Bacteremic pneumonia caused by a single clone of Streptococcus pneumoniae with different optochin susceptibilities

Emergence of Neoteric Serotypes Among Multidrug Resistant Strains of Streptococcus pneumoniae Prevalent in Egypt

Background

Streptococcus pneumoniae is still one of the major causes of morbidity and mortality worldwide. The prevalent serotype distribution had shown variation along different studies conducted at different time intervals. In order to efficiently assess the epidemiology of the diseases for effective preventive and treatment strategies, serotype prevalence need to be periodically reassessed.

Objectives

Conducting a reassessment of the prevalent S. pneumoniae serotypes in Egypt as an essential step in the search for a regional vaccine. In addition, monitoring the antibiotic susceptibility patterns of pneumococcal strains currently causing infections as an evaluation of therapeutic strategies applied.

Materials and Methods

A total of 100 specimens of different sources were collected in Cairo, Egypt, from 2011 to 2013, representing almost all different types of diseases caused by S. pneumoniae such as meningitis, pneumonia, otitis media and sinusitis. Conventional and molecular identification methods were performed, the antimicrobial susceptibility patterns were assessed and serotyping was done using PCR assays to identify the most prevalent types. In addition, detection of certain virulence genes for the most prevalent serotypes was carried out.

Results

Our results revealed that in Egypt, currently, the most prevalent serotypes were serogroup 6 and serotype 19F as they represented 58% of all isolates. High rates of resistance were found to different antibiotic classes. The lytA and psaA genes were found to be more sensitive for S. pneumoniae identification than ply.

Conclusions

Our study illustrates the importance of constantly monitoring the prevalent serotypes in any region in order to aid in the development of more effective vaccines.

The mystery of the fourth clone: comparative genomic analysis of four non-typeable Streptococcus pneumoniae strains with different susceptibilities to optochin

Optochin-resistant pneumococci can be rarely caught in clinical microbiology laboratories because of the routine identification of all such strains as viridans group non-pneumococci. We were lucky to find four non-typeable Streptococcus pneumoniae clones demonstrating the different susceptibilities to optochin: one of them (Spn_13856) was resistant to optochin, while the other three (Spn_1719, Spn_27, and Spn_2298) were susceptible. Whole genome nucleotide sequences of these strains were compared to reveal the differences between the optochin-resistant and optochin-susceptible strains. Two adjacent genes coding maltose O-acetyltransferase and uridine phosphorylase which were presented in the genomes of all optochin-susceptible strains and missed in the optochin-resistant strain were revealed. Non-synonymous substitutions in 14 protein-coding genes were discovered, including the Ala49Ser mutation in the C-subunit of the F0 part of the ATP synthase rotor usually associated with pneumococcal optochin resistance. Modeling of a process of optochin interaction with the F0 part of the ATP synthase rotor indicates that the complex of optochin with "domain C" composed by wild-type C-subunits is more stable than the same complex composed of Ala49Ser mutant C-subunits.

Phenotypic and molecular characterization of optochin-resistant Streptococcus pneumoniae isolates from Brazil, with description of five novel mutations in the ATPC gene

Optochin (Opt) susceptibility is used largely for the identification of Streptococcus pneumoniae in diagnostic laboratories. Opt-resistant (Opt(r)) S. pneumoniae isolates have been reported, however, indicating the potential for misidentification of this important pathogen. Point mutations in the atpC gene have been associated with the emergence of Opt(r) S. pneumoniae, but data on the characterization of such atypical variants of S. pneumoniae are still limited. The present report describes the results of a polyphasic approach to identifying and characterizing 26 Opt(r) S. pneumoniae isolates recovered from patients or carriers living in Brazil. Sixteen isolates consisted of heterogeneous populations, and 10 isolates were homogeneously Opt(r). The isolates had different serotypes and antimicrobial susceptibility profiles. They also presented diverse genetic characteristics, as indicated by pulsed-field gel electrophoresis (PFGE), multilocus variable-number tandem-repeat analysis (MLVA), and pspA gene typing. Except for Opt MICs (4- to 64-fold higher among Opt(r) variants), Opt(r) and Opt-susceptible (Opt(s)) subpopulations originating from the same culture had identical characteristics. Sequencing of the atpC gene of the Opt(r) variants revealed 13 different nucleotide changes distributed among eight different codons. Changes in codon 49 were the most frequent, suggesting that this might be a hot spot for optochin resistance-conferring mutations. On the other hand, five novel types of mutations in the atpC gene (Met13Ile, Gly18Ser, Gly20Ala, Ala31Val, and Ala49Gly) were identified. In silico prediction modeling indicated that the atpC gene mutations corresponded to alterations in the transmembrane region of the ATPase, leading to a higher hydrophobicity profile in α-helix 1 and to a lower hydrophobicity profile in α-helix 2.

Optochin resistance in Streptococcus pneumoniae induced by frozen storage in glycerol

Susceptibility to optochin is frequently the only test used to differentiate Streptococcus pneumoniae from other alpha-hemolytic streptococci isolated from clinical specimens. The current study shows that storage of S. pneumoniae isolates in tryptic soy broth containing 15% glycerol at -70 degrees C can lead to optochin resistance. This optochin resistance was sometimes reversible by growing the bacteria in broth. Optochin-susceptible and optochin-resistant variants of individual S. pneumoniae isolates have similar pulsed-field gel electrophoresis pattern. However, optochin-resistant S. pneumoniae isolates exhibit differences in ultrastructure compared with optochin-susceptible variants. This study demonstrates that the frozen storages of S. pneumoniae in glycerol may affect the optochin phenotype. Thus, this characteristic should not be the only one used for identification of S. pneumoniae after frozen storage of isolates.

Emergence of optochin resistance among Streptococcus pneumoniae in Portugal

In most clinical microbiology laboratories optochin susceptibility is used in the screening and identification of Streptococcus pneumoniae. We report the characterization of 32 optochin-resistant S. pneumoniae strains from 10 laboratories that constituted 3.2% of all isolates recovered in 2005 in 30 laboratories in Portugal. Resistant isolates consisted of bile-soluble optochin-susceptible and optochin-resistant subpopulations with identical antimicrobial susceptibility patterns, capsular types and pulsed-field gel electrophoresis (PFGE) profiles. The most frequent serotypes--1, 19A, 11A, 3, 8, and 15A--were all common serotypes present in infection and colonization isolates in the country. The PFGE profiles of the 32 isolates corresponded to those of previously identified clones and confirmed that the emergence of these strains could not be attributed to clonal expansion. Clinical laboratories must be aware that optochin-resistant pneumococci are presently circulating in the community. Because accurate identification of S. pneumoniae is essential for correct diagnosis and adequate therapy of patients, we recommend that at least the bile solubility test should be routinely performed in cases of suspected pneumococcal etiology, even if the isolates are optochin-resistant.

Molecular characterization of disease-associated streptococci of the mitis group that are optochin susceptible

Eight optochin-susceptible (Opt(s)) alpha-hemolytic (viridans) streptococcus isolates were characterized at the molecular level. These isolates showed phenotypic characteristics typical of both viridans streptococci and Streptococcus pneumoniae. Comparison of the sequence of housekeeping genes from these isolates with those of S. pneumoniae, Streptococcus mitis, Streptococcus oralis, and Streptococcus pseudopneumoniae suggested that the Opt(s) isolates corresponded to streptococci of the mitis group. Besides, the Opt(s) streptococci were negative by a Gen-Probe AccuProbe pneumococcus test and hybridized with specific pneumococcal probes (lytA and ply) but also with ant, a gene not present in most S. pneumoniae strains. Moreover, the isolates were insoluble in 1% sodium deoxycholate but completely dissolved in 0.1% deoxycholate. Sequence analysis of the lytA gene revealed that the Opt(s) streptococci carried lytA alleles characteristic of those present in nonpneumococcal streptococci of the mitis group. The determination of the partial nucleotide sequence embracing the atp operon encoding the F(o)F(1) H(+)-ATPase indicated that the optochin susceptibility of the isolates was due to the acquisition of atpC, atpA, and part of atpB from S. pneumoniae by horizontal gene transfer.

Use of the housekeeping genes, gdh (zwf) and gki, in multilocus sequence typing to differentiate Streptococcus pneumoniae from Streptococcus mitis and Streptococcus oralis

Polymerase chain reaction and sequencing of the housekeeping genes, gdh (zwf) and gki, based on the primers and alleles from multilocus sequence typing can be used to delineate and support the identity of clinical isolates of Streptococcus pneumoniae and differentiate from the closely related Streptococcus mitis and Streptococcus oralis.

Phenotypic and genotypic discrepancy of Streptococcus pneumoniae strains isolated from Asian countries

Non-typeable isolates of Streptococcus pneumoniae collected from Asian countries were characterized by optochin susceptibility test, bile solubility test, multilocus sequence typing of housekeeping genes, amplification of virulence-related genes, 16S rDNA-RsaI digestion, and 16S rDNA sequencing. Six of 54 non-typeable pneumococcal isolates showed divergence of gene sequences of recP and xpt from typical pneumococcal strains. Of these six atypical pneumococcal strains, two showed different results in optochin susceptibility or bile solubility test from typical pneumococcal strains. All six isolates showed high sequence dissimilarities of multilocus sequence typing, 16S rDNA sequences, and lytA sequences from typical S. pneumoniae strains. Data from this study suggest that classic tests such as optochin susceptibility and bile solubility tests may lead to incorrect identification of S. pneumoniae. These atypical strains may belong to different bacterial species from S. pneumoniae.

Accuracy of phenotypic and genotypic testing for identification of Streptococcus pneumoniae and description of Streptococcus pseudopneumoniae sp. nov

We have identified an unusual group of viridans group streptococci that resemble Streptococcus pneumoniae. DNA-DNA homology studies suggested that a subset of these isolates represent a novel species that may be included in the S. oralis-S. mitis group of viridans group streptococci. We suggest that this novel species be termed Streptococcus pseudopneumoniae. A combination of phenotypic and genetic reactions allows its identification. S. pseudopneumoniae strains do not have pneumococcal capsules, are resistant to optochin (inhibition zones, less than 14 mm) when they are incubated under an atmosphere of increased CO2 but are susceptible to optochin (inhibition zones, >14 mm) when they are incubated in ambient atmospheres, are not soluble in bile, and are positive by the GenProbe AccuProbe Pneumococcus test. The bile solubility test is more specific than the optochin test for identification of S. pneumoniae. Genetic tests for pneumolysin (ply) and manganese-dependent superoxide dismutase (sodA) and identification tests with a commercial probe, AccuProbe Pneumococcus, do not discriminate between the new species and S. pneumoniae.

Pyelonephritis and urosepsis caused by Streptococcus pneumoniae

This report presents the case of a patient with a massive pyelonephritis and a urosepsis caused by Streptococcus pneumoniae. This case is unusual as the focus was distant from the respiratory tract, the usual primary site of infection caused by this organism. No other primary site of infection was documented.

Genetic characterization of optochin-susceptible viridans group streptococci

Two clinical isolates of viridans group streptococci (VS) with different degrees of susceptibility to optochin (OPT), i.e., fully OPT-susceptible (Opt(s)) VS strain 1162/99 (for which the MIC was equal to that for Streptococcus pneumoniae, 0.75 micro g/ml) and intermediate Opt(s) VS strain 1174/97 (MIC, 6 micro g/ml) were studied. Besides being OPT susceptible, they showed characteristics typical of VS, such as bile insolubility; lack of reaction with pneumococcal capsular antibodies; and lack of hybridization with rRNA (AccuProbe)-, lytA-, and pnl-specific pneumococcal probes. However, these VS Opt(s) strains and VS type strains hybridized with ant, a gene not present in S. pneumoniae. A detailed characterization of the genes encoding the 16S rRNA and SodA classified isolates 1162/99 and 1174/97 as Streptococcus mitis. Analysis of the atpCAB region, which encodes the c, a, and b subunits of the F(0)F(1) H(+)-ATPase, the target of optochin, revealed high degrees of similarity between S. mitis 1162/99 and S. pneumoniae in atpC, atpA, and the N terminus of atpB. Moreover, amino acid identity between S. mitis 1174/97 and S. pneumoniae was found in alpha helix 5 of the a subunit. The organization of the chromosomal region containing the atp operon of the two Opt(s) VS and VS type strains was spr1284-atpC, with spr1284 being located 296 to 556 bp from atpC, whereas in S. pneumoniae this distance was longer than 68 kb. In addition, the gene order in S. pneumoniae was IS1239-74 bp-atpC. The results suggest that the full OPT susceptibility of S. mitis 1162/99 is due to the acquisition of atpC, atpA, and part of atpB from S. pneumoniae and that the intermediate OPT susceptibility of S. mitis 1174/97 correlates with the amino acid composition of its a subunit.

Meningitis due to mixed infection with penicillin-resistant and penicillin-susceptible strains of Streptococcus pneumoniae

Streptococcus pneumoniae is the major cause of bacterial meningitis. We report a case of meningitis due to a mixed infection with two distinct strains of S. pneumoniae: one penicillin-resistant strain of serotype 9V and one penicillin-susceptible strain of serotype 7. The two strains exhibited different pulsed-field gel electrophoresis profiles.

Identification of Streptococcus pneumoniae revisited

The sensitivities and specificities of several different diagnostic assays for Streptococcus pneumoniae were assessed using 99 clinical isolates of S. pneumoniae and 101 viridans streptococci and were as follows: Pneumoslide, 99 and 87%, respectively; Directigen, 100 and 85%, respectively; Phadebact, 100 and 98%, respectively; deoxycholate drop test, 99 and 98%, respectively; deoxycholate tube test, 100 and 99%, respectively; optochin, 99 and 98%, respectively; and Gram Positive Identification Card, 90 and 96%, respectively. Identification of clinical isolates of S. pneumoniae should be confirmed using one or more diagnostic assays with well-documented high (e.g., > or =95%) sensitivities and specificities.