Oropharyngeal Specimens Research Articles

Meningococcal carriage among a university student population – United States, 2015

ObjectivesSeveral outbreaks of serogroup B meningococcal disease have occurred among university students in recent years. In the setting of high coverage of the quadrivalent meningococcal conjugate vaccine and prior to widespread use of serogroup B meningococcal vaccines among adolescents, we conducted surveys to characterize the prevalence and molecular characteristics of meningococcal carriage among university students. MethodsTwo cross-sectional oropharyngeal carriage surveys were conducted among undergraduates at a Rhode Island university. Isolates were characterized using slide agglutination, real-time polymerase chain reaction (rt-PCR), and whole genome sequencing. Adjusted prevalence ratios and 95% confidence intervals were calculated using Poisson regression to determine risk factors for carriage. ResultsA total of 1837 oropharyngeal specimens were obtained from 1478 unique participants. Overall carriage prevalence was 12.7–14.6% during the two survey rounds, with 1.8–2.6% for capsular genotype B, 0.9–1.0% for capsular genotypes C, W, or Y, and 9.9–10.8% for nongroupable strains by rt-PCR. Meningococcal carriage was associated with being male, smoking, party or club attendance, recent antibiotic use (inverse correlation), and recent respiratory infections. ConclusionsIn this university setting, the majority of meningococcal carriage was due to nongroupable strains, followed by serogroup B. Further evaluation is needed to understand the dynamics of serogroup B carriage and disease among university students.

Clinical Characteristics of Hospitalized Infants With Laboratory-Confirmed Pertussis in Guatemala

Pertussis is an important cause of hospitalization and death in infants too young to be vaccinated (aged <2 months). Limited data on infant pertussis have been reported from Central America. The aim of this study was to characterize acute respiratory illnesses (ARIs) attributable to Bordetella pertussis among infants enrolled in an ongoing surveillance study in Guatemala. As part of a population-based surveillance study in Guatemala, infants aged <2 months who presented with ARI and required hospitalization were enrolled, and nasopharyngeal and oropharyngeal swab specimens were obtained. For this study, these specimens were tested for B pertussis using real-time polymerase chain reaction (PCR). Among 301 infants hospitalized with ARI, we found 11 with pertussis confirmed by PCR (pertussis-positive infants). Compared to pertussis-negative infants, pertussis-positive infants had a higher mean admission white blood cell count (20900 vs 12579 cells/μl, respectively; P = .024), absolute lymphocyte count (11517 vs 5591 cells/μl, respectively; P < .001), rate of admission to the intensive care unit (64% vs 35%, respectively; P = .054), and case fatality rate (18% vs 3%, respectively; P = .014). Ten of the 11 pertussis-positive infants had cough at presentation; the majority (80%) of them had a cough duration of <7 days, and only 1 had a cough duration of >14 days. Fever (temperature ≥ 38°C) was documented in nearly half (45%) of the pertussis-positive infants (range, 38.0-38.4°C). In this study of infants <2 months of age hospitalized with ARI in Guatemala, pertussis-positive infants had a high rate of intensive care unit admission and a higher case fatality rate than pertussis-negative infants.

Utility and Challenges of a Multi-pathogen Diagnostic Platform for Characterizing Public Health Threats of Severe Acute Respiratory Infections in Six Countries

BackgroundPneumonia causes significant morbidity and mortality worldwide. Comprehensive etiology studies of pneumonia in adults are limited; however, new diagnostics enable simultaneous detection of multiple pathogens in respiratory specimens. Characterizing the public health threat of severe acute respiratory infection (SARI) may enhance global health security. We studied potential etiologies of SARI among adults in six countries over a 12-month period using multi-pathogen diagnostics.MethodsWe enrolled SARI cases (acute onset of fever and cough, requiring hospitalization, in an adult) from Global Disease Detection sites in Bangladesh, China, Egypt, Guatemala, Kenya, and Thailand and healthy frequency-matched controls (2 controls: 5 cases) by time (onset), age group (18–49, 50–64, 65+ years), and catchment area. Demographics, clinical data, and nasopharyngeal and oropharyngeal specimens were collected from cases and controls. Specimens were tested for 16 viruses and 14 bacteria using Taqman® Array Card, which uses real-time reverse transcriptase polymerase chain reaction.ResultsWe enrolled 2,388 cases and 1,135 controls from Oct 2013 through Oct 2015. Age distribution (Figure) and seasonality varied by site: enrollment peaked in summer months in Bangladesh, Thailand, and China, and in winter months in Egypt, but was stable throughout the year in Guatemala and Kenya. Case fatality rate across all study locations was 2.3% (range 0–7.0%). One or more pathogens was detected in 76% of cases and in 67% of controls; ≥2 pathogens were detected in 42% of cases and 37% of controls. Pathogens more commonly detected among cases than controls included influenza A (OR 13.3, CI 7.0–25.2; 12.8% of cases vs. 1.1% of controls), influenza B (OR: 27.0, CI 8.6–84.8; 8.1% vs. 0.3%), and respiratory syncytial virus (RSV) (OR: 9.4, CI 3.4–25.8; 4.0% vs. 0.4%).ConclusionIn this SARI study, frequent detection of multiple pathogens in the oro- and nasopharynx of both cases and controls made etiology attribution difficult. Influenza and RSV, however, were likely to be causes of SARI. Because upper respiratory tract specimens may not accurately reflect disease in the lung, better specimens are needed to determine pneumonia etiology, particularly for bacteria.Disclosures All authors: No reported disclosures.

