Accuracy of Sensititre YeastOne echinocandins epidemiological cut-off values for identification of FKS mutant Candida albicans and Candida glabrata: a ten year national survey of the Fungal Infection Network of Switzerland (FUNGINOS).

OBJECTIVES: Echinocandins represent the first-line treatment of candidaemia. Acquired echinocandin resistance is mainly observed among Candida albicans and Candida glabrata and is associated with FKS hotspot mutations. The commercial Sensititre YeastOne™ (SYO) kit is widely used for antifungal susceptibility testing, but interpretive clinical breakpoints are not well defined. We determined echinocandins epidemiological cut-off values (ECV) for C. albicans/glabrata tested by SYO and assessed their ability to identify FKS mutants in a national survey of candidaemia. METHODS: Bloodstream isolates of C. albicans and C. glabrata were collected in 25 Swiss hospitals from 2004 to 2013 and tested by SYO. FKS hotspot sequencing was performed for isolates with an MIC≥ECV for any echinocandin. RESULTS: In all, 1277 C. albicans and 347 C. glabrata were included. ECV 97.5% of caspofungin, anidulafungin and micafungin were 0.12, 0.06 and 0.03 µg/mL for C. albicans, and 0.25, 0.12 and 0.03 µg/mL for C. glabrata, respectively. FKS hotspot sequencing was performed for 70 isolates. No mutation was found in the 52 'limit wild-type' isolates (MIC=ECV for at least one echinocandin). Among the 18 'non-wild-type' isolates (MIC>ECV for at least one echinocandin), FKS mutations were recovered in the only two isolates with MIC>ECV for all three echinocandins, but not in those exhibiting a 'non-wild-type' phenotype for only one or two echinocandins. CONCLUSION: This 10-year nationwide survey showed that the rate of echinocandin resistance among C. albicans and C. glabrata remains low in Switzerland despite increased echinocandin use. SYO-ECV could discriminate FKS mutants from wild-type isolates tested by SYO in this population.

Candida species distribution and antifungal susceptibility testing according to European Committee on Antimicrobial Susceptibility Testing and new vs. old Clinical and Laboratory Standards Institute clinical breakpoints: a 6-year prospective candidaemia survey from the fungal infection network of Switzerland.

We analyzed the species distribution of Candida blood isolates (CBIs), prospectively collected between 2004 and 2009 within FUNGINOS, and compared their antifungal susceptibility according to clinical breakpoints defined by the European Committee on Antimicrobial Susceptibility Testing (EUCAST) in 2013, and the Clinical and Laboratory Standards Institute (CLSI) in 2008 (old CLSI breakpoints) and 2012 (new CLSI breakpoints). CBIs were tested for susceptiblity to fluconazole, voriconazole and caspofungin by microtitre broth dilution (Sensititre® YeastOne™ test panel). Of 1090 CBIs, 675 (61.9%) were C. albicans, 191 (17.5%) C. glabrata, 64 (5.9%) C. tropicalis, 59 (5.4%) C. parapsilosis, 33 (3%) C. dubliniensis, 22 (2%) C. krusei and 46 (4.2%) rare Candida species. Independently of the breakpoints applied, C. albicans was almost uniformly (>98%) susceptible to all three antifungal agents. In contrast, the proportions of fluconazole- and voriconazole-susceptible C. tropicalis and F-susceptible C. parapsilosis were lower according to EUCAST/new CLSI breakpoints than to the old CLSI breakpoints. For caspofungin, non-susceptibility occurred mainly in C. krusei (63.3%) and C. glabrata (9.4%). Nine isolates (five C. tropicalis, three C. albicans and one C. parapsilosis) were cross-resistant to azoles according to EUCAST breakpoints, compared with three isolates (two C. albicans and one C. tropicalis) according to new and two (2 C. albicans) according to old CLSI breakpoints. Four species (C. albicans, C. glabrata, C. tropicalis and C. parapsilosis) represented >90% of all CBIs. In vitro resistance to fluconazole, voriconazole and caspofungin was rare among C. albicans, but an increase of non-susceptibile isolates was observed among C. tropicalis/C. parapsilosis for the azoles and C. glabrata/C. krusei for caspofungin according to EUCAST and new CLSI breakpoints compared with old CLSI breakpoints.

