The pan-genome of the emerging multidrug-resistant pathogen Corynebacterium striatum

Corynebacterium striatum, a common constituent of the human skin microbiome, is now considered an emerging multidrug-resistant pathogen of immunocompromised and chronically ill patients. However, little is known about the molecular mechanisms in the transition from colonization to the multidrug-resistant (MDR) invasive phenotype in clinical isolates. This study performed a comprehensive pan-genomic analysis of C. striatum, including isolates from "normal skin microbiome" and from MDR infections, to gain insights into genetic factors contributing to pathogenicity and multidrug resistance in this species. For this, three novel genome sequences were obtained from clinical isolates of C. striatum of patients from Brazil, and other 24 complete or draft C. striatum genomes were retrieved from GenBank, including the ATCC6940 isolate from the Human Microbiome Project. Analysis of C. striatum strains demonstrated the presence of an open pan-genome (α = 0.852803) containing 3816 gene families, including 15 antimicrobial resistance (AMR) genes and 32 putative virulence factors. The core and accessory genomes included 1297 and 1307 genes, respectively. The identified AMR genes are primarily associated with resistance to aminoglycosides and tetracyclines. Of these, 66.6% are present in genomic islands, and four AMR genes, including aac(6')-ib7, are located in a class 1-integron. In conclusion, our data indicated that C. striatum possesses genomic characteristics favorable to the invasive phenotype, with high genomic plasticity, a robust genetic arsenal for iron acquisition, and important virulence determinants and AMR genes present in mobile genetic elements.

Ecogenomics of the Marine Benthic Filamentous Cyanobacterium Adonisia

Turfs are among the major benthic components of reef systems worldwide. The nearly complete genome sequences, basic physiological characteristics, and phylogenomic reconstruction of two phycobiliprotein-rich filamentous cyanobacteria strains isolated from turf assemblages from the Abrolhos Bank (Brazil) are investigated. Both Adonisia turfae CCMR0081^T (= CBAS 745^T) and CCMR0082 contain approximately 8 Mbp in genome size and experiments identified that both strains exhibit chromatic acclimation. Whereas CCMR0081^T exhibits chromatic acclimation type 3 (CA3) regulating both phycocyanin (PC) and phycoerythrin (PE), CCMR0082 strain exhibits chromatic acclimation type 2 (CA2), in correspondence with genes encoding specific photosensors and regulators for PC and PE. Furthermore, a high number and diversity of secondary metabolite synthesis gene clusters were identified in both genomes, and they were able to grow at high temperatures (28 °C, with scant growth at 30 °C). These characteristics provide insights into their widespread distribution in reef systems.

Rapid screening of marine bacterial symbionts using MALDI-TOF MS

Matrix-Assisted Laser Desorption Ionization Time-Of-Flight Mass Spectrometry (MALDI-TOF MS) is a rapid, cost-effective and high-throughput method for bacteria characterization. However, most previous studies focused on clinical isolates. In this study, we evaluated the use of MALDI-TOF MS as a rapid screening tool for marine bacterial symbionts. A set of 255 isolates from different marine sources (corals, sponge, fish and seawater) was analyzed using cell lysates to obtain a rapid grouping. Cluster analysis of mass spectra and 16S rRNA showed 18 groups, including Vibrio, Bacillus, Pseudovibrio, Alteromonas and Ruegeria. MALDI-TOF distance similarity scores ≥ 60% and ≥ 70% correspond to ≥ 98.7% 16S rRNA gene sequence similarity and ≥ 95% pyrH gene sequence similarity, respectively. MALDI-TOF MS is a useful tool for Vibrio species groups' identification.

Description of Alteromonas abrolhosensis sp. nov., isolated from sea water of Abrolhos Bank, Brazil

Two Gram-negative, motile, aerobic bacteria isolated from waters of the Abrolhos Bank were classified through a whole genome-based taxonomy. Strains PEL67E^T and PEL68C shared 99% 16S rRNA and dnaK sequence identity with Alteromonas marina SW-47^T and Alteromonas macleodii ATCC 27126^T. In silico DNA-DNA Hybridization, i.e. genome-to-genome distance (GGD), average amino acid identity (AAI) and average nucleotide identity (ANI) showed that PEL67E^T and PEL68C had identity values between 33-36, 86-88 and 83-84%, and 85-86 and 83%, respectively, towards their close neighbors A. macleodii ATCC 27126^T and A. marina SW-47^T. The DNA G + C contents of PEL67E^T and PEL68C were 44.5%. The phenotypic features that differentiate PEL67E^T and PEL68C strains from their close neighbors were assimilation of galactose and activity of phosphatase, and lack of mannitol, maltose, acetate, xylose and glycerol assimilation and lack of lipase, α and β-glucosidase activity. The new species Alteromonas abrolhosensis is proposed. The type strain is PEL67E^T (= CBAS 610^T = CAIM 1925^T).

Genomic analysis of a nontoxigenic, invasive Corynebacterium diphtheriae strain from Brazil

We report the complete genome sequence and analysis of an invasive Corynebacterium diphtheriae strain that caused endocarditis in Rio de Janeiro, Brazil. It was selected for sequencing on the basis of the current relevance of nontoxigenic strains for public health. The genomic information was explored in the context of diversity, plasticity and genetic relatedness with other contemporary strains.

Infective endocarditis in Rio de Janeiro, Brazil: a 5-year experience at two teaching hospitals

INTRODUCTION

Despite the recent advances in diagnosis and treatment, mortality rates due to infective endocarditis (IE) remain high if not aggressively treated with antibiotics, whether or not associated with surgery. Data on the prevalence, epidemiology and etiology of IE from developing countries remain scarce. The aim of this observational, prospective cohort study was to report a 5-year experience of IE at two teaching hospitals in Rio de Janeiro, Brazil.

MATERIAL AND METHODS

Demographical, anamnestic and microbiological characteristics of 71 IE patients were evaluated during the period of January 2009 to March 2013.

RESULTS

The mean age of the IE patients was 49.8 ± 2.4 years, of which 41 (57.7%) were males. The median time between the onset of symptoms and diagnosis of IE was 35.8 ± 4.8 days. A total of 31 (43.6%) cases of community-acquired infective endocarditis (CAIE) and 40 (56.3%) cases of healthcare-acquired infective endocarditis (HAIE) were observed. Staphylococcus aureus (30%) was the predominant cause of IE. Streptococcus spp. (45.1 %) was the predominant cause of the CAIE while S. aureus (32.5%) and Enterococcus spp. (27.2 %) were the main etiological agents of HAIE. For 64 (90.1 %) patients with native valve endocarditis, the mitral valve was the most commonly affected (48.3%). The main source of IE in this cohort was intravascular catheter. The tricuspid valve and renal chronic insufficiency were more frequent in patients with HAIE than CAIE (p = 0.001). The risk factors associated with in-hospital mortality rate (46.4%) in IE patients were: age over 45 (OR 3.4; 95% CI 1.03-11.24; p = 0.04) and chronic renal insufficiency (OR 38.3; 95% CI 3.2-449.4; p = 0.004).

CONCLUSIONS

At two main teaching hospitals in Brazil, Streptococcus spp. was the principal pathogen of CAIE while S. aureus and Enterococcus spp. were the most frequent causes of HAIE. IE remains a serious disease associated with high in-hospital mortality rate (46.6%); especially, in individuals over 45 years of age and with renal failure. Data suggest that early surgery may improve the outcome of IE patients.

A case report and literature overview: Abiotrophia defectiva aortic valve endocarditis in developing countries

A fatal case of aortic valve endocarditis due to Abiotrophia defectiva was reported in Brazil. An overview of cases of endocarditis and other human infections related to A. defectiva in developing countries was also accomplished.

