Characterization of an epidemic carbapenem-resistant Pseudomonas aeruginosa producing SPM-1 metallo-beta-lactamase in a hospital located in Rio de Janeiro, Brazil

Metallo-beta-lactamase production is emerging worldwide as an important mechanism of carbapenem resistance among nonfermentative Gram-negative isolates, and this mechanism is becoming frequently observed in Brazil. This study documents the occurrence and characteristics of an epidemic SPM-1-producing Pseudomonas aeruginosa strain in a teaching hospital located in Rio de Janeiro City, Brazil. The bla (SPM-1) gene and a class 1 integron were detected in 13 isolates, representing 20% of the 65 imipenem-resistant P. aeruginosa isolates obtained from January, 2000, to August, 2001. DNA sequencing revealed that this integron carries three gene cassettes that confer resistance to antimicrobials, aacA4, bla (OXA-56), and aadA7, and an orf1 encoding a putative transposase. All 13 SPM-producing P. aeruginosa isolates had closely related pulsed-field gel electrophoresis (PFGE) profiles, designated as clonal group A, suggesting nosocomial spread of the strain. This clonal group was the same as that observed in other SPM-1-producing P. aeruginosa isolates from distinct Brazilian states. The dissemination of this clone throughout Brazil could not be explained by transfer of infected patients and/or sharing of common health-care staff. It is likely that the spread of these strains occurred indirectly via the community.     

Outbreaks of multidrug-resistant Pseudomonas aeruginosa in community hospitals in Japan

We previously reported an outbreak in a neurosurgery ward of catheter-associated urinary tract infection with multidrug-resistant (MDR) Pseudomonas aeruginosa strain IMCJ2.S1, carrying the 6'-N-aminoglycoside acetyltransferase gene [aac(6')-Iae]. For further epidemiologic studies, 214 clinical isolates of MDR P. aeruginosa showing resistance to imipenem (MIC >or= 16 microg/ml), amikacin (MIC >or= 64 microg/ml), and ciprofloxacin (MIC >or= 4 microg/ml) were collected from 13 hospitals in the same prefecture in Japan. We also collected 70 clinical isolates of P. aeruginosa that were sensitive to one or more of these antibiotics and compared their characteristics with those of the MDR P. aeruginosa isolates. Of the 214 MDR P. aeruginosa isolates, 212 (99%) were serotype O11. We developed a loop-mediated isothermal amplification (LAMP) assay and a slide agglutination test for detection of the aac(6')-Iae gene and the AAC(6')-Iae protein, respectively. Of the 212 MDR P. aeruginosa isolates, 212 (100%) and 207 (98%) were positive in the LAMP assay and in the agglutination test, respectively. Mutations of gyrA and parC genes resulting in amino acid substitutions were detected in 213 of the 214 MDR P. aeruginosa isolates (99%). Of the 214 MDR P. aeruginosa isolates, 212 showed pulsed-field gel electrophoresis patterns with >or=70% similarity to that of IMCJ2.S1 and 83 showed a pattern identical to that of IMCJ2.S1, indicating that clonal expansion of MDR P. aeruginosa occurred in community hospitals in this area. The methods developed in this study to detect aac(6')-Iae were rapid and effective in diagnosing infections caused by various MDR P. aeruginosa clones.     

Fusarium species in sandy soil from Ipanema Beach,Rio de Janeiro,Brazil

The presence of the genus Fusarium was investigated in sandy soil from Ipanema Beach, Rio de Janeiro, RJ, Brazil during a period of one year in order to determine the diversity, and seasonal distribution of species. A total of 123 strains were isolated, for a total of 34 different species, with higher incidence in spring and winter. The species detected in greater numbers during the various seasons of the year were, in decreasing order, F. solani var. solani, F. oxysporum var. oxysporum and F. sacchari var. subglutinans, described in the literature (GUARRO and GENÉ 1992) as infectious agents for humans and animals. Few species were detected in summer and fall, probably due to the higher rainfull occurring during these seasons.     

