Neonatal sepsis is a severe clinical syndrome characterized by systemic signs of infection, shock and system organ failure; diagnosis is confirmed on positive culture from a normally sterile site(s). There are few reports comparing incidence, mortality, and risk factors between clinically diagnosed sepsis and that confirmed by culture.
All infants diagnosed with early- (within first 72 h after birth) or late-onset (72 h–4 weeks after birth) neonatal sepsis between 1997 and 1999 from four neonatal centers in South Korea, were investigated.
The estimated incidence rate of neonatal sepsis during the 3 years was 30.5 per 1000 live births for clinical sepsis and 6.1 per 1000 live births for sepsis with positive culture, with case-fatality rates of 4.7% and 2.2%, respectively. When only early-onset sepsis was considered, the incidence and fatality rates were 25.1 per 1000 live births and 6.1% for clinical sepsis, and 4.3 per 1000 live births and 2.5% for culture-confirmed sepsis, respectively. For the 179 patients (185 causative organisms) of proven sepsis, Staphylococcus spp. including S. aureus were the most frequent isolates. In early-onset clinical sepsis, having very low birthweight (≤1500 g), a low Apgar score at 5 min (≤7), and being male were related to higher rates of case-fatality (relative risk: 11.3, 6.8 and 2.5, respectively)
Clinical sepsis was more common than culture-confirmed sepsis and had a higher case-fatality rate. It seems prudent to take rapid and decisive steps toward better management of the high-risk group whether the sepsis is clinically diagnosed or culture confirmed.
case fatality rate; epidemiology; newborns; sepsis; South Korea
We determined host and pathogen risk factors for urinary-source bacteremia in a prospective study of patients with Escherichia coli bacteriuria. Both host (urinary retention; history of urogenital surgery) and pathogen factors (a capsule characteristic) were independent predictors of bacteremia.
Background. The urinary tract is the most common source for Escherichia coli bacteremia. Mortality from E. coli urinary-source bacteremia is higher than that from urinary tract infection. Predisposing factors for urinary-source E. coli bacteremia are poorly characterized.
Methods. In order to identify urinary-source bacteremia risk factors, we conducted a 12-month prospective cohort study of adult inpatients with E. coli bacteriuria that were tested for bacteremia within ±1 day of the bacteriuria. Patients with bacteremia were compared with those without bacteremia. Bacterial isolates from urine were screened for 16 putative virulence genes using high-throughput dot-blot hybridization.
Results. Twenty-four of 156 subjects (15%) had E. coli bacteremia. Bacteremic patients were more likely to have benign prostatic hyperplasia (56% vs 19%; P = .04), a history of urogenital surgery (63% vs 28%; P = .001), and presentation with hesitancy/retention (21% vs 4%; P = .002), fever (63% vs 38%; P = .02), and pyelonephritis (67% vs 41%; P = .02). The genes kpsMT (group II capsule) (17 [71%] vs 62 [47%]; P = .03) and prf (P-fimbriae family) (13 [54%] vs 40 [30%]; P = .02) were more frequent in the urinary strains from bacteremic patients. Symptoms of hesitancy/retention (odds ratio [OR], 7.8; 95% confidence interval [CI], 1.6–37), history of a urogenital procedure (OR, 5.4; 95% CI, 2–14.7), and presence of kpsMT (OR, 2.9; 95% CI, 1–8.2) independently predicted bacteremia.
Conclusions. Bacteremia secondary to E. coli bacteriuria was frequent (15%) in those tested for it. Urinary stasis, surgical disruption of urogenital tissues, and a bacterial capsule characteristic contribute to systemic invasion by uropathogenic E. coli.
Escherichia coli is a common cause of asymptomatic and symptomatic bacteriuria in hospitalized patients. Asymptomatic bacteriuria (ASB) is frequently treated with antibiotics without a clear indication. Our goal was to determine patient and pathogen factors suggestive of ASB.
We conducted a 12-month prospective cohort study of adult inpatients with E. coli bacteriuria seen at a tertiary care hospital in St. Louis, Missouri, USA. Urine cultures were taken at the discretion of treating physicians. Bacterial isolates were tested for 14 putative virulence genes using high-throughput dot-blot hybridization.
