Use of pulsed-field gel electrophoresis, enterobacterial repetitive intergenic consensus typing, and automated ribotyping to assess genomic variability among strains of nontypeable Haemophilus influenzae

Genotype and virulence gene analyses of Bacillus cereus group clinical isolates from the Chinese softshell turtle (Pelodiscus sinensis) in Taiwan

Chinese softshell turtles (Pelodiscus sinensis) (CST) are susceptible to infections by bacteria belonging to the Bacillus cereus group (Bcg). Bcg includes several closely related species, two of which, B. cereus and B. thuringiensis, are pathogens of aquatic animals or insects. In the present study, we collected 57 Bcg isolates obtained from diseased CST from 2016 to 2019 in Kaohsiung and Pingtung, the areas with the most CST farms in Taiwan. All isolates were divided into four genotypes with two restriction enzymes, SmaI and NotI, by pulsed-field gel electrophoresis and enterobacterial repetitive intergenic consensus-polymerase chain reaction (ERIC-PCR). Representative isolates from each genotype were subjected to phylogenetic tree analysis using 16S rDNA and pyruvate carboxylase genes as phylogenetic markers, and these CST isolates appeared in different clades. PCR was performed targeting six selected virulence genes, four of which were detected in CST isolates, including cytotoxin K (1/57), hblC of the haemolysin BL complex (46/57), nheA of the non-haemolytic enterotoxin complex (52/57) and enterotoxin FM (57/57), whereas cereulide synthetase and cereulide peptide synthase-like genes were not detected in any isolates.

The host immune response contributes to Haemophilus influenzae virulence

BACKGROUND

There is compelling evidence that infections with non-typeable Haemophilus influenzae (NTHi) are associated with exacerbations in COPD patients. However, NTHi has also been isolated frequently during clinically stable disease. In this study we tested the hypothesis that genetically distinct NTHi isolates obtained from COPD patients differ in virulence which could account for dissimilarities in the final outcome of an infection (stable vs. exacerbation).

RESULTS

NTHi isolates (n = 32) were obtained from stable COPD patients, or during exacerbations. Genetically divergent NTHi isolates were selected and induction of inflammation was assessed as an indicator of virulence using different in vitro models. Despite marked genomic differences among NTHi isolates, in vitro studies could not distinguish between NTHi isolates based on their inflammatory capacities. Alternatively, when using a whole blood assay results demonstrated marked inter-, but not intra-individual differences in cytokine release between healthy volunteers irrespective of the origin of the NTHi isolate used.

CONCLUSION

Results suggest that the individual immune reactivity might be an important predictor for the clinical outcome (exacerbation vs. no exacerbation) following NTHi infection.

Genetic diversity of the ftsI gene in β-lactamase-nonproducing ampicillin-resistant and β-lactamase-producing amoxicillin-/clavulanic acid-resistant nasopharyngeal Haemophilus influenzae strains isolated from children in South Korea

Haemophilus influenzae frequently colonizes the nasopharynx of children and adults, which can lead to a variety of infections. We investigated H. influenzae carriage in the nasopharynx of 360 children, in terms of (1) the prevalence of strains with decreased susceptibility, and (2) the presence of amino acid substitutions in PBP3. One hundred twenty-three strains were isolated (34.2%, 123/360), 122 of which were classified as nontypable H. influenzae (NTHi). Of these, β-lactamase-nonproducing ampicillin-susceptible strains accounted for 26.2%, β-lactamase-producing-ampicillin-resistant strains for 9.0%, β-lactamase-nonproducing ampicillin-resistant (BLNAR) strains for 40.2%, and β-lactamase-producing amoxicillin-/clavulanic acid-resistant (BLPACR) for 24.6%, respectively. Pulsed field gel electrophoresis (PFGE) patterns were so diverse that they were clustered into 41 groups. The amino acid substitutions in the transpeptidase domain (292 amino acids) of ftsI in BLNAR isolates showed that group IIb accounted for 30.6%, IIc for 8.2%, IId for 16.3%, III for 32.7%, and the others for 12.2%. Moreover, groups IIb (56.7%; 17/30) and III (23.3%; 7/30) were prevalent among BLPACR strains. They were subclassified into more diverse sequence subtypes by analysis of the entire PBP3 (610 amino acids). Groups IIb, IIc, IId, and III exhibited 13, four, six, and four sequence subtypes, respectively. Such a genetic diversity is likely indicative of significant potential for decreased antimicrobial susceptibility in nasopharyngeal-colonizing NTHi strains.

Prevalence and characteristics of Staphylococcus aureus in Connecticut swine and swine farmers

This study explores the characteristics of Staphylococcus aureus (S. aureus) in swine and their human handlers in a convenience sample of 35 farms in Connecticut. Husbandry practices are clearly different from better-known concentrated animal feeding operations (CAFOs) with less intensive rearing conditions. Nasal samples were collected from 263 pigs and nine humans on 35 farms during the 2010 rearing season. Samples were analysed using established microbiology methods, and resulting methicillin-sensitive (MSSA) and resistant (MRSA) isolates were typed by pulsed-field gel electrophoresis (PFGE) and spa typing. PCR was used to detect the presence of the Panton-Valentine Leukocidin (PVL) gene, a cytotoxin usually associated with CA-MRSA infection. A farm assessment form and questionnaire were used to obtain the information about husbandry practices and human exposure risk, respectively. Staphylococcus aureus colonized swine and humans were found in 51% (18/35) of the farms sampled at a rate of 30% (85/259) and 22% (2/9), respectively. Eight pigs and two humans were MRSA positive on five farms. MRSA in swine was related to healthcare-associated (HA), community-associated (CA) or livestock-associated (LA) MRSA strains, whereas humans were colonized with HA-MRSA. On the basis of spa typing, there was evidence of human-animal transmission thereby signifying humanosis/reverse zoonoses. The PVL gene was found in 88% (7/8) of MRSA swine isolates, the first time this gene has been seen in colonized pigs sampled on US farm. MSSA isolates belonged to six spa types: t337 (41%), t034 (12%), t334 (12%), t4529 (12%), t8760 (18%) and t1166 (6%) including LA strains. This is the first time spa type t8760 has been reported and the only MSSA with the PVL gene. In summary, MRSA including LA strains (LA-MRSA) can be found on small farms with different husbandry practices from CAFOs, suggesting that preventive measures for zoonotic MRSA infection should address a range of animal production.

Haemophilus influenzae and Haemophilus haemolyticus in tonsillar cultures of adults with acute pharyngotonsillitis

OBJECTIVE

The aim of this study was to evaluate the clinical implication of Haemophilus haemolyticus, one of the closest relative of Haemophilus influenzae, on acute pharyngotonsillitis.

METHODS

We applied polymerase chain reaction (PCR) for 16S ribosomal DNA (rDNA) and IgA protease gene (iga) to distinguish H. haemolyticus and H. influenzae.

RESULTS

Among the 199 Haemophilus spp. isolated from 214 patients with acute pharyngotonsillitis, 52 (24.3%) H. influenzae strains and 23 (10.7%) H. haemolyticus strains were identified by polymerase chain reaction (PCR) for 16S rDNA and IgA protease gene (iga). All H. haemolyticus strains showed hemolysis on horse blood agar and there were no other Haemophilus spp., nonhemolytic H. haemolyticus and H. influenzae variant strains that had absent iga gene. H. hemolyticus showed close genetic relationship with H. influenzae evaluated by pulsed field gel electrophoresis (PFGE). The cases of acute pharyngotonsillitis showing WBC=7000/mm(3) or CRP=8 mg/dl were frequently found among cases with H. influenzae rather than cases with H. haemolyticus.

CONCLUSION

H. haemolyticus is a pharyngeal commensal that is isolated frequently from adults with acute pharyngotonsillitis.

Multilocus sequence typing and pulsed field gel electrophoresis of otitis media causing pathogens

Streptococcus pneumoniae, Haemophilus influenzae, and Moraxella catarrhalis are the three leading bacteria species associated with otitis media. Defining the molecular epidemiology of bacteria known to cause otitis media is of great importance, in both clinical and research settings. PFGE and MLST provide data for the characterization of isolates' genetic relatedness, yet they differ in the types of studies for which they are most useful. Consequently, knowledge of both techniques is important for laboratories intending to study the molecular epidemiology of otitis media-associated bacterial pathogens.

Genetic diversity of paired middle-ear and pharyngeal nontypeable Haemophilus influenzae isolates from children with acute otitis media

Pulsed-field gel electrophoresis was used to determine genetic diversities of multiple nontypeable Haemophilus influenzae isolates from throat and ear specimens of eight children with otitis media. From five children, all ear and throat isolates were identical. The bacterial populations in these specimens showed less diversity than populations in throat isolates of healthy children.

Pharyngeal colonization dynamics of Haemophilus influenzae and Haemophilus haemolyticus in healthy adult carriers

Haemophilus influenzae is an important cause of respiratory infections, including acute otitis media, sinusitis, and chronic bronchitis, which are preceded by asymptomatic H. influenzae colonization of the human pharynx. The aim of this study was to describe the dynamics of pharyngeal colonization by H. influenzae and an intimately related species, Haemophilus haemolyticus, in healthy adults. Throat specimens from four healthy adult carriers were screened for Haemophilus species; 860 isolates were identified as H. influenzae or H. haemolyticus based on the porphyrin test and on dependence on hemin and NAD for growth. Based on tests for hemolysis, for the presence of the 7F3 epitope of the P6 protein, and for the presence of iga in 412 of the isolates, 346 (84%) were H. influenzae, 47 (11%) were H. haemolyticus, 18 (4%) were nonhemolytic H. haemolyticus, and 1 was a variant strain. Carriers A and B were predominantly colonized with nontypeable H. influenzae, carrier C predominantly with b(-) H. influenzae mutants, and carrier D with H. haemolyticus. A total of 358 H. influenzae and H. haemolyticus isolates were genotyped by pulsed-field gel electrophoresis (PFGE) following SmaI or EagI digestion of their DNA, and the carriers displayed the following: carrier A had 11 unique PFGE genotypes, carrier B had 15, carrier C had 7, and carrier D had 10. Thus, adult H. influenzae and H. haemolyticus carriers are colonized with multiple unique genotypes, the colonizing strains exhibit genetic diversity, and we observed day-to-day and week-to-week variability of the genotypes. These results appear to reflect both evolutionary processes that occur among H. influenzae isolates during asymptomatic pharyngeal carriage and sample-to-sample collection bias from a large, variable population of colonizing bacteria.

Diversity of ampicillin resistance genes and antimicrobial susceptibility patterns in Haemophilus influenzae strains isolated in Korea

By Etest determination of the susceptibilities of 229 Haemophilus influenzae strains isolated in Korea to 10 antibiotics, the isolates were found to be antibiotic nonsusceptible in the following order: ampicillin (58.1%), trimethoprim-sulfamethoxazole (52%), cefaclor (41.1%), clarithromycin (25.8%), chloramphenicol (14.0%), amoxicillin-clavulanic acid (13.5%), meropenem (11.7%), cefixime (10.9%), cefuroxime (9.2%), and levofloxacin (1.3%). The prevalences of each resistance class were 23.6% for beta-lactamase-negative ampicillin-susceptible (BLNAS) strains; 37.6% for strains with the TEM-1 type beta-lactamase gene; 1.3% for strains with the ROB-1 type beta-lactamase gene; 29.3% for the beta-lactamase-negative ampicillin-resistant (BLNAR) strains with a mutation in the ftsI gene, which encodes PBP 3; and 8.3% for beta-lactamase-positive amoxicillin-clavulanate-resistant (BLPACR) strains, which showed both resistance mechanisms (i.e., a beta-lactamase gene and a mutation in the ftsI gene). The MIC50s of all beta-lactams, including cephem and meropenem agents, for the BLNAR strains were two to three times higher than those for the BLNAS strains. This study confirms that the prevalence of BLNAR and BLPACR strains is relatively high and for the first time confirms the presence of H. influenzae strains carrying blaROB-1 in Korea. Even though mutations in another gene(s) might be involved in beta-lactam resistance, these results suggest that mutations in the ftsI gene are important for the development of resistance to beta-lactams in H. influenzae strains in Korea.

