The effective identification of bacterial and fungal isolates is essential for microbiological monitoring in environments like speleotherapeutic caves. This study compares MALDI-TOF MS and the ...OmniLog ID System, two high-throughput culture-based identification methods. MALDI-TOF MS identified 80.0% of bacterial isolates to the species level, while the OmniLog ID System identified 92.9%. However, species-level matches between the methods were only 48.8%, revealing considerable discrepancies. For discrepant results, MALDI-TOF MS matched molecular identification at the genus level in 90.5% of cases, while the OmniLog ID System matched only in 28.6%, demonstrating MALDI-TOF MS’s superiority. The OmniLog ID System had difficulties identifying genera from the order Micrococcales. Fungal identification success with MALDI-TOF MS was 30.6% at the species level, potentially improvable with a customised spectral library, compared to the OmniLog ID System’s 16.7%. Metagenomic approaches detected around 100 times more microbial taxa than culture-based methods, highlighting human-associated microorganisms, especially Staphylococcus spp. In addition to Staphylococcus spp. and Micrococcus spp. as indicators of cave anthropisation, metagenomics revealed another indicator, Cutibacterium acnes. This study advocates a multi-method approach combining MALDI-TOF MS, the OmniLog ID System, culture-based, and metagenomic analyses for comprehensive microbial identification. Metagenomic sampling on nitrocellulose filters provided superior read quality and microbial representation over liquid sampling, making it preferable for cave air sample collection.
Candidatus Neoehrlichia mikurensis (CNM) is an emerging tick-born pathogen and usually causes symptomatic infection only in immunocompromised patients. Apart from one described case found in the ...literature where cultivation was successful, all cases so far were diagnosed by using broad-range 16S rDNA PCR. Due to the obscurity of the pathogen, diagnostic workup in CNM is prolonged and challenging. More awareness is need about this emerging infectious disease in countries with high prevalence of tick-borne diseases as standard microbiological methods are not successful in confirming the diagnosis.
Summary
To investigate epidemiology of invasive pneumococcal disease (IPD) in the central part of Slovenia in a population with no routine pneumococcal vaccination, we carried out serotyping of ...isolates by sequential multiplex polymerase chain reaction (PCR) and genotyping by repetitive sequence-based PCR (rep-PCR) and some by multilocus sequence typing. IPD was confirmed in 134 (26.5 %) of 510 acutely ill patients, either by a positive blood culture or real-time PCR (rt-PCR). In 94 patients, isolates were available for typing (24 from blood and 70 from nasopharynx). They belonged to 12 different serotypes; the most prevalent were 14 (27.6 % isolates), 9V, 3 (12.7 % each), 7F (9.5 %), 19A, and 1 (7.4 % each) followed by 4, 6A/B, 19F, 23F, 18C, and 33F. Genotyping yielded 34 rep-PCR genotypes and 13 subtypes; six were found in serotype 14, one in 9V, four each in 3, 19A, and 6A/B, three each in 7F and 1, and two each in 4, 19F, 23F, and 18C. Serotype 9V was the most homogenous and 14 and 19A were heterogenous and had two divergent clonal groups each. The most common genotypes belonged to virulent widespread clones, like ST162, ST9, ST15, ST156, ST191, and ST1377; however, sporadic clones were also observed.
Bacteremia induced by wound myiasis is uncommon and therefore rarely suspected by clinicians when treating patients with neglected wounds. We present a case of Ignatzschineria larvae bacteremia as a ...complication of Lucilia sp. maggot wound myiasis in a young male migrant. This is the first reported human case of Ignatzschineria bacteremia in Slovenia and one of the 2 described in the literature where the fly larvae infesting the wounds of the patient with Ignatzschineria bacteremia were not only suspected to be Lucilia sp. but also entomologically identified.
Antibacterial activity of three members of a benzoxazine series of histidine kinase inhibitors ( 4a , 4b and 6 ) was studied on standard strains, and with 4b also on clinical isolates of enterococci.