Immunohistochemistry Analysis of CD44, EGFR, and p16 in Oral Cavity and Oropharyngeal Squamous Cell Carcinoma.

Objectives We analyze the relationship between CD44, epidermal growth factor receptor (EGFR), and p16 expression in oral cavity and oropharyngeal cancers in a diverse population. We also describe whether particular patterns of staining are associated with progression-free survival and overall survival. Study Design Prospective study, single-blind to pathologist and laboratory technologist. Setting Hospital based. Subjects and Methods Immunohistochemistry, comprising gross staining and cellular expression, was performed and interpreted in a blinded fashion on 24 lip/oral cavity and 40 oropharyngeal cancer specimens collected between 2007 and 2012 from participants of a larger study. Information on overall survival and progression-free survival was obtained from medical records. Results Nineteen cases were clinically p16 positive, 16 of which were oropharyngeal. Oral cavity lesions were more likely to exhibit strong CD44 membrane staining ( P = .0002). Strong CD44 membrane and strong EGFR membrane and/or cytoplasmic staining were more common in p16-negative cancers ( P = .006). Peripheral/mixed gross p16 staining pattern was associated with worse survival than the universal staining on univariate and multivariate analyses ( P = .006, P = .030). This held true when combining gross and cellular localization for p16. For CD44, universal gross staining demonstrated poorer overall survival compared with the peripheral/mixed group ( P = .039). CD44 peripheral/mixed group alone and when combined with universal p16 demonstrated the best survival on multivariate analysis ( P = .010). Conclusion In a diverse population, systematic analysis applying p16, CD44, and EGFR gross staining and cellular localization on immunohistochemistry demonstrates distinct patterns that may have prognostic potential exceeding current methods. Larger studies are warranted to investigate these findings further.

Use of Single-dose Azithromycin to Control a Community Outbreak of emm26.3 Group A Streptococcus Invasive Disease—Alaska, 2017

Background In July 2016, invasive infections caused by a rare subtype of group A Streptococcus (iGAS; subtype emm26.3) were detected among the estimated 700–1000 homeless persons in Anchorage, Alaska. An increase in case numbers of emm26.3 iGAS was detected in October, including one death. We implemented a mass antibiotic intervention at homeless service facilities in Anchorage to prevent further cases of emm26.3 iGAS.Methods We defined cases as the isolation of emm26.3 GAS from a normally sterile body site, or nonsterile sites in the case of necrotizing fasciitis or toxic shock syndrome. We identified cases through routine laboratory-based surveillance and conducted antimicrobial susceptibility testing on all invasive isolates. From February 13–18, 2017, we evaluated persons accessing homeless services at six facilities in Anchorage and offered a single oral dose of 1 gram of azithromycin for iGAS prophylaxis. We concurrently collected oropharyngeal (OP) and wound swab specimens on a subset of participants. The swab collection was repeated at the same locations 4 weeks after the intervention. Swabs were cultured for GAS and emm-typed.ResultsFrom October 1, 2016 through February 18, 2017, we detected 31 cases among homeless persons. All emm26.3 iGAS isolates were erythromycin susceptible. We evaluated 484 persons at homeless services facilities and provided azithromycin to 394 (81%). Of 289 swab participants, 9 (3.1%) had baseline emm26.3 OP colonization. Of participants with wounds, 3/71 (4.2%) had emm26.3 wound colonization. At follow-up, 3/298 (1.0%) participants had emm26.3 OP colonization and 1/63 (1.6%) had emm26.3 wound colonization (P-value for change in any colonization = 0.05). Colonization by other emm-types, primarily erythromycin non-susceptible emm11, was 5.1% at baseline and 5.0% at follow-up. In the 6 weeks post-intervention, we detected 1 case among homeless persons (0.2 cases/week post- vs. 1.6 cases/week pre-intervention, P = 0.01 for change).Conclusion We reached a substantial proportion of the Anchorage homeless population with an antibiotic intervention to prevent iGAS. While possible that the outbreak was waning, the intervention was temporally associated with reduced case counts and colonization prevalence.Disclosures All authors: No reported disclosures.

HPV-Positive Oropharyngeal Cancer Via p16 Immunohistochