Capsulation loci of non-serotype b encapsulated Haemophilus influenzae

Invasive Haemophilus influenzae disease in the vaccine era in Rio de Janeiro, Brazil

BACKGROUND

Haemophilus influenzae (Hi) serotype b (Hib) conjugate vaccine was incorporated into the infant immunisation schedule in Brazil in 1999, where Hib was one of the major etiologic sources of community-acquired bacterial meningitis.

OBJECTIVES

The purpose of this study is to describe the molecular epidemiology of invasive Hi disease in Rio de Janeiro state, Brazil, before and after vaccine introduction.

METHODS

Surveillance data from 1986 to 2014 were analysed. Hi isolates recovered from cerebrospinal fluid (CSF) or blood from 1993 to 2014 were serotyped by slide agglutination, genotyped by multilocus sequence typing (MLST), and the capsule type evaluation, differentiation of serologically non-typeable isolates, and characterisation of the capsule (cap) locus was done by polymerase chain reaction. Antimicrobial susceptibility testing was performed using E-test.

FINDINGS

From 1986 to 1999 and from 2000 to 2014, 2580 and 197 (42% without serotype information) confirmed cases were reported, respectively. The case fatality rate was 17% and did not correlate with the strain. Hib and b- variant isolates belonged to ST-6, whereas serotype a isolates belonged to the ST-23 clonal complex. Serotype a appeared to emerge during the 2000s. Non-encapsulated isolates were non-clonal and distinct from the encapsulated isolates. Ampicillin-resistant isolates were either of serotype b or were non-encapsulated, and all of them were β-lactamase-positive but amoxicillin-clavulanic acid susceptible.

MAIN CONCLUSIONS

Although Hi meningitis became a relatively rare disease in Rio de Janeiro after the introduction of the Hib conjugate vaccine, the isolates recovered from patients have become more diverse. These results indicate the need to implement an enhanced surveillance system to continue monitoring the impact of the Hib conjugate vaccine.

Utilization of a real-time PCR approach for Haemophilus influenzae serotype determination as an alternative to the slide agglutination test

Our laboratory has developed a simple two-step multiplex real-time PCR for use on isolates of Haemophilus influenzae for molecular serotype identification and the detection of capsular gene targets. The assay consists of a 2-plex real-time PCR targeting the capsule transport gene (bexA), and serotype b specific gene (bcsB), and a 5-plex real-time PCR detecting serotypes a, c, d, e, and f targeting Region II serotype-specific genes. Both real-time PCR assays are highly sensitive (<8 CFU) for all serotypes and 100% specific when tested by a panel of more than 40 bacterial organisms. A retrospective study of 214 isolates received between 1998 and 2011 were tested and compared against the traditional slide agglutination test (SAT) resulting in 100% concordance. We demonstrate that this two-step real-time PCR approach is more sensitive than previously published PCR assays and provides a simple alternative to the SAT. Reliable, rapid and sensitive H. influenzae serotyping is critical for identifying new emerging strains for epidemiological surveillance.

Use of bexB to detect the capsule locus in Haemophilus influenzae

Haemophilus influenzae strains are classified as typeable or nontypeable H. influenzae (NTHI) based upon the presence or absence of capsule. In addition to serotyping, which is subject to false-positive results, typeable strains can be identified through the detection of the capsular export gene bexA and one of six capsule-specific genes, but this method is resource intensive, especially in characterizing large numbers of strains. To address these challenges, we developed a bexB-based method to differentiate true NTHI strains from typeable strains. We validated a PCR-based method to detect bexB in 10 strains whose capsule status was well defined. Among 40 strains that were previously serotype positive in clinical microbiology laboratories, 5 lacked bexA, bexB, and capsule type-specific genes by PCR analysis and thus likely represent false-positive serotyping results. Among 94 additional otitis media, commensal, and serotype b-negative invasive strains, 85 were bexA and bexB negative and 9 contained either a complete or partial capsule locus, i.e., 8 were bexA and bexB positive and 1 was bexA negative but bexB positive. Finally, we adapted the method for use in a high-throughput DNA hybridization-based microarray method, which showed 98.75 and 97.5% concordance to the PCR methods for bexA and bexB, respectively. In addition, bexB showed 84% or greater nucleotide identity among strains containing the capsule locus. In this study, we demonstrate that bexB is a reliable proxy for the capsule locus and that its detection provides a simple and reliable method for differentiating strains that lack the entire capsule locus from those containing a partial or complete capsule locus.

Poor clinical outcome for meningitis caused by Haemophilus influenzae serotype A strains containing the IS1016-bexA deletion

Since the introduction of Haemophilus influenzae type b (Hib) conjugate vaccines, meningitis caused by serotypes other than Hib has gained in importance. We conducted active hospital-based surveillance for meningitis over an 11-year period in Salvador, Brazil. H. influenzae isolates were serotyped and analyzed by polymerase chain reaction, pulsed-field gel electrophoresis, and DNA sequencing to identify strains with a specific deletion (IS1016) in the bexA gene (IS1016-bexA). We identified 43 meningitis cases caused by non-type b H. influenzae: 28 (65%) were caused by type a (Hia), 9 (21%) were caused by noncapsulated strains, and 3 (7%) each were caused by types e and f. Hia isolates clustered in 2 clonal groups; clonal group A strains (n = 9) had the IS1016-bexA deletion. Among children <5 years of age, meningitis caused by Hia from clonal group A had higher case-fatality than meningitis caused by clonal group B. Despite small numbers, these results indicate that the presence of the IS1016-bexA deletion is associated with enhanced virulence in non-type b H. influenzae.

Haemophilus influenzae meningitis 5 years after introduction of the Haemophilus influenzae type b conjugate vaccine in Brazil

The long-term impact of Haemophilus influenzae type b (Hib) conjugate vaccine, introduced throughout Latin America in the late 1990s, has not been evaluated. Active surveillance for H. influenzae meningitis was performed from August 9, 1996 to August 8, 2004 in Metropolitan Salvador, Brazil. Five years after the introduction of Hib conjugate vaccine, Hib meningitis incidence decreased from 2.39 to 0.06 cases per 100,000 population (98%) overall, and from 60.9 to 3.1 cases per 100,000 population (95%) in children <1 year of age. A transient serotype replacement phenomenon was observed associated with a small increase of meningitis due to two H. influenzae type a clonal groups. These findings indicate that Hib immunization campaign has led to the virtual elimination of Hib disease in this region.

Invasive Infections with Haemophilus influenzae Serotype a Containing an IS1016-bexA Partial Deletion: Possible Association with Virulence

BACKGROUND

Recent reports of invasive Haemophilus influenzae non-b capsular serotypes in the era since development of conjugate vaccines have prompted concern about serotype replacement. Unusual clusters of invasive infection due to H. influenzae serotype a with clinical features that resemble those of infection due to H. influenzae serotype b have been described. A unique feature often associated with more-virulent H. influenzae serotype a isolates is the IS1016-bexA partial deletion, which was previously identified in the capsule locus of H. influenzae serotype b strains. We report the clinical, epidemiologic, and molecular genetic features of 2 cases of severe disease caused by H. influenzae serotype a.

METHODS

Invasive H. influenzae isolates were serotyped with standard serological methods, and molecular typing was done with PCR. The capsular genotype of each isolate was characterized with PCR, partial sequencing, and Southern blot hybridization. Further strain typing was performed with pulsed-field gel electrophoresis.

RESULTS

We identified 2 children with severe invasive disease due to H. influenzae serotype a. Both H. influenzae serotype a isolates contained the identical pulsed-field gel electrophoresis pattern and capsular genotype. An IS1016-bexA partial deletion in the capsule gene locus similar to that found in H. influenzae serotype b was identified in both isolates by means of PCR and sequencing of the IS1016-bexA junction.

CONCLUSIONS

We describe 2 cases of severe invasive disease due to H. influenzae serotype a with the putative virulence-enhancing IS1016-bexA partial deletion and duplication of the capsule locus. Our data support the hypothesis that this mutation may be associated with virulence in non-b capsular serotypes of H. influenzae.

Molecular characterisation of Haemophilus influenzae type a and untypeable strains isolated simultaneously from cerebrospinal fluid and blood: novel use of quantitative real-time PCR based on the cap copy number to determine virulence

This study investigated the genetic structure of the cap region of an isolate of Haemophilus influenzae serotype a (Hia) from the cerebrospinal fluid (CSF) of a child with meningitis. In addition, the genetic structure of the cap region of a non-serotypeable H. influenzae isolate, obtained simultaneously from the blood of the same patient, was determined. According to restriction fragment length polymorphism analysis, the CSF and blood isolates were identical, with the exception of a single band shift of c. 35 kb. PCR analyses suggested that the CSF isolate possessed the IS1016-bexA gene and cap region II, whereas the blood isolate only had the IS1016 element. Furthermore, Southern analysis of DNA from both isolates showed that the CSF isolate carried the cap gene(s), while the blood isolate did not. Using a novel quantitative real-time PCR approach for determining the cap copy number, it was demonstrated that the CSF isolate had two intact tandem repeats of the cap gene containing three copies of IS1016, whereas the blood isolate had only one copy of IS1016. This study provided evidence that H. influenzae serotypes other than serotype b can cause serious disease, and that the virulence of these non-serotype b strains relates primarily to the cap gene copy number and the structure of the cap locus. Therefore, the quantitative real-time PCR assay described in this study should be useful for the rapid and definitive identification of strains of H. influenzae type a that represent a risk for serious disease.

Prevalence and serotype distribution of encapsulated Haemophilus influenzae isolates from patients with lower respiratory tract infections in Poland

Among 1,272 H. influenzae isolates obtained from patients with lower respiratory tract infections, 5.6% were found to be encapsulated. The most common were serotypes b (40.3%) and e (38.9%) followed by serotypes f (16.7%) and d (4.1%). All encapsulated isolates within a particular serotype showed high genetic homogeneity and did not produce beta-lactamases.

Serotypes of Haemophilus influenzae strains isolated from pediatric patients with respiratory tract infections

Capsular serotypes of 122 respiratory Haemophilus influenzae strains were identified utilizing antigenic examinations (Slide Agglutination Test [SAT] and counter immuno-electrophoresis [CIE]), and PCR method. Results of the two methods were compared to find disagreement. Clinical and bacteriological characteristics of encapsulated strains were analyzed. By utilizing PCR assay, 3 (2.5%) serotype b, 1 (0.8%) serotype f and 118 (96.7%) non-typeable strains were found among 122 tested strains. Discrepancy between the results of antigenic examinations and PCR assay was found in one strain. That strain gave positive results by antigenic tests with capsular type c antiserum but it was determined to be capsular type f by PCR. No serotype b- strain was detected. All the encapsulated strains displayed biotype I. All the serotype b strains produced beta-lactamase, but none of those was sulbactam/ampicillin and amoxicillin/clavulanic acid resistant. The serotype f strain was beta-lactamase non-producing ampicillin susceptible. The patients suffered from respiratory infections due to encapsulated strains displayed safe clinical manifestations and good clinical responses to antibiotic treatments using beta-lactams. In pre-vaccination era, PCR is considered to be a useful method for determination of serotypes of respiratory H. influenzae, which may contribute to reducing a possibility of clonal transmission of serotype b strains among children community, which is one of the potential risk factors for pediatric invasive infections.

PCR-based capsular serotype determination of Haemophilus influenzae strains recovered from Japanese paediatric patients with invasive infection

The serotypes of 53 isolates of Haemophilus influenzae from children with invasive infections were determined by a conventional slide agglutination test (SAT) and a recently proposed PCR-based method for serotyping H. influenzae. The PCR assay identified 47 (88.7%) type b isolates, one (1.9%) type e isolate and five (9.4%) non-typeable isolates. The only discrepancy between the methods was an isolate that was non-typeable by SAT, but was identified as serotype e by PCR. Of 41 isolates from patients with meningitis, 39 (95.1%) were type b. Of the five non-typeable isolates, three (60%) were from the blood of patients with septicaemic pneumonia and two (40%) were from the cerebrospinal fluid of patients with meningitis. None of the non-typeable isolates appeared to be a capsule-deficient mutant of an encapsulated H. influenzae strain. Overall, the study confirmed the usefulness of this PCR method for the serotyping of invasive H. influenzae isolates.

Emergence of nonencapsulated and encapsulated non-b-type invasive Haemophilus influenzae isolates in Portugal (1989-2001)

Phenotypes and genetic relatedness of invasive Haemophilus influenzae strains were evaluated from 1989 through 2001. Among 119 isolates, multidrug resistance decreased (from 50 to 0%), the level of H. influenzae serotype b (Hib) strains declined (from 81 to 16%), the level of noncapsulated strains rose (from 19 to 80%), and the first invasive H. influenzae serotype f strain was described. This study documents changes in invasive H. influenzae infections in Portugal, i.e., the emergence of non-type-b strains that are genetically diverse and unrelated to Hib.

Evaluation of methodology for serotyping invasive and nasopharyngeal isolates of Haemophilus influenzae in the ongoing surveillance in Brazil

To assess the magnitude of discrepant results obtained by routine Haemophilus influenzae serotyping, 258 isolates, collected by the epidemiological surveillance system in Brazil from individuals with invasive diseases or carriage, were evaluated by two slide agglutination (SlAg) methods: SlAg method 1, by which strains were initially screened with a serotype b-specific antiserum, and SlAg method 2, by which strains were tested against all serotype-specific antisera in parallel. Investigators comparing results of the two SlAg methods with those obtained by capsule type-specific PCR were blinded to the method used. The serotype prevalence rates found by the three methods were significantly different, involving discrepancies mainly between serotype b and noncapsulated (NC) isolates. For invasive isolates (n = 131), the overall agreement rate between SlAg method 1 or 2 and PCR was 68.0 or 88.3%, respectively, whereas for colonizing isolates (n = 127) the corresponding rate was 46.5 or 94.2%, respectively. SlAg method 2 improved the ascertainment of serotypes over that obtained with SlAg method 1, demonstrating good correlation with PCR. Use of the polyvalent antiserum as a screening reagent for SlAg for invasive and colonizing isolates showed poor discriminatory power, with a sensitivity of 65.8% and a specificity of 91.7%. We stress the importance of using a well-standardized SlAg methodology and suggest that reference laboratories should utilize PCR routinely to confirm SlAg results and to check all nonspecific SlAg reactions and apparent NC isolates by SlAg in order to provide reliable data on the prevalence of H. influenzae serotypes in the H. influenzae type b vaccine era.

Pgi genotyping is a surrogate for serotyping of encapsulated Haemophilus influenzae

Study of the epidemiology of invasive infections caused by encapsulated Haemophilus influenzae has been complicated by the poor sensitivity and specificity of the serologic assays used to identify specific capsular polysaccharides. The population structure of these bacteria is highly clonal, however, and serotype is highly correlated with other genetic characteristics. We sought to determine if alleles of the highly conserved phosphoglucose isomerase (pgi) gene correspond to the serotypes of encapsulated H. influenzae strains. pgi alleles of 52 well-characterized encapsulated H. influenzae isolates were amplified by PCR, sequenced, and compared to one another and to additional previously reported H. influenzae pgi alleles. Overall, 83% of the strains possessed pgi alleles associated with the major serotype a, b, e, and f clonotypes that cause the most invasive disease in the United States. Six strains (four type a and two type f) had unusual pgi alleles, which suggested that these strains belonged to less common clonotypes of encapsulated bacteria or were actually nontypeable strains. pgi genotyping may provide a simple and stable surrogate for capsular serotyping. Further studies correlating pgi typing with the expression of capsule are likely to increase our understanding of the epidemiology and pathogenesis of these infections.

Prevalence and distribution of adhesins in invasive non-type b encapsulated Haemophilus influenzae

Adhesion to the respiratory epithelium plays an important role in Haemophilus influenzae infection. The distribution of H. influenzae adhesins in type b and nontypeable strains has been characterized, but little is known about the prevalence of these factors in non-type b encapsulated strains. We analyzed 53 invasive type a, type e, and type f strains for the presence of hap, hia, hmw, and hif genes; Hap, Hia, and HMW1/2 adhesins; and hemagglutinating pili. The hap gene was ubiquitous, and homologs of hmw and hia were present in 7 of 53 (13.2%) and 45 of 53 (84.9%) strains, respectively. Hap was detected in 28 of 45 (62.2%) hap(+) strains, HMW1/2 was detected in 5 of 7 (71.4%) hmw(+) strains, and Hia was detected in 31 of 45 (68.8%) hia(+) strains. The hif gene cluster was present in 26 of 53 strains (49.1%), and 21 of 26 hif(+) strains (80.8%) agglutinated (HA) red blood cells. Nine isolates exhibited HA but lacked the hif gene cluster. The distribution of adhesin genes correlated with the genetic relatedness of the strains. Strains belonging to one type a clonotype and the major type e clonotype possessed hia but lacked the hif cluster. Strains belonging to the second type a clonotype possessed both hia and hif genes. All type f strains belonging to the major type f clonotype possessed hia and lacked hifB. Although the specific complement of adhesin genes in non-type b encapsulated H. influenzae varies, most invasive strains express Hap and Hia, suggesting these adhesins may be especially important to the virulence of these organisms.

Invasive type e Haemophilus influenzae disease in Italy

We describe the first reported cases of invasive type e Haemophilus influenzae disease in Italy. All five cases occurred in adults. The isolates were susceptible to ampicillin and eight other antimicrobial agents. Molecular analysis showed two distinct type e strains circulating in Italy, both containing a single copy of the capsulation locus.