Molecular epidemiology of methicillin-resistant Staphylococcus aureus in Switzerland: sampling only invasive isolates does not allow a representative description of the local diversity of clones.

We conducted a molecular study of MRSA isolated in Swiss hospitals, including the first five consecutive isolates recovered from blood cultures and the first ten isolates recovered from other sites in newly identified carriers. Among 73 MRSA isolates, 44 different double locus sequence typing (DLST) types and 32 spa types were observed. Most isolates belonged to the NewYork/Japan, the UK-EMRSA-15, the South German and the Berlin clones. In a country with a low to moderate MRSA incidence, inclusion of non-invasive isolates allowed a more accurate description of the diversity.

Tuberculosis caused by Mycobacterium microti in South American camelids.

BACKGROUND: Infection with Mycobacterium microti can cause chronic disease in animals and threaten human health through its zoonotic potential. OBJECTIVE: To describe clinical findings, diagnostic investigations, necropsy, and epidemiology results in South American camelids (SAC) infected with M. microti, member of the Mycobacterium tuberculosis complex. ANIMALS: Eleven SAC with tuberculous lesions. METHODS: Description of 10 llamas and 1 alpaca, aged 4-18 years, from 6 herds with a history of wasting and weakness admitted to the Vetsuisse-Faculty of Berne over 8 years. RESULTS: Clinical signs included weight loss, recumbency, and anorexia in late stages of the disease. Respiratory problems were seen in 6 animals of 11. No consistent hematologic abnormalities were identified. Suspect animals were examined in detail by abdominal ultrasonography and thoracic radiology. Abnormal findings such as enlarged mediastinal, mesenteric, or hepatic lymph nodes were seen only in animals with advanced disease. Single comparative intradermal tuberculin test with bovine protein purified derivate (PPD) and avian PPD was negative in all animals. At necropsy, typical tuberculous lesions were found, and confirmed by bacteriological smear and culture, molecular methods, or both. CONCLUSIONS AND CLINICAL IMPORTANCE: Infection caused by M. microti should be considered a differential diagnosis in chronic debilitating disease with or without respiratory signs in SAC. Antemortem confirmation of the diagnosis remains challenging at any stage of infection. Because cases of M. microti infection have been reported in immunocompromized human patients, the zoonotic potential of the organism should be kept in mind when dealing with this disease in SAC.

Species identification of non-tuberculous mycobacteria from humans and cattle of Chad.

In Chad, during a study on tuberculosis in humans and cattle, 52 non-tuberculous mycobacteria (NTM) strains were isolated. By means of INNO-LiPA, PRA-hsp65 amplification and sequencing of 16S rDNA, NTM species of 25/52 isolates were identified. M. fortuitum complex (8) was the most frequent species, followed by M. nonchromogenicum (4) and M. avium complex (4). PRA method could identify M. fortuitum 3rd variant among isolates derived from cattle specimens. This finding could confirm the existence of farcy in the Chadian cattle population as M. fortuitum 3rd variant and putitative pathogen M. farcinogenes can't be distinguished by the methods used in this study. Half of the NTM isolates could not be specified and we considered them as contaminants from the environment.

[Streptococcus milleri. An early sign of cancer in otorhinolaryngologic patients?]. / Streptococcus milleri. Ein Hinweis auf Karzinome im HNO-Bereich?

The Streptococcus milleri group, which also includes S. anginosus, S. intermedius and S. constellatus, is found in the oropharynx and gastrointestinal tract mucosa. Recent isolations of S. milleri DNA sequences have been made from both gastric and oesophageal carcinoma. There are only a few publications on the isolation of viable bacteria and S. milleri DNA, and their role in carcinogenesis, in otorhinolaryngologic malignoma. We present four patients with a cervical abscess and the isolation of S. milleri -group bacteria, without signs of malignancy or other risk factors. After a delay of several months, squamous cell carcinoma of the oropharynx was diagnosed in three patients and a neck metastasis without primary tumor in the fourth.

Non-tuberculous mycobacteria: patterns of isolation. A multi-country retrospective survey.

OBJECTIVE: To collect data on non-tuberculous mycobacteria (NTM) isolated from clinical laboratories in different countries to establish: 1) whether the isolation of NTM was increasing, 2) which species were increasing, and 3) whether there was any pattern of geographical distribution. DESIGN: In 1996, the Working Group of the Bacteriology and Immunology Section of the International Union Against Tuberculosis and Lung Disease contacted 50 laboratories in different countries for the necessary information. RESULTS: The number of patients reported with NTM was 36099 from 14 countries. Mycobacterium avium complex, M. gordonae, M. xenopi, M. kansasii and M. fortuitum were the five species most frequently isolated. There was a significant upward trend for M. avium complex and M. xenopi. Pigmented mycobacteria predominated in Belgium, the Czech Republic and the Mediterranean coast of Spain. Non-chromogenic mycobacteria were found to be predominant in the area of the Atlantic coast of Brazil and in Turkey, the United Kingdom, Finland and Denmark. CONCLUSIONS: There was an increase in the number of NTM isolated from clinical samples of patients. Isolation of the most frequent species is constantly changing in most of the geographical areas, and newer species are emerging due to better diagnostic techniques to detect and identify NTM.

Generalized tuberculosis in llamas (Lama glama) due to Mycobacterium microti.

Necropsy of two llamas revealed numerous caseous nodules containing abundant acid-fast bacilli (AFB) in various organs. The AFB were identified by spoligotyping as Mycobacterium microti, vole type. Infection caused by M. microti should be considered in the differential diagnosis of debilitating diseases in New World camelids.

[First isolation of tuberculous mycobacteria in man and animals in Chad]. / Premiers isolements de mycobactéries tuberculeuses chez l'homme et l'animal au Tchad.

This report describes the first successful isolation and identification of mycobacterial infection in humans and animals of Chad. All mycobacterial strains from human specimens were M. tuberculosis and strains from animal specimens (cattle) were M. bovis. None of the 10 of M. tuberculosis strains tested for antibiotic resistance were multidrug resistant. Due to the intrinsic resistance of M. bovis to pyrazinamide and the growing number of tuberculosis cases in HIV-infected people in Africa and elsewhere, more information on the potential of M. bovis for human infection is needed to guide disease control policy.

False-positive Mycobacterium tuberculosis culture revealed by restriction fragment length polymorphism analysis.

BACKGROUND: The microbiological analysis of respiratory specimens is the most reliable approach to diagnose active pulmonary tuberculosis. PATIENT AND METHODS: We report a 60-year-old female patient (index patient) who underwent diagnostic bronchoscopy for chronic cough. No acid-fast bacilli were detected in bronchial washings. Although cough subsided with symptomatic treatment, Mycobacterium tuberculosis grew on egg-based media after 12 weeks. A false-positive culture result was suspected. Chart review and DNA fingerprinting were carried out. RESULTS: The bronchoscope used to examine the index patient was previously used for a 30-year-old patient (source patient) with smear- and culture-positive pulmonary tuberculosis. Restriction fragment length polymorphism (RFLP) analysis based on the IS 6110 element confirmed that the two strains were identical. CONCLUSION: Cross-contamination is a reason for false-positive cultures with M. tuberculosis and should be suspected in patients with a low clinical probability for active tuberculosis.

Ocular manifestation of disseminated Mycobacterium simiae infection in a cat.

Disseminated mycobacterial disease was diagnosed in an eight-year-old domestic shorthaired cat, with involvement of the skin, lungs, lymph nodes and one eye. Mycobacterium simiae was cultured from skin biopsies on solid agar and in liquid media. This organism is known to cause pulmonary, cutaneous or disseminated infection in human patients with acquired immunodeficiency syndrome but has never been encountered as a pathogen in companion animals. Combination treatment with rifampicin, enrofloxacin and clarithromycin resulted in complete clinical remission within six months, with no side effects. No recurrence was observed in a 22-month follow-up period.

Evaluation of a commercial line probe assay for identification of mycobacterium species from liquid and solid culture.

