequencing. To evaluate the affinities of the PBPs to imipenem, steady-state concentration-response experiments were carried out using imipenem in a competition assay with Bocillin-FL. The effect of the carbonyl cyanide m-chlorophenylhydrazone (CCCP) on imipenem susceptibility was assessed using broth dilution and viable cell counting. Using whole-genome sequencing, we explored the potential roles of outer membrane protein P2 (OmpP2), LytM proteins and the dcw gene cluster in imipenem heteroresistance.

RESULTS

All 46 imipenem-heteroresistant isolates (IMI^hR) harboured amino acid substitutions in the ftsI gene, which encodes PBP3, corresponding to 25 different mutation patterns that varied from the ftsI gene mutation patterns found in imipenem-susceptible isolates. Among all PBPs, the highest affinity to imipenem was documented for PBP3 (IC₅₀, 0.004 μg/mL). Different amino acid substitutions and insertions were noted in OmpP2, suggesting a relationship with imipenem heteroresistance. The IMI^hR isolates were affected by CCCP differently and displayed a higher percentage of killing by imipenem in CCCP-treated cells at concentrations ranging between 0.5 and 8 μg/mL.

CONCLUSIONS

The present study provides robust evidence indicating that in combination with the altered PBP3, the slowed drug influx and its enhanced efflux due to the loss of regulation led to the development of imipenem heteroresistance in NTHi.

Rapid molecular determination of methicillin resistance in staphylococcal bacteraemia improves early targeted antibiotic prescribing: a randomized clinical trial

Empiric therapy of methicillin-susceptible Staphylococcus aureus (MSSA) infections with vancomycin is associated with poorer outcome than targeted therapy with β-lactams. Our objective was to evaluate whether rapid determination of methicillin resistance shortens the time from Gram stain to targeted antimicrobial therapy in staphylococcal bacteraemia, thereby reducing vancomycin overuse. This was a single-centre open parallel RCT. Gram-positive cocci in clusters in positive blood culture underwent real-time PCR for rapid species and methicillin resistance determination parallel to conventional microbiology. Patients were randomized 1:1 so that clinicians would be informed of PCR results (intervention group) or not (control group). Eighty-nine patients (intervention 48, control 41) were analysed. MRSA was identified in seven patients, MSSA in 46, and CoNS in 36. PCR results were highly concordant (87/89) with standard microbiology. Median time (hours) from Gram stain to transmission of methicillin-susceptibility was 3.9 (2.8-4.3) vs. 25.4 (24.4-26-7) in intervention vs. control groups (p <0.001). Median time (hours) from Gram stain to targeted treatment was similar for 'all staphylococci' [6 (3.8-10) vs. 8 (1-36) p 0.13] but shorter in the intervention group when considering S. aureus only [5 (3-7) vs. 25.5 (3.8-54) p <0.001]. When standard susceptibility testing was complete, 41/48 (85.4%) patients in the intervention group were already receiving targeted therapy compared with 23/41 (56.1%) in the control group (p 0.004). There was no significant effect on clinical outcomes. Rapid determination of methicillin resistance in staphylococcal bacteraemia is accurate and reduces significantly the time to targeted antibiotic therapy in the subgroup of S. aureus, thereby avoiding unnecessary exposure to vancomycin.

Ampicillin-resistant Haemophilus influenzae isolates in Geneva: serotype, antimicrobial susceptibility, and β-lactam resistance mechanisms

