Genomic diversity among Streptococcus agalactiae isolates detected by a degenerate oligonucleotide-primed amplification assay

Phenotype, genotype and pathogenicity of Streptococcus agalactiae isolated from cultured tilapia (Oreochromis spp.) in Taiwan

Tilapia (Oreochromis spp.) is globally used as an aquaculture fish species due to its high growth rate and disease resistance. However, it faces an increased risk of streptococcosis. Streptococcus agalactiae, also known as group B streptococcus (GBS), is the most important tilapia pathogen in Asia. Studies of Str. agalactiae infection in Taiwan are still unclear. Thus, this study aimed to explore the phenotype, genotype and pathogenicity of Str. agalactiae isolated from cultured tilapia in Taiwan in 2016-2018. The analysis revealed that 85% of the strains displayed β-haemolysis and 15% showed γ-haemolysis, with the same capsule level, and were positive for the CAMP test. The Rapid ID 32 Strep test showed a similarity of Rapid ID 32 Strep is more than 99.5% to GBS. Genotypic distribution by molecular serotyping detected only serotype Ia from all isolates, despite the regional differences. Pulsed-field gel electrophoresis (PFGE) was categorized into 3 and 10 clusters by restriction enzymes SmaI and ApaI, respectively. Virulence genes and antimicrobial resistance genes presented the same profile in all isolates. The challenge test with 10⁶  CFU/fish (LD₅₀ ), administered intraperitoneally, showed that the β-haemolysis strains had a higher mortality rate than γ-haemolysis, although they were from the same cluster from PFGE, year and region.

Phenotypic and Genotypic Characterization of Resistance to Macrolides and Lincosamides in Streptococcus agalactiae Isolated from Pregnant Women in Misiones, Argentina

The aim of this work was to determine the susceptibility, molecular profile, and clonal relationship in Streptococcus agalactiae (group B Streptococcus [GBS]) isolated from vaginal-rectal swab samples. We worked with 200 isolates collected from pregnant women between 35 and 37 weeks of gestation. The macrolide-lincosamide-streptogramin B (MLS_B) resistance phenotypes were determined using the double-disc assay. Susceptibility to erythromycin (ERI) and clindamycin (CLI) was performed with the E-test. Resistance genes ermB and ermTR were detected by polymerase chain reaction. Clonal studies were performed using the random amplification of polymorphic DNA. Twelve (6%) of the isolates were resistant to ERI and 10 (5%) of them to CLI. Fifty percent of the resistant strains corresponded to serotype III, 25% to serotype V, and the remaining 25% to serotype Ia, II, and nontypeable strains. The cMLS_B phenotype was detected in eight strains (66.67%) and the iMLS_B phenotype in four (33.33%). The minimum inhibitory concentration values were between 1.5 and 16 μg/mL for ERI, and between 1 and 32 μg/mL for CLI. Out of the 25 strains susceptible to ERI and CLI, the presence of the ermB gene was detected in eight of them and the ermTR gene in one strain. The ermB gene was detected in the 12 strains that initially had some macrolide resistance phenotype. The ermTR gene was detected in three out of the four strains with the iMLS_B phenotype. The resistance to macrolides in the province of Misiones is due to multiclonal spread. The phenotypic and genotypic characterization of macrolide resistance in GBS strains are crucial to contribute to the correct intrapartum prophylactic antibiotic therapy of allergic pregnant women and the epidemiological surveillance of these strains.

Genomic Insights Into the Distribution and Evolution of Group B Streptococcus

Streptococcus agalactiae, also known as Group B Streptococcus (GBS), is a bacteria with truly protean biology. It infects a variety of hosts, among which the most commonly studied are humans, cattle, and fish. GBS holds a singular position in the history of bacterial genomics, as it was the substrate used to describe one of the first major conceptual advances of comparative genomics, the idea of the pan-genome. In this review, I describe a brief history of GBS and the major contributions of genomics to understanding its genome plasticity and evolution as well as its molecular epidemiology, focusing on the three hosts mentioned above. I also discuss one of the major recent paradigm shifts in our understanding of GBS evolution and disease burden: foodborne GBS can cause invasive infections in humans.

Genotyping of Streptococcus agalactiae (group B streptococci) isolated from vaginal and rectal swabs of women at 35-37 weeks of pregnancy

BACKGROUND

Group B streptococci (GBS), or Streptococcus agalactiae, are the leading bacterial cause of meningitis and bacterial sepsis in newborns. Here we compared different culture media for GBS detection and we compared the occurrence of different genotypes and serotypes of GBS isolates from the vagina and rectum.

METHODS

Streptococcus agalactiae was cultured separately from both rectum and vagina, for a total of 150 pregnant women, i) directly onto Columbia CNA agar, or indirectly onto ii) Granada agar resp. iii) Columbia CNA agar, after overnight incubation in Lim broth.

RESULTS

Thirty six women (24%) were colonized by GBS. Of these, 19 harbored GBS in both rectum and vagina, 9 only in the vagina and 8 exclusively in the rectum. The combination of Lim broth and subculture on Granada agar was the only culture method that detected all GBS positive women. Using RAPD-analysis, a total of 66 genotypes could be established among the 118 isolates from 32 women for which fingerprinting was carried out. Up to 4 different genotypes in total (rectal + vaginal) were found for 4 women, one woman carried 3 different genotypes vaginally and 14 women carried two 2 different genotypes vaginally. Only two subjects were found to carry strains with the same genotype, although the serotype of both of these strains was different.Eighteen of the 19 subjects with GBS at both sites had at least one vaginal and one rectal isolate with the same genotype.We report the presence of two to four different genotypes in 22 (61%) of the 36 GBS positive women and the presence of identical genotypes in both sites for all women but one.

CONCLUSION

The combination of Lim broth and subculture on Granada medium provide high sensitivity for GBS detection from vaginal and rectal swabs from pregnant women. We established a higher genotypic diversity per individual than other studies, with up to four different genotypes among a maximum of 6 isolates per individual picked. Still, 18 of the 19 women with GBS from both rectum and vagina had at least one isolate from each sampling site with the same genotype.

Selection, recombination, and virulence gene diversity among group B streptococcal genotypes

Transmission of group B Streptococcus (GBS) from mothers to neonates during childbirth is a leading cause of neonatal sepsis and meningitis. Although subtyping tools have identified specific GBS phylogenetic lineages that are important in neonatal disease, little is known about the genetic diversity of these lineages or the roles that recombination and selection play in the generation of emergent genotypes. Here, we examined genetic variation, selection, and recombination in seven multilocus sequence typing (MLST) loci from 94 invasive, colonizing, and bovine strains representing 38 GBS sequence types and performed DNA sequencing and PCR-based restriction fragment length polymorphism analysis of several putative virulence genes to identify gene content differences between genotypes. Despite the low level of diversity in the MLST loci, a neighbor net analysis revealed a variable range of genetic exchange among the seven clonal complexes (CCs) identified, suggesting that recombination is partly responsible for the diversity observed between genotypes. Recombination is also important for several virulence genes, as some gene alleles had evidence for lateral gene exchange across divergent genotypes. The CC-17 lineage, which is associated with neonatal disease, is relatively homogeneous and therefore appears to have diverged independently with an exclusive set of virulence characteristics. These data suggest that different GBS genetic backgrounds have distinct virulence gene profiles that may be important for disease pathogenesis. Such profiles could be used as markers for the rapid detection of strains with an increased propensity to cause neonatal disease and may be considered useful vaccine targets.

Comparative time-kill study of doxycycline, tigecycline, sulbactam, and imipenem against several clones of Acinetobacter baumannii

To assess potential alternative options for the treatment of infections caused by Acinetobacter baumannii, we performed time-kill studies of doxycycline and tigecycline using several isolates recovered from patients residing in 10 different cities in Argentina. Imipenem and sulbactam were also included for comparison purposes. Eleven isolates representing 5 distinctive clones, or isolates with different susceptibility patterns within the same clone, were selected. Tubes containing cation-supplemented Mueller-Hinton broth with and without antibiotics were seeded with a log-phase inoculum of roughly 5 x 10(5) CFU/mL. By using the viable counts determined at 2-, 4-, 6-, 8-, and 24-h intervals after inoculation, a 24-h time-kill curve was constructed for each isolate. No bactericidal activity (defined as a >or=3-log(10) CFU/mL decrease in the viable cell counts with respect to the original inoculum) was observed at any time with sulbactam (4 microg/mL) or tigecycline (1 microg/mL), whereas low bactericidal rate (18% of the isolates) was shown for doxycycline (1 microg/mL) and sulbactam (16 microg/mL) after 24 h of incubation. Doxycycline (4 microg/mL) and tigecycline (8 microg/mL) displayed bactericidal activity at 24 h of incubation against 36% and 54% of the isolates, respectively, including the carbapenem-resistant isolate. Corresponding values for imipenem (1 and 4 microg/mL) against the 10 carbapenem-susceptible isolates were 60% and 90%, respectively. The present study confirms the in vitro efficacy of imipenem against A. baumannii, suggests that doxycycline could be a suitable, cost-effective, alternative option in some instances, and sheds light on the potential role of tigecycline in the treatment of infections with this organism.

