Identification and antimicrobial susceptibility of Streptomyces and other unusual Actinobacteria clinical isolates in Spain.

Two hundred and eighty-six isolates from human clinical samples were identified between 1996 and 2019 as belonging to 8 families, 19 genera and 88 species of Actinobacteria. The most identified genera were Streptomyces (182 strains from 45 species), Actinomadura (29 strains, 5 species), Nocardiopsis (21 strains, 6 species) and Dietzia (18 strains, 5 species). The rest of the identified genera (15) contained 27 species with 36 isolates. Of the species studied, only 13/88 had been documented previously as isolates from clinical samples, and in some cases, as true pathogens. In this sense, a literature review of the species found in infections or in clinical samples without clear involvement in pathology has been carried out. Finally, the susceptibility to 8 antimicrobial agents has been studied. Streptomyces showed high resistance (80.8%) against cefotaxime and cotrimoxazole (55.5%), and no isolate resistance to amikacin and linezolid have been found. Lower percentages of resistance have been found in other genera, except in Dietzia (100% against cotrimoxazole and 44.4% against erythromycin). The greatest resistance in these genera was to cotrimoxazole (29.8) and erythromycin (27,9%), and no resistance to linezolid has been found in these genera. In Microbispora, Nonomuraea and Umezawaea, no resistant isolates have been found against any antibiotic studied. Only 3/104 isolates were resistant to amikacin in Amycolatopsis, Crossiella, and Micromonosopora. One isolate of Amycolatopsis was resistant to imipenem.

Paenibacillus spp. isolated from human and environmental samples in Spain: detection of 11 new species.

One hundred thirty-six isolates, 88 human and 48 environmental, that met the requirements to belong to the genus Paenibacillus were identified using a polyphasic taxonomic approach known as 16S rRNA plus phenotypic traits. Thirty-seven Paenibacillus species were identified; some had not been previously reported from clinical samples. The main species were P. pabuli (13 isolates), P. provencensis (11), P. phoenicis (9) and P. lautus (8). P. pabuli (11/13) and P. provencensis (8/11) were mainly environmental isolates, while P. phoenicis (9/9) and P. lautus (6/8) were mainly human isolates. Despite the difficulties in assigning to human Paenibacillus isolates a role as a pathogen or contaminant, here 25% of the isolates were involved in true infections, especially in those cases that affected abscesses, wound exudates, ocular infections and diverse fluids. In addition, 15 isolates were identified as 11 'Candidatus' to a new species, all of them from human specimens except one that was obtained from laboratory air. The antimicrobial susceptibility testing showed 95.6% of isolates were resistant to ampicillin, 44% were resistant to cotrimoxazole, 20 to 30% were resistant to cefotaxime and vancomycin and 13% were resistant to rifampicin and erythromycin.

Characterization and antimicrobial susceptibility of one antibiotic-sensitive and one multidrug-resistant Corynebacterium kroppenstedtii strain isolated from patients with granulomatous mastitis.

Human infections associated with Corynebacterium kroppenstedtii are rarely reported, and this organism is usually described as antibiotic sensitive. Almost all published cases of C. kroppenstedtii infections have been associated with breast pathology in women and have been described in New Zealand, France, Canada, India and Japan. Here we describe the microbiologic characteristics of two strains isolated from two women diagnosed of granulomatous mastitis in Spain. One C. kroppenstedtii isolate was antibiotic sensitive while the other was multidrug resistant. Biochemical identification was possible using a wide battery of methods including API Coryne V2.0, API Strep, API NH, API NE, matrix-assisted laser desorption/ionization time-of-flight mass spectrometry and 16S rRNA gene amplification and sequencing. Antimicrobial susceptibility to 28 antibiotics as determined by Etest showed one isolate being sensitive to benzylpenicillin, ciprofloxacin, moxifloxacin, gentamicin, vancomycin, clindamycin, tetracycline, linezolid and rifampin. The second isolate showed resistance to ciprofloxacin, moxifloxacin, clindamycin, tetracycline and rifampin. The multidrug-resistant isolate contained the erm(X), tet(W), cmx, aphA1-IAB, strAB and sul1 resistance genes known from the R plasmid pJA144188 of Corynebacterium resistens. These genes were absent in the genome of the antibiotic-sensitive isolate. This report confirms the tropism of this microorganism for women's breasts and presents the first description of a multidrug-resistant C. kroppenstedtii strain.