Adenoviruses in faeces of children with acute gastroenteritis in Rio de Janeiro, Brazil

Faeces from 746 children less than 5 years old with acute gastroenteritis were screened for the presence of adenovirus particles or antigens by immunoelectron microscopy (IEM) and enzyme immunoassay (EIA). Thirty-five samples were positive by both IEM and EIA, two only by IEM, and two only by EIA, giving a total of 39 (5.2%) samples with positive results. Of these, 25 could be propagated in HEp2 cells and were neutralized by one of the antisera to adenovirus types 1 to 18. The remaining 14 samples could be propagated only in the 293 permanent line of human cells transformed by adenovirus type 5 DNA [Graham et al, 1977] and were not neutralized by antisera to adenovirus types 1 to 31. An EIA carried out by the antibody-capture technique, using antiserum specific for "enteric" adenoviruses [Johansson et al, 1979], gave positive results with all isolates that could be propagated only in 293 cells and with none of those capable of growing in HEp2 cells.     

Effectiveness of first-line antiretroviral therapy in the IPEC cohort,Rio de Janeiro,Brazil

Background

While Brazil has had a long-standing policy of free access to antiretroviral therapy (ART) for all in need, the epidemiological impact of ART on human immunodeficiency virus (HIV) RNA suppression in this middle-income country has not been well evaluated. We estimate first-line ART effectiveness in a large Brazilian cohort and examine the socio-demographic, behavioral, clinical and structural factors associated with virologic suppression.

Methods

Virologic suppression on first-line ART at 6, 12, and 24 months from start of ART was defined as having a viral load measurement ≤400 copies/mL without drug class modification and/or discontinuation. Drug class modification and/or discontinuation were defined based on the class of a particular drug. Quasi-Poisson regression was used to quantify the association of factors with virologic suppression.

Results

From January 2000 through June 2010, 1311 patients started first-line ART; 987 (75%) patients used NNRTI-based regimens. Virologic suppression was achieved by 77%, 76% and 68% of patients at 6, 12 and 24 months, respectively. Factors associated with virologic suppression at 12 months were: >8 years of formal education (compared to <4 years, risk ratio (RR) 1.13, 95% confidence interval (95% CI) 1.03-1.24), starting ART in 2005-2010 (compared to 2000-2004, RR 1.25 95% CI 1.15-1.35), and clinical trial participation (compared to no participation, RR 1.08 95% CI 1.01-1.16). Also at 12 months, women showed less virologic suppression compared to heterosexual men (RR 0.90 95% CI 0.82-0.99). For the 24-month endpoint, in addition to higher education, starting ART in the later period, and clinical trial participation, older age and an NNRTI-based regimen were also independently associated with virologic suppression.

Conclusions

Our results show that in Brazil, a middle-income country with free access to treatment, over three-quarters of patients receiving routine care reached virologic suppression on first-line ART by the end of the first year. Higher education, more recent ART initiation and clinical trial participation were associated with improved outcomes both for the 12-month and the 24-month endpoints, suggesting that further studies are needed to understand what aspects relating to these factors lead to higher virologic suppression.

     

Incident HIV infection in a high-risk, homosexual, male cohort in Rio de Janeiro, Brazil.