The median age of the 287 study patients was 65 (19–101) years; 78% were female. Seventy percent had community-acquired bacteriuria. One-hundred ten (38.3%) patients had ASB and 177 (61.7%) had symptomatic urinary tract infection (sUTI). Asymptomatic patients were more likely than symptomatic patients to have congestive heart failure (p = 0.03), a history of myocardial infarction (p = 0.01), chronic pulmonary disease (p = 0.045), peripheral vascular disease (p = 0.04), and dementia (p = 0.03). Patients with sUTI were more likely to be neutropenic at the time of bacteriuria (p = 0.046). Chronic pulmonary disease [OR 2.1 (95% CI 1.04, 4.1)] and dementia [OR 2.4 (95% CI 1.02, 5.8)] were independent predictors for asymptomatic bacteriuria. Absence of pyuria was not predictive of ASB. None of the individual virulence genes tested were associated with ASB nor was the total number of genes.
Asymptomatic E. coli bacteriuria in hospitalized patients was frequent and more common in patients with dementia and chronic pulmonary disease. Bacterial virulence factors could not discriminate symptomatic from asymptomatic bacteriurias. Asymptomatic E. coli bacteriuria cannot be predicted by virulence screening.
Escherichia coli; Bacteriuria; Urinary tract infection; Asymptomatic; Virulence factors
Antibiotic-resistant infections complicate treatment and increase morbidity and mortality. Mathematical modeling has played an integral role in improving our understanding of antibiotic resistance. In these models, parameter sensitivity is often assessed, while model structure sensitivity is not. To examine the implications of this, we first reviewed the literature on antibiotic-resistance modeling published between 1993 and 2011. We then classified each article's model structure into one or more of 6 categories based on the assumptions made in those articles regarding within-host and population-level competition between antibiotic-sensitive and antibiotic-resistant strains. Each model category has different dynamic implications with respect to how antibiotic use affects resistance prevalence, and therefore each may produce different conclusions about optimal treatment protocols that minimize resistance. Thus, even if all parameter values are correctly estimated, inferences may be incorrect because of the incorrect selection of model structure. Our framework provides insight into model selection.
anti-bacterial agents; bacteria; bacterial infections; basic reproduction number; drug resistance; humans; models, theoretical
Men who have sex with men (MSM) have higher rates of HIV and other sexually transmitted infections (STI) than women and heterosexual men. This elevated risk persists across age groups and reflects biological and behavioral factors, yet there have been few direct comparisons of sexual behavior patterns between these populations.
We compared sexual behavior patterns of MSM and male and female heterosexuals aged 18–39 using 4 population-based random digit dialing surveys. A 1996–1998 survey in 4 U.S. cities and 2 Seattle surveys (2003, 2006) provided estimates for MSM; a 2003–2004 Seattle survey provided data about heterosexual men and women.
Sexual debut occurred earlier among MSM than heterosexuals. MSM reported longer cumulative lifetime periods of new partner acquisition than heterosexuals, and a more gradual decline in new partnership formation with age. Among MSM, 86% of 18–24 year olds and 72% of 35–39 year olds formed a new partnership during the prior year, compared to 56% of heterosexual men and 34% of women at ages 18–24, and 21% and 10%, respectively, at ages 35–39. MSM were also more likely to choose partners >5 years older and were 2–3 times as likely as heterosexuals to report recent concurrent partnerships. MSM reported more consistent condom use during anal sex than heterosexuals reported during vaginal sex.
MSM have longer periods of partnership acquisition, a higher prevalence of partnership concurrency, and more age-disassortative mixing than heterosexuals. These factors likely help explain higher HIV/STI rates among MSM, despite higher levels of condom use.
men who have sex with men; heterosexuals; sexual behavior; HIV; STI
Cocolonization with methicillin-resistant Staphylococcus aureus (MRSA) and vancomycin-resistant enterococci (VRE) is a precursor to vancomycin-resistant S. aureus emergence. MRSA/VRE cocolonization incidence is higher among skilled nursing facility residents with functional disability and indwelling devices and occurs more frequently in wounds than other anatomical sites.
Background. Methicillin-resistant Staphylococcus aureus (MRSA) remains sensitive to vancomycin; when vancomycin-resistant S. aureus (VRSA) emerges, treatment becomes more complex. VRSA emergence is attributed to conjugative transfer of the vancomycin-resistance gene cluster from vancomycin-resistant enterococci (VRE) to MRSA. Because cocolonization with MRSA and VRE precedes VRSA development, this study investigates the epidemiology of cocolonization in skilled nursing facility (SNF) residents at high risk for MRSA or VRE colonization.
Methods. A prospective observational study conducted at 15 SNFs in southeast Michigan. Overall, 178 residents (90 with indwelling urinary catheters and/or feeding tubes and 88 device-free) were cultured monthly for MRSA and VRE, and clinical data were recorded.
Results. The incidence of MRSA/VRE cocolonization among residents with indwelling devices was 6.5 per 100 resident-months; 5.2 (95% confidence interval [CI]: 1.49–18.1) times that among those without devices. MRSA/VRE cocolonization in the device group occurred most frequently in wounds (4.1 per 100 resident-months). In a logistic regression analysis limited to residents with devices, functional disability (rate ratio [RR], 1.3; 95% CI: 1.1–1.4) and wound presence (RR, 3.4; 95% CI: 1.4–8.6) were independent risk factors of cocolonization.
Conclusions. In a population of SNF residents, individuals with indwelling devices who also had functional disability or wounds were at greatest risk of MRSA/VRE cocolonization. These individuals should be routinely monitored for the presence of VRSA colonization.
We demonstrate the feasibility of using qPCR on DNA extracted from vaginal Gram stain slides to estimate the presence and relative abundance of specific bacterial pathogens. We first tested Gram stained slides spiked with a mix of 108 cfu/ml of Escherichia coli and 105 cfu/ml of Lactobacillus acidophilus. Primers were designed for amplification of total and species-specific bacterial DNA based on 16S ribosomal gene regions. Sample DNA was pre-amplified with nearly full length 16S rDNA ribosomal gene fragment, followed by quantitative PCR with genera and species-specific 16S rDNA primers. Pre-amplification PCR increased the bacterial amounts; relative proportions of Escherichia coli and Lactobacillus recovered from spiked slides remained unchanged. We applied this method to forty two archived Gram stained slides available from a clinical trial of cerclage in pregnant women at high risk of preterm birth. We found a high correlation between Nugent scores based on bacterial morphology of Lactobacillus, Gardenerella and Mobiluncus and amounts of quantitative PCR estimated genus specific DNA (rrn copies) from Gram stained slides. Testing of a convenience sample of eight paired vaginal swabs and Gram stains freshly collected from healthy women found similar qPCR generated estimates of Lactobacillus proportions from Gram stained slides and vaginal swabs. Archived Gram stained slides collected from large scale epidemiologic and clinical studies represent a valuable, untapped resource for research on the composition of bacterial communities that colonize human mucosal surfaces.
Group B Streptococcus (GBS) remains a major cause of neonatal sepsis and is an emerging cause of invasive bacterial infections. The 9 known serotypes vary in virulence, and there is little cross-immunity. Key parameters for planning an effective vaccination strategy, such as average length of immunity and transmission probabilities by serotype, are unknown. We simulated GBS spread in a population using a computational model with parameters derived from studies of GBS sexual transmission in a college dormitory. Here we provide estimates of the duration of immunity relative to the transmission probabilities for the 3 GBS serotypes most associated with invasive disease: Ia, III, and V. We also place upper limits on the durations of immunity for serotype Ia (570 days), III (1125 days) and V (260 days). Better transmission estimates are required to establish the epidemiological parameters of GBS infection and determine the best vaccination strategies to prevent GBS disease.
vaccines; modeling; Streptococcus agalactiae; group B Streptococcus
Skin, the largest human organ, is a complex and dynamic ecosystem inhabited by a multitude of microorganisms. Host demographics and genetics, human behavior, local and regional environmental characteristics, and transmission events may all potentially drive human skin microbiota variability, resulting in an alteration of microbial community structure. This alteration may have important consequences regarding health and disease outcomes among individuals. More specifically, certain diversity patterns of human microbiota may be predictive or diagnostic of disease. The purpose of this review is to briefly describe the skin microbiota, outline the potential determining factors driving its variability, posit the likelihood of an association between the resulting microbial community structure on the skin with disease outcomes among individuals, and finally, to present some challenges and implications for studying the skin microbiota.
microbial ecology; epidemiology; diversity; transmission; skin
Approximately 25% of hospitalized patients have a urinary catheter, and catheter associated urinary tract infection is the most common nosocomial infection in the US, causing >1 million cases/year. However, the natural history of the biofilms that rapidly form on urinary catheters and lead to infection is not well described.
We characterized the dynamics of catheter colonization among catheters collected from 3 women and 5 men in a trauma burn unit with different indwelling times using TRFLP and culture. All patients received antibiotic therapy. Results: Colony-forming units increased along the extraluminal catheter surface from the catheter balloon to the urethra, but no trend was apparent for the intraluminal surface. This suggests extraluminal bacteria come from periurethral communities while intraluminal bacteria are introduced via the catheter or already inhabit the urine/bladder. Richness of operational taxonomic units (OTUs) increased over time on the intraluminal surface, but was constant extraluminally.
OTU community composition was explained best by time rather than axial location or surface. Our results suggest that catheter colonization can be very dynamic, and possibly have a predictable succession.
Urinary tract infection; Microbial ecology; Biofilms; Urinary catheter
Our objective was to characterize 46 unique, erythromycin-sensitive, and clindamycin-resistant Streptococcus agalactiae strains from S. Korea that displayed a novel phenotype in double-disk diffusion assay. We used polymerase chain reaction to determine presence of erythromycin and clindamycin resistance genes, disc diffusion assays to determine resistance phenotype, and microbroth dilution to determine minimal inhibitory concentration. We detected a novel phenotype in the double-disk diffusion assay for inducible resistance among 46 S. agalactiae strains that were both erythromycin sensitive and clindamycin resistant. Thirty-two strains with the novel phenotype tested positive for erm(B) by DNA–DNA hybridization; sequencing of the erm(B) gene revealed mutations in the ribosomal binding site region in the erm(B) open reading frame, which is consistent with a lack of erythromycin resistance phenotype. Although identified from patients at multiple hospitals, genotyping suggested that the strains are closely related. The new phenotype shows increased sensitivity to clindamycin in the presence of erythromycin.
Among otherwise healthy college women with a newly-diagnosed acute UTI, drinking 8 oz of 27% cranberry juice twice a day did not decrease the 6-month incidence of a second UTI compared to those drinking a placebo.
Background. A number of observational studies and a few small or open randomized clinical trials suggest that the American cranberry may decrease incidence of recurring urinary tract infection (UTI).
Methods. We conducted a double-blind, placebo-controlled trial of the effects of cranberry on risk of recurring UTI among 319 college women presenting with an acute UTI. Participants were followed up until a second UTI or for 6 months, whichever came first. A UTI was defined on the basis of the combination of symptoms and a urine culture positive for a known uropathogen. The study was designed to detect a 2-fold difference between treated and placebo groups, as was detected in unblinded trials. We assumed 30% of participants would experience a UTI during the follow-up period.
Results. Overall, the recurrence rate was 16.9% (95% confidence interval, 12.8%–21.0%), and the distribution of the recurrences was similar between study groups, with the active cranberry group presenting a slightly higher recurrence rate (20.0% vs 14.0%). The presence of urinary symptoms at 3 days, 1–2 weeks, and at ≥1 month was similar between study groups, with overall no marked differences.
Conclusions. Among otherwise healthy college women with an acute UTI, those drinking 8 oz of 27% cranberry juice twice daily did not experience a decrease in the 6-month incidence of a second UTI, compared with those drinking a placebo.
To identify obstetric and maternal factors related to Group B Streptococcus (GBS) colonization in pregnant women in Korea.
The study was conducted between the years 2006-2008 in four hospitals, Cheil and Eulji hospital in Seoul, and Motae and Eulji hospital in Daejeon. We recruited 2,644 pregnant women between 35 to 37 weeks of gestation who had visited for antenatal care. Participants completed a questionnaire, and urine, vaginal and rectal specimens were obtained and cultured using selective broth media. After delivery, medical records were reviewed.
GBS colonization was significantly associated with hospital, age group, education, frequency of pregnancy, and premature rupture of membranes (PROM, more than 18 hours). After adjustment for other variables, Cheil hospital (odds ratio [OR], 2.05; 95% confidence interval [CI], 1.20-3.52), and the first pregnancy (OR, 2.32; 95% CI, 1.12-4.81) remained significant. History of vaginitis showed marginal significance (OR, 1.50; 95% CI, 0.98-2.29).
To prevent GBS infection of neonates, clinicians should be alert to the potentially higher risk of GBS colonization in pregnant women in their first pregnancy, and women with premature rupture of membranes (PROM) (18 hours+) or who have a history of vaginitis.
Colonization; Pregnant women; Risk factors; Screening; Streptococcus agalactiae
The evolution of antibiotic resistance (AR) increases treatment cost and probability of failure, threatening human health worldwide. The relative importance of individual antibiotic use, environmental transmission and rates of introduction of resistant bacteria in explaining community AR patterns is poorly understood. Evaluating their relative importance requires studying a region where they vary. The construction of a new road in a previously roadless area of northern coastal Ecuador provides a valuable natural experiment to study how changes in the social and natural environment affect the epidemiology of resistant Escherichia coli. We conducted seven bi-annual 15 day surveys of AR between 2003 and 2008 in 21 villages. Resistance to both ampicillin and sulphamethoxazole was the most frequently observed profile, based on antibiogram tests of seven antibiotics from 2210 samples. The prevalence of enteric bacteria with this resistance pair in the less remote communities was 80 per cent higher than in more remote communities (OR = 1.8 [1.3, 2.3]). This pattern could not be explained with data on individual antibiotic use. We used a transmission model to help explain this observed discrepancy. The model analysis suggests that both transmission and the rate of introduction of resistant bacteria into communities may contribute to the observed regional scale AR patterns, and that village-level antibiotic use rate determines which of these two factors predominate. While usually conceived as a main effect on individual risk, antibiotic use rate is revealed in this analysis as an effect modifier with regard to community-level risk of resistance.
antibiotic resistance; Escherichia coli; transmission models; Ecuador; community
Partnership formation and dissolution rates are primary determinants of sexually transmitted infection (STI) transmission dynamics.
The authors used data on persons' lifetime sexual experiences from a 2003-2004 random digit dialing survey of Seattle residents aged 18-39 years (N=1,194) to estimate age- and gender-specific partnership formation and dissolution rates. Partnership start and end dates were used to estimate participants' ages at the start of each partnership and partnership durations, and partnerships not enumerated in the survey were imputed.
Partnership formation peaked at age 19 at 0.9 (95% CI: 0.76, 1.04) partnerships per year and decreased to 0.1-0.2 after age 30 for women and peaked at age 20 at 1.4 (95% CI: 1.08, 1.64) and declined to 0.5 after age 30 for men. Nearly a quarter (23.7%) of partnerships ended within 1 week and over one-half (51.2%) ended within 12 weeks. Most (63.5%) individuals aged 30-39 had not formed a new sexual partnership in the past 3 years.
A large proportion of the heterosexual population is no longer at substantial STI risk by their early 30s, but similar analyses among high-risk populations may give insight into reasons for the profound disparities in STI rates across populations.
heterosexual; partnerships; mathematical modeling; random digit dialing survey; sexually transmitted diseases; epidemiology
Persistent E. coli asymptomatic bacteriuria (ASB) is common among persons with diabetes mellitus, but duration of colonization and re-colonization rates are unknown. We estimated duration of colonization and re-colonization among successively isolated E. coli from asymptomatic diabetic women and compared the virulence profiles to uropathogenic and commensal E. coli.
105 women with diabetes were enrolled in a randomized controlled clinical trial for treatment of ASB in Manitoba, Canada and followed at least every three months for up to three years. We analyzed 517 isolates from 70 women with repeated E. coli ASB for genetic similarity using ERIC-PCR. Unique strains were screened for uropathogenic virulence characteristics using dot blot hybridization, and compared to different collections of E. coli isolates.
On average, there were differences between women assigned to treatment for ASB, those only treated for symptomatic infections and untreated women in: a) follow-up time with bacteriuria (29%, 31% and 66%, p=<0.001), b) duration of bacteriuria (2.2, 2.5 and 3.7 months, p=0.04) and c) carriage of unique isolates (2.4, 2.8 and 4 months, p=0.03). Women assigned to antibiotic treatment usually had recurrent infection (76%), 64% of the time with a genetically new E. coli strain. Virulence characteristics of these isolates were comparable to those of fecal isolates from healthy women.
Treatment may reduce the overall proportion of time infected in the long-term and carriage of a unique strain, but most treatment regimens were followed by subsequent re-colonization. Infecting strains did not have virulence factors characteristic of uropathogenic E. coli.
urinary tract infection; diabetes; virulence; colonization; ERIC-PCR typing
Genotypic analyses of Streptococcus mutans using fingerprinting methods depend on a few genetic loci being different but do not reveal the underlying genome-wide differences between strains. We used comparative genomic hybridization (CGH) with 70-mer oligonucleotide microarrays containing open reading frames (ORFs) from S. mutans UA159 to examine the genetic diversity of 44 isolates from nine children selected from a local study population in Eastern Iowa. Unique strains (clones) within each child initially identified by AP-PCR were confirmed by CGH. There was a wide range of variation in the hybridization patterns of the 1948 ORFs among test isolates examined. Between 87 and 237 ORFs failed to give a positive signal among individual isolates. A total of 323 of the UA159 ORFs were absent from one or more of the test strains. These 323 variable genes seemed to be distributed across the entire UA 159 genome and across all the predicted functional categories. This set of very close geographically and temporally collected S. mutans isolates had a degree of gene content variations as high as a global set of strains examined in a previous publication (Waterhouse et al., 2007). Comparing the frequency of these variable genes, the majority of which have unknown function, among strains of different origins (i.e. different caries status) could help determine their relevance in S. mutans cariogenicity.
Dental Caries; S. mutans; CGH (comparative genomic hybridization)
The prevalence of group B streptococcus (GBS) among pregnant women and disease burdens in neonates and adults are increasing in Korea. Colonizing isolates, collected by screening pregnant women (n=196), and clinical isolates collected from clinical patients throughout Korea (n=234), were serotyped and screened for antibiotic resistance. Serotype III (29.8%) and V (27.7%) predominated, followed by Ia (17.0%). Antibiotic resistance was higher among clinical than colonizing isolates for erythromycin (35.1% and 26.9%; P=0.10) and for clindamycin (49.4% and 42.1%; P=0.17). erm(B) occurred in 91.9% of erythromycin resistant isolates, and 84.0% of isolates resistant to clindamycin. Only five isolates (4.2%) resistant to erythromycin were susceptible to clindamycin; by contrast, and unique to Korea, 34% of isolates resistant to clindamycin were erythromycin susceptible. Among these 60 erythromycin-susceptible & clindamycin-resistant isolates, 88% was serotype III, and lnu(B) was found in 89% of strains. Four fifths of the serotype V isolates were resistant to both erythromycin and clindamycin. Further characterization of the genetic assembly of these resistance conferring genes, erm(B) and lnu(B), will be useful to establish the clonal lineages of multiple resistance genes carrying strains.
Drug Resistance, Microbial; Genotype; Pregnant Women; Streptococcus Agalactiae; Serotyping
The occurrence and spread of antibiotic-resistant bacteria (ARB) are pressing public health problems worldwide, and aquatic ecosystems are a recognized reservoir for ARB. We used culture-dependent methods and quantitative molecular techniques to detect and quantify ARB and antibiotic resistance genes (ARGs) in source waters, drinking water treatment plants, and tap water from several cities in Michigan and Ohio. We found ARGs and heterotrophic ARB in all finished water and tap water tested, although the amounts were small. The quantities of most ARGs were greater in tap water than in finished water and source water. In general, the levels of bacteria were higher in source water than in tap water, and the levels of ARB were higher in tap water than in finished water, indicating that there was regrowth of bacteria in drinking water distribution systems. Elevated resistance to some antibiotics was observed during water treatment and in tap water. Water treatment might increase the antibiotic resistance of surviving bacteria, and water distribution systems may serve as an important reservoir for the spread of antibiotic resistance to opportunistic pathogens.
Mycobacterium tuberculosis lipases, a diverse class of enzymes involved in lipid metabolism, may have an important role in tuberculosis (TB) pathogenesis. We explored the association of large sequence polymorphism (LSP) in one of the M. tuberculosis lipase-encoding genes, lipR (Rv3084), with patient characteristics using a population-based sample of clinical isolates to elucidate the potential role of lipR in TB pathogenesis. LSP in lipR were found in 104 (15.6%) of 665 isolates, of which 96% belonged to principal genetic group 3. When linkage by molecular type and epidemiologic evidence were compared, molecularly clustered cases infected with a lipR LSP isolate were more often epidemiologically linked than clustered cases infected with a lipR wild-type isolate. Further epidemiologic and functional studies are necessary to determine if the association between this lipR LSP and recent transmission we identified in this population reflects a functional role of lipR in TB transmission and pathogenesis, the lipR polymorphism acting as a marker for strains that have been recently introduced into this geographical region, or a yet unidentified mechanism.
lipR; large sequence polymorphisms; tuberculosis transmission and pathogenesis; molecular epidemiology of tuberculosis
ESBL; Escherichia coli; community acquired; persistence; urinary tract infection; bacteria; letter
Periodontitis is considered a consequence of a pathogenic microbial infection at the periodontal site and host susceptibility factors. Periodontal research supports the association of Actinobacillus actinomycetemcomitans, Porphyromonas gingivalis, Prevotella intermedia, and Bacteroides forsythus, and periodontitis; however causality has not been demonstrated. In pursuit of the etiology of periodontitis, we hypothesized that the intracellular bacteria, Chlamydia trachomatis, may play a role. As a first step, a cross-sectional study of dental school clinic patients with established periodontitis were assessed for the presence of C. trachomatis in the oral cavity, and in particular from the lining epithelium of periodontal sites. C. trachomatis was detected using a direct fluorescent monoclonal antibody (DFA) in oral specimens from 7% (6/87) of the patients. Four patients tested positive in specimens from the lining epithelium of diseased periodontal sites, one patient tested positive in healthy periodontal sites, and one patient tested positive in the general mucosal specimen. In conclusion, this study provides preliminary evidence of C. trachomatis in the periodontal sites. Planned studies include the use of a more precise periodontal epithelial cell collection device, the newer nucleic acid amplification techniques to detect C. trachomatis, and additional populations to determine the association of C. trachomatis and periodontitis.
Chlamydia; Chlamydia trachomatis; Fluorescent antibody technique; Periodontal diseases; Periodontitis
Probe hybridization array typing (PHAT) is a previously validated, high-throughput, highly discriminatory binary typing method based on the presence or absence of genetic material. To increase the utility of PHAT, we identified a refined PHAT probe set using 24 known and potential Escherichia coli virulence genes, by which groups similar to multilocus sequence typing (MLST) clonal groups (CGs) could be determined. We PHAT typed 1,132 E. coli isolates, representing at least 62 MLST CGs and diverse disease states, using a “library-on-a-slide” microarray format. Using 24 PHAT probes, all 62 MLST CGs in the representative E. coli collection were distinguished. For major CGs, PHAT correctly classified all sequence types within CG7 and CG17 but misclassified between one and four sequence types for CG13, CG14, CG23, CG38, and CG58, giving an overall sensitivity and specificity of 80.4 and 98.7%, respectively. After application of the PHAT classification to the whole collection, MLST validation of the PHAT probe classification resulted in sensitivities from 0.0 to 100.0% and specificities from 75.0 to 100.0% for individual CGs and an overall sensitivity and specificity of 64.7 and 88.3%, respectively. The refined PHAT probe set is capable of classifying isolates into groups in a manner similar to major clonal complexes of MLST, indicating coevolution between the chromosomal background and the flexible gene pool. Further refinement is needed to distinguish between closely related groups. For analysis of large bacterial collections, PHAT is a relatively time- and cost-efficient method and is ideal for a first level of analysis.
The Mycobacterium tuberculosis PE_PGRS multigene family is thought to be involved in antigenic variation, which can be generated by differential regulation of expression and a high frequency of genetic polymorphism. PE_PGRS16 and PE_PGRS26 are inversely regulated during persistent M. tuberculosis infection, suggesting that differential regulation of the expression of these two PE_PGRS genes may have a role in latency. To understand how genetic diversity, in addition to differential regulation, contributes to antigenic variability, we investigated the sequence variations in the PE_PGRS16 and PE_PGRS26 genes among 200 clinical M. tuberculosis strains, in comparison to the sequenced laboratory strain H37Rv, using PCR and DNA sequencing. Among the 200 strains, 102 (51%) and 100 (50%) had sequence variations within the PE_PGRS16 gene and the PE_PGRS26 gene, respectively. In-frame insertions and deletions, frameshifts, and SNPs were observed in both the PE_PGRS16 gene and the PE_PGRS26 gene. However, the frequency of frameshifts and in-frame deletions differed between the two PE_PGRS genes. Examining the profile of the PE_PGRS16, PE_PGRS26, and the previously investigated PE_PGRS33 amino acid sequences for each of the 200 strains, 72 different profiles were observed with frequencies ranging from 0.5% to 13%. In conclusion, a remarkable level of genetic diversity exists in the PE_PGRS16 and PE_PGRS26 genes of M. tuberculosis clinical strains. The significant sequence variations in the two PE_PGRS genes observed in this study could impact the function of these two PE_PGRS proteins and be associated with differences in the ability of the tubercle bacilli to remain persistent within the host.