Phenotypic, molecular characterization, antimicrobial susceptibility and draft genome sequence of Corynebacterium argentoratense strains isolated from clinical samples.

During a 12-year period we isolated five Corynebacterium argentoratense strains identified by phenotypic methods, including the use of matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF) and 16S rRNA gene sequencing. In addition, antimicrobial susceptibility was determined, and genome sequencing for the detection of antibiotic resistance genes was performed. The organisms were isolated from blood and throat cultures and could be identified by all methods used. All strains were resistant to cotrimoxazole, and resistance to ß-lactams was partly present. Two strains were resistant to erythromycin and clindamycin. The draft genome sequences of theses isolates revealed the presence of the erm(X) resistance gene that is embedded in the genetic structure of the transposable element Tn5423. Although rarely reported as a human pathogen, C. argentoratense can be involved in bacteraemia and probably in other infections. Our results also show that horizontal transfer of genes responsible for antibiotic resistance is occurring in this species.

Increase in isolation of Burkholderia contaminans from Spanish patients with cystic fibrosis.

Species of the Burkholderia cepacia complex are associated with opportunistic infection in patients with cystic fibrosis. For years now, B. multivorans and B. cenocepacia have been the most frequently isolated species within the complex in such patients. However, between 2008 and 2012, the overall incidence of these species in Spain (17.7% and 12.5% respectively) was overtaken by that of B. contaminans (36.5%). The population structure of B. contaminans isolates from Spanish patients with cystic fibrosis was analysed using multilocus sequence typing and pulsed-field gel electrophoresis (PFGE). Three major known sequence types (ST102, ST404 and ST482) and a new one (ST771) were identified among 59 isolates. In addition, PFGE detected 17 pulsotypes. Susceptibility to antibiotics was examined using the Etest. Cotrimoxazole and ceftazidime were the most active antibiotics against B. contaminans, inhibiting growth in 88% and 86% of the isolates, respectively. In addition, this species showed less resistance to most of the antibiotics tested than did either B. multivorans or B. cenocepacia isolates recovered from similar Spanish patients.

First report of bacteremia by Janibacter terrae in humans.

The genus Janibacter comprises nine different species mainly found in the environment. Only two human infections by these microorganisms have been previously reported, one by J. melonis and another one by an undescribed Janibacter sp. Herewith we report the first human cases of infection by J. terrae in four bacteremic patients. The microorganisms were isolated from two consecutive blood cultures taken from four febrile patients with several underlying conditions. All patients were treated with antibiotics, two of them with favorable outcome. Two severely immunocompromised patients died, and one was treated with an antibiotic in vitro active against the isolate. Janibacter terrae was identified by phenotypic and 16S rDNA amplification methods. This report includes also the first data on antimicrobial susceptibility of this opportunistic pathogen. Clinical microbiologists should be aware of this microorganism which can be identified by phenotypic and molecular methods.

Contamination of liquid soap for hospital use with Raoultella planticola.

This article reports the contamination of a batch of liquid soap for hospital use with Raoultella planticola. The micro-organism was first identified as Klebsiella pneumoniae due to the inability of automated systems to characterize this species. There is a need to strengthen the inspection of cosmetic products to be used in the hospital setting. It is recommended that hospitalized patients at the highest risk of infection should use antimicrobial soaps for personal hygiene. The incidence of infections due to R. planticola is unknown as it is usually misclassified as Klebsiella spp. by automated systems.

Meningitis caused by Abiotrophia defectiva: case report and literature review.

The genus Abiotrophia comprises fastidious Gram-positive bacteria previously classified as nutritionally variant streptococci (NVS). The isolation of NVS from the central nervous system (CNS) is very rare. We describe a case of meningitis due to Abiotrophia defectiva in a patient who underwent a total hip arthroplasty 4 days previously. It is possible that the organism could be introduced through the spinal anesthesia. We also review all cases of CNS infections caused by NVS.

Two simultaneous botulism outbreaks in Barcelona: Clostridium baratii and Clostridium botulinum.

Botulism is a severe neuroparalytic disorder that can be potentially life-threatening. In Barcelona, Spain, no outbreaks had been reported in the past 25 years. However, in September 2011, two outbreaks occurred involving two different families. A rare case of Clostridium baratii which produced a neurotoxin F outbreak was detected in five family members who had shared lunch, and several days before that another family was affected by C. botulinum toxin A which was probably present in homemade pâté.

Dermabacter hominis: a usually daptomycin-resistant gram-positive organism infrequently isolated from human clinical samples.

During a 12-year period, Dermabacter hominis was isolated from 21 clinical samples belonging to 14 patients attending a tertiary hospital in León, Spain. Samples included blood cultures (14), peritoneal dialysis catheter exit sites (three), cutaneous abscesses (two), an infected vascular catheter (one) and a wound swab (one). Identification was made by API Coryne™ V2.0, Biolog™ GP2 and 16S rRNA gene amplification. Six febrile patients had positive blood cultures (one, two or three sets) and all of them were treated with teicoplanin (two patients), vancomycin, ampicillin plus gentamicin, amoxicillin/clavulanic acid and ciprofloxacin (one each). An additional patient with a single positive blood culture was not treated, the finding being considered non-significant. In the remaining seven patients the organism was isolated from a single specimen and three of them received antimicrobial treatment (ciprofloxacin, ceftriaxone plus vancomycin and amoxicillin/clavulanic acid). At least ten patients had several underlying diseases and conditions, and no direct mortality was observed in relation to the isolated organism. All isolates were susceptible to vancomycin, rifampin and linezolid. Resistance to other antibiotics varied: erythromycin (100%), clindamycin (78.5%), ciprofloxacin (21.4%) and gentamicin, quinupristin-dalfopristin, benzylpenicillin and imipenem 7.1% each. Thirteen isolates were highly resistant to daptomycin with MICs ranging from 8 to 48 (MIC90 = 32 mg/L); only one was daptomycin-sensitive (MIC = 0.19 mg/L).

Identification, molecular characterisation and antimicrobial susceptibility of genomovars of the Burkholderia cepacia complex in Spain.

Burkholderia spp. strains collected in Spain over a 13-year period from patients with cystic fibrosis (CF) (n = 148), non-CF patients (n = 103) and from environmental sources (n = 64) were characterised. One hundred and forty-one of the examined strains were involved in seven suspected nosocomial disease outbreaks. Strains were identified by their 16s rRNA and recA genes. Their genetic relatedness, the possession of cable pili and the B. cepacia epidemic strain marker (BCESM), and their susceptibility to antimicrobial agents were studied using pulsed-field gel electrophoresis (PFGE), cblA and esmR genes analysis, and by the E-test, respectively. The genomovar distribution for the 315 strains was as follows: B. stabilis 29.5 %, B. cepacia 14.9 %, B. multivorans 11.1 %, B. cenocepacia IIIA 9.5 %, B. vietnamiensis 3.8 %, B. cenocepacia IIIB 3.5 %, and B. ambifaria and B. pyrrocinia 0.3 % each. The genetic diversity of the B. cepacia complex (Bcc) was ample, with 57 different SpeI types, showing a genetic similarity of 36.4-96.6 %. No strain carried cblA, whereas 25 B. cenocepacia genotypes harboured BCESM (23 from patients with CF). Antimicrobial resistance rates to tobramycin (TOB; 86 %) and imipenem (IPM; 67 %) were high. The strains from patients with CF showed significantly greater resistance to piperacillin (PIP), levofloxacin (LVX) and co-trimoxazole (SXT) than those isolated from non-CF patients (p < 0.05). In conclusion, B. cenocepacia was the most prevalent genomovar found in patients with CF (19.1 %), whereas B. cepacia was the most common among non-CF patients (20.7 %). B. stabilis (47.6 %) was the most common environmental genomovar. Susceptibility to antimicrobial agents depended on genomovar status and strain origin.

[Molecular characterization of Streptococcus pyogenes from invasive disease and streptococcal toxic shock syndrome episodes]. / Caracterización molecular de Streptococcus pyogenes causantes de enfermedad invasora y síndrome de shock tóxico estreptocócico.

Streptococcus pyogenes causes a variety of common human diseases, including pharyngitis, scarlet fever and impetigo. Nevertheless, the past decades have witnessed a worldwide resurgence in invasive disease and streptococcal toxic shock syndrome (STSS). The objective of the present study is to evaluate the genetic diversity, virulence gene distribution (spe, sme and ssa genes) and susceptibility pattern of 10 S. pyogenes isolates causing invasive disease and STSS. The isolates were recovered from blood cultures of hospitalized patients at Hospital Santamarina and Nueva Clínica Chacabuco, Tandil, Buenos Aires, Argentina between 12/2000-04/2005. Two pulse field gel electrophoretic patterns predominated. The most frequent one included 5 characteristic isolates of emm1-T1 type, toxin gene profile speA, speB, speF, speG and smeZ. The second pattern included 2 characteristic isolates of emm3-TNT type (speB, speF, speG). The other 3 isolates corresponded to types emm49-TNT (speB, speC, speF, speG), emm75-T25 (speB, speF, speG) and emm83-TNT (speB, speF, speG, ssa, smeZ). All isolates were susceptible to penicillin, cefotaxime, erythromycin, clindamycin, chloramphenicol, tetracycline and rifampicin. The data from the present study demonstrated genetic diversity among the strains. Types emm1 and emm3 were prevalent in invasive disease. The empirical treatment with the combination of penicillin and clindamicin is still valid.

A possible novel Francisella genomic species isolated from blood and urine of a patient with severe illness.

Two identical isolates were recovered in pure culture from the blood and urine of a patient suffering from severe septicaemia associated with obstructive pyelonephritis secondary to lithotripsy. Preliminary phenotypic and genotypic characterizations based on serological, biochemical and sequence analyses following PCR amplification of selected gene regions indicate that this organism represents a potential new Francisella genomic species.

Outbreak of multiresistant Acinetobacter baumannii in a polyvalent intensive care unit: clinical, epidemiological analysis and PFGE-printing evolution.

An outbreak of multidrug-resistant Acinetobacter baumannii (MRAB) occurred over the course of a 27-week period in our adult polyvalent intensive care unit (ICU). Twenty-one patients were affected, and 72 strains were identified from different clinical samples. The strains were resistant to all antibiotics except for colistin and ampicillin/sulbactam. Forty-nine MRAB strains collected from 18 patients were analysed by pulsed-field gel electrophoresis (PFGE). This analysis revealed four highly-related PFGE types (genetic similarity index >90%) termed 1, 2, 3 and 4, that were isolated in 13, seven, one, and three patients, respectively. A single PFGE type was identified from five of ten patients with successive isolation of MRAB; in the other five patients, two or three PFGE types were detected. This suggested phased evolution of PFGE types 2, 3 and 4 from PFGE type 1. Global mortality was high (13 patients; 62%). Non-survivors had higher APACHE II scores than survivors on the date that MRAB was isolated (OR = 1.57; 95% CI [1.02, 2.44]). The outbreak was controlled after implementation of an extensive infection control program.

Isolation of Corynebacterium ureicelerivorans from normally sterile sites in humans.

Fifteen Corynebacterium ureicelerivorans isolates were recovered in pure culture from six patients during a five-year period. Five patients had bacteremia and the other was an infection of ascitic fluid. The API Coryne numerical profile obtained corresponds to the profile for C. bovis, while Biolog GP2 identified four out of the six isolates as C. jeikeium. The organisms were molecular identified by 16S rDNA and rpoB. The present report also includes information on new phenotypic tests and, for the first time, antimicrobial susceptibility data of C. ureicelerivorans and their rpoB sequences. All macrolide-resistant isolates presented a constitutive MLS phenotype. This organism must be differentiated from other slow-growing, lipophilic, and urea-splitting corynebacteria.

Pneumonia due to Nocardia cyriacigeorgica in a patient with Crohn's disease treated with infliximab.

Infliximab, an anti-tumor necrosis factor α (TNF-α) antibody, is useful in the treatment of rheumatoid arthritis, Crohn's disease etc. It has been related to increases in the rate of several infections. We present the case of a 53-year-old woman diagnosed with community-acquired pneumonia due to Nocardia cyriacigeorgica who was taking infliximab, azathioprine and prednisone for Crohn's disease.