An HIV seroincidence study was conducted to identify a high-risk population for HIV prevention trials. Inclusion criteria were male gender, homosexual behavior, age between 18 and 50 years, and negative HIV serostatus; 862 study subjects were screened and 753 were enrolled and observed during follow-up for a mean of 1.5 years. In this population, 34 people had HIV seroconversions for an overall annual seroincidence of 3.1% (95% confidence interval [CI], 2.1%-4.1%). Among study subjects <20 years old, annual incidence was 8.4% (95% CI, 1.7%-15%). Independent risk factors for seroconversion were age <25 years (p = .01), hepatitis B core antibody seropositivity (p > .01), sex at first encounter in the preceding 6 months (p = .11), and a history of gonorrhea or condyloma in the 6 months before seroconversion (p = .04 and p = .08, respectively). At enrollment, 85% of the eventual seroconverters said they would participate in a vaccine trial; all agreed to participate when told there would be a placebo arm. Follow-up rates were 97%, 91%, and 88% at 6, 12, and 18 months, respectively. The HIV-1 subtype was B for each of the first 17 seroconverters. These data demonstrate the suitability of this cohort for HIV prevention trials, based on high HIV incidence and retention rates, and a willingness to participate in such trials.     

First detection of autochthonous Zika virus transmission in a HIV-infected patient in Rio de Janeiro,Brazil

Since May 2015, Brazil’s Ministry of Health has reported autochthonous transmission of Zika virus (ZIKV) in some states of the country. Simultaneous circulation of Dengue, Chikungunya and ZIKV in the country hinder both the diagnosis and the therapeutic approach of patients seeking care with acute febrile illnesses especially in patients with comorbidities. The association between HIV infection and endemic diseases has been described especially in tropical regions with varying levels of complications, although there has been no report of ZIKV in HIV-infected patients. We report the first autochthonous case of laboratory confirmed ZIKV infection in a HIV-infected patient in Rio de Janeiro, Brazil. He evolved with only mild symptoms and recovered well without major laboratory abnormalities. Phylogenetic analysis of the ZIKV detected in the patient sera clustered within the Asian clade. To the best of our knowledge, this is the first time that Zika virus co-infection is reported in a HIV-infected patient.     

Patient-provider communication and reproductive health among HIV-positive women in Rio de Janeiro, Brazil

Objective

To qualitatively assess the influence of patient-provider communication on contraceptive choice among HIV-positive women in the context of universal antiretroviral therapy (ART) access.

Methods

Focus group discussions (FGD; n = 3), in-depth (IDI; n = 15) and freelist interviews (FLI; n = 36) were conducted with HIV-positive women aged 18-40 years recruited from public health units in Rio de Janeiro/Brazil.

Results

Of 70 participants, 49 used ART and the median time since HIV diagnosis was 6 years (range: 1-18). The majority of participants (71.4%) reported some degree of dissatisfaction with their health providers (usually lack of open dialogue) and a few reported experiences of stigma/prejudice during appointments. Intra, interpersonal and social factors modulated behaviors and reproductive health decisions, and those issues were rarely addressed by providers during HIV clinical care.

Conclusion

Despite dramatic increases in survival and life quality after universal ART implementation in Brazil, reproductive health issues are neglected by multiple cadres of HIV health providers. Communication on reproductive health issues remains fragmented and potentially contradictory, compromising care in these settings.

Practice implications

Adequate provider training to address reproductive health-related issues in a comprehensive, culturally sensitive manner and improved integration of HIV and reproductive health care are urgently needed in this setting.     

Diversity of microfungi in the sandy soil of Ipanema Beach,Rio de Janeiro,Brazil

The mycobiota of the sandy soil of Ipanema Beach, Rio de Janeiro, Brazil, was investigated in 144 sand samples collected at four different sites along the sea coast, divided into three subsites. for a period of one year. A total of 4285 yeast colonies and of 6956 of colonies filamentous fungi were isolated using conventional media and techniques. Representatives of the filamentous fungi corresponding to a total of 1334 colonies were identified and assigned to 34 genera and 170 species. The genera of highest incidence and their respective numbers of species were as follows: Aspergillus, 30.4%, 32 spp.; Penicillium, 16.2%, 35 spp.; Fusarium, 12,6%, 33 spp.: Trichoderma, 6.4%, 7 spp.; Paecilomyces, 3.7%, 10 spp.: Cladosporium, 3.1 %, 8 spp. and Acremonium, 1.0%, 8 spp. Several other genera and species were detected at quite low occurrences. Non-sporulating fungi (18.3%) and Coelomycetes (Sphaeropsidales) (1.9%) were also detected. Most of the genera detected belonged to the Deuteroycotina, with fewer proportions belonging to the Ascomycotina and Zygomycotina. Moniliaceae was represented by the largest number of species and Dematiaceae was represented by the largest number of genera. In terms of seasonal distribution, the largest number of filamentous fungi was isolated during the winter and the smallest number the Summer.     