New qnr gene cassettes associated with superintegron repeats in Vibrio cholerae O1

A novel qnr determinant emerged in ciprofloxacin-resistant Vibrio cholerae O1 from the Amazon region of Brazil. This qnrVC1 was in a typical class 1 integron. Its attC showed 89% identity with V. parahaemolyticus superintegron repeats. Analysis showed V. cholerae O1 carrying qnrVC2 associated with a V. cholerae superintegron repeat.

Coexistence of epidemic colistin-only-sensitive clones of Pseudomonas aeruginosa, including the blaSPM clone, spread in hospitals in a Brazilian Amazon City

Nosocomial outbreaks caused by multidrug-resistant (MDR) Pseudomonas aeruginosa have been associated to fibrocystic patients and isolates harboring metallo-beta-lactamase (MBL) genes. Genotyping is an important tool for interpreting bacterial nosocomial outbreaks and implementing adequate control strategies. The aim of this study was to evaluate whether an outbreak of MDR P. aeruginosa occurring in different hospitals was due to a unique clone or independent isolates. From 2000 to 2003, 108 P. aeruginosa were recovered from colonized/infected inpatients in hospitals of São Luís, Maranhão, Brazil. The susceptibility test was performed with antipseudomonal drugs, and the presence of MBL genes were verified by PCR. Isolates were genotyped by pulsed-field gel electrophoresis (PFGE). The majority of strains was multiresistant including a great number presenting the colistin-only-sensitive (COS) profile. PFGE analysis revealed 54 genotypes, with predominance of three major COS clones (A, C, and E) coexisting at different moments and hospitals. Clone A harbored the bla(SPM) gene. Eight unique genotypes also had the COS profile. Other eight MDR genotypes presented isolates with differences in resistance profiles. Here we detected, for the first time, the coexistence of COS P.aeruginosa genotypes disseminated in several hospitals during long periods, attacking patients under various clinical conditions.

Emergence of dhfrXVb and blaCARB-4 gene cassettes in class 1 integrons from clinical Pseudomonas aeruginosa isolated in Amazon region

Integrons play a role in horizontal acquisition and expression of genes, as well as gene reservoir, contributing for the resistance phenotype, particularly relevant to bacteria of clinical importance. We aimed to determine the composition and the organization of the class 1 integron variable region present in Pseudomonas aeruginosa clinical isolates from Brazil. Strains carrying class 1 integrons were resistant to the majority of antibiotics tested, except to imipenem and ceftazidime. Sequence analysis of the integron variable region revealed the presence of the blaCARB-4 gene into two distinct cassette arrays: aacA4-dhfrXVb-blaCARB-4 and aadB-aacA4-blaCARB-4. dhfrXVb gene cassette, which is rare in Brazil and in P. aeruginosa species, was found in one isolate. PFGE analysis showed the spread of blaCARB-4 among P. aeruginosa clones. The occurrence of blaCARB-4 and dhfrXVb in Brazil may contribute for developing resistance to clinically important antibiotics, and shows a diversified scenarium of these elements occurring in Amazon clinical settings, where no study about integron dynamics was performed to date.

Class 1 integrons in Pseudomonas aeruginosa isolates from clinical settings in Amazon region, Brazil

A hundred and six Pseudomonas aeruginosa isolates from clinical cases were screened using PCR for the presence of integrons and associated resistance gene cassettes. Forty-four isolates harboured class 1 integrons (41.5%), of which 29 isolates (66%) also carried gene cassettes. The aacA gene was most frequently found within class 1 integrons (69%), followed by blaOXA family genes (52%). From class 1 integron-positive strains, we detected a total of 15 isolates (34%) carrying no gene cassettes. Restriction fragment-length polymorphism analysis of the integrons variable region revealed some identical structures, as well as distinct profiles indicating heterogeneity among these cassette regions. Multiresistance was observed in 71% of isolates, nevertheless no strong correlation was observed between integron presence and multiresistance. This is the first report showing class 1 integron prevalence and gene cassette content in P. aeruginosa isolates from clinical settings in the Brazilian Amazon.

Differentiation of environmental and clinical isolates of Vibrio mimicus from Vibrio cholerae by multilocus enzyme electrophoresis

In this study, we demonstrated that analyzed strains of Vibrio mimicus and Vibrio cholerae could be separated in two groups by using multilocus enzyme electrophoresis (MEE) data from 14 loci. We also showed that the combination of four enzymatic loci enables us to differentiate these two species. Our results showed that the ribosomal intergenic spacer regions PCR-mediated identification system failed, in some cases, to differentiate between V. mimicus and V. cholerae. On the other hand, MEE proved to be a powerful molecular tool for the discrimination of these two species even when atypical strains were analyzed.

Genetic relationships among the different phenotypes of Streptococcus dysgalactiae strains

The species Streptococcus dysgalactiae was proposed to accommodate a heterogeneous group of streptococci associated with infections in animals and human beings. This taxon is now considered to include animal isolates of alpha-haemolytic group C streptococci, previously called S. dysgalactiae; animal and human isolates of beta-haemolytic group C streptococci, previously called 'S. equisimilis'; beta-haemolytic group L strains associated with infections in animals and, rarely, in humans; and beta-haemolytic group G strains isolated from humans. DNA-DNA reassociation experiments (hydroxyapatite method) and multilocus enzyme electrophoresis (MEE) were performed on reference strains and clinical isolates to determine the genetic relationships among these different phenotypic categories. DNA-DNA hybridization tests showed that they were related at the species level, despite the phenotypic and host heterogeneity. Both genotypic and phenotypic characterization indicated that S. dysgalactiae could be separated into two major sub-groups. The first sub-group contained alpha-haemolytic strains that showed levels of DNA relatedness with the type strain of S. dysgalactiae ranging from 84 to 90% and from 82 to 88% under optimal (55 degrees C) and stringent (70 degrees C) conditions, respectively. The second sub-group contained beta-haemolytic strains showing levels of relatedness ranging from 71 to 79% (55 degrees C) and from 62 to 73% (70 degrees C). Percentage divergence varied from 0.5 to 1.0% (alpha-haemolytic group) and from 2.0 to 3.5% (beta-haemolytic group). A dendrogram based on phenotypic similarity between the enzyme bands produced by MEE showed a Jaccard similarity coefficient of 0.45 between the subclusters formed by the two sub-groups. The results of phenotypic and genotypic characterization were consistent with a published proposal to divide S. dysgalactiae into two subspecies, S. dysgalactiae subsp. dysgalactiae and S. dysgalactiae subsp. equisimilis, with a few modifications.

Biochemical properties and whole-cell protein profiles of group G streptococci isolated from dogs

Whole-cell protein profiles obtained by SDS-PAGE were used in conjunction with physiological tests to differentiate strains of Streptococcus canis isolated from dogs. Fermentation of trehalose and lactose, aesculin hydrolysis together with production of beta-D-glucuronidase and alpha-D-galactosidase allowed the demonstration of nine different biotypes. However, visual analysis of the protein patterns and comparison by the coefficient of Dice showed minor differences in band patterns among strains. Only two different profiles were observed. Although a correlation between biotyping and protein profile has been found, this kind of analysis did not provide the basis for a typing method.

The effect of subminimal inhibitory concentrations of penicillin on growth rate and haemolysin activity of group G Streptococcus

The influence of the subminimal inhibitory concentrations (1/3 and 1/4 of the MIC) of penicillin on growth rate and on haemolysin production of a strain of group G Streptococcus was studied. It was shown that 1/3 of the MIC almost completely inhibited the bacterial growth, but it was not able to inhibit haemolysin activity in the culture supernate. The generation time of bacteria grown in 1/4 of the MIC was approximately twice longer than that of the control culture. In all cultures, the haemolysin, after being produced (or liberated), reached a peak and decreased to low levels, which could suggest that group G Streptococcus produces some end products of metabolism that are able to inhibit haemolysin activity.