Probe hybridization array typing: a binary typing method for Escherichia coli

The ability to distinguish between Escherichia coli strains is critical for outbreak investigations. Binary typing, based on the presence or absence of genetic material, provides a high-throughput alternative to gel- and PCR-based typing techniques that generate complex banding patterns and lack uniform interpretation criteria. We developed, validated, and determined the discriminatory power of an E. coli binary typing method, probe hybridization array typing (PHAT). In PHAT, the absence or presence of genetic material is identified by using DNA hybridization to produce a reproducible and portable fingerprint for each genome. PHAT probes were generated from genome subtractive hybridization experiments. We PHAT typed the ECOR collection of strains from a variety of geographical locations, and 33 rectal E. coli strains selected from college-aged women with urinary tract infection. In the set of 33 human rectal strains, the discriminatory power of PHAT (98%) equaled that of multilocus sequence typing (MLST) and pulsed-field gel electrophoresis. However, for ECOR strains, which include nonhuman strains, the current set of PHAT probes was less discriminating than MLST, ribotyping, and enterobacterial repetitive intergenic consensus sequence PCR (80% versus 97, 92, and 97%, respectively). When we limited the analysis to ECOR strains of B2 and D lineage, which are associated with human infection, current PHAT probes were highly discriminatory (94%). PHAT can be applied in a high-throughput format (i.e., "library on a slide"), the discriminatory ability can be varied based on the probe set, and PHAT is readily adapted to other bacterial species with high variation in genetic content.

[Molecular characterization of invasive Haemophilus influenzae strains isolated in Tunisia]

We reported a molecular characterization of 25 Haemophilus influenzae strains derived from cases of meningitis and sepsis in children aged less than five years hospitalized in pediatric wards from three hospitals in the Sahel area (Tunisia) during the period 1997-2002. These strains were biotyped and subjected to a capsular typing by Slide agglutination serotyping and Polymerase Chain Reaction (PCR). The genetic polymorphism of these strains was also studied in Arbitrarily Primed Polymerase Chain Reaction (AP-PCR) with two sets of primers: RAP IV and 217 delta(2) as in Pulsed Field Gel Electrophoresis after digestion of the total DNA with the restriction enzyme SmaI (PFGE SmaI). Nineteen strains among 25 (76%) were of biotype I. The bexA gene was highlighted in 13 strains (52%) and in all the cases it was of the type b. Twelve strains (48%) were shown to be unencapsulated by PCR. AP-PCR RAP IV (23 genotypes/25 with a discrimination index ID=0.993) had shown nearly the same discriminatory power than PFGE (20 genotypes/21 strains with a discrimination index ID=0.995). We thus note, how capsular typing by PCR is more sensitive than slide agglutination serotyping. We also note the genetic diversity of the invasive strains isolated with a remarkable presence of non typable strains. AP PCR seems to be an alternative of choice for the epidemiologic follow-up of the Haemophilus influenzae invasive infections.

Molecular characterization of Haemophilus ducreyi isolates from different geographical locations

The technique of random amplified polymorphic DNA (RAPD) was adapted and optimized to study Haemophilus ducreyi isolates. A panel of 43 strains isolated from chancroid patients from different countries in Africa, Europe, North America, and Asia were characterized. The strains were also studied with respect to lipooligosaccharide (LOS) migration and immunoblotting patterns and the presence of cytolethal distending toxin genes. The RAPD method with the OPJ20 primer generated nine banding patterns (1 to 9). The majority of the isolates were clustered into two major profiles, 14 and 13 strains into profiles 1 and 2, respectively, and just a few strains revealed patterns 3 and 4. The isolates from Thailand were exceptional in that they showed greater diversity and were represented by six different RAPD patterns, i.e., patterns 3 and 5 to 9. The LOS migration and immunoblotting analyses revealed two different patterns, which indicated long and short forms of LOS; the former was found in 20/23 tested strains. Two strains that expressed the short form of LOS were grouped into RAPD pattern 4. The absence of cdtABC genes was observed in only 4/23 strains, and three of these isolates were assigned to RAPD pattern 4. Our results showed limited genotypic and phenotypic variations among H. ducreyi strains, as supported by the conserved RAPD and LOS profiles shared by the majority of the studied strains. However, the RAPD method identified differences between strains, including those from different geographic areas, which indicate the potential of RAPD as an epidemiological tool for the typing of H. ducreyi isolates in countries where chancroid is endemic.

