Genomic Insights into the expansion of Carbapenem-Resistant Klebsiella pneumoniae within Portuguese Hospitals

Carbapenem-resistant Klebsiella pneumoniae complex (CR-KP) are a public health concern, causing infections with a high mortality rate, limited therapeutic options and challenging infection control strategies. In Portugal CR-KP rate has increased steeply, but the factors associated to this expansion are poorly explored. To address this question we compared, by phylogenetic and resistome analysis, the draft genomes of 200 CR-KP isolates collected in 2017-2019 from five hospitals in the Lisbon region, Portugal. We found that CR-KP belonged mainly to ST13 (29%), ST17 (15%), ST348 (13%), ST231 (12%) and ST147 (7%). Carbapenem resistance was conferred mostly by KPC-3 (74%) or OXA-181 (18%) presence, which were associated with IncF/IncN and IncX plasmids, respectively. Almost all isolates were multidrug resistant harbouring resistance determinants to aminoglycosides, beta-lactams, trimethoprim, fosfomycin, quinolones and sulphonamides. In addition, 11% of isolates were resistant to colistin. Colonizing and infection isolates were highly related and most colonized patients (89%) reported a previous hospitalization. Moreover, among the 171 events of cross-dissemination identified, by cgMLST data analysis (<5 alleles), 41 occurred between different hospitals and 130 within the same hospital. Our results suggest that CR-KP dissemination in the Lisbon region result from acquisition of carbapenemases in mobile genetic elements, influx of CR-KP into the hospitals by colonized ambulatory patients and transmission of CR-KP within and between hospitals. Our data reinforces that the prudent use of carbapenems, patients screening at hospital entrance, and improvement of infection control will be needed to decrease the burden of CR-KP infection in Portugal.

In-hospital mortality during the wild-type, alpha, delta, and omicron SARS-CoV-2 waves: a multinational cohort study in the EuCARE project

Background

Investigating outcomes of hospitalised COVID-19 patients throughout the pandemic is crucial to understand the impact of different SARS-CoV-2 variants. We compared 28-day in-hospital mortality of Wild-type, Alpha, Delta, and Omicron variant infections. Whether the difference in risk by variant varied by age was also evaluated.

Methods

We conducted a cohort study including patients ≥18 years, hospitalised between 2020 and 02-01 and 2022-10-15 with a SARS-CoV-2 positive test, from nine countries. Variant was classified based on sequenced viruses or from national public metadata. Mortality was compared using the cumulative incidence function and subdistribution hazard ratios (SHR) adjusted for age, sex, calendar time, and comorbidities. Results were shown age-stratified due to effect measure modification (P < 0.0001 for interaction between age and variant).

Findings

We included 38,585 participants: 19,763 Wild-type, 6387 Alpha, 3640 Delta, and 8795 Omicron. The cumulative incidence of mortality decreased throughout the study period. Among participants ≥70 years, the adjusted SHR (95% confidence interval) for Delta vs. Omicron was 1.66 (1.29-2.13). This estimate was 1.66 (1.17-2.36) for Alpha vs. Omicron, and 1.34 (0.92-1.95) for Wild-type vs. Omicron. These were 1.21 (0.81-1.82), 1.21 (0.68-2.17), and 0.98 (0.53-1.82) among unvaccinated participants. When comparing Omicron sublineages, the aSHR for BA.1 was 1.92 (1.43-2.58) compared to BA.2 and 1.52 (1.11-2.08) compared to BA.5.

Interpretation

The herein observed decrease in in-hospital mortality seems to reflect a combined effect of immunity from vaccinations and previous infections, although differences in virulence between SARS-CoV-2 variants may also have contributed.

Funding

European Union's Horizon Europe Research and Innovation Programme.

Characterization of Lophomonas spp. Infection in a Population of Critical Care Patients

Lophomonas are flagellated protozoa that have been increasingly associated with upper and lower airway infection in humans. The prevalence and characterization of this disease in the critically ill remains poorly understood. We present a series of eleven ICU patients with confirmed Lophomonas spp. identification in respiratory samples.

European candidaemia is characterised by notable differential epidemiology and susceptibility pattern: Results from the ECMM Candida III study

The objectives of this study were to assess Candida spp. distribution and antifungal resistance of candidaemia across Europe. Isolates were collected as part of the third ECMM Candida European multicentre observational study, conducted from 01 to 07-07-2018 to 31-03-2022. Each centre (maximum number/country determined by population size) included ∼10 consecutive cases. Isolates were referred to central laboratories and identified by morphology and MALDI-TOF, supplemented by ITS-sequencing when needed. EUCAST MICs were determined for five antifungals. fks sequencing was performed for echinocandin resistant isolates. The 399 isolates from 41 centres in 17 countries included C. albicans (47.1%), C. glabrata (22.3%), C. parapsilosis (15.0%), C. tropicalis (6.3%), C. dubliniensis and C. krusei (2.3% each) and other species (4.8%). Austria had the highest C. albicans proportion (77%), Czech Republic, France and UK the highest C. glabrata proportions (25-33%) while Italy and Turkey had the highest C. parapsilosis proportions (24-26%). All isolates were amphotericin B susceptible. Fluconazole resistance was found in 4% C. tropicalis, 12% C. glabrata (from six countries across Europe), 17% C. parapsilosis (from Greece, Italy, and Turkey) and 20% other Candida spp. Four isolates were anidulafungin and micafungin resistant/non-wild-type and five resistant to micafungin only. Three/3 and 2/5 of these were sequenced and harboured fks-alterations including a novel L657W in C. parapsilosis. The epidemiology varied among centres and countries. Acquired echinocandin resistance was rare but included differential susceptibility to anidulafungin and micafungin, and resistant C. parapsilosis. Fluconazole and voriconazole cross-resistance was common in C. glabrata and C. parapsilosis but with different geographical prevalence.

EuCARE-hospitalised study protocol: a cohort study of patients hospitalised with COVID-19 in the EuCARE project

BACKGROUND

Severe acute respiratory syndrome coronavirus 2 (SARS CoV-2), the virus responsible for coronavirus disease 2019 (COVID-19), can lead to hospitalisation, particularly in elderly, immunocompromised, and non-vaccinated or partially vaccinated individuals. Although vaccination provides protection, the duration of this protection wanes over time. Additional doses can restore immunity, but the influence of viral variants, specific sequences, and vaccine-induced immune responses on disease severity remains unclear. Moreover, the efficacy of therapeutic interventions during hospitalisation requires further investigation. The study aims to analyse the clinical course of COVID-19 in hospitalised patients, taking into account SARS-CoV-2 variants, viral sequences, and the impact of different vaccines. The primary outcome is all-cause in-hospital mortality, while secondary outcomes include admission to intensive care unit and length of stay, duration of hospitalisation, and the level of respiratory support required.

METHODS

This ongoing multicentre study observes hospitalised adult patients with confirmed SARS-CoV-2 infection, utilising a combination of retrospective and prospective data collection. It aims to gather clinical and laboratory variables from around 35,000 patients, with potential for a larger sample size. Data analysis will involve biostatistical and machine-learning techniques. Selected patients will provide biological material. The study started on October 14, 2021 and is scheduled to end on October 13, 2026.

DISCUSSION

The analysis of a large sample of retrospective and prospective data about the acute phase of SARS CoV-2 infection in hospitalised patients, viral variants and vaccination in several European and non-European countries will help us to better understand risk factors for disease severity and the interplay between SARS CoV-2 variants, immune responses and vaccine efficacy. The main strengths of this study are the large sample size, the long study duration covering different waves of COVID-19 and the collection of biological samples that allows future research.

TRIAL REGISTRATION

The trial has been registered on ClinicalTrials.gov. The unique identifier assigned to this trial is NCT05463380.

Pantoea in Peritoneal Dialysis: A Rare Cause of Peritonitis

Peritonitis is the most common complication of peritoneal dialysis (PD) and an important cause of PD failure. There are numerous etiological agents, mostly bacteria. Pantoea spp is a rare cause of peritonitis.

We describe three cases of Pantoea peritonitis in three PD patients. Previous reports have identified risk factors such as close contact with plants and animals. We review the typical clinical presentation and prognosis. It is fulcral to teach patients about the risks regarding proximity to plants and animals to prevent this type of infection.

Deep dermatophytosis caused by Trichophyton rubrum in immunocompromised patients

In immunosuppressed patients, dermatophytosis can be more invasive, affecting the dermis and subcutaneous tissues. The authors describe the cases of two patients with kidney and heart transplanted, respectively, that developed a deep dermatophytosis caused by Trichophyton rubrum, confirmed by culture and DNA sequencing. Both patients had concomitant onychomycosis, and both were treated with itraconazole for about two months, which was interrupted due to pharmacological interactions with the immunosuppressive drugs and switched to terbinafine, leading to clinical resolution within four months. Deep dermatophytosis should be considered when dealing with immunocompromised patients, especially when a superficial dermatophytosis is present. Oral treatment is necessary and terbinafine is a preferable option in solid organ transplant recipients because it has less pharmacological interactions.

Imported Malaria in Portugal: Prevalence of Polymorphisms in the Anti-Malarial Drug Resistance Genes pfmdr1 and pfk13

Malaria is one of the ‘big three’ killer infectious diseases, alongside tuberculosis and HIV. In non-endemic areas, malaria may occur in travelers who have recently been to or visited endemic regions. The number of imported malaria cases in Portugal has increased in recent years, mostly due to the close relationship with the community of Portuguese language countries. Samples were collected from malaria-infected patients attending Centro Hospitalar Lisboa Ocidental (CHLO) or the outpatient clinic of Instituto de Higiene e Medicina Tropical (IHMT-NOVA) between March 2014 and May 2021. Molecular characterization of Plasmodium falciparum pfk13 and pfmdr1 genes was performed. We analyzed 232 imported malaria cases. The majority (68.53%) of the patients came from Angola and only three patients travelled to a non-African country; one to Brazil and two to Indonesia. P. falciparum was diagnosed in 81.47% of the cases, P. malariae in 7.33%, P. ovale 6.47% and 1.72% carried P. vivax. No mutations were detected in pfk13. Regarding pfmdr1, the wild-type haplotype (N86/Y184/D1246) was also the most prevalent (64.71%) and N86/184F/D1246 was detected in 26.47% of the cases. The typical imported malaria case was middle-aged male, traveling from Angola, infected with P. falciparum carrying wild type pfmdr1 and pfk13. Our study highlights the need for constant surveillance of malaria parasites imported into Portugal as an important pillar of public health.

Foodborne Origin and Local and Global Spread of Staphylococcus saprophyticus Causing Human Urinary Tract Infections

Staphylococcus saprophyticus is a primary cause of community-acquired urinary tract infections (UTIs) in young women. S. saprophyticus colonizes humans and animals but basic features of its molecular epidemiology are undetermined. We conducted a phylogenomic analysis of 321 S. saprophyticus isolates collected from human UTIs worldwide during 1997–2017 and 232 isolates from human UTIs and the pig-processing chain in a confined region during 2016–2017. We found epidemiologic and genomic evidence that the meat-production chain is a major source of S. saprophyticus causing human UTIs; human microbiota is another possible origin. Pathogenic S. saprophyticus belonged to 2 lineages with distinctive genetic features that are globally and locally disseminated. Pangenome-wide approaches identified a strong association between pathogenicity and antimicrobial resistance, phages, platelet binding proteins, and an increased recombination rate. Our study provides insight into the origin, transmission, and population structure of pathogenic S. saprophyticus and identifies putative new virulence factors.

Staphylococcus saprophyticus From Clinical and Environmental Origins Have Distinct Biofilm Composition

Biofilm formation has been shown to be critical to the success of uropathogens. Although Staphylococcus saprophyticus is a common cause of urinary tract infections, its biofilm production capacity, composition, genetic basis, and origin are poorly understood. We investigated biofilm formation in a large and diverse collection of S. saprophyticus (n = 422). Biofilm matrix composition was assessed in representative strains (n = 63) belonging to two main S. saprophyticus lineages (G and S) recovered from human infection, colonization, and food-related environment using biofilm detachment approach. To identify factors that could be associated with biofilm formation and structure variation, we used a pangenome-wide association study approach. Almost all the isolates (91%; n = 384/422) produced biofilm. Among the 63 representative strains, we identified eight biofilm matrix phenotypes, but the most common were composed of protein or protein-extracellular DNA (eDNA)-polysaccharides (38%, 24/63 each). Biofilms containing protein-eDNA-polysaccharides were linked to lineage G and environmental isolates, whereas protein-based biofilms were produced by lineage S and infection isolates (p < 0.05). Putative biofilm-associated genes, namely, aas, atl, ebpS, uafA, sasF, sasD, sdrH, splE, sdrE, sdrC, sraP, and ica genes, were found with different frequencies (3-100%), but there was no correlation between their presence and biofilm production or matrix types. Notably, icaC_1 was ubiquitous in the collection, while icaR was lineage G-associated, and only four strains carried a complete ica gene cluster (icaADBCR) except one that was without icaR. We provided evidence, using a comparative genomic approach, that the complete icaADBCR cluster was acquired multiple times by S. saprophyticus and originated from other coagulase-negative staphylococci. Overall, the composition of S. saprophyticus biofilms was distinct in environmental and clinical isolates, suggesting that modulation of biofilm structure could be a key step in the pathogenicity of these bacteria. Moreover, biofilm production in S. saprophyticus is ica-independent, and the complete icaADBCR was acquired from other staphylococci.

Transcontinental Dissemination of the L2b/D-Da Recombinant Chlamydia trachomatis Lymphogranuloma venereum (LGV) Strain: Need of Broad Multi-Country Molecular Surveillance

Previously, we identified a Chlamydia trachomatis lymphogranuloma venereum (LGV) recombinant strain possessing a non-LGV ompA genotype. Here, culture-independent genome sequencing confirms its circulation in Europe, Middle East, and North America, and unveils emergence of antibiotic resistance. Broad surveillance is needed.

Trends on Aspergillus Epidemiology-Perspectives from a National Reference Laboratory Surveillance Program

Identification of Aspergillus to species level is important since sibling species may display variable susceptibilities to multiple antifungal drugs and also because correct identification contributes to improve the knowledge of epidemiological studies. Two retrospective laboratory studies were conducted on Aspergillus surveillance at the Portuguese National Mycology Reference Laboratory. The first, covering the period 2017–2018, aimed to study the molecular epidemiology of 256 Aspergillus isolates obtained from patients with respiratory, subcutaneous, or systemic infections and from environmental samples. The second, using our entire collection of clinical and environmental A. fumigatus isolates (N = 337), collected between 2012 and 2019, aimed to determine the frequency of azole-resistant A. fumigatus isolates. Aspergillus fumigatus sensu stricto was the most frequent species in both clinical and environmental samples. Overall, and considering all Aspergillus sections identified, a high frequency of cryptic species was detected, based on beta-tubulin or calmodulin sequencing (37% in clinical and 51% in environmental isolates). Regarding all Fumigati isolates recovered from 2012–2019, the frequency of cryptic species was 5.3% (18/337), with the identification of A. felis (complex), A. lentulus, A. udagawae, A. hiratsukae, and A. oerlinghauensis. To determine the frequency of azole resistance of A. fumigatus, isolates were screened for azole resistance using azole-agars, and 53 possible resistant isolates were tested by the CLSI microdilution reference method. Nine A. fumigatus sensu stricto and six Fumigati cryptic isolates showed high minimal inhibitory concentrations to itraconazole, voriconazole, and/or posaconazole. Real-time PCR to detect cyp51A mutations and sequencing of cyp51A gene and its promoter were performed. The overall frequency of resistance to azoles in A. fumigatus sensu stricto was 3.0%. With this retrospective analysis, we were able to detect one azole-resistant G54R mutant A. fumigatus environmental isolate, collected in 2015. The TR₃₄/L98H mutation, linked to environmental transmission route of azole resistance, was the most frequently detected mutation (N = 4; 1.4%). Our findings underline the demand for correct identification and susceptibility testing of Aspergillus isolates.

Short Communication: HIV and Tuberculosis Co-Infection Among Migrants in Portugal: A Brief Study on Their Sociodemographic, Clinical, and Genomic Characteristics

HIV and tuberculosis (TB) are among the global deadliest diseases. Migrant populations are particularly vulnerable to these infections. Yet, literature is still scarce on the epidemiology of HIV-TB co-infection among migrants. In this study, we characterized native and migrant HIV patients followed in Portuguese hospitals, who were diagnosed with TB, regarding their sociodemographic, clinical, and genomic characteristics. Among 67 patients with HIV and TB diagnoses, there were 24 migrants, most from sub-Saharan Africa. Most patients had CD4+ T cell counts below 350 cells/μL, and were diagnosed simultaneously for HIV and TB. When compared to natives, migrants presented a higher proportion of non-B HIV-1 infections. Patients infected with these non-B HIV-1 strains presented higher viral loads, which can have an important impact for the transmissibility and pathogenicity of both diseases. Future studies should investigate different HIV strains and consequences for TB and HIV transmission and disease outcomes, especially among vulnerable populations.

Distinct epidemiology and resistance mechanisms affecting ceftolozane/tazobactam in Pseudomonas aeruginosa isolates recovered from ICU patients in Spain and Portugal depicted by WGS

Objectives

To analyse the epidemiology, the resistome and the virulome of ceftolozane/tazobactam-susceptible or -resistant Pseudomonas aeruginosa clinical isolates recovered from surveillance studies in Portugal (STEP, 2017–18) and Spain (SUPERIOR, 2016–17).

Methods

P. aeruginosa isolates were recovered from intra-abdominal, urinary tract and lower respiratory tract infections in ICU patients admitted to 11 Portuguese and 8 Spanish hospitals. MICs were determined (ISO-standard broth microdilution, EUCAST 2020 breakpoints). A subset of 28 ceftolozane/tazobactam-resistant P. aeruginosa isolates were analysed and compared with 28 ceftolozane/tazobactam-susceptible P. aeruginosa strains by WGS.

Results

Clonal complex (CC) 235 (27%) and CC175 (18%) were the most frequent, followed by CC244 (13%), CC348 (9%), CC253 (5%) and CC309 (5%). Inter-hospital clonal dissemination was observed, limited to a geographical region (CC235, CC244, CC348 and CC253 in Portugal and CC175 and CC309 in Spain). Carbapenemases were detected in 25 isolates (45%): GES-13 (13/25); VIM type (10/25) [VIM-2 (4/10), VIM-20 (3/10), VIM-1 (2/10) and VIM-36 (1/10)]; and KPC-3 (2/25). GES-13-CC235 (13/15) and VIM type-CC175 (5/10) associations were observed. Interestingly, KPC-3 and VIM-36 producers showed ceftolozane/tazobactam-susceptible phenotypes. However, ceftolozane/tazobactam resistance was significantly associated with GES-13 and VIM-type carbapenemase production. Six non-carbapenemase producers also displayed ceftolozane/tazobactam resistance, three of them showing known ceftolozane/tazobactam resistance-associated mutations in the PBP3 gene, ftsI (R504C and F533L). Overall, an extensive virulome was identified in all P. aeruginosa isolates, particularly in carbapenemase-producing strains.

Conclusions

GES-13-CC235 and VIM type-CC175 were the most frequent MDR/XDR P. aeruginosa clones causing infections in Portuguese and Spanish ICU patients, respectively. Ceftolozane/tazobactam resistance was mainly due to carbapenemase production, although mutations in PBP-encoding genes may additionally be involved.

OP0317 ACCURACY OF THE OMERACT DEFINITIONS FOR IDENTIFICATION OF CALCIUM PYROPHOSPHATE CRYSTALS WITH ULTRASOUND: FINAL RESULTS OF THE OMERACT US IN CPPD SUB-TASK FORCE STUDY

Background:

The OMERACT Ultrasound (US) in calcium pyrophosphate deposition disease (CPPD) sub-task force has been working on the use of US in CPPD since 2014 first creating definitions for CPPD identification and then assessing the reliability[1].

Objectives:

Objective of this study is to assess the diagnostic accuracy (truth) of US in CPPD.

Methods:

Consecutive patients waiting to undergo knee replacement surgery due to osteoarthritis were enrolled in 12 centres from 6 countries. Each patient underwent US examination of the knee, focusing on the menisci and the hyaline cartilage, the day prior to surgery, scoring each site for presence/absence of CPP as defined previously[1]. After surgery, the menisci and the condyles were retrieved and examined microscopically. Six samples were collected, both from the surface and from the internal part of menisci and cartilage trying to cover a large part of it. All slides were observed under transmitted light microscopy and by compensated polarised microscopy. A dichotomous score was given for the presence/absence of CPP. US and microscopic analysis were performed by different operators, blind to each other’s findings. Sensitivity and specificity of US were calculated using microscopic findings as the gold standard.

Results:

101 patients have been enrolled in the study. 33 patients have been excluded due to loss of anatomical pieces at surgery. The mean age of the remaining 68 pts was 71yo (±8), 44 women, 34 were affected by CPPD according to microscopy. Overall and per site diagnostic US accuracy results are presented in table 1

Diagnostic accuracySensitivitySpecificityPositive Predictive valueNegative Predictive valueGlobal0.750.910.590.690.87Medial meniscus0.820.870.770.770.87Lateral meniscus0.750.830.680.680.83Medial cartilage0.860.790.920.880.85Lateral cartilage0.820.710.880.770.84Medial side (combined cartilage and meniscus)0.820.880.760.790.87Lateral side (combined cartilage and meniscus)0.780.880.690.730.86

Conclusion:

Our results demonstrate that US is an accurate exam for identification of CPPD. The best combination of sensitivity and specificity is achieved by examining the medial aspect of the knee.

References:

[1]Filippou G, Scirè CA, Adinolfi A,et al.Identification of calcium pyrophosphate deposition disease (CPPD) by ultrasound: reliability of the OMERACT definitions in an extended set of joints—an international multiobserver study by the OMERACT Calcium Pyrophosphate Deposition Disease Ultrasound Subtask Force.Ann Rheum Dis2018;:annrheumdis-2017-212542. doi:10.1136/annrheumdis-2017-212542

Disclosure of Interests:

Georgios Filippou: None declared, Anna Scanu: None declared, Antonella Adinolfi: None declared, Carmela Toscano: None declared, Dario Gambera: None declared, Raquel Largo: None declared, Esperanza Naredo: None declared, Emilio Calvo: None declared, Gabriel Herrero-Beaumont: None declared, Pascal Zufferey: None declared, Christel Madelaine-Bonjour: None declared, Daryl MacCarter: None declared, Stanley Makman: None declared, Zachary Weber: None declared, Fabiana Figus: None declared, Ingrid Möller: None declared, Marwin Gutierrez: None declared, Carlos Pineda: None declared, Denise Clavijo Cornejo: None declared, Héctor García: None declared, Victor Ilizaliturri: None declared, Jaime Mendoza Torres: None declared, Raul Pichardo: None declared, Luis Carlos Rodriguez Delgado: None declared, Emilio Filippucci Speakers bureau: Dr. Filippucci reports personal fees from AbbVie, personal fees from Bristol-Myers Squibb, personal fees from Celgene, personal fees from Roche, personal fees from Union Chimique Belge Pharma, personal fees from Pfizer, outside the submitted work., Edoardo Cipolletta: None declared, Teodora Serban: None declared, Catalin Cirstoiu: None declared, Florentin Ananu Vreju: None declared, Dun Grecu: None declared, Gael Mouterde: None declared, Marcello Govoni: None declared, Leonardo Punzi: None declared, Nemanja Damjanov Grant/research support from: from AbbVie, Pfizer, and Roche, Consultant of: AbbVie, Gedeon Richter, Merck, Novartis, Pfizer, and Roche, Speakers bureau: AbbVie, Gedeon Richter, Merck, Novartis, Pfizer, and Roche, Lene Terslev Speakers bureau: LT declares speakers fees from Roche, MSD, BMS, Pfizer, AbbVie, Novartis, and Janssen., Carlo Alberto Scirè: None declared, Annamaria Iagnocco Grant/research support from: Abbvie, MSD and Alfasigma, Consultant of: AbbVie, Abiogen, Alfasigma, Biogen, BMS, Celgene, Eli-Lilly, Janssen, MSD, Novartis, Sanofi and Sanofi Genzyme, Speakers bureau: AbbVie, Alfasigma, BMS, Eli-Lilly, Janssen, MSD, Novartis, Sanofi

Epidemiology and genetic variability of respiratory syncytial virus in Portugal, 2014-2018

INTRODUCTION

Respiratory syncytial virus (RSV) is associated with substantial morbidity and mortality since it is a predominant viral agent causing respiratory tract infections in infants, young children and the elderly. Considering the availability of the RSV vaccines in the coming years, molecular understanding in RSV is necessary.

OBJECTIVE

The objective of the present study was to describe RSV epidemiology and genotype variability in Portugal during the 2014/15-2017/18 period.

MATERIAL AND METHODS

Epidemiological data and RSV-positive samples from patients with a respiratory infection were collected through the non-sentinel and sentinel influenza surveillance system (ISS). RSV detection, subtyping in A and B, and sequencing of the second hypervariable region (HVR2) of G gene were performed by molecular methods. Phylogenetic trees were generated using the Neighbor-Joining method and p-distance model on MEGA 7.0.

RESULTS

RSV prevalence varied between the sentinel (2.5%, 97/3891) and the non-sentinel ISS (20.7%, 3138/16779), being higher (P < 0.0001) among children aged <5 years. Bronchiolitis (62.9%, 183/291) and influenza-like illness (24.6%, 14/57) were associated (P < 0.0001) with RSV laboratory confirmation among children aged <6 months and adults ≥65 years, respectively. The HVR2 was sequenced for 562 samples. RSV-A (46.4%, 261/562) and RSV-B (53.6%, 301/562) strains clustered mainly to ON1 (89.2%, 233/261) and BA9 (92%, 277/301) genotypes, respectively, although NA1 and BA10 were also present until 2015/2016.

CONCLUSION

The sequence and phylogenetic analysis reflected the relatively high diversity of Portuguese RSV strains. BA9 and ON1 genotypes, which have been circulating in Portugal since 2010/2011 and 2011/2012 respectively, predominated during the whole study period.

Genomic Study of a Clostridium difficile Multidrug Resistant Outbreak-Related Clone Reveals Novel Determinants of Resistance

Background:Clostridium difficile infection (CDI) is prevalent in healthcare settings. The emergence of hypervirulent and antibiotic resistant strains has led to an increase in CDI incidence and frequent outbreaks. While the main virulence factors are the TcdA and TcdB toxins, antibiotic resistance is thought to play a key role in the infection by and dissemination of C. difficile.

Methods: A CDI outbreak involving 12 patients was detected in a tertiary care hospital, in Lisbon, which extended from January to July, with a peak in February, in 2016. The C. difficile isolates, obtained from anaerobic culture of stool samples, were subjected to antimicrobial susceptibility testing with Etest^®strips against 11 antibiotics, determination of toxin genes profile, PCR-ribotyping, multilocus variable-number tandem-repeat analysis (MLVA) and whole genome sequencing (WGS).

Results: Of the 12 CDI cases detected, 11 isolates from 11 patients were characterized. All isolates were tcdA^-/tcdB⁺ and belonged to ribotype 017, and showed high level resistance to clindamycin, erythromycin, gentamicin, imipenem, moxifloxacin, rifampicin and tetracycline. The isolates belonged to four genetically related MLVA types, with six isolates forming a clonal cluster. Three outbreak isolates, each from a different MLVA type, were selected for WGS. Bioinformatics analysis showed the presence of several antibiotic resistance determinants, including the Thr82Ile substitution in gyrA, conferring moxifloxacin resistance, the substitutions His502Asn and Arg505Lys in rpoB for rifampicin resistance, the tetM gene, associated with tetracycline resistance, and two genes encoding putative aminoglycoside-modifying enzymes, aadE and aac(6′)-aph(2″). Furthermore, a not previously described 61.3 kb putative mobile element was identified, presenting a mosaic structure and containing the genes ermG, mefA/msrD and vat, associated with macrolide, lincosamide and streptogramins resistance. A substitution found in a class B penicillin-binding protein, Cys721Ser, is thought to contribute to imipenem resistance.

Conclusion: We describe an epidemic, tcdA^-/tcdB⁺, multidrug resistant clone of C. difficile from ribotype 017 associated with a hospital outbreak, providing further evidence that the lack of TcdA does not impair the infectious potential of these strains. We identified several determinants of antimicrobial resistance, including new ones located in mobile elements, highlighting the importance of horizontal gene transfer in the pathogenicity and epidemiological success of C. difficile.

Epidemiologia das infeções fúngicas superficiais em Portugal - revisão de 3 anos (2014-2016)

Introdução: As infeções fúngicas superficiais são as dermatoses infeciosas mais frequentes e a sua incidência continua a aumentar. Os dermatófitos são os principais agentes causais apresentando, contudo, uma distribuição geográfica variável.Material e Métodos: O presente estudo teve como objetivo a caracterização epidemiológica das infeções fúngicas superficiais diagnosticadas nos Serviços/Unidades de Dermatologia pertencentes ao Serviço Nacional de Saúde Português entre janeiro de 2014 e dezembro 2016 através da análise retrospetiva dos resultados das culturas realizadas durante esse período.Resultados: Foram estudados 2375 isolamentos, pertencentes a 2319 doentes. O dermatófito mais frequentemente isolado foi o Trichophyton rubrum (53,6%), tendo sido o principal agente causal da tinha da pele glabra (52,4%) e das onicomicoses (51,1%). Relativamente às tinhas do couro cabeludo, globalmente o Microsporum audouinii foi o agente mais prevalente (42,6%), seguido do Trichophyton soudanense (22,1%). Enquanto na área metropolitana de Lisboa estes dermatófitos foram os principais agentes de tinha do couro cabeludo, nas regiões Norte e Centro o agente mais frequente foi o Microsporum canis (58,5%). Os fungos leveduriformes foram os principais responsáveis pelas onicomicoses das mãos (76,7%).Conclusão: Os resultados deste estudo estão globalmente concordantes com a literatura científica. O Trichophyton rubrum apresenta-se como o dermatófito mais frequentemente isolado em cultura. Na tinha do couro cabeludo, na área metropolitana de Lisboa, as espécies antropofílicas de importação assumem particular destaque.

Assessing preschoolers interactive behaviour: A validation study of the "Coding System for Mother-Child Interaction"

BACKGROUND

The preschool years are a period of great developmental achievements, which impact critically on a child's interactive skills. Having valid and reliable measures to assess interactive behaviour at this stage is therefore crucial. The aim of this study was to describe the adaptation and validation of the child coding of the Coding System for Mother-Child Interactions and discuss its applications and implications in future research and practice.

METHODS

Two hundred twenty Portuguese preschoolers and their mothers were videotaped during a structured task. Child and mother interactive behaviours were coded based on the task. Maternal reports on the child's temperament and emotional and behaviour problems were also collected, along with family psychosocial information.

RESULTS

Interrater agreement was confirmed. The use of child Cooperation, Enthusiasm, and Negativity as subscales was supported by their correlations across tasks. Moreover, these subscales were correlated with each other, which supports the use of a global child interactive behaviour score. Convergent validity with a measure of emotional and behavioural problems (Child Behaviour Checklist 1 ½-5) was established, as well as divergent validity with a measure of temperament (Children's Behaviour Questionnaire-Short Form). Regarding associations with family variables, child interactive behaviour was only associated with maternal behaviour.

CONCLUSIONS

Findings suggest that this coding system is a valid and reliable measure for assessing child interactive behaviour in preschool age children. It therefore represents an important alternative to this area of research and practice, with reduced costs and with more flexible training requirements. Attention should be given in future research to expanding this work to clinical populations and different age groups.

Human gastric hyperinfection by Anisakis simplex: A severe and unusual presentation and a brief review

Anisakiasis is an emerging marine food-borne zoonosis resulting from the accidental ingestion of Anisakis larvae, through the consumption of raw or undercooked infected seafood products. The first case of human gastric hyperinfection by Anisakis simplex with an unusual and severe presentation, occurring in a Portuguese woman, is described in this article. Over 140 anisakid larvae were removed by gastroscopy. Massive infection is uncommon in areas where the consumption of raw fish is not part of the traditional diet, as is the case in Portugal. The increased consumption of raw seafood products is considered a health determinant in the rise in cases of anisakiasis. However, clinicians should be aware of the emergence of these infections, not only because of the new dietary habits of the population, but also because of the high prevalence of Anisakis larvae in the different fish species usually consumed by the population, collected on the Portuguese coast.

Prevention and Control of Antimicrobial Resistant Healthcare-Associated Infections: The Microbiology Laboratory Rocks!

In Europe, each year, more than four milion patients acquire a healthcare-associated infection (HAI) and almost 40 thousand die as a direct consequence of it. Regardless of many stategies to prevent and control HAIs, they remain an important cause of morbidity and mortality worldwide with a significant economic impact: a recent estimate places it at the ten billion dollars/year. The control of HAIs requires a prompt and efficient identification of the etiological agent and a rapid communication with the clinician. The Microbiology Laboratory has a significant role in the prevention and control of these infections and is a key element of any Infection Control Program. The work of the Microbiology Laboratory covers microbial isolation and identification, determination of antimicrobial susceptibility patterns, epidemiological surveillance and outbreak detection, education, and report of quality assured results. In this paper we address the role and importance of the Microbiology Laboratory in the prevention and control of HAI and in Antibiotic Stewardship Programs and how it can be leveraged when combined with the use of information systems. Additionally, we critically review some challenges that the Microbiology Laboratory has to deal with, including the selection of analytic methods and the proper use of communication channels with other healthcare services.

Molecular and epidemiologic study of Clostridium difficile reveals unusual heterogeneity in clinical strains circulating in different regions in Portugal

Clostridium difficile infection (CDI) represents a great healthcare burden in developed countries. The emergence of the epidemic PCR ribotype (RT) 027 and its acquired fluoroquinolones resistance have accentuated the need for an active surveillance of CDI. Here we report the first countrywide study of CDI in Portugal with the characterization of 498 C. difficile clinical isolates from 20 hospitals in four regions in Portugal regarding RT, virulence factors and antimicrobial susceptibility. We identified 96 RTs with marked variations between and within regions, as only six RTs appeared in all four regions. RT027 was the most frequent RT overall (18.5%) and among healthcare facility-associated isolates (19.6%), while RT014 was the most common among community-associated isolates (12%). The north showed a high RT diversity among isolates and a low moxifloxacin (MXF) resistance rate (11.9%), being the only region in which RT027 was not predominant. In contrast, the isolates from the centre presented the highest RT027 frequency, and 53.4% were resistant to MXF. Overall, MXF resistance (33.2%) was associated (p <0.001) with the presence of binary toxin genes and mutations in tcdC regardless of the RT. Both traits appeared in almost 30% of the strains. RT027 showed a reduced susceptibility to metronidazole (p <0.01), and RT126 had higher minimum inhibitory concentrations to vancomycin (p = 0.03) compared to other RTs. The present study highlights an unusual heterogeneity of RTs in Portugal, with a high frequency of hypervirulent RTs and the emergence of virulence factors in non-027 RTs, emphasizing the need for a surveillance system for CDI in Portugal.

Dirofilariasis by Dirofilaria repens: an imported case and a brief review

Human infections caused by Dirofilaria repens, a cosmopolitan zoonotic parasitosis endemic in Southern and Eastern Europe and Asia still is an underdiagnosed infection due to parasite identification difficulties. Here, we report the first human case of subcutaneous dirofilariasis by D. repens diagnosed in Portugal. This was probably an imported case from India, as judged by epidemiological and clinical data. With this presentation we aim to alert clinicians for the emergence of vector-borne zoonoses associated with global warming and international travel. This case showed that differential diagnosis of D. repens in subcutaneous nodules is needed, in order to avoid further complications.

Infeções do Trato Urinário numa Coorte de Transplantados Renais

<strong>Introduction:</strong> Urinary tract infection is the most common infectious complication following renal transplantation and its frequency is insufficiently studied in Portugal. The aim of this study was to characterize the incidence of urinary tract infections and recurrent urinary tract infections in renal transplant recipients.<br /><strong>Material and Methods:</strong> This was a retrospective cohort observational study, obtained from clinical files of all patients who received a renal transplant at the Hospital of Santa Cruz, from January 2004 to December 2005, with a mean follow-up period of five years or until date of graft loss, death or loss of follow-up. After a descriptive analysis of the population, we used bivariate tests to identify risk factors for urinary tract infections.<br /><strong>Results:</strong> A total of 127 patients were included, with a 593 patients.year follow-up. We detected 53 patients (41.7%) presenting with at least one episode of urinary tract infection; 21 patients (16.5%) had recurrent urinary tract infection. Female gender was the only risk factor associated with the occurrence of urinary tract infections (p &lt; 0.001, OR = 7.08, RR = 2.95) and recurrent urinary tract infections (p &lt; 0.001, OR = 4.66, RR = 2.83). Escherichia coli (51.6%), Klebsiella pneumoniae (15.5%) and Enterobacter spp (9.9%) were the<br />most frequently identified pathogens. Patients did not reveal an increased mortality or allograft loss. However, urinary tract infections were the most important cause of hospital admissions.<br /><strong>Discussion:</strong> Female gender was the only risk factor for urinary tract infections in this population. Escherichia coli was the most frequent agent isolated.<br /><strong>Conclusion:</strong> Despite preventive measures, urinary tract infections remain an important cause of morbidity and hospital admissions.<br /><strong>Keywords:</strong> Urinary Tract Infections; Postoperative Complications; Risk Factors; Kidney Transplantation; Portugal.

Permeation of naproxen from saturated solutions and commercial formulations through synthetic membranes

The release of naproxen through synthetic membranes, mounted in modified Franz-type diffusion cells, was evaluated, either from saturated solutions or from commercially available topical formulations containing 10% naproxen. The results obtained showed that the porous type synthetic membranes chosen (cellulose acetate and polyethersulphone) can be used for assessing product performance in quality control procedures. The formulations interacted with the solid membranes (silicone and EVA) to change their diffusional characteristics. However, transfer in the membrane, and not the formulation was rate controlling. These membranes could not therefore be used in assessing product release performance for quality control.

Orbital and spin photon angular momentum transfer in liquid crystals

All-optical angular control of the molecular alignment in liquid-crystal films is demonstrated using a laser beam having an elliptically shaped intensity profile. The material birefringence is unimportant, as proven by the fact that good alignment is obtained with unpolarized light. This raises the possibility of achieving optical angular control of transparent isotropic bodies. A general theoretical approach, based on light and matter angular momentum conservation, shows that the optical alignment is due to the internal compensation between the transfer of the orbital and the spin part of angular momentum of the incident photons to the material.

Topical delivery of caffeine from some commercial formulations

Permeation of caffeine through human skin and artificial membranes (mounted in modified Franz type diffusion cells) was evaluated, either from saturated solutions or from commercially available topical formulations (all containing 3% caffeine). Data interpretation of the caffeine diffusion through human skin does not implicate transfer through pores despite caffeine being a relatively polar molecule. No correlation was found between transfer though the synthetic membranes (cellulose acetate impregnated with isopropyl myristate and silicone rubber soaked in isopropyl myristate) and that observed through skin. The synthetic membranes can be used for assessing product performance in quality assurance but will give little indication of its performance in vivo. The study investigated the percutaneous permeation of caffeine through human skin in order to obtain a mechanistic interpretation of its route of permeation. Synthetic membranes were also examined to determine if they could be used as models for human skin. Different commercial formulations investigated to determine the significance of enhancement strategies.

[A case of retroperitoneal fibrosis with spontaneous regression]

Retroperitoneal fibrosis has an unknown pathogenesis. Medical treatment should be preferred to surgery. However, surgical treatment is required when an ureteral involvement is present. A case of retroperitoneal fibrosis with spontaneous regression is reported. Current knowledge on pathogenesis, diagnosis and preferred treatment is outlined.

[Multicenter study of isolated micro-organisms resistant to antimicrobials in 10 Portuguese hospitals in 1994]

In 1994, Microbiology Laboratories of ten Portuguese hospitals analysed isolated microorganisms found in blood and urine samples and studied antimicrobial susceptibilities of the most frequent bacterial pathogens. From 63780 blood samples, the most frequent were Staphylococcus spp. and from 69189 urine samples significant numbers of Escherichia coli, Enterococcus spp., Pseudomonas aeruginosa and Candida spp. were isolated. Escherichia coli strains (c.7000) revealed a low percentage of resistance to antibiotics with the exceptions of ampicillin (48%) and co-trimoxazol (25%). Klebsiella pneumoniae isolates (c.2000) revealed important resistance to ampicillin (98%), cephalotin (31%), co-trimoxazol (38%) and gentamicin (28%), while values for 3rd generation cephalosporins varied among hospitals, with several strains showing phenotype of extended-spectrum beta-lactamase. A great variation in resistance values of P. aeruginosa (c.4000) was found in relation to the antibiotics as well as to the hospitals. Resistance to methicillin in S. aureus (c.6000) was high, reaching an average of 47%, and it was even higher with S. epidermidis (c.3000) and S. haemolyticus (c.650). Only vancomycin was always active against these strains. In E. faecalis (c.2500) resistance was of 2% to ampicillin, 35% to gentamicin, 45% to streptomycin and 1% to vancomycin. E. faecium isolates (c.300) showed the most worrying results with 70% resistance to ampicillin, 42% to gentamicin, 59% to streptomycin and 9% (30 strains isolated in 5 hospitals) to vancomycin. Vancomycin resistant strains were also resistant to all other antibiotics.

[Carotid thromboendarterectomy: personal experience and review of the literature]

Carotid endoarterectomy (CEA) is known to prevent cerebrovascular accidents. Between February 1987 and December 1993 we performed 97 CEA on 82 patients (62 male and 20 female, median age 66 +/- 7.6 years) 95.1% reported previous hemispheric neurological accidents; 4.9% were asymptomatic. Operative indications for asymptomatic patients were high degree stenosis (> 70%) of the internal carotid artery and ulcerated plaques with a moderate degree (50%) of stenosis. Major events (transient ischemic attack and stroke) were recorded in 73.2% cases. Preoperative investigations consisted of Duplex scan, arteriography, and cerebral CT scan or NMR. Operative mortality was 2.06% (2 cases) and perioperative stroke was 5.1% (5 cases). The sensibility, sensitivity and accuracy of Duplex scan to detect ulcerated plaques was 88.7%, 85.2% and 87.5% respectively. At a median follow-up of 33 months (range 6-81 months) 74 (92.5%) patients are free of strokes whereas 1 patient died for stroke. In our series the annual incidence of stroke was 0.5%. Our results suggest that Duplex scan is a reliable exam to investigate the carotid axis and CEA is a safe operation that prevents future cerebrovascular accidents.

[Salivary IgA in a group of children with recurrent respiratory infections]

Salivary IgA were examined in a group of children with recurring respiratory infections (RRI) in order to complete research into the immunological profile of such children. IgA assays were performed in 21 children suffering from RRI both in the remission period (Summer) and during infections (Winter). No children revealed any real disorder in basic salivary IgA. Salivary IgA levels were however about ten times higher in the Winter (the infection period). In a control group of 15 healthy children in the same age range, IgA levels were also high in the winter but still lower than those found in the RRI group. It is therefore concluded that children with RRI do not, as has often been suggested, present any basic disorder in salivary IgA, but that the response of secretory IgA is far more sensitive to infection than the system as a whole.