Use of PCR in Diagnosis of Human American Tegumentary Leishmaniasis in Rio de Janeiro, Brazil

In Brazil, the most common etiological agent of American tegumentary leishmaniasis is Leishmania (Viannia) braziliensis. In general, diagnostic techniques envisage the visualization of the parasite, but that technique has a low sensitivity. The main purpose of the present work was to evaluate the PCR as a routine tool for the diagnosis of leishmaniasis. Biopsy specimens from cutaneous or mucosal lesions were taken from 230 individuals from areas where Leishmania is endemic: 216 patients who had a clinical picture suggestive of leishmaniasis and 14 individuals with cutaneous lesions due to other causes. Each specimen was processed for histopathologic examination, culture, touch preparation, and DNA isolation. Oligonucleotides that amplify the conserved region of the minicircle molecules of Leishmania were used in a hot-start PCR. While at least one conventional technique was positive for Leishmania for 62% (134 of 216) of the patients, PCR coupled to hybridization was positive for 94% (203 of 216) of the patients. The 14 patients whose clinical picture was not suggestive of leishmaniasis had negative results by all techniques. The impact of the PCR was striking in mucosal disease. While the disease in only 17% (4 of 24) of the patients could be diagnosed by conventional techniques, PCR was positive for 71% (17 of 24) of the patients. Hybridization showed that all cases of disease were caused by parasites belonging to the Viannia subgenus. Altogether, the results indicate that PCR is a valuable tool for the diagnosis of leishmaniasis on a routine basis and is likely to provide valuable epidemiological information about the disease in countries where it is endemic.     

Molecular epidemiology of Pseudomonas aeruginosa colonization in a burn unit: persistence of a multidrug-resistant clone and a silver sulfadiazine-resistant clone

To study the epidemiology of Pseudomonas aeruginosa colonization in a 32-bed burn wound center (BWC), 321 clinical and 45 environmental P. aeruginosa isolates were collected by prospective surveillance culture over a 1-year period and analyzed by serotyping, drug susceptibility testing, and amplified fragment length polymorphism (AFLP) analysis. Among 441 patients treated at the center, 70 (16%) were colonized with P. aeruginosa, including 12 (17%) patients who were colonized on admission and 58 (83%) patients who acquired the organism during their stay. Of the 48 distinct AFLP genotypes found, 21 were found exclusively in the environment, 15 were isolated from individual patients only, and 12 were responsible for the colonization of 57 patients, of which 2 were also isolated from the environment, but secondary to patient carriage. Polyclonal P. aeruginosa colonization with strains of two to four genotypes, often with different antibiotic susceptibility patterns, was observed in 19 patients (27%). Two predominant genotypes were responsible for recurrent outbreaks and the colonization of 42 patients (60% of all colonized patients). The strain with one of those genotypes appeared to be endemic to the BWC and developed multidrug resistance (MDR) at the end of the study period, whereas the strain with the other genotype was antibiotic susceptible but resistant to silver sulfadiazine (SSD(r)). The MDR strain was found at a higher frequency in sputum samples than the SSD(r) strain, which showed a higher prevalence in burn wound samples, suggesting that anatomic habitat selection was associated with adaptive resistance to antimicrobial drugs. Repeated and thorough surveys of the hospital environment failed to detect a primary reservoir for any of those genotypes. Cross-acquisition, resulting from insufficient compliance with infection control measures, was the major route of colonization in our BWC. In addition to the AFLP pattern and serotype, analysis of the nucleotide sequences of three (lipo)protein genes (oprI, oprL, and oprD) and the pyoverdine type revealed that all predominant strains except the SSD(r) strain belonged to recently identified clonal complexes. These successful clones are widespread in nature and therefore predominate in the patient population, in whom variants accumulate drug resistance mechanisms that allow their transmission and persistence in the BWC.     

Genetic diversity of porcine enteric caliciviruses in pigs raised in Rio de Janeiro State, Brazil

Porcine enteric caliciviruses (PEC) belong to the genera Norovirus and Sapovirus within the family Caliciviridae. They are enteric pathogens and are considered potential zoonotic agents. In this study, the circulation of PEC was evaluated by RT-PCR of stool samples and intestinal contents of pigs raised in Rio de Janeiro State, Brazil. Both porcine norovirus (PoNoV) and porcine sapovirus (PoSaV) were detected. The PoNoV strains were classified as genogroup II, genotypes 11, 18 and 19. The PoSaV strains were classified as genogroups III and VII, though some strains could not be classified into any established genogroup, potentially representing a new one. PEC were detected mainly in animals without clinical signs of gastroenteritis.     

NGS-based typings for 7 HLA loci in three populations from Rio de Janeiro,RJ, Brazil

We investigated HLA class I (HLA-A, -B, and -C) and class II (HLA-DRB1, -DQB1, -DPA1, and -DPB1) alleles by NGS-based typing among 759 Brazilian individuals from three populations in the Rio de Janeiro city based on their self-declared skin color (Caucasian, N = 521, AFND-ID: 3730; Parda, N = 170, AFND-ID: 3728; Black, N = 68, AFND-ID: 3727) to calculate allelic and haplotypic frequencies, plus linkage disequilibrium. Only HLA-DRB1 locus deviated from Hardy-Weinberg equilibrium (in Caucasian and Black populations). The three populations shared the most frequent allele on HLA-A, -C, -DRB1, -DPA1, and -DPB1. Genotype and frequency data are available in the Allele Frequencies Net Database.     

Discovery of a novel Mycobacterium tuberculosis lineage that is a major cause of tuberculosis in Rio de Janeiro, Brazil

The current study evaluated Mycobacterium tuberculosis isolates from Rio de Janeiro, Brazil, for genomic deletions. One locus in our panel of PCR targets failed to amplify in approximately 30% of strains. A single novel long sequence polymorphism (>26.3 kb) was characterized and designated RD(Rio). Homologous recombination between two similar protein-coding genes is proposed as the mechanism for deleting or modifying 10 genes, including two potentially immunogenic PPE proteins. The flanking regions of the RD(Rio) locus were identical in all strains bearing the deletion. Genetic testing by principal genetic group, spoligotyping, variable-number tandem repeats of mycobacterial interspersed repetitive units (MIRU-VNTR), and IS6110-based restriction fragment length polymorphism analysis cumulatively support the idea that RD(Rio) strains are derived from a common ancestor belonging solely to the Latin American-Mediterranean spoligotype family. The RD(Rio) lineage is therefore the predominant clade causing tuberculosis (TB) in Rio de Janeiro and, as indicated by genotypic clustering in MIRU-VNTR analysis, the most significant source of recent transmission. Limited retrospective reviews of bacteriological and patient records showed a lack of association with multidrug resistance or specific risk factors for TB. However, trends in the data did suggest that RD(Rio) strains may cause a form of TB with a distinct clinical presentation. Overall, the high prevalence of this genotype may be related to enhanced virulence, transmissibility, and/or specific adaptation to a Euro-Latin American host population. The identification of RD(Rio) strains outside of Brazil points to the ongoing intercontinental dissemination of this important genotype. Further studies are needed to determine the differential strain-specific features, pathobiology, and worldwide prevalence of RD(Rio) M. tuberculosis.