Conservation and diversity of HMW1 and HMW2 adhesin binding domains among invasive nontypeable Haemophilus influenzae isolates

The pathogenesis of nontypeable Haemophilus influenzae (NTHi) begins with adhesion to the rhinopharyngeal mucosa. In almost 80% of NTHi clinical isolates, the HMW proteins are the major adhesins. The prototype HMW1 and HMW2 proteins, identified in NTHi strain 12, exhibit different binding specificities. The two binding domains have been localized in regions of maximal sequence dissimilarity (40% identity, 58% similarity). Two areas within these binding domains have been found essential for full level adhesive activity (designated the core-binding domains). To investigate the conservation and diversity of the HMW1 and HMW2 core-binding domains among isolates, PCR and DNA sequencing were used. First, we separately amplified the hmw1A-like and hmw2A-like structural genes in nine invasive NTHi isolates, discovering two new hmwA alleles, whose sequences are herein reported. Then, the hmw1A-like and hmw2A-like PCR products were used as the template in nested PCR to produce amplicons encompassing the encoding sequences of the two core-binding domains. In-depth sequence analysis was then performed among sequences of each group, with the support of specific computer programs. Overall, extensive sequence diversity among isolates was highlighted. However, similarity plots showed patterns consisting of peaks of relatively high similarity alternating with strongly divergent regions. The phylogenetic tree clearly indicated the HMW1-like and HMW2-like core-binding domain sequences as two clusters. Distinct sets of conserved amino acid motifs were identified within each group of sequences using the MEME/MOTIFSEARCH tool. Since HMW adhesins could represent candidates for future vaccines, identification of specific patterns of conserved motifs in otherwise highly variable regions is of great interest.

Hypermutable Haemophilus influenzae with mutations in mutS are found in cystic fibrosis sputum

Hypermutable bacterial pathogens exist at surprisingly high prevalence and benefit bacterial populations by promoting adaptation to selective environments, including resistance to antibiotics. Five hundred Haemophilus influenzae isolates were screened for an increased frequency of mutation to resistance to rifampicin, nalidixic acid and spectinomycin: of the 14 hypermutable isolates identified, 12 were isolated from cystic fibrosis (CF) sputum. Analysis by enterobacterial repetitive intergenic consensus (ERIC)-PCR and ribotyping identified eight distinct genetic fingerprints. The hypermutable phenotype of seven of the eight unique isolates was associated with polymorphisms in conserved sites of mutS. Four of the mutant mutS alleles were cloned and failed to complement the mutator phenotype of a mutS : : TSTE mutant of H. influenzae strain Rd KW20. Antibiotic susceptibility testing of the hypermutators identified one beta-lactamase-negative ampicillin-resistant (BLNAR) isolate with two isolates producing beta-lactamase. Six isolates from the same patient with CF, with the same genetic fingerprint, were clonal by multilocus sequence typing (MLST). In this clone, there was an evolution to higher MIC values for the antibiotics administered to the patient during the period in which the strains were isolated. Hypermutable H. influenzae with mutations in mutS are prevalent, particularly in the CF lung environment, and may be selected for and maintained by antibiotic pressure.

Genetic and molecular characterization of beta-lactamase-negative ampicillin-resistant Haemophilus influenzae with unusually high resistance to ampicillin

Previous studies with beta-lactamase-negative, ampicillin-resistant (BLNAR) Haemophilus influenzae from Japan, France, and North America indicate that mutations in ftsI encoding PBP3 confer ampicillin MICs of 1 to 4 micro g/ml. Several BLNAR strains with ampicillin MICs of 4 to 16 micro g/ml recently isolated from North America were studied. Pulsed-field gel electrophoresis identified 12 unique BLNAR strains; sequencing of their ftsI transpeptidase domains identified 1 group I and 11 group II mutants, as designated previously (K. Ubukata, Y. Shibasaki, K. Yamamoto, N. Chiba, K. Hasegawa, Y. Takeuchi, K. Sunakawa, M. Inoue, and M. Konno, Antimicrob. Agents Chemother. 45:1693-1699, 2001). Geometric mean ampicillin MICs for several clinical isolates were 8 to 10.56 micro g/ml. Replacement of the ftsI gene in H. influenzae Rd with the intact ftsI from several clinical isolates resulted in integrants with typical BLNAR geometric mean ampicillin MICs of 1.7 to 2.2 micro g/ml. Cloning and purification of His-tagged PBP3 from three clinical BLNAR strains showed significantly reduced Bocillin binding compared to that of PBP3 from strain Rd. Based on these data, changes in PBP3 alone could not account for the high ampicillin MICs observed for these BLNAR isolates. In an effort to determine the presence of additional mechanism(s) of ampicillin resistance, sequencing of the transpeptidase regions of pbp1a, -1b, and -2 was performed. While numerous changes were observed compared to the sequences from Rd, no consistent pattern correlating with high-level ampicillin resistance was apparent. Additional analysis of the resistant BLNAR strains revealed frame shift insertions in acrR for all four high-level, ampicillin-resistant isolates. acrR was intact for all eight low-level ampicillin-resistant and four ampicillin-susceptible strains tested. A knockout of acrB made in one clinical isolate (initial mean ampicillin MIC of 10.3 micro g/ml) lowered the ampicillin MIC to 3.67 micro g/ml, typical for BLNAR strains. These studies illustrate that BLNAR strains with high ampicillin MICs exist that have combined resistance mechanisms in PBP3 and in the AcrAB efflux pump.

Partial analysis of the genomes of two nontypeable Haemophilus influenzae otitis media isolates

In 1995, The Institute for Genomic Research completed the genomic sequence of a rough derivative of Haemophilus influenzae serotype d, strain KW20. This sequence, though extremely useful in understanding the basic biology of H. influenzae, has yet to provide significant insight into our understanding of disease caused by nontypeable H. influenzae (NTHI), because serotype d strains are not generally pathogens. In contrast, NTHI strains are frequently mucosal pathogens and are the primary pathogens of chronic otitis media as well as a significant cause of acute otitis media in children. Thus, it is of great importance to further understand their biology. We used a DNA-based microarray approach to identify genes present in a clinical isolate of NTHI that were absent from strain Rd. We also sequenced the genome of a second NTHI isolate from a child with chronic otitis media to threefold coverage and then used an array of bioinformatics tools to identify genes present in this NTHI strain but absent from strain Rd. These methods were complementary in approach and results. We identified, in both strains, homologues of H. influenzae lav, an autotransported protein of unknown function; tnaA, which encodes tryptophanase; as well as a homologue of Pasteurella multocida tsaA, which encodes an alkyl peroxidase that may play a role in protection against reactive oxygen species. We also identified a number of putative restriction-modification systems, bacteriophage genes and transposon-related genes. These data provide new insight that complements and extends our ongoing analysis of NTHI virulence determinants.

Implications of molecular genotyping of Helicobacter pylori isolates from different human populations by genomic fingerprinting of enterobacterial repetitive intergenic consensus regions for strain identification and geographic evolution

Biogeographic partitioning of the genome is typical of the gastric pathogen Helicobacter pylori. Such population-specific evolution could serve as a model for understanding host-pathogen interaction and the impact of genetic drift and recombination on insular populations. With a total of 320 isolates from six geographic regions (Japan, India, England, Spain, Ireland, Africa, and Peru) analyzed by enterobacterial repetitive intergenic consensus (ERIC)-based genotyping, we examined genetic affinities among various H. pylori populations in the world. Several strain-specific and region-specific differences were observed by ERIC-based typing. Polymorphic ERIC patterns indicated that the ERIC sequences are in fact dispersed in the H. pylori chromosome at different locations separated by various distances. Phylogenetic analysis of 61 representative isolates revealed three distinct genetic clusters populated by isolates with shared ERIC types independent of the cag right-junction motif type and vacA allele status. Among the notable genetic relationships were the genotypic similarities between Irish and Japanese and between Peruvian and Japanese isolates. Insular genotypic characteristics of Irish isolates amid genetic similarity to East Asian, as well as North European, strains have been once again proved in this study. Peruvian genotypes were more similar to those of Japanese isolates than to those of Iberian or European isolates. Given the current debate on the origin and age of present-day H. pylori, this is a significant finding that supports the possibility of ancient colonization of Amerindians with East Asian strains. Genotypic data presented here will be additionally helpful in realizing the importance of H. pylori geographical genomics in the development of gastroduodenal pathology.

Comparison of usefulness of randomly amplified polymorphic DNA and amplified-fragment length polymorphism techniques in epidemiological studies on nasopharyngeal carriage of non-typable Haemophilus influenzae

Randomly amplified polymorphic DNA (RAPD) and automated amplified-fragment length polymorphism (AFLP) techniques with fluorescently labelled primers were used to type non-serotypable Haemophilus influenzae (NTHI) isolates. Eighty-seven isolates from healthy children attending day-care centres or living at orphanages in southern Poland were investigated. Through comparison of the AFLP data with RAPD analysis, it has been concluded that the discriminatory power of AFLP for NTHI typing is higher than RAPD. Generally, the NTHI isolates analysed were highly heterogeneous, as detected with a HindIII/TaqI AFLP genotyping scheme on intra/inter similarity levels of 94 and 96 % using Pearson's correlation coefficient. The range of similarity values found for isolates from children permanently residing at a particular day-care centre was much wider than that for isolates from orphanages. AFLP can efficiently access NTHI strain diversity and can monitor their turn-over for comparative typing in local and inter-local epidemiological investigations.

Evaluation of genotyping large numbers of Escherichia coli isolates by enterobacterial repetitive intergenic consensus-PCR

We analyzed a large collection of Escherichia coli isolates typed by enterobacterial repetitive intergenic consensus (ERIC)-PCR with BioNumerics gel analysis software. However, the interexperimental variation of ERIC-PCR caused the computer software to classify repeated isolates as different. ERIC-PCR should not be used as the sole determinant of genetic similarity when typing large numbers of bacterial isolates via computer software.

Diversity and sharing of Haemophilus influenzae strains colonizing healthy children attending day-care centers

BACKGROUND

Children attending day-care centers (DCCs) are at risk for Haemophilus influenzae nasopharyngeal colonization and acute otitis media. The degree to which a given strain circulates within a day-care center and the heterogeneity of strains among DCCs in a geographic area are not well-characterized. This study describes the prevalence rates of H. influenzae colonization in a large number of children attending day-care centers and examines the genetic diversity of colonizing strains and the degree of sharing among children.

METHODS

Throat cultures were collected from 198 healthy children <3 years old attending 16 day-care centers in Michigan. All H. influenzae isolates were genetically typed by enterobacterial repetitive intergenic consensus PCR as the initial screening technique to identify unique strains within each child. Pulsed field gel electrophoresis was used subsequently to examine the genetic diversity of strains between children.

RESULTS

There were 127 (64%) children colonized with H. influenzae. Wide variation in rates of colonization was identified among day-care centers (0 to 95%). A total of 179 genetically unique H. influenzae strains were isolated, and 47 children (37%) were colonized with 2 or more genetically distinct H. influenzae organisms. Evidence of sharing of the same strain in different children was found in 13 of 15 colonized DCCs and 23% of genotypically unique strains were shared.

CONCLUSION

The degree of sharing of H. influenzae among children in this study suggests transmission of these potentially pathogenic microorganisms in day-care centers.

Typing of nonencapsulated haemophilus strains by repetitive-element sequence-based PCR using intergenic dyad sequences

Intergenic dyad sequences (IDS) are short repeated elements that have been described for several Haemophilus genomes and for only two other bacterial genera. We developed a repetitive-element sequence-based PCR using an IDS-specific primer as a typing method (IDS-PCR) for nonencapsulated Haemophilus strains and compared this technique with pulsed-field gel electrophoresis (PFGE) of DNA restricted with SmaI. IDS-PCR was rapid, easy to perform, and reproducible, with a high discriminatory capacity for nontypeable Haemophilus influenzae (NTHI) strains. The 69 NTHI strains tested generated 65 different banding patterns. Epidemiologically related strains gave similar or identical fingerprints, and all of the unrelated strains except two showed different patterns. These results were in agreement with those obtained by PFGE. For 20 genital strains usually identified as being biotype IV NTHI and belonging to a cryptic genospecies of Haemophilus with remarkable genetic homogeneity, four bands were significantly present and six bands were significantly absent from the fingerprints. The 20 strains were gathered in 11 closely related profiles, whereas PFGE provided no band when DNA was treated with SmaI. IDS-PCR improved the differentiation previously obtained within this species by ribotyping and multilocus enzyme electrophoresis. Our findings suggest that IDS-PCR is a rapid, reliable, and discriminatory method for typing NTHI strains and is currently the most efficient method for distinguishing strains within the cryptic genospecies of HAEMOPHILUS: