Application of molecular typing to the epidemiology of Streptococcus pneumoniae

Description of optochin-resistant Streptococcus pneumoniae due to an uncommon mutation in the atpA gene and comparison with previously identified atpC mutants from Brazil

Optochin susceptibility testing is a major assay used for presumptive identification of Streptococcus pneumoniae. Still, atypical optochin-resistant (Opt^r) pneumococci have been reported and this phenotype has been attributed to nucleotide substitutions in the genes coding for the F₀F₁ATPase. While substitutions in the atpC gene (c-subunit of ATPase) are more common and better characterized, data on mutations in the atpA (a-subunit) are still limited. We have characterized five Opt^r isolates presenting alterations in the atpA (Trp206Cys in four isolates and Trp206Ser in one isolate), constituting the first report of such mutations in Brazil. Most of the Opt^r isolates consisted of heterogeneous populations. Except for Opt MICs and the nucleotide changes in the atpA gene, Opt^r and Opt^s subpopulations originating from the same culture had identical characteristics. In addition, we compared phenotypic and genetic characteristics of these atpA mutants with those of atpC mutants previously identified in Brazil. No structural alterations were detected among predicted proteins, regardless of mutations in the coding gene, suggesting that, despite the occurrence of mutations, protein structures tend to be highly conserved, ensuring their functionalities. Phylogenetic analysis revealed that atypical Opt^r strains are true pneumococci and Opt resistance does not represent any apparent selective advantage for clinical isolates.

Important Mutations Contributing to High-Level Penicillin Resistance in Taiwan19F-14, Taiwan23F-15, and Spain23F-1 of Streptococcus pneumoniae Isolated from Taiwan

Penicillin-resistant Streptococcus pneumoniae is a serious concern worldwide. In this study, we analyzed the cause of β-lactam resistance in pandemic multidrug-resistant clones. A total of 41 penicillin-nonsusceptible clinical isolates were collected from 1996 to 2012. Sero- and molecular typing confirmed that these isolates were clonal types of Taiwan^19F-14, Taiwan^23F-15, and Spain^23F-1. Sero-switching was found in four isolates. All isolates were multidrug resistant. Sequencing analysis of the penicillin binding proteins (PBPs) was performed on PBP1a, 2b, and 2x, and a large number of mutations were identified in comparing to clinical penicillin-susceptible isolates and the recipient strain R6 used for homologous recombination. The T₄₅₁A substitution was the key amino acid in PBP2b that contributed to penicillin resistance. T₃₃₈A in PBP2x played a role in resistance and reached the highest level of resistance when combined with other mutations in PBP2x. High-level penicillin resistance could not be obtained without the combination of mutations in PBP1a with PBP2b and 2x. The amino acid substitutions in PBP1a, 2b, and 2x were the crucial factors for β-lactam resistance.

Genotyping Streptococcus pneumoniae

ABSTRACT 

Streptococcus pneumoniae is a potentially deadly human pathogen associated with high morbidity, mortality and global economic burden. The universally used bacterial genotyping methods are multilocus sequence typing and pulsed field gel electrophoresis. However, another highly discriminatory, rapid and less expensive genotyping technique, multilocus variable number of tandem repeat analysis (MLVA), has been developed. Unfortunately, no universal MLVA protocol exists, and some MLVA protocols do not amplify certain loci for all pneumococcal serotypes, leaving genotyping profiles incomplete. A number of other genotyping or characterization methods have been developed and will be discussed. This review examines the various protocols for genotyping S. pneumoniae and highlights the current direction technology and research is heading to understand this bacterium.

Site-specific disease potential of individual Streptococcus pneumoniae serotypes in pediatric invasive disease, acute otitis media and acute conjunctivitis

BACKGROUND

Recent studies have shown that some Streptococcus pneumoniae serotypes possess a higher potential to cause invasive disease than others. However, it is unknown whether disease potential for specific serotypes is similar for mucosal disease. Our objective was to assess the disease potential of individual S. pneumoniae serotypes causing invasive pneumococcal disease (IPD), acute otitis media (AOM) and acute conjunctivitis (AC) in children.

METHODS

Serotypes of pneumococcal isolates from children with IPD, AOM and AC were compared with those carried by healthy children aged <3 years. All children resided in the same area and were studied during the same period. Odds ratios for disease were calculated for each diagnosis following multivariate analysis, including gender, age, ethnic group, previous antibiotic treatment and year variability.

RESULTS

A total of 5,500 isolates were collected: 189 from blood or cerebrospinal fluid, 3,200 from middle ear fluid, 348 from conjunctiva and 1,763 from nasopharynx of healthy children. A significant positive association with IPD was demonstrated for serotypes 1, 5 and 12F; with AOM for serotypes 1, 3, 5, 12F, 19A and 19F; and with AC for serotype 3 and nontypeable S. pneumoniae. A significant negative association with IPD was demonstrated for nontypeable S. pneumoniae and with AOM for serotypes 6A, 6B, 15A and nontypeable S. pneumoniae.

CONCLUSIONS

Our results reflect the importance of the polysaccharide capsule in site-specific disease potential and provide useful information regarding disease potential of nonvaccine serotypes shown to be involved in carriage replacement after vaccination with the 7-valent conjugate vaccine.

Managing acute lower respiratory tract infections in an era of antibacterial resistance

Respiratory tract infections account for more than 116 million office visits and an estimated 3 million visits to hospital EDs annually. Patients presenting at EDs with symptoms suggestive of lower respiratory tract infections of suspected bacterial etiology are often severely ill, thus requiring a rapid presumptive diagnosis and empiric antimicrobial treatment. Traditionally, clinicians have relied on beta-lactam or macrolide antibiotics to manage community-acquired lower respiratory tract infections. However, the emerging resistance of Streptococcus pneumoniae to beta-lactams and/or macrolides may affect the clinical efficacy of these agents. Inappropriate use of antibiotics and use of agents with an overly broad spectrum of antimicrobial activity have contributed to the emergence of antibiotic resistance. When treating respiratory infections, clinicians need to prescribe antimicrobial agents only for those individuals with infections of suspected bacterial etiology; to select agents with a targeted spectrum of activity that ensures coverage against typical S pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis strains, including antibiotic-resistant strains and atypical pathogens; and to consider agents with specific chemical properties that limit the development of antimicrobial resistance and that achieve concentrations at sites of infection that exceed those required for bactericidal activity. Newer classes of antimicrobial agents, such as the oxazolidinones and ketolides, will likely play a significant role in this era of antimicrobial resistance.

Loop-mediated isothermal amplification method targeting the lytA gene for detection of Streptococcus pneumoniae

It is difficult to separate Streptococcus pneumoniae from the genotypically similar species Streptococcus mitis and Streptococcus oralis, which are commensals of the human oral cavity. A novel nucleic acid amplification technique, loop-mediated isothermal amplification (LAMP), which amplifies DNA under isothermal conditions (63 degrees C) with high specificity, efficiency, and rapidity, was examined regarding its applicability for detecting S. pneumoniae. An S. pneumoniae-specific LAMP primer targeting the lytA gene was designed. The primer specificity was validated using 10 Streptococcus and 7 non-Streptococcus species. Within 60 min, the assay could detect 10 or more copies of purified S. pneumoniae DNA with a sensitivity 1,000 times that of conventional PCR. Clinical isolates of 21 other strains (3 S. oralis, 17 S. mitis, and 1 Streptococcus species) that harbor virulence-factor-encoding genes (lytA or ply) were tried to differentiate S. pneumoniae. The detection of S. pneumoniae in clinical isolates was more selective using the LAMP method than using conventional PCR. Therefore, LAMP appears to be a sensitive and reliable means of diagnosing S. pneumoniae infection.

Analysis of the genetic structure of nontypeable pneumococcal strains isolated from conjunctiva

More than 50% of the nontypeable (NT) pneumococcal strains received in our laboratory for reference purposes are isolated in sporadic cases of conjunctivitis. To determine the genetic structure of the population of these NT conjunctival strains, we analyzed 75 pneumococci (40 NT and 35 typeable) isolated from conjunctivas and 30 (15 NT and 15 typeable) isolated from other sources. The NT and typeable conjunctival strains grouped in separate clusters, whereas NT and typeable pneumococci isolated from other sources were similarly distributed. NT conjunctival strains belonged to two well-differentiated clonal lineages. The first, represented by three newly described sequence types, featured fully antibiotic susceptible strains and appeared to be characteristic of conjunctival tissue; the second, represented by the previously described ST344, had a pattern of multiresistance to penicillin, tetracycline, and erythromycin and shared a genetic background with some NT strains isolated from other sources.

Comparison of serotyping, pulsed field gel electrophoresis and amplified fragment length polymorphism for typing of Streptococcus pneumoniae

The aim of the present study was to compare serotyping, PFGE and AFLP for typing of Streptococcus pneumoniae with regard to discriminatory power, typeability and typing system concordance. Thirty-four isolates from cerobrospinal fluid and 34 time-matched blood culture isolates collected from in-patients at two hospitals in western Norway during the period from January 1994 to May 2002 were included in the study. The discriminatory powers of serotyping, PFGE and AFLP were 0.93, 0.99 and 0.95, respectively. The typeabilities for serotyping, PFGE and AFLP were 1, 1 and 0.99, respectively. A good concordance was shown between all the typing methods. Serotyping would most probably have a higher discriminatory power if further subtyping had been performed. PFGE was more discriminatory than AFLP, and AFLP grouped more-distantly related isolates together. The two typing methods thus provided different information, and therefore both could be useful adjuncts to serotyping for the characterization of S. pneumoniae.

Molecular genetic methods in diagnosis and direct characterization of acute bacterial central nervous system infections

Acute bacterial infection of the central nervous system requires rapid and adequate management. Etiological diagnosis is hence crucial. Moreover, the epidemic threat of certain bacteria necessitates a reliable characterization of the involved bacterial strains to follow the spread of epidemic strains. Conventional identification and characterization of etiological agents are basically based on culture and identification of bacterial markers most frequently by serological assays. Molecular identification and characterization of bacteria have been employed. They provide more reliable analysis of bacterial isolates. Molecular methods for non-culture diagnosis of bacterial infections have recently been developed. In many cases, the molecular assays have decreased the identification time of positive cultures and rescued detection of pathogens in culture-negative clinical samples.

Antibiotic-resistant invasive pediatric Streptococcus pneumoniae clones in Israel

Antibiotic-resistant international clones of Streptococcus pneumoniae are increasingly reported in different parts of the world. We investigated the spread of these clones through an active surveillance performed at the Israeli Streptococcal National Center during 1998 and 1999. Isolates were tested for antibiotic susceptibility, serotyped, and genotyped by random amplified polymorphic DNA analysis and pulsed-field gel electrophoresis. Of 437 isolates, 276 (63.4%) were antibiotic resistant and 156 (35%) were penicillin nonsusceptible (PNS). The PNS isolates were less frequently encountered in southern Israel (27 of 136 [20%]) than in other regions (127 of 301 [42%]). Among 276 antibiotic-resistant isolates, 43 fingerprint patterns were observed. The most common clones were 9V/14-a (19.2%), 5-a (17.8%), and 1-a (10%). The 9V/14-a clone was less common, while the 1-a clone was more frequent in the south than in other regions. The 5-a clone was more common in Jerusalem than in other regions. Among the Jewish and Arab populations the most frequent clones were 9V/14-a (20%) and 1-a (25%), respectively. Three international clones, 9V/14-a-Spain(9V)-3, 6B-a-Spain(6B)-2, and 5-a-Colombia(5)-19, comprised 40% of all antibiotic-resistant isolates and 56% of all PNS isolates. The seven-valent conjugate vaccine covers 58% of the most common clones, all highly PNS clones, and 94% of the multidrug-resistant clones in Israel, while the nine-valent vaccine covers all of them. The most common antibiotic-resistant invasive pediatric S. pneumoniae clones-mainly the three international ones-contribute significantly to increases in antibiotic resistance. Their geographic distribution varies within the country and between the different populations.

Using cpsA-cpsB sequence polymorphisms and serotype-/group-specific PCR to predict 51 Streptococcus pneumoniae capsular serotypes

Streptococcus pneumoniae polysaccharide and protein-conjugate vaccines are available against the most commonly isolated pneumococcal serotypes. Ongoing surveillance of invasive pneumococcal disease is needed in order to monitor changes in distribution of serotypes. Based on previously published sequences of capsular polysaccharide synthesis (cps) gene clusters of 16 pneumococcal serotypes, a molecular capsular typing (MCT) system has been developed, based on a combination of partial cpsA-cpsB sequencing and serotype- or serogroup-specific PCR, targeting the genes wzy and wzx (except for serotype 3). In this study, 151 S. pneumoniae isolates of known serotype (representing 51 serotypes) and 276 recent clinical isolates were used to develop MCT and compare it with conventional serotyping (CS) (total 427 isolates). On the basis of 376 heterogeneity sites in the cpsA-cpsB region, 89 sequence types (ST) were identified, of which 76 corresponded to a single serotype and 11 contained two serotypes. The correct serotypes in two of the latter (10A-23F-g and 23F-23A) were identified using serotype 23F-specific PCR. Limited CS was required for 92 (22 %) isolates to distinguish between the two serotypes in the nine other mixed ST (6A-6B-g, 6A-6B-q, 15B-22F, 33F-33A, 17F-35B, 18B-18C, 13-20, 25F-38, 31-42). MCT is a specific, objective and practical method that can predict the serotype of most S. pneumoniae isolates; it will facilitate epidemiological studies. Further study of the relationship between MCT and CS is needed in order to improve our understanding of serotype differentiation and to improve MCT methods further.

Penicillin susceptibility and molecular characteristics of clinical isolates of Streptococcus pneumoniae at the University of Malaya Medical Center, Kuala Lumpur, Malaysia

OBJECTIVE

To determine the prevalence of penicillin resistance and molecular characteristics of pneumococcal isolates at the University of Malaya Medical Center.

METHODS

From March 1999 to July 2000, 100 clinical isolates of Streptococcus pneumoniae were obtained from 93 patients of various ages and from various body sites. The minimum inhibitory concentrations (MICs) for penicillin and ceftriaxone were determined by E test, and results were interpreted according to guidelines recommended by the National Committee for Clinical Laboratory Standards (NCCLS). Fifty isolates were further serotyped, and analyzed by pulsed-field gel electrophoresis (PFGE) and polymerase chain reaction/restriction fragment length polymorphism (PCR-RFLP) of the penicillin-binding protein (pbp) 2b and 2x genes.

RESULTS

The majority of the isolates were from respiratory sites. Thirty-one isolates showed decreased susceptibility to penicillin (PRSP), and many of these also showed decreased susceptibility to ceftriaxone. Twelve serogroup/types (SGTs) were present, with 19F being the most common. PFGE analysis identified two dominant profiles, consisting mainly of PRSPs that had common serotypes (19F) and pbp gene patterns within their respective groups, although PCR-RFLP analysis showed different patterns of pbp genes among the PRSPs as compared to penicillin-susceptible strains, which had a uniform pattern.

CONCLUSION

PRSPs were genetically related as shown by PFGE and serotype. The consistency of pbp gene patterns, observed among many of the PRSPs within their respective PFGE profiles, supported their relatedness as established by PFGE.

Penicillin susceptibility and epidemiological typing of invasive pneumococcal isolates in the Republic of Ireland

A national study was undertaken to investigate the incidence of invasive pneumococcal disease in the Republic of Ireland and to examine the associated isolates. In 1999, 144 S. pneumoniae isolates, all recovered from cases of invasive disease, were received from 12 microbiology laboratories. The incidence of invasive pneumococcal disease was estimated to be 6.6/100000 population. All isolates were analyzed for serotype, penicillin susceptibility, chromosomal relatedness (by using pulsed-field gel electrophoresis [PFGE]), and penicillin-binding protein (pbp) fingerprinting. Several findings of note were observed regarding the pneumococcal population in Ireland. First, isolates of 25 different serotypes were represented, with serotypes 14, 9V, 8, 5, 4, and 3 being the most common. This finding, together with the pbp fingerprinting and PFGE typing results, indicated the clonal spread of strains of these serotypes in Ireland. Second, 27 (18.7%) isolates had reduced susceptibility to penicillin, and 74% of these were serotype 9V. Of these, 80% appeared to belong to the same clone. This could suggest the spread of the international Spanish/French 9V penicillin-resistant clone into Ireland. Third, nine different pbp genotypes were identified, four of which were new. Two pbp genotypes accounted for the majority of isolates dividing them according to their penicillin susceptibility status but irrespective of serotype and PFGE type. This is strong evidence for the occurrence of horizontal transfer of pbp genes between strains, observed with both penicillin-susceptible and penicillin-nonsusceptible isolates. Fourth, there was evidence of serotype transformation since isolates, indistinguishable by pbp fingerprinting and PFGE typing, expressed different capsular types.

Emergence of penicillin-nonsusceptible Streptococcus pneumoniae invasive clones in Canada

Distinctive international clones of penicillin-nonsusceptible and multidrug-resistant Streptococcus pneumoniae are increasingly being reported. We investigated the spread of these clones in Canada through an active surveillance that was carried out at 11 Canadian pediatric tertiary care centers from 1991 to 1998. All penicillin-nonsusceptible isolates were serotyped, tested for antibiotic susceptibility, and genotyped by pulsed-field gel electrophoresis (PFGE) and random amplified polymorphic DNA (RAPD). Forty-five penicillin-nonsusceptible S. pneumoniae isolates were evaluated. Eleven serotype 9V isolates and six serotype 14 isolates displayed identical RAPD and PFGE fingerprint profiles. Twelve (70%) of these isolates were encountered in Quebec. The 9V/14 clone and the Spanish-French clone had similar PFGE fingerprint patterns. Eight isolates of serotype 23F and two isolates of serogroup 14 had the same fingerprint profiles and displayed resistance to three or more antibiotic drug classes. This clone was first detected in Calgary (Alberta) and in 1996 appeared simultaneously in various regions of Canada. This clone showed a PFGE fingerprint pattern similar to that of the Spanish-U.S. 23F clone. Our data show the emergence across Canada of two international clones of penicillin-nonsusceptible S. pneumoniae: (i) serotypes 9V and 14 related to the Spanish-French clone and (ii) the 23F Spanish-U.S. clone. The source of the first clone was in Quebec and the second international clone was probably originated from the United States. The exact reasons for the successful spread of these clones within Canada and their contribution to increased resistance to antibiotics have yet to be explored.

Random amplified polymorphic DNA analysis applied to acute otitis media caused by penicillin non-susceptible Streptococcus pneumoniae

The spread of penicillin non-susceptible Streptococcus pneumoniae (PNSSP) is an emerging problem for the treatment of acute otitis media (AOM). Attendance of children at day care centers, as well as the spread of PNSSP, is a risk factor for AOM. The status of the spread of PNSSP during the acute infection phase of AOM has not been evaluated. We examined the clonality of samples from seven children in a day care center who simultaneously developed AOM caused by PNSSP. The seven isolates from the children, and six control samples were grouped by serotyping, by determining resistance to antimicrobial agents, and by genotyping, carried out by sequencer-based random amplified polymorphic DNA (RAPD), and validated by bootstrap analysis. There was no evidence to indicate the direct dissemination of PNSSP among these patients in the day care center, although the simultaneous occurrence of PNSSP AOM had initially suggested a clonal outbreak. The possible presence of a common ancestral strain suggested the importance of surveillance during the carrier state. The result of RAPD genotyping was highly reproducible, as validated by the high bootstrap score. The use of an automated sequencer, in combination with a careful choice of primers, and commercially established kits, played a significant role in the reproducibility of the studies.

Comparison of automated ribotyping to pulsed-field gel electrophoresis for genetic fingerprinting of Streptococcus pneumoniae

Fifty-two isolates of Streptococcus pneumoniae were characterized by pulsed-field gel electrophoresis (PFGE) and automated ribotyping by using HindIII and PvuII. HindIII ribotypes correlated well with PFGE. PvuII produced fewer bands and was less discriminatory. Automated ribotyping with HindIII is an accurate method for genetic fingerprinting of S. pneumoniae and can complement PFGE.

Sensitive and specific method for rapid identification of Streptococcus pneumoniae using real-time fluorescence PCR

Molecular surveillance of pathogens has shown the need for rapid and dependable methods for the identification of organisms of clinical and epidemiological importance. As the leading cause of community-acquired pneumonia, Streptococcus pneumoniae was used as a model organism to develop and refine a real-time fluorescence PCR assay and enhanced DNA purification method. Seventy clinical isolates of S. pneumoniae, verified by latex agglutination, were screened against 26 negative control clinical isolates employing a TaqMan assay on a thermocycler (LightCycler). The probe, constructed from the lytA gene, correctly detected all S. pneumoniae genomes without cross-reaction to negative controls. The speed and ease of this approach will make it adaptable to identification of many bacterial pathogens and provide potential for adaptation to direct detection from patient specimens.

Comparison of results generated by serotyping, pulsed-field restriction analysis, ribotyping, and repetitive-sequence PCR used to characterize penicillin-resistant pneumococci from the United States

One hundred forty-seven isolates of Streptococcus pneumoniae with high-level penicillin resistance collected during a national surveillance program in the United States were characterized by serotyping, pulsed-field restriction analysis, ribotyping, and repetitive-sequence (BOX element) PCR. The results generated by each method were compared by frequency of association to examine whether relationships existed between the various typing methods and statistically to determine association with the geographic source of the isolate or the age of the patient from whom the isolate was obtained. When the data were examined by pairwise analysis of individual strain classifications produced by each typing method, no statistically significant relationships between strain type, geographic location, or patient age were identified, suggesting that distinct clones of penicillin-resistant S. pneumoniae have been widely distributed throughout the United States. However, we did observed shared expression of two or three typing markers at a high frequency (>50%) among clusters of strains, indicating a certain level of concordance between the various typing methods used to classify penicillin-resistant S. pneumoniae.

Genetic relatedness among nontypeable pneumococci implicated in sporadic cases of conjunctivitis

Nontypeable Streptococcus pneumoniae is a common cause of epidemic conjunctivitis. A previous molecular fingerprinting study identified a clone of nontypeable pneumococcus that was responsible for a recent outbreak of conjunctivitis. In the present study, we examined the extent to which pneumococci that cause sporadic cases of conjunctivitis are related to this epidemic strain. Using arbitrarily primed BOX-PCR, we have determined that, of 10 nontypeable pneumococci causing sporadic conjunctivitis, 5 were clonal and closely related to a previous outbreak strain, whereas 5 others were genetically diverse.

Decreased susceptibility of Streptococcus pneumoniae to fluoroquinolones in Canada. Canadian Bacterial Surveillance Network

BACKGROUND

Fluoroquinolones are now recommended for the treatment of respiratory tract infections due to Streptococcus pneumoniae, particularly when the isolates are resistant to beta-lactam antibiotics. Although pneumococci with reduced susceptibility to fluoroquinolones have been identified, their prevalence has not been determined in a defined population.

METHODS

We performed susceptibility testing on 7551 isolates of S. pneumoniae obtained from surveillance in Canada in 1988 and from 1993 to 1998. Pneumococci with reduced susceptibility to fluoroquinolones (defined as a minimal inhibitory concentration of ciprofloxacin of at least 4 microg per milliliter) were further characterized. We also examined antibiotic prescriptions dispensed in Canadian retail pharmacies.

RESULTS

Between 1988 and 1997, fluoroquinolone prescriptions increased from 0.8 to 5.5 per 100 persons per year. The prevalence of pneumococci with reduced susceptibility to fluoroquinolones increased from 0 percent in 1993 to 1.7 percent in 1997 and 1998 (P=0.01). Among adults, the prevalence increased from 1.5 percent in 1993 and 1994 combined to 2.9 percent in 1997 and 1998 combined. The prevalence was higher in isolates from older patients (2.6 percent among those 65 years of age or older vs. 1.0 percent among those 15 to 64 years of age, P<0.001) and among those from Ontario (1.5 percent, vs. 0.4 percent among those from the rest of Canada; P< 0.001). Fluoroquinolone use was greatest among the elderly and in Ontario. The 75 isolates (17 serotypes) of pneumococci with reduced susceptibility to fluoroquinolones were submitted by 40 laboratories in eight provinces. Reduced susceptibility to fluoroquinolones was associated with resistance to penicillin.

CONCLUSIONS

The prevalence of pneumococci with reduced susceptibility to fluoroquinolones is increasing in Canada, probably as a result of selective pressure from the increased use of fluoroquinolones.