The purpose of this study was to analyze the molecular mechanisms of ampicillin-resistant Haemophilus influenzae isolated in Geneva, Switzerland. We investigated the association between specific patterns of amino acid substitutions in penicillin-binding protein 3 (with or without β-lactamase production) and β-lactam susceptibility. Another main focus for this study was to compare the accuracy of disk diffusion and Etest methods to detect resistance to ampicillin and amoxicillin/clavulanic acid. The antibiotic susceptibility to β-lactam antibiotics of 124 H. influenzae isolates was determined by disk diffusion and Etest methods, and interpreted by European Committee on Antimicrobial Susceptibility Testing (EUCAST) and Clinical and Laboratory Standards Institute (CLSI) breakpoints. Alterations in PBP3 were investigated by sequencing the ftsI gene. Of the 124 clinical isolates analyzed, ampicillin resistance was found in 36% (45 out of 124). The rate of resistance to amoxicillin/clavulanic acid was 9% and 0.8%, using EUCAST and CLSI breakpoints respectively. For the 78 β-lactamase negative ampicillin-susceptible (BLNAS) isolates for which the Etest method indicated a high degree of susceptibility (MIC ≤ 1 mg/L), the disk diffusion method revealed resistance to ampicillin and amoxicillin/clavulanic acid in 33 cases (42%). Most common amino acid substitutions were Asn526Lys and Val547Ile, followed by Asp569Ser, Ala502Val, Asp350Asn, Met377Ile, Ile449Val, and Arg517His. The patterns observed were classified into six groups (IIa, IIb, IIc, IId, III-like, and miscellaneous). Continued characterization of both invasive and respiratory H. influenzae isolates is necessary in order to observe changes in the microbiology and epidemiology of this pathogen that could lead to clinical failure when treated by empirical antibiotic therapy.

[Diagnosis of bacterial gastroenteritis]

The etiologic agents of acute gastroenteritis are diverse. The diagnosis of bacterial pathogens is particularly challenging given the large amount of vastly diverse indigenous gastrointestinal organisms present in stool. Multiple methods must be used by the clinical microbiology laboratories to diagnose the cause of acute gastroenteritis, including bacterial cultures, ELISA, and microscopy. Due to the limitations of conventional methods, there is still room for improvement in the detection of pathogens by using the molecular methods. This paper discusses these different diagnostic approaches and limitations.

[Rapid tests during respiratory infection: an aid to non-prescription of antibiotics? ]

Due to overuse, we are about to reach the end of the antibiotic era. Each of us is responsible to limit their usage to a minimum. Respiratory infections are the first cause of antibiotic prescriptions. The use of new simple tests available at the bedside can be very useful in this context. The development of sophisticated molecular diagnostic tools, such as "multiorganism" panels, may revolutionize our approach to respiratory infections. The key will be to interpret the results correctly, with due consideration of the statement, "Treat patients, not lab results".

[Which benefits for the clinician to implement MALDI-TOF/MS in the bacteriology laboratory?]

Mass spectrometry (MALDI-TOF/MS) is a recent technology especially adapted to identify microbial pathogens. It has rapidly established itself as a must for most medical bacteriology laboratories. Its ease of use and speed of execution typically permit providing pathogen identification one day earlier to the clinicians. MALDI-TOF/MS facilitates identification of filamentous fungi and mycobacteria that require particular lab expertise when using conventional methods. This paper highlights the multiple advantages that MALDI-TOF/MS can bring to the physicians in their practice.

[ESBL and carbapenemases in Enterobacteriaceae]

Carbapenemase-producing enterobacteria (CPE) spread all over the world during the last years, causing serious infections with increasing frequency. Very few new drugs active against CPE are expected to be clinically available. Studies summarized in this review show that there is yet room to improve our therapeutic approaches, in the treatment of infections due to CPE.

[Epidemiology and clinical implications of carbapenemase-producing bacteria in Switzerland]

The emergence and global dissemination of carbapenemases represents a major threat to public health. Switzerland has not been spared; we report a case-series of four patients hospitalised in our institution colonised with carbapenemase-producing bacteria. Infections caused by carbapenemase-producing Enterobacteriaceae limit therapeutic options and increase mortality. Detection of carbapenemases is also a challenge for laboratories. It is imperative to implement stringent infection control measures in order to prevent epidemics at the hospital level.

Retropharyngeal abscess in adults

OBJECTIVES

Retropharyngeal abscess in adults can be life-threatening. The otolaryngologist is on the front line in making the diagnosis and treatment of this disease. The aim of this study is to review the clinical features, the diagnostic tools and the management of retropharyngeal abscesses in adults.

PATIENTS AND METHODS

Retrospective study of retropharyngeal abscesses in adults admitted in the ENT department from 2005 to 2010.

RESULTS

In total 4 patients were included in this study: mean age of 53 years (range 45 to 62 years), sex ration F/M = 3. Cultures obtained from the abscesses identified group A beta-hemolytic streptococci susceptible to amoxicilline-clavulanate in three cases. The treatment consisted in surgical drainage of the collection and intravenous antibiotics.

CONCLUSIONS

Retropharyngeal abscesses in adults are critical infections requiring prompt diagnosis and treatment. Computed tomography scan was the crucial tool for the diagnosis, notably to differentiate cellulitis from abscesses. The management includes intravenous broad-spectrum antibiotics associated, if necessary, with surgical drainage in cases of persistent abscess. The outcome is usually good.

Application and use of various mass spectrometry methods in clinical microbiology

When confronted with a septic patient or dealing with an emerging epidemic, clinicians, infection control specialists and microbiologists have often felt an immense 'need for speed' while waiting for culture results. Various mass spectrometry (MS) applications are about to answer most of their demands. Matrix-assisted laser desorption ionization (MALDI) time-of-flight (TOF) MS of whole bacterial cells has already greatly shortened the time needed for identification of a positive culture in major diagnostic laboratories in Europe. MS is described in this article, with a special emphasis on the different systems currently commercially available for routine identification. MALDI-TOF MS remains, however, limited by the previous time-consuming culture steps, and is not suited for strain typing in epidemic contexts. These limitations can be overcome by other applications of MS in microbiology. MALDI-resequencing is a rapid method for genotyping, offering comparable results to multilocus sequence typing. New systems of broad-range PCR, associated with analyses of amplicons by electrospray ionization MS, might allow nearly full automation for the direct identification of pathogens in blood, thus bypassing the culture stage. This article describes various applications of MS methods in clinical microbiology, and provides a comparative table of these technologies.

[Supernumerary axillary breast: a case report]

We report on a case of polymastia in a 14-year-old girl in whom surgical exploration of an axillary mass histologically documented a supernumerary breast. Through this observation and review of the literature, the authors describe the pathological and management aspects of polymastia.

[Hydatid cyst of the kidney in children: a retrospective study of 10 cases]

INTRODUCTION

The hydatid cyst disease of the kidney is rare in children, it ranks third among the liver and the lung.

MATERIAL

We report a series of 10 pediatric case of hydatid cyst of the kidney, managed in the department of surgery pediatric of Rabat, between 1990 and 2008.

RESULTS

The median age was 9 years (4-15 years). The clinical presentation was pain (7 cases) and/or abdominal mass (6 cases). Diagnostic accuracy has been improved since the wide use of ultrasonography in eight cases. In all cases, the resection of the prominent dome was usually sufficient.

CONCLUSION

In the light of these 10 observations, the ultrasonography may be sufficient and the surgical conservative treatment is still necessary.

[Pediatric osteo-articular infections with negative culture results: what about Kingella kingae?]

Kingella kingae is an emerging pathogen that is recognized as a causative agent of septic arthritis and osteomyelitis, primarily in infants and children. The bacterium is best detected by rapid inoculation in blood culture systems or by real-time PCR assays. Pathogenesis of the agent was linked recently to the production of a potent cytotoxin, known as RTX, which is toxic to a variety of human cell types. The locus encoding the RTX toxin is thought to be a putative virulence factor, and is, apparently, essential for inducing cytotoxic effects on respiratory epithelial, synovial and macrophage-like cells. Herein, we describe a novel real-time PCR assay that targets the RTX toxin gene. The assay exhibited a sensitivity of 30 c.f.u., which is 10-fold more sensitive than a previously published semi-nested broad-range 16S rRNA gene PCR, and showed no crossreactivity with several related species and common osteoarticular pathogens. Its clinical impact is illustrated by three pediatric cases.