...Susceptibility to each compound was tested using a broth macrodilution method with a range of dilutions from 0.016 to 128 microg/ml on four standard strains (Escherichia coli ATCC 25922, Pseudomonas aeruginosa ATCC 27853, Staphylococcus aureus ATCC 29213 and Enterococcus faecalis ATCC 29212) and in the case of 4b also on 52 clinical isolates of enterococci (7 vancomycin-susceptible E. faecalis, 15 vancomycin-susceptible Enterococcus faecium and 30 vancomycin-resistant E. faecium), and on two additional standard strains (S. aureus ATCC 43300 and E. faecalis ATCC 51299).
Neither of the compounds inhibited the growth of E. coli ATCC 25922 or P. aeruginosa ATCC 27853. Compound 4b inhibited the growth of S. aureus ATCC 29213 at 8 microg/ml, S. aureus ATCC 43300 at 32 microg/ml, E. faecalis ATCC 29212, and E. faecalis ATCC 51299 at 16 microg/ml, while 4a and 6 did so at higher concentrations. For clinical isolates of enterococci, the minimal inhibitory concentrations of 4b were in the range of 0.5-16 microg/ml.
Compound 4b promises to be a potentially useful antimicrobial agent for vancomycin-susceptible and -resistant enterococci.
Malignant syphilis (MS) is a rare form of secondary syphilis with grotesque skin lesions, systemic manifestation and life-threatening complications. This article presents a case of MS in an ...immunocompetent 41-year-old female, who initially manifested with a generalized nonpruritic erythematous rash and systemic symptoms. She was mistreated for generalized impetigo and hepatitis attributed to chronic alcoholism. After partial recovery and a 3-month latent period, she developed infiltrated plaques with crusts on the trunk, head and neck; pharyngitis and laryngeal lesions; generalized lymphadenopathy and nonspecific systemic symptoms. Serologic tests confirmed syphilis, and cerebrospinal fluid analyses indicated the presence of anti-treponemal antibodies. Urine drug screening was positive for cannabinoids. The polymerase chain reaction from skin biopsy samples identified
, confirmed with Warthin-Starry staining. Immunohistochemical analysis was uncharacteristic. Tertiary syphilis, neurosyphilis, ocular syphilis and otosyphilis were excluded. However, the patient was treated for neurosyphilis with benzylpenicillin (18 million IU intravenously daily, 14 days) and corticosteroids. No Jarisch-Herxheimer reaction occurred. Ten months after treatment, residual scars were visible, and 1 year later, she attempted suicide. Since MS can resemble other diseases, it should be suspected in a mentally ill patient with chronic drug abuse, systemic nonspecific manifestations and dermatological abnormalities, including the head and neck region.
Acinetobacter baumannii
primarily causes colonization, yet it can be an opportunistic pathogen associated with hospital-acquired infections. Many countries report rapid spread of carbapenem-resistant
...Acinetobacter baumannii
(CRAb) which limits treatment options, with colistin frequently being the last line treatment option. The aim of our study was to evaluate a recently developed rapid method, namely the Rapid ResaPolymyxin test, for detection of colistin resistance (ColR) in
Acinetobacter baumannii
. This test was used for rapid screening of colistin resistance in a clinical setting where there is endemicity of CRAb isolates. A total of 82
A. baumannii
clinical isolates were included in the evaluation. The majority of them were resistant to carbapenems (75/82, 91.5%). A total of 37 isolates (45.1%) were resistant to colistin, all being resistant to carbapenems. None of the ColR isolates carried the plasmid-mediated
mcr-1
to
-5
genes. The Rapid ResaPolymyxin NP test reached a 95.1% categorical agreement with results of reference broth microdilution method, with 93.3% sensitivity and specificity, and positive and negative predictive values being respectively at 92.3% and 97.7%. The Rapid ResaPolymyxin NP test performed well on our collection of clinical and surveillance CRAb isolates from the Central Slovenia region. The test is inexpensive and easy to integrate into laboratory workflow. The main value of the test is rapid categorization of susceptibility and resistance which has important implications with respect to the treatment strategy as well as the infection control measures.
Summary
Early postoperative prosthetic valve endocarditis due to
Stenotrophomonas maltophilia
was diagnosed in seven patients (two men) aged from 68 to 84 years (mean age 78.1 years) over a ...three-year period. All patients had undergone aortic valve replacement.
S. maltophilia
was isolated from at least two blood cultures per patient. Four patients experienced CNS embolic complications. Three patients died. All patients were treated with ceftazidime, one in combination with amikacin, one with ciprofloxacin and one with levofloxacin. Because a common source of infection in the operating theater was suspected, 24 environmental samples were taken, of which two contained
S. maltophilia
. Six of the seven clinical isolates from the patients and two isolates from the environment were analyzed using molecular typing by pulsed-field gel electrophoresis (PFGE). The patients' isolates were resistant to gentamicin, ciprofloxacin, trimethoprim/sulfamethoxazole and, except in one case, to amikacin and piperacillin/tazobactam and susceptible to ceftazidime and levofloxacin. In contrast, the environmental isolates were resistant to ceftazidime, showed intermediate susceptibility to ciprofloxacin, and were susceptible to trimethoprim/sulfamethoxazole. PFGE demonstrated indistinguishable or closely related (1–3 band difference) PFGE patterns in isolates from the patients, but a different pattern in the environmental isolates. No common source of infection was found despite intensive investigation. Extensive cleaning and other measures of infection control were carried out and no new cases were recorded in the two year follow-up period.
Staphylococcus aureus is one of the most important human pathogens and methicillin-resistant variants (MRSAs) are a major cause of hospital and community-acquired infection. We aimed to map the ...geographic distribution of the dominant clones that cause invasive infections in Europe.
In each country, staphylococcal reference laboratories secured the participation of a sufficient number of hospital laboratories to achieve national geo-demographic representation. Participating laboratories collected successive methicillin-susceptible (MSSA) and MRSA isolates from patients with invasive S. aureus infection using an agreed protocol. All isolates were sent to the respective national reference laboratories and characterised by quality-controlled sequence typing of the variable region of the staphylococcal spa gene (spa typing), and data were uploaded to a central database. Relevant genetic and phenotypic information was assembled for interactive interrogation by a purpose-built Web-based mapping application. Between September 2006 and February 2007, 357 laboratories serving 450 hospitals in 26 countries collected 2,890 MSSA and MRSA isolates from patients with invasive S. aureus infection. A wide geographical distribution of spa types was found with some prevalent in all European countries. MSSA were more diverse than MRSA. Genetic diversity of MRSA differed considerably between countries with dominant MRSA spa types forming distinctive geographical clusters. We provide evidence that a network approach consisting of decentralised typing and visualisation of aggregated data using an interactive mapping tool can provide important information on the dynamics of MRSA populations such as early signalling of emerging strains, cross border spread, and importation by travel.
In contrast to MSSA, MRSA spa types have a predominantly regional distribution in Europe. This finding is indicative of the selection and spread of a limited number of clones within health care networks, suggesting that control efforts aimed at interrupting the spread within and between health care institutions may not only be feasible but ultimately successful and should therefore be strongly encouraged.
Abstract
Infectious spondylodiscitis is diagnosed with increasing frequency. It is most commonly caused by Staphylococcus aureus. The aim of the present study was to determine clinical differences ...between S. aureus and non-S. aureus spondylodiscitis and, by using spa typing, to determine whether certain clones of S. aureus predominate. During the y 2002-2006, 70 patients (45 male, 25 female) were diagnosed with spondylodiscitis and treated at the Department of Infectious Diseases, University Medical Centre Ljubljana. The age range was 13-95 y (mean age 63.4 y). Cultures were positive in 59 (85%) patients; S. aureus was isolated from blood and/or vertebral disc in 42 (60%) and other bacteria were isolated in 17 (25%). In patients with S. aureus spondylodiscitis, the infection was more likely to be haematogenous. These patients were more likely at risk for epidural abscess. Thirty S. aureus isolates from blood were typed with the spa typing molecular method. All of them were methicillin-susceptible. We identified 20 spa types. Seven spa types (t005, t015, t026, t091, t116, t449 and t474) were identified more than once, while 13 were sporadic. Among the sporadic spa types, 6 were newly identified in this study and introduced as new types into the spa server database. A heterogeneity of S. aureus isolates from spondylodiscitis was detected in this study. Thus no specific clone was identified that might be more likely to cause infection of the spine.
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