The performance of a commercial line probe assay (LiPA) (Inno-LiPA Mycobacteria; Innogenetics, Belgium) for the detection and identification of Mycobacterium species from liquid and solid culture was evaluated at five routine clinical laboratories. The LiPA method is based on the reverse hybridization principle, in which the mycobacterial 16S-23S ribosomal RNA (rRNA) spacer region is amplified by polymerase chain reaction (PCR). Amplicons are subsequently hybridized with oligonucleotide probes arranged on a membrane strip and detected by a colorimetric system. The test detects the presence of Mycobacterium species and specifically identifies Mycobacterium tuberculosis complex, Mycobacterium kansasii, Mycobacterium xenopi, Mycobacterium gordonae, Mycobacterium avium complex, Mycobacterium avium, Mycobacterium intracellulare, Mycobacterium scrofulaceum, and Mycobacterium chelonae - Mycobacterium abscessus complex. The results of LiPA were compared with the results obtained using traditional biochemical and molecular tests (DNA probe-based techniques, PCR restriction enzyme analysis of the 65 kDa heat-shock protein gene, and sequencing of the 16S rDNA). A total of 669 isolates, 642 of which were identified as Mycobacterium species and 27 as non- Mycobacterium species, were tested by LiPA. After analysis of 14 initially discordant results and exclusion of one isolate, concordant results were obtained for 636 of 641 Mycobacterium isolates (99.2% accuracy). All Mycobacterium species reacted with the MYC ( Mycobacterium species) probe (100% sensitivity), and all non- Mycobacterium species were identified as such (100% specificity).

Multidrug-resistant tuberculosis in prison inmates, Azerbaijan.

In a tuberculosis (TB) program in the Central Penitentiary Hospital of Azerbaijan, we analyzed 65 isolates of Mycobacterium tuberculosis by IS6110-based restriction fragment-length polymorphism (RFLP) and spoligotyping. From 11 clusters associated with 33 patients, 31 isolates had an IS6110-based banding pattern characteristic of the Beijing genotype of M. tuberculosis. In addition, 15 M. tuberculosis isolates with similar RFLP patterns constituted a single group by spoligotyping, matching the Beijing genotype. Multidrug resistance, always involving isoniazid and rifampin, was seen in 34 (52.3%) of 65 isolates, with 28 belonging to the Beijing genotype.

Laboratory diagnosis of mycobacterial infections: new tools and lessons learned.

Even in the 21st century, tuberculosis continues to be a problem. Although the number of cases continues gradually to decrease in the United States, cases get more difficult to treat, specifically those that are multiple-drug resistant. Infection of one-third of the world's population ensures that tuberculosis will not disappear in the near future. In light of this, it will be useful to know the goals for the health care system and how these goals may be accomplished. Laboratory testing in the mycobacteriology field is experiencing more changes today than ever before. Determining what assays will be most useful to the clinician is a challenge, and acceptance of the new technology by the medical community an even greater one. Clinicians must use the best available resources to determine the most appropriate care for their patients and work together with the laboratory to ensure that the communication channels are open. This review focuses on current state-of-the-art resources useful for accurate and rapid laboratory diagnosis of mycobacterial infections.

Application of the Sherlock Mycobacteria Identification System using high-performance liquid chromatography in a clinical laboratory.

There is a growing need for a more accurate, rapid, and cost-effective alternative to conventional tests for identification of clinical isolates of Mycobacterium species. Therefore, the ability of the Sherlock Mycobacteria Identification System (SMIS; MIDI, Inc.) using computerized software and a Hewlett-Packard series 1100 high-performance liquid chromatograph to identify mycobacteria was compared to identification using phenotypic characteristics, biochemical tests, probes (Gen-Probe, Inc.), gas-liquid chromatography, and, when necessary, PCR-restriction enzyme analysis of the 65-kDa heat shock protein gene and 16S rRNA gene sequencing. Culture, harvesting, saponification, extraction, derivatization, and chromatography were performed following MIDI's instructions. Of 370 isolates and stock cultures tested, 327 (88%) were given species names by the SMIS. SMIS software correctly identified 279 of the isolates (75% of the total number of isolates and 85% of the named isolates). The overall predictive value of accuracy (correct calls divided by total calls of a species) for SMIS species identification was 85%, ranging from only 27% (3 of 11) for M. asiaticum to 100% for species or groups including M. malmoense (8 of 8), M. nonchromogenicum (11 of 11), and the M. chelonae-abscessus complex (21 of 21). By determining relative peak height ratios (RPHRs) and relative retention times (RRTs) of selected mycolic acid peaks, as well as phenotypic properties, all 48 SMIS-misidentified isolates and 39 (91%) of the 43 unidentified isolates could be correctly identified. Material and labor costs per isolate were $10.94 for SMIS, $26.58 for probes, and $42.31 for biochemical identification. The SMIS, combined with knowledge of RPHRs, RRTs, and phenotypic characteristics, offers a rapid, reasonably accurate, cost-effective alternative to more traditional methods of mycobacterial species identification.

Can the API (RAPID) Coryne system be used for identification of rapidly growing mycobacteria?

Fifty-six strains of rapidly growing mycobacteria (RGM) and 14 strains of aerobic actinomycetes as quality controls (QC) were tested in the API (RAPID) Coryne system version 2. Both groups yielded codes with low identification scores, considerable overlaps, and similar diagnoses. No species-specific codes were observed. Thus, the system would not be useful for the identification of RGM.

Resistance to antimicrobial agents in Mycobacterium tuberculosis.

According to the World Health Organization (WHO) more people will currently die of tuberculosis (TB) than in any other year in history. Of equal concern are the emergence and nosocomial transmission of multidrug-resistant (MDR) strains of Mycobacterium tuberculosis. Only recently, with the advent of new molecular biological techniques, the mechanisms of drug resistance in TB bacilli are more and more understood. In M. tuberculosis, the primary mechanism of drug resistance seems to be exclusively confined to chromosomal DNA and not, as in other bacteria, to mobile genetic elements as well.

[Sensitivity of bacteria to antibiotics (Zurich, 2000)]. / Die Empfindlichkeit von Bakterien gegen Antibiotika (Zürich, 2000).

This paper describes the frequency of susceptibility of Gram-negative and Gram-positive bacteria against antibacterial agents. Data are based on all susceptibility tests performed at the Department of Medical Microbiology of the University of Zurich in 2000. The evaluation of the results from 1987 to 2000 shows that susceptibilities against the antimicrobial agents tested have not markedly changed with the following exceptions: 7% of Staphylococcus aureus are resistant against methicillin, 8% of pneumococci have a reduced susceptibility to penicillin, 1% is resistant to penicillin, and 10% are resistant to macrolides. 9% of group A streptococci are resistant to macrolides. Quinolone resistance is markedly high in the medical practice with 10% of E. coli strains and 32% of Campylobacter sp. Strains of Klebsiella pneumoniae and E. coli producing extended spectrum betalactamases are isolated occasionally. Of all strains of Mycobacterium tuberculosis isolated from clinical specimens in 2000, 4% were multi-drug resistant. The tables may be a help for the physician in his decision for a "calculated chemotherapy" of bacterial infections.

Surveillance of antituberculosis drug resistance in Switzerland 1995-1997: the central link.

The purpose of the present paper is to investigate the usefulness of routine notification of antituberculosis drug susceptibilities. In Switzerland, laboratories have to report susceptibilities to isoniazid, rifampicin, ethambutol, and pyrazinamide to the Federal Office of Public Health. All clinical and laboratory information on every single tuberculosis case is routinely linked. Proportions of drug resistance were calculated and logistic regression was applied to evaluate the role of potential risk factors. Eighty percent (1056) of all culture-positive tuberculosis cases reported between October 1995 and December 1997 were analysed. The strains of 66 (6.3%) patients had resistances to at least one drug. Risk factors identified were previous antituberculosis treatment (adjusted odds ratio 7.3, 95% confidence interval 3.9-13.6), male sex (1.4, 1.1-2.0), and age <65 yrs (1.5, 1.0-2.3). Fourteen cases (1.3%), 13 of them foreign-born, were resistant to at least isoniazid and rifampicin. Reporting of drug susceptibilities allows routine assessment of the proportion of drug resistant tuberculosis and populations at risk. This proportion was found to be small in Switzerland. Risk factors were previous treatment for tuberculosis, male sex, and age <65 yrs. Resistance to at least isoniazid and rifampicin was predominantly found in foreign-born patients.