Use of a serotype-specific DNA microarray for identification of group B Streptococcus (Streptococcus agalactiae)

Epidemiology of group B streptococcal infection in pregnant women and diseased infants in mainland China

Group B Streptococcus (GBS) is a leading cause of neonatal sepsis and an important cause of maternal disease in many countries; however, no accurate population-based epidemiological data on GBS is yet available in mainland China. In this systematic literature review, we obtained published data regarding the maternal GBS colonization rate, incidence of invasive GBS disease in infants, clinical screening, and the associated GBS typing and clinical outcomes in China. The maternal GBS colonization rate in mainland China ranged from 3.7 to 14.52%, and the incidence of invasive GBS disease in infants was 0.55-1.79 per 1000 live births, with a case fatality risk ranging from 6.45 to 7.1%. Serotype III was the dominant serotype that was observed in GBS isolates. GBS detection and identification has become more commonplace, due to the availability of polymerase chain reaction and DNA microarray technologies. Immunizing pregnant women against GBS is an emerging approach through which newborns are protected from GBS. The available data suggest that five GBS serotypes (Ia, Ib, II, III, and V) account for the majority of the cases of GBS disease in mainland China. Furthermore, conjugate vaccines comprising some or all of these serotypes are of potential value in the prevention of GBS infection.

Development and Assessment of a Diagnostic DNA Oligonucleotide Microarray for Detection and Typing of Meningitis-Associated Bacterial Species

Meningitis is commonly caused by infection with a variety of bacterial or viral pathogens. Acute bacterial meningitis (ABM) can cause severe disease, which can progress rapidly to a critical life-threatening condition. Rapid diagnosis of ABM is critical, as this is most commonly associated with severe sequelae with associated high mortality and morbidity rates compared to viral meningitis, which is less severe and self-limiting. We have designed a microarray for detection and diagnosis of ABM. This has been validated using randomly amplified DNA targets (RADT), comparing buffers with or without formamide, in glass slide format or on the Alere ArrayTube^TM (Alere Technologies GmbH) microarray platform. Pathogen-specific signals were observed using purified bacterial nucleic acids and to a lesser extent using patient cerebral spinal fluid (CSF) samples, with some technical issues observed using RADT and glass slides. Repurposing the array onto the Alere ArrayTube^TM platform and using a targeted amplification system increased specific and reduced nonspecific hybridization signals using both pathogen nucleic and patient CSF DNA targets, better revealing pathogen-specific signals although sensitivity was still reduced in the latter. This diagnostic microarray is useful as a laboratory diagnostic tool for species and strain designation for ABM, rather than for primary diagnosis.

Identification of Group B Streptococcus Capsule Type by Use of a Dual Phenotypic/Genotypic Assay

The group B streptococcus (GBS) capsular polysaccharide (CPS) is an important virulence factor which is also used for GBS typing. There are 10 CPS types (Ia, Ib, and II to IX). GBS that do not phenotypically type are considered nontypeable. All genes required for CPS synthesis are found on the GBS cps operon, which contains a highly variable CPS-determining region (cpsG-cpsK). The objective of this study was development of an assay to detect sialic acid on the GBS cell surface, followed by a genotypic PCR CPS typing assay. Sialic acid is located at the terminal end of the side chain of all known GBS CPS types. Sialic acid can be bound to commercially available lectins such as slug Limax flavus lectin. Biotinylated L. flavus-streptavidin-peroxidase complex was used in an enzyme immunoassay and dot blot assay to detect sialic acid. This was followed by a PCR typing scheme that was developed to target the serotype-determining region of the cps locus for Ia, Ib, and II to IX. Sialic acid from the CPS types Ia, Ib, and II to IX was detectable on the GBS cell surfaces of all previously identified CPS-typed GBS strains assayed. This was followed by the real-time PCR typing assay which successfully identified CPS Ia, Ib, and II to IX types. The combination of phenotypic and genotypic assays provides an accurate tool for detection of CPS expression and assignment of CPS typing. These assays have the potential to be used for CPS typing in large-scale epidemiological studies.

Multiplex PCR-based reverse line blot assay for simultaneous detection of 22 virulence genes in uropathogenic Escherichia coli

Urinary tract infections (UTIs) are among the most common bacterial infections and are responsible for significant morbidity and health care costs worldwide. The main bacterial cause of uncomplicated UTI is Escherichia coli, which possesses numerous virulence factors (VFs). Many studies of the pathogenesis of E. coli UTI have centered on VF genes. Hence, the development of better molecular assays to study VF genes would facilitate these studies. We developed a highly sensitive and specific multiplex PCR-based reverse line blot (mPCR/RLB) assay to simultaneously detect 22 VF genes of uropathogenic E. coli and then used it to characterize 180 isolates from nonpregnant women of child-bearing age with cystitis and 153 fecal isolates from similar-age healthy women, in regional New South Wales, Australia. The assay accurately identified all VF genes (of the 22 under study) known to be present in 30 previously characterized control strains. The detection limits were 28 ng of DNA from E. coli isolates and 50 CFU/ml in mock-infected urine specimens containing known concentrations of E. coli. Cystitis isolates (compared to the fecal isolates) showed a significantly higher prevalence of 18 individual VF genes and contained significantly more VF genes per isolate (median number, 18.5 versus 6.5 [P = 0.001]). Discordance between paired probes for a given VF gene occurred in several clinical test isolates but no reference strains and among the test isolates was associated with fecal source (10% of VF genes versus 2% for cystitis isolates [P < 0.001]). This novel mPCR/RLB method is a potentially powerful tool for investigating the prevalence and distribution of VFs in E. coli.

Use of a DNA microarray for detection and identification of bacterial pathogens associated with fishery products

We established a microarray for the simultaneous detection and identification of diverse putative pathogens often associated with fishery products by targeting specific genes of Listeria monocytogenes, Salmonella, Shigella, Staphylococcus aureus, Streptococcus pyogenes, Vibrio cholerae, Vibrio parahaemolyticus, Vibrio vulnificus, and Yersinia enterocolitica and the 16S-23S rRNA gene internal transcribed spacer (ITS) region of Proteus mirabilis and Proteus vulgaris. The microarray contained 26 specific probes and was tested against a total of 123 target bacterial strains that included 55 representative strains, 68 clinical isolates, and 45 strains of other bacterial species that belonged to 8 genera and 34 species, and it was shown to be specific and reproducible. A detection sensitivity of 10 ng DNA or 10 CFU/ml for pure cultures of each target organism demonstrated that the assay was highly sensitive and reproducible. Mock and real fishery product samples were tested by the microarray, and the accuracy was 100%. The DNA microarray method described in this communication is specific, sensitive, and reliable and has several advantages over traditional methods of bacterial culture and antiserum agglutination assays.

Development of a DNA microarray for detection and serotyping of enterotoxigenic Escherichia coli

Enterotoxigenic Escherichia coli (ETEC) is a common pathogen worldwide causing infectious diarrhea, especially traveler's diarrhea. Traditional physiological assays, immunoassays, and PCR-based methods for the detection of ETEC target the heat-labile enterotoxin and/or the heat-stable enterotoxin. Separate serotyping methods using antisera are required to determine the ETEC serogroup. In this study, we developed a DNA microarray that can simultaneously detect enterotoxin genes and the 19 most common O serogroup genes in ETEC strains. The specificity and reproducibility of this approach were verified by hybridization to 223 strains: 50 target reference or clinical strains and 173 other strains, including those belonging to other E. coli O serogroups and closely related species. The sensitivity of detection was determined to be 50 ng of genomic DNA or 10(8) CFU per ml of organisms in pure culture. The random PCR strategy used in this study with minimal bias provides an effective alternative to multiplex PCR for the detection of pathogens using DNA microarrays. The assay holds promise for applications in the clinical diagnosis and epidemiological surveillance of pathogenic microorganisms.

Acute bacterial meningitis in infants and children

Bacterial meningitis continues to be an important cause of mortality and morbidity in neonates and children throughout the world. The introduction of the protein conjugate vaccines against Haemophilus influenzae type b, Streptococcus pneumoniae, and Neisseria meningitidis has changed the epidemiology of bacterial meningitis. Suspected bacterial meningitis is a medical emergency and needs empirical antimicrobial treatment without delay, but recognition of pathogens with increasing resistance to antimicrobial drugs is an important factor in the selection of empirical antimicrobial regimens. At present, strategies to prevent and treat bacterial meningitis are compromised by incomplete understanding of the pathogenesis. Further research on meningitis pathogenesis is thus needed. This Review summarises information on the epidemiology, pathogenesis, new diagnostic methods, empirical antimicrobial regimens, and adjunctive treatment of acute bacterial meningitis in infants and children.

The variation of O antigens in gram-negative bacteria

The O antigen, consisting of many repeats of an oligosaccharide unit, is part of the lipopolysaccharide (LPS) in the outer membrane of Gram-negative bacteria. It is on the cell surface and appears to be a major target for both immune system and bacteriophages, and therefore becomes one of the most variable cell constituents. The variability of the O antigen provides the major basis for serotyping schemes of Gram-negative bacteria. The genes responsible for the synthesis of O antigen are usually in a single cluster known as O antigen gene cluster, and their location on the chromosome within a species is generally conserved. Three O antigen biosynthesis pathways including Wzx/Wzy, ABC-transporter and Synthase have been discovered. In this chapter, the traditional and molecular O serotyping schemes are compared, O antigen structures and gene clusters of well-studied species are described, processes for formation and distribution of the variety of O antigens are discussed, and finally, the role of O antigen in bacterial virulence.

Streptococcus agalactiae pulsed-field gel electrophoresis patterns cross capsular types

Streptococcus agalactiae is a genetically diverse organism; when typed by pulsed-field gel electrophoresis (PFGE), multiple types appear within a single serotype. We tested whether S. agalactiae PFGE types correspond to a specific serotype within individuals, and different individuals from the same geographic area. A total of 872 S. agalactiae isolates from 152 healthy individuals were classified by PFGE and capsular serotype. Serotype V was the most homogeneous (Simpson's diversity index 0.54); and types III, II and Ib were mostly heterogeneous (Simpson's diversity index 0.90). Within an individual, isolates with the same PFGE patterns had identical capsular types, but across individuals the same PFGE types sometimes occurred in different serotypes. Capsular type alone is insufficient to define epidemiological relatedness. Although PFGE types appear to be a valid surrogate for capsular typing of isolates from the same individual, it is not a valid surrogate for serotype in isolates from different individuals.

Acquisition and transmission of group B Streptococcus during pregnancy

Group B Streptococcus (GBS) is a major cause of neonatal sepsis and meningitis. We followed up 78 pregnant couples for < or =2 months to estimate the risk of GBS transmission. Among couples with discordant GBS status, we observed 1 male-to-female transmission event (1 of 3 couples in which the woman was GBS negative at enrollment), but no female-to-male transmission events (0 of 8 couples in which the man was GBS negative at enrollment).

Population structure of invasive and colonizing strains of Streptococcus agalactiae from neonates of six U.S. Academic Centers from 1995 to 1999

The purpose of this study was to describe the population structure of group B streptococci (GBS) isolated from infected and colonized neonates during a prospective active-surveillance study of early-onset disease in six centers in the United States from July 1995 to June 1999 and to examine its relationship to bovine strains of GBS. The phylogenetic lineage of each GBS isolate was determined by multilocus sequence typing, and isolates were clustered into clonal complexes (CCs) using the eBURST software program. A total of 899 neonatal GBS isolates were studied, of which 129 were associated with invasive disease. Serotype Ia, Ib, and V isolates were highly clonal, with 92% to 96% of serotype Ia, Ib, and V isolates being confined to single clonal clusters. In contrast, serotype II and III isolates were each comprised of two major clones, with 39% of serotype II and 41% of serotype III isolates in CC 17 and 41% of serotype II and 54% of serotype III isolates in CC 19. Further analysis demonstrates that the CC 17 serotype II and III GBS are closely related to a previously described "ancestral" lineage of bovine GBS. While 120 (93%) of invasive GBS were confined to the same lineages that colonized neonates, 9 (7%) of the invasive GBS isolates were from rare lineages that comprised only 2.7% of colonizing lineages. These results are consistent with those for other geographic regions that demonstrate the highly clonal nature of GBS infecting and colonizing human neonates.

Characterisation of invasive group B streptococci based on investigation of surface proteins and genes encoding surface proteins

The joint distributions of the six genes bca, bac, epsilon/alp1, alp2, alp3 and rib (encoding alpha-C-protein, beta-C-protein, epsilon/Alp1, Alp2, Alp3, and Rib, respectively) and the proteins alpha-C-protein, beta-C-protein and Rib were investigated in invasive isolates of group B streptococcus (GBS). In total, 297 invasive isolates (123 from neonates, 174 from adults) from south-west Sweden were collected during a 13-year period. Genes were detected using multiplex and specific PCRs, and expression of the surface proteins was demonstrated using monoclonal antibodies. The genes studied were found alone or in combinations in 294 (99%) of the invasive isolates. The most common genes were rib (n = 127 isolates, 43%), alp3 (n = 78, 26%) and epsilon/alp1 (n = 42, 14%). The bac gene was never found alone, but was found in combination with one other gene in 36 isolates. The surface proteins studied were detected alone or in combinations in 152 (51%) isolates, with the most common being Rib (n = 80, 27%), alpha-C-protein (n = 68, 23%) and beta-C-protein (n = 24, 8%). Several genes were associated significantly with particular serotypes (e.g., epsilon/alp1 with serotype Ia; bca and bac with serotypes Ib and II; rib with serotype III; alp3 with serotype V). Overall, it was concluded that demonstration of different genes and surface proteins of GBS strains can be useful in epidemiological studies and in formulation of vaccines, but disappointingly, no single gene or surface protein included in the study was sufficiently common for it to be considered as the basis for a successful GBS vaccine.

Multiplex PCR-based reverse line blot hybridization assay (mPCR/RLB)--a practical epidemiological and diagnostic tool

Combining multiplex PCR, sequentially, with reverse line blot hybridization (mPCR/RLB) is a convenient, objective way to identify up to 43 targets in 43 individual specimens simultaneously (using a 45-lane membrane format). It is more flexible and less expensive than DNA microarray. The number of targets is adequate for epidemiological and most clinical diagnostic applications; based on the same target (43) and specimen numbers (43), it is much more practical than conventional uniplex PCR (uPCR) and mPCR. We have used the protocol to identify and subtype bacteria, viruses and fungi and identify pathogens in clinical specimens; potentially, it could be used for many other applications, such as detection of mutations in, or identification of alleles of, eukaryotic genes. Development of each assay involves (i) careful primer and probe design, based on literature and sequence database searches, which are critical to success of the assay; and (ii) bench-top evaluation, using known samples, controls and dilution series, to confirm sensitivity, specificity and reproducibility. The assay takes about one and half working days to complete; about 4 h for the mPCR and 6 h for the RLB, including a total of 4 h 'hands-on' time.

Reevaluating the serotype II capsular locus of Streptococcus agalactiae

We report a novel sequence of the serotype II capsular locus of group B streptococcus that resolves inconsistencies among the results of various groups and the sequence in GenBank. This locus was found in diverse lineages and presents genes consistent with the complete synthesis of the type II polysaccharide.

Identification of less-common Streptococcus pneumoniae serotypes by a multiplex PCR-based reverse line blot hybridization assay

We developed a multiplex PCR-based reverse line blot (mPCR/RLB) assay to identify 50 uncommon pneumococcal serotypes. In combination with a previously described mPCR/RLB assay (3), all 90 pneumococcal serotypes can be identified individually (32 serotypes) or, because of predictable cross-reactions, to within small groups of two to five related serotypes (58 serotypes), which can be distinguished using serotype-specific antisera.

Methodologies towards the development of an oligonucleotide microarray for determination of Salmonella serotypes

A DNA-based microarray designed to detect somatic (O) and flagellar (H) antigens present in the five most commonly isolated Salmonella serovars within Canada was developed as an alternative to the traditional Kauffmann-White serotyping scheme currently used to serotype salmonellae. Short oligonucleotide probes were designed based on publicly available sequence data of selected genes responsible for O and H antigen biosynthesis. These targets included: antigen-specific sequences within the flagella (H) antigen phase 1 (fliC) and phase 2 (fljB) genes and somatic (O) antigen biosynthesis genes within the rfb cluster (Groups B--rfbJ, C1--wbaA, C2--rfbJ, D1--rfbS). A prototype microarray with 117 O and H antigen-specific probes and controls was used to assess probe performance against two pools of gene target PCR amplicons. A set of 31 of these antigen-specific probes (8 O and 23 H) with high specific signal and low non-specific signal were selected based on t-test (p-value <0.01) and log(2) ratio distribution analysis to create a prototype microarray. The microarray was tested against 16 Salmonella strains of known serotype. Based on the strains tested in this study, these probes successfully identified and differentiated 11 of the 12 antigens targeted. The prototype DNA-based typing microarray described here has the potential to be an automated alternative to the traditional antigen-antibody serotyping scheme currently used for Salmonella.

Molecular epidemiology and distribution of serotypes, surface proteins, and antibiotic resistance among group B streptococci in Italy

Group B streptococci (GBS) comprising three different sets of isolates (31 invasive, 36 noninvasive, and 24 colonizing isolates) were collected in Italy during the years 2002 to 2005. Clonal groups were established by pulsed-field gel electrophoresis (PFGE), and selected isolates were studied by multilocus sequence typing (MLST). GBS isolates were also characterized by classical and molecular techniques for serotyping and protein gene and antibiotic resistance profiling. Some serotypes were significantly associated with a particular isolate population: serotype Ia more frequently corresponded to invasive strains than other strains, serotype V was more frequently encountered among noninvasive strains, and nontypeable strains were more common among isolates from carriers. Four major clonal groups accounted for 52.7% of all isolates: PFGE type 1/clonal complex 1 (CC1) comprised mainly serotype V isolates carrying the alp3 gene, PFGE type 2/CC23 encompassed serotype Ia isolates with the alp1 or alpha gene, PFGE type 3/CC17 comprised serotype III isolates carrying the rib gene, and PFGE type 4/CC19 consisted mainly of serotype II isolates possessing the rib gene. The same serotypes were shared by isolates of different clonal groups, and conversely, isolates belonging to the same clonal groups were found to be of different serotypes, presumably due to capsular switching by the horizontal transfer of capsular genes. Erythromycin resistance (prevalence, 16.5%; 15 resistant isolates of 91) was restricted to strains isolated from patients with noninvasive infections and carriers, while tetracycline resistance was evenly distributed (prevalence, 68.1%; 62 resistant isolates of 91). Most erythromycin-resistant GBS strains were of serotype V, were erm(B) positive, and belonged to the PFGE type 1/CC1 group, suggesting that macrolide resistance may have arisen both by clonal dissemination and by the horizontal transfer of resistance genes.

Multiplex PCR assay for rapid and accurate capsular typing of group B streptococci

We developed a simple, specific, and sensitive two-multiplex-PCR assay that enabled the detection of all known group B streptococcal (GBS) capsular polysaccharides. This test is well adapted for GBS capsular polysaccharide typing in large-scale epidemiological studies.