A composite transposon associated with erythromycin and clindamycin resistance in group B Streptococcus

Group B Streptococcus (GBS) resistant to erythromycin and clindamycin has been isolated with increasing frequency since the mid-1990s. This work studied GBS isolates from three US cities to determine the genetic basis of the macrolide resistance phenotype. ermB genes were amplified from five isolates collected in Boston, Pittsburgh and Seattle from infant and adult sources. Gene-walking methods were used to determine the chromosomal location of ermB and to identify associated genes. Southern mapping and random amplified polymorphic DNA (RAPD) analyses were used to distinguish the isolates. The ermB gene was present on the chromosome within a composite Tn917/Tn916-like transposon similar to one identified in Streptococcus pneumoniae. Four strains from Boston and Pittsburgh were serotype V and identical by Southern hybridization and RAPD analysis. The Seattle isolate was serotype Ib, with different patterns on RAPD analysis and Southern mapping. The composite transposon was integrated at an identical chromosomal site in all five isolates. The presence of this composite transposon in both GBS and pneumococci suggests that ermB-mediated macrolide resistance in streptococci may be due to the horizontal transfer of a mobile transposable element, and raises concern for further dissemination of high-grade erythromycin and clindamycin resistance among streptococcal species.

Genomic diversity and evolution within the species Streptococcus agalactiae

Streptococcus agalactiae is a leading cause of invasive infections in neonates, and responsible for bovine mastitis. It is also a commensal bacterium adapted to asymptomatic colonization of the mammalian gut and of the genitourinary tract. Here, we report the analysis of a collection of 75 strains of human and animal origin by using serotyping, multilocus sequence typing, whole genome DNA-array hybridizations and sequence comparison of putatively virulence-associated loci. Although the most variable parts of the genome are the previously predicted genomic islands, significant genetic variations were present in the genome backbone. Evolution within genes encoding surface and secreted proteins and those involved in the biosynthesis of different capsular types is mainly due to recombination events leading to the replacement of a locus of several genes or to the allelic exchange of the internal part of a gene. These two processes, which led to a broad diversity of surface protein patterns, are probably involved in the diversity of interactions with the host and its immune system. According to gene content comparisons and phylogeny, recent gene replacements by horizontal gene transfer may occur but are rare events. Although specific gene patterns, with respect to the origin of the strains and the epidemiological characteristics, were not identified, we show that the recently described hypervirulent ST-17 lineage is a homogeneous group. The study highlights for the first time that this lineage contains a specific and conserved set of surface proteins, probably accounting for its high capacity to cause infections in newborns.

Evaluation of randomly amplified polymorphic DNA and pulsed field gel electrophoresis techniques for molecular typing of Dermatophilus congolensis

This study aimed to evaluate molecular typing methods useful for standardization of strains in experimental work on dermatophilosis. Fifty Dermatophilus congolensis isolates, collected from sheep, cattle, horse and a deer, were analyzed by randomly amplified polymorphic DNA (RAPD) method using twenty-one different primers, and the results were compared with those obtained by typing with a pulsed field gel electrophoresis (PFGE) method using the restriction digest enzyme Sse8387I. The typeability, reproducibility and discriminatory power of RAPD and Sse8387I-PFGE typing were calculated. Both typing methods were highly reproducible. Of the two techniques, Sse8387I-PFGE was the least discriminating (Dice Index (DI), 0.663) and could not distinguish between epidemiologically related isolates, whereas RAPD showed an excellent discriminatory power (DI, 0.7694-0.9722). Overall, the degree of correlation between RAPD and PFGE typing was significantly high (r, 0.8822). We conclude that the DNA profiles generated by either RAPD or PFGE can be used to differentiate epidemiologically unrelated isolates. The results of this study strongly suggest that at least two independent primers are used for RAPD typing in order to improve its discriminatory power, and that PFGE is used for confirmation of RAPD results.