[Mesenchymal hamartoma of the liver in a child: a case report]

Mesenchymal hamartoma of the liver is a rare, benign tumor that presents mostly before the age of 2 years. Its pathogenesis is poorly understood. We present the case of a 2.5-year-old female patient who had a large cystic mass of the liver of which the hamartomatous nature was confirmed by the pathological examination of the surgical specimen. We discuss the clinicopathological, imaging, and histological features of this unusual tumor through a review of the literature.

Neuropathies périphériques sans cryoglobulinémie révélatrices de l’hépatite virale C

INTRODUCTION

Peripheral neuropathies are the most common neurological complication of viral hepatitis C infection with mixed cryoglobulinemia.

CASES REPORT

We report five cases (three men, two women) of peripheral neuropathies revealing viral hepatitis C infection without cryoglobulinemia; the patients' mean age was 56 years. Paresthesias were the most frequent symptom. Electroneuromyographic examination found one case of polyneuropathy and four cases of multiplex mononeuropathies; the complement level was normal in all patients and the rheumatoid factor positive in two cases. Etiological investigations for peripheral neuropathy remained negative. Treatment and outcome were variable.

DISCUSSION

Negative cryoglobulinemia in cases of VHC infection with neurological features has been described in the last few years, suggesting the possibility of other mechanisms such as direct action of the virus on the nervous system. There is no consensus on the treatment and outcome is variable.

CONCLUSION

Peripheral neuropathy may reveal VHC infection, underscoring the need for VHC serology testing in etiological investigations for peripheral neuropathies.

[Thyroid tuberculosis]

OBJECTIVES

The aims of this study were to emphasize the difficulties of diagnosing thyroid tuberculosis because of its non specific symptoms and to encourage physicians to seek it more frequently.

MATERIAL AND METHODS

Six cases of thyroid tuberculosis diagnosed within a 3-year period were included in a retrospective study.

RESULTS

There were two men and four women, mean age 45 years. Four patients underwent lobo-isthmectomy with frozen section analysis which enabled us to rectify the diagnosis. Medical treatment was based on a 6-month course of bactericidal chemotherapy. Outcome was favorable in all the cases with 17 months average follow up.

CONCLUSION

Symptoms of thyroid tuberculosis are misleading, pathologic findings are of increasing importance for diagnosis, which with the new serology techniques may improve further.

The localised aggressive periodontitis prevalence in Morocco

This work concerns a retrospective study of prevalence records and the clinical characteristics of localised aggressive periodontitis in the breast of consultants in the periodontitis service in Dental Medicine Faculty of Rabat (Morocco) from 1997 to 1999.

Hydrothermal recharge and discharge across 50 km guided by seamounts on a young ridge flank

Hydrothermal circulation within the sea floor, through lithosphere older than one million years (Myr), is responsible for 30% of the energy released from plate cooling, and for 70% of the global heat flow anomaly (the difference between observed thermal output and that predicted by conductive cooling models). Hydrothermal fluids remove significant amounts of heat from the oceanic lithosphere for plates typically up to about 65 Myr old. But in view of the relatively impermeable sediments that cover most ridge flanks, it has been difficult to explain how these fluids transport heat from the crust to the ocean. Here we present results of swath mapping, heat flow, geochemistry and seismic surveys from the young eastern flank of the Juan de Fuca ridge, which show that isolated basement outcrops penetrating through thick sediments guide hydrothermal discharge and recharge between sites separated by more than 50 km. Our analyses reveal distinct thermal patterns at the sea floor adjacent to recharging and discharging outcrops. We find that such a circulation through basement outcrops can be sustained in a setting of pressure differences and crustal properties as reported in independent observations and modelling studies.