Rare serotype c Haemophilus influenzae invasive isolate: characterization of the first case in Portugal.

We report for the first time in Portugal a serotype c Haemophilus influenzae isolated from an adult, with HIV-1 infection. Whole-genome sequencing characterized the isolate as clonal complex ST-7, albeit with a novel MLST (ST2754) due to a unique atpG profile. Integration of this genome with other available H. influenzae serotype c genomes from PubMLST revealed its overall genetic distinctiveness, with the closest related isolate being identified in France in 2020. This surveillance study, involving collaboration among hospitals and reference laboratory, successfully contributed to the identification and characterization of this rare serotype.

Sustained increase of paediatric invasive Streptococcus pyogenes infections dominated by M1UK and diverse emm12 isolates, Portugal, September 2022 to May 2023.

Since autumn 2022, observed numbers of paediatric invasive group A Streptococcus infections in Portugal (n = 89) were higher than in pre-COVID-19 seasons. Between September 2022 and May 2023, the dominant diagnoses were pneumonia (25/79), mostly with empyema (20/25), and sepsis (22/79). A number of cases required admission to intensive care (27/79) and surgery (35/79), and the case fatality rate was 5.1% (4/79). Genomic sequencing (n = 55) revealed multiple genetic lineages, dominated by the M1UK sublineage (26/55) and more diverse emm12 isolates (12/55).

Haemophilus influenzae Type b Vaccine Failure in Portugal: A Nationwide Multicenter Pediatric Survey.

BACKGROUND: Despite the high effectiveness of the Haemophilus influenzae type b (Hib) vaccine in preventing invasive disease (ID) in children, Hib vaccine failures (VFs) cases may still occur. This study aimed to characterize the Hib-VF cases in Portugal in a 12-year period and trying to identify the possible associated risk factors. METHODS: Prospective descriptive nationwide surveillance study. Bacteriologic and molecular studies were performed at the same Reference Laboratory. Clinical data were collected by the referring pediatrician. RESULTS: Hib was identified in 41 children with ID and 26 (63%) were considered VF. Nineteen (73%) cases occurred in children less than 5 years old; 12 (46%) occurred before the Hib vaccine booster dose at 18 months of age. Comparing the first and the last 6-year periods of the study, the incidence rate of Hib, VF and total H. influenzae (Hi) ID significantly raised ( P < 0.05). VF cases corresponded, respectively, to 13.5% (7/52) and 22% (19/88) of total Hi-ID cases ( P = 0.232). Two children died due to epiglottitis and 1 acquired sensorineural hearing loss. Only 1 child had an inborn error of immunity. The immunologic workup performed in 9 children revealed no significant abnormalities. All 25 Hib-VF strains analyzed belonged to the same clonal complex 6. CONCLUSIONS: In Portugal, more than 95% of children are vaccinated against Hib, but severe Hib-ID cases still occur. No predisposing factors were clearly identified to justify the increased number of VF in recent years. Along with continued Hi-ID surveillance, Hib colonization and serologic studies should be implemented.

Haemophilus influenzae Carriage among Healthy Children in Portugal, 2015-2019.

Haemophilus influenzae is an important cause of mucosal and invasive infections and a common colonizer of the upper respiratory tract. As there are no recent data on H. influenzae carriage in Portugal, we aimed to characterize carriage samples and investigate possible parallelisms with disease isolates. Between 2016-2019, 1524 nasopharyngeal samples were obtained from children (0-6 years) attending day-care. H. influenzae were serotyped and screened for ß-lactamase production. Strains producing ß-lactamase and/or those that were encapsulated were further characterized by antibiotype; encapsulated strains were also investigated for MLST and the presence of antimicrobial resistance and virulence genes (extracted from whole genome sequencing). The overall carriage rate was 84.1%. Most isolates (96.7%) were nonencapsulated. Encapsulated strains were of serotypes f (1.8%), e (1.1%), a (0.3%), and b (0.1%). MLST showed clonality within serotypes. Although the lineages were the same as those that were described among disease isolates, colonization isolates had fewer virulence determinants. Overall, 7.5% of the isolates were ß-lactamase positive; one isolate had blaTEM-82, which has not been previously described in H. influenzae. A single isolate, which was identified as H. parainfluenzae, had an incomplete f-like cap locus. In conclusion, circulation of serotype b is residual. The few encapsulated strains are genetically related to disease-causing isolates. Thus, surveillance of H. influenzae carriage should be maintained.

Phylogenetic Structure and Comparative Genomics of Multi-National Invasive Haemophilus influenzae Serotype a Isolates.

Recent reports have indicated a rise of invasive disease caused by Haemophilus influenzae serotype a (Hia) in North America and some European countries. The whole-genome sequences for a total of 410 invasive Hia isolates were obtained from 12 countries spanning the years of 1998 to 2019 and underwent phylogenetic and comparative genomic analysis in order to characterize the major strains causing disease and the genetic variation present among factors contributing to virulence and antimicrobial resistance. Among 410 isolate sequences received, 408 passed our quality control and underwent genomic analysis. Phylogenetic analysis revealed that the Hia isolates formed four genetically distinct clades: clade 1 (n = 336), clade 2 (n = 13), clade 3 (n = 3) and clade 4 (n = 56). A low diversity subclade 1.1 was found in clade 1 and contained almost exclusively North American isolates. The predominant sequence types in the Hia collection were ST-56 (n = 125), ST-23 (n = 98) and ST-576 (n = 51), which belonged to clade 1, and ST-62 (n = 54), which belonged to clade 4. Clades 1 and 4 contained predominantly North American isolates, and clades 2 and 3 predominantly contained European isolates. Evidence of the presence of capsule duplication was detected in clade 1 and 2 isolates. Seven of the virulence genes involved in endotoxin biosynthesis were absent from all Hia isolates. In general, the presence of known factors contributing to ß-lactam antibiotic resistance was low among Hia isolates. Further tests for virulence and antibiotic susceptibility would be required to determine the impact of these variations among the isolates.

Molecular epidemiology of invasive Haemophilus influenzae disease in Portugal: an update of the post-vaccine period, 2011-2018.

Haemophilus influenzae reference laboratory from Portugal characterized the entire collection of 260 H. influenzae invasive isolates received between 2011 and 2018, with the purpose of updating the last published data (2002-2010). Capsular serotypes and antimicrobial susceptibility patterns were determined. The ftsI gene encoding the transpeptidase domain of PBP3 was sequenced for ß-lactamase-negative ampicillin-resistant (BLNAR) isolates. Multilocus sequence typing (MLST) was performed to examine genetic relatedness among isolates. The majority of H. influenzae invasive isolates are nonencapsulated (NTHi-79.2%). Among encapsulated isolates (20.8%), the most characterized serotype was serotype b (13.5%), followed by serotype f (3.1%), serotype a (2.7%), and serotype e (1.5%). In contrast to NTHi that mainly affected the elderly (64.0%; ≥ 65 years old), most encapsulated isolates were characterized in preschool children (55.6%). Comparing the two periods, ß-lactamase production increased from 10.4 to 13.5% (p = 0.032) and low-BLNAR (MIC ≥ 1 mg/L) isolates from 7.7 to 10.5% (p = 0.017). NTHi showed high genetic diversity (60.7%), in opposition to encapsulated isolates that were clonal within each serotype. Interestingly, ST103 and ST57 were the predominant STs among NTHi, with ST103 being associated with ß-lactamase-producers and ST57 with non-ß-lactamase-producers. In Portugal, susceptible and genetically diverse NTHi H. influenzae continues to be responsible for invasive disease, mainly in the elderly. Nevertheless, we are now concerned with Hib circulating in children we believe to have been vaccinated. Our data reiterates the need for continued surveillance, which will be useful in the development of public health prevention strategies.

Cross-sectional study of adenoidal biofilms in a paediatric population and its clinical implications

INTRODUCTION: Adenoids are nasopharyngeal lymphoid tissue with a relevant role in host defence against infection of upper respiratory tract. Nevertheless, adenoids are also a reservoir of microorganisms that can cause infections of upper respiratory tract and otitis particularly in children. OBJECTIVE: Evaluate and compare the association between biofilm assembly on adenoids and the incidence of recurrent infections in a paediatric population submitted to adenoidectomy by either infectious or non-infectious indication. METHODS: Scanning electron microscopy was used to assess biofilms on adenoid surface; biofilm assembly in vitro was monitored by crystal violet assay; antibiotic susceptibility was assessed following EUCAST guidelines; Hinfluenzae capsular typing was performed by PCR. RESULTS: Biofilms were present in 27.4% of adenoid samples and no statistical difference was found between infectious and non-infectious groups. In vitro, the most clinically relevant bacteria, H.influenzae, S.aureus, S.pyogenes, S.pneumoniae and M.catarrhalis, were mostly moderate biofilm assemblers (71.7%). 55.3% of these bacteria were intermediate/resistant to at least one of the tested antibiotics. No association was found between the ability to assemble biofilms in vitro and the presence of biofilms on adenoids nor antibiotic resistance. All H.influenzae were characterized as non-typeable. CONCLUSION: The presence of biofilms on adenoid surface was independent from clinical sample background. Bacterial ability to assemble biofilms in vitro cannot be used to predict biofilm assembly in vivo. The lack of correlation between biofilm formation and infectious respiratory diseases found contributes to question the relevance of biofilms on the pathogenesis of infectious diseases.

Role of inter-species recombination of the ftsI gene in the dissemination of altered penicillin-binding-protein-3-mediated resistance in Haemophilus influenzae and Haemophilus haemolyticus.

OBJECTIVES: To screen the ftsI gene sequences obtained from clinical isolates of non-typeable Haemophilus influenzae (NTHi) and Haemophilus haemolyticus for the presence of mosaic ftsI gene structures, and to evaluate the role of inter-species recombination of the ftsI gene in the formation and distribution of resistant ftsI genes. METHODS: The ftsI genes of 100 Haemophilus isolates comprising genetically defined ß-lactamase-negative ampicillin-susceptible (gBLNAS), ß-lactamase-positive ampicillin-resistant (gBLPAR), ß-lactamase-negative ampicillin-resistant (gBLNAR) and ß-lactamase-positive amoxicillin/clavulanate-resistant (gBLPACR) isolates of NTHi (n = 50) and H. haemolyticus (n = 50) were analysed in this study. Both the flanking regions and the full-length ftsI gene sequences of all study isolates were screened for mosaic structures using H. influenzae Rd and H. haemolyticus ATCC 33390 as reference parental sequences, and bioinformatics methods were used for recombination analysis using SimPlot. RESULTS: Of the 100 clinical isolates analysed 34% (34/100) harboured mosaic ftsI gene structures containing distinct ftsI gene fragments similar to both reference parental sequences. The inter-species recombination events were exclusively encountered in the ftsI gene of gBLNAR/gBLPACR isolates of both NTHi and H. haemolyticus, and were always associated with the formation of a mosaic fragment at the 3' end of the ftsI gene. There was no evidence supporting horizontal gene transfer (HGT) involving the entire ftsI gene among the clinical isolates in vivo. CONCLUSIONS: We provide evidence for the HGT and inter-species recombination of the ftsI gene among gBLNAR/gBLPACR isolates of NTHi and H. haemolyticus in a clinical setting, highlighting the importance of recombination of the ftsI gene in the emergence of altered penicillin-binding protein 3 and BLNAR-mediated resistance.

Polymorphism in ftsI gene and {beta}-lactam susceptibility in Portuguese Haemophilus influenzae strains: clonal dissemination of beta-lactamase-positive isolates with decreased susceptibility to amoxicillin/clavulanic acid.

OBJECTIVES: The aim of this study was to characterize ampicillin resistance mechanisms in clinical isolates of Haemophilus influenzae from Portugal. Association between specific patterns of amino acid substitutions in penicillin-binding protein 3 (PBP3) (with or without ß-lactamase production) and ß-lactam susceptibility as well as genetic relatedness among isolates were investigated. METHODS: Two-hundred and forty non-consecutive H. influenzae isolates chosen according to their different ampicillin MICs [101 ß-lactamase-non-producing ampicillin-resistant (BLNAR) isolates, 80 ß-lactamase-producing ampicillin-resistant (BLPAR) isolates and 59 ß-lactamase-non-producing ampicillin-susceptible (BLNAS) isolates] were analysed. The ß-lactamase-encoding bla(TEM-1) gene was detected by PCR. The ftsI gene encoding PBP3 was sequenced. Genetic relatedness among isolates was examined by PFGE. RESULTS: Of the 240 H. influenzae isolates, 141 had mutations in the transpeptidase domain of the ftsI gene, including most BLNAR strains (94/101, 93.1%) and a high percentage of BLPAR strains (47/80, 58.8%). As previously reported, the latter have been described as ß-lactamase-positive amoxicillin/clavulanic acid resistant (BLPACR). The most common amino acid substitutions were identified near the KTG motif: N526K (136/141, 96.5%), V547I (124/141, 87.9%) and N569S (121/141, 85.8%). The 141 strains were divided into 31 ftsI mutation patterns and included six groups (I, IIa, IIb, IIc, IId and III-like). BLNAR strains were genetically diverse but close genetic relationships were demonstrated among BLPACR strains. CONCLUSIONS: This study shows that the non-enzymatic mechanism of resistance to ß-lactams is widespread among H. influenzae isolates in Portugal. Clonal dissemination of BLPACR strains showing high resistance to ampicillin and reduced susceptibility to amoxicillin/clavulanic acid was documented.