Molecular epidemiology of group B streptococcal infections

Streptococcus agalactiae (GBS) is a causative agent of sepsis and meningitis in newborns and diseases in pregnant women and nonpregnant adults. Various approaches, including both nongenetic and genetic techniques, are currently used for the study of epidemiology of GBS infections. In the present paper the different methods of molecular epidemiology of GBS infections are reviewed, and several novel approaches are introduced. The advantages and disadvantages of molecular methods are discussed and compared with traditional serotyping technique. The possible use of the molecular approaches for identification of different genetic lineages in GBS as well as for identification and control of the epidemiologically actual clones is discussed.

Macrorestriction analysis of Streptococcus agalactiae (group B Streptococcus) isolates from Malaysia

Streptococcus agalactiae or group B streptococci (GBS) often colonize the gastrointestinal and urogenital tracts of women, who may transmit these organisms to their offspring during the birth process. Using PFGE analysis, the genetic diversity of GBS was studied for strains isolated from pregnant women and their newborn infants in a teaching hospital. A total of 48 different PFGE profiles were obtained from 123 strains, with one profile (S1) appearing to be predominant among both groups studied. There was good overall correlation between the profiles obtained for strains from mother-infant pairs and for strains isolated from different body sites in the same individual. Occasional discrepancies seen in related body sites and among mother-infant pairs suggest concurrent carriage of different strains in the same individual as well as the possibility of an environmental source of organism for the neonate. The overall results demonstrated that many variants of GBS strains occur in Malaysia.

Late-onset and recurrent neonatal Group B streptococcal disease associated with breast-milk transmission

The purpose of the study was to determine the epidemiological relationships in three unrelated cases of neonatal late-onset Group B streptococcal (GBS) disease and maternal breast-milk infection with GBS. All deliveries were by cesarean section; case 1 was at term, and cases 2 and 3 were at 32- and 33-wk gestation, respectively. Case 1 relates to a mother with clinical mastitis and recurrent GBS infection in a 20-day-old male infant. Following antibiotic therapy and cessation of breast-feeding, the infant recovered without sequelae. Case 2 refers to a mother with clinical mastitis and the occurrence of late-onset GBS disease in 5-wk-old male twins. Despite intervention, one infant died and the second became ill. Following antibiotic therapy and cessation of breast-feeding, the surviving infant recovered without sequelae. Case 3 refers to a mother with sub-clinical mastitis and late-onset GBS infection occurring in a 6-day-old female twin. Following intervention, the infant recovered but suffered a bilateral thalamic infarction resulting in developmental delay and a severe seizure disorder. Following recovery of GBS from an inapparent mastitis and cessation of breast-feeding, the second infant remained well. Blood cultures from all affected infants and maternal breast milk were positive for GBS. Epidemiological relationships between neonatal- and maternal-derived GBS isolates were confirmed by a random amplified polymorphic DNA polymerase chain reaction assay (RAPD-PCR). This study is significant in that it has demonstrated that maternal milk (in cases of either clinical or sub-clinical mastitis) can be a potential source of infection resulting in either late-onset or recurrent neonatal GBS disease.

Towards a genotyping system for Streptococcus agalactiae (group B streptococcus): use of mobile genetic elements in Australasian invasive isolates

This study forms part of the development of an integrated genotyping system for Streptococcus agalactiae (group B streptococcus, GBS) that can be used to study the population genetics of the organism and the pathogenesis and epidemiology of GBS disease. In recent previous studies, two sets of markers, the capsular polysaccharide synthesis (cps) gene cluster and surface protein antigen genes, have been used to assign molecular serotypes (MS) and protein-gene profiles (PGP) to more than 200 isolates. In the present study, five mobile genetic elements (MGE) have been used as a third set of markers, to characterize further 194 invasive isolates, recovered from blood or cerebrospinal fluid (CSF). Of these, 97 % contained one or more of the five MGE, the distribution of which was related to MS and PGP, as illustrated by MS III, which is divisible into four serosubtypes with different combinations of the MGE (or none). Fifty-six different genotypes and eight genetic clusters were identified, each with different combinations of the three sets of molecular markers. Five predominant genotypes (Ia-1, Ib-1, III-1, III-2 and V-1) contained 62 % of the isolates and five of the eight genetic clusters contained 92 % of the isolates. The 17 CSF isolates were relatively widely distributed between 10 genotypes and across seven of the eight clusters. Further study is needed to determine whether these genotypes or clusters share common markers of increased virulence. In future, comparison of invasive with colonizing strains of GBS may elucidate the significance of these findings.

Molecular detection of Histoplasma capsulatum var. capsulatum in human clinical samples

We developed a seminested PCR for the diagnosis of histoplasmosis that amplifies a portion of the Histoplasma capsulatum H antigen gene. This assay is highly sensitive and specific, being able to detect genomic material corresponding to less than 10 yeast cells without cross-reaction against other bacterial or fungal pathogens.

Can composition and structural features of oligonucleotides contribute to their wide-scale applicability as random PCR primers in mapping bacterial genome diversity?

Among current genotypic methodologies, random amplification of polymorphic DNA (RAPD or AP-PCR) represents a widely employed assay for the evaluation of bacterial genomic diversity. A common bottleneck of this technique, however, is represented by the screening of useful informative primers to discriminate among isolates of a particular bacterial species. In an attempt to simplify this process, we evaluated here the utility of degenerate oligonucleotides to act as informative AP-PCR primers. For this purpose, a number of features (G+C contents, degeneracy rate, modifications at the 5' end) of related degenerate primers was tested for their effects in the generation of informative arrays from a set of bacterial genomes. Our results indicate that a combination of a wide base composition and a common palindromic structure at the 5' end of the sequences that compose the degenerate primers tested here beneficially resulted for the generation of informative arrays aimed to evaluate the bacterial genome heterogeneity.

Molecular characterization of methicillin-resistant coagulase-negative staphylococci from a neonatal intensive care unit

OBJECTIVE

To evaluate clonal dissemination of methicillin-resistant coagulase-negative staphylococci (CNS).

SETTING

Neonatal intensive care unit of a 180-bed, university-affiliated general hospital.

PATIENTS

Neonates admitted to the neonatal intensive care unit between March 1999 and October 2000, from whom CNS were isolated as a unique pathogen. Patients from other wards from whom epidemiologically unrelated staphylococci strains were obtained served as control-patients.

METHODS

Conventional methods were used for phenotypic characterization of CNS. Methicillin resistance was determined by mecA polymerase chain reaction (PCR) amplification. Genotypic characterization was done by random amplification of DNA with degenerated primers (RAPD) and repetitive element sequence-based PCR (rep-PCR).

RESULTS

Forty methicillin-resistant CNS isolates obtained from neonates were characterized as Staphylococcus epidermidis (33), S. hominis (5), S. warneri (1), and S. auricularis (1). Both RAPD and rep-PCR indicated the presence of 4 different clones among the 33 S. epidermidis isolates. In turn, the 4 randomly selected, epidemiologically unrelated methicillin-resistant CNS strains obtained from control-patients showed 3 new profiles by RAPD and 2 by rep-PCR, which differed from the corresponding patterns mentioned earlier. Persistence of S. hominis in a neonate could be assessed by both genotypic techniques.

CONCLUSIONS

The molecular characterization of the methicillin-resistant CNS studied indicated dissemination of one particular methicillin-resistant CNS clone among the neonates in the ward studied. Although RAPD showed a superior power to discriminate among methicillin-resistant CNS isolates, both RAPD and rep-PCR detected intraspecific and interspecific genomic diversity.

Characterization of Streptococcus agalactiae isolates of bovine and human origin by randomly amplified polymorphic DNA analysis

Streptococcus agalactiae is considered one of the major causes of bovine intramammary infections. It is also found in the vaginas of women without any apparent clinical symptoms, but reports of neonatal infections, causing significant morbidity, are relatively frequent. The aim of this study was to evaluate the genetic diversity of S. agalactiae strains isolated from bovine milk and from asymptomatic women in Québec, Canada, by randomly amplified polymorphic DNA (RAPD) analysis. A total of 185 bovine isolates and 38 human isolates were first serotyped for capsular polysaccharide by double diffusion in agarose gel (bovine isolates) and coagglutination (human isolates). Strains were then studied by RAPD using 3 primers, designated OPS11, OPB17, and OPB18, which were selected from 12 primers. Thirty-eight percent of bovine isolates and 82% of human isolates could be serotyped. Prevalent serotypes were type III (28%) for bovine isolates and types V (26%) and III (24%) for human isolates. RAPD results showed that, taken together, all isolates (of bovine and human origin) shared 58% similarity. Ninety-four percent of these isolates were clustered in four groups (I, II, III, and IV) with 70% similarity among them. Three clusters, A (48 isolates), B (14 isolates), and C (32 isolates), with 79 to 80% similarity were identified within group IV, whereas the three other groups did not present any clusters. Despite some clustering of human isolates, relatively high diversity was seen among them. Relatively high heterogeneity was observed with the RAPD profiles, not only for field strains belonging to different serotypes but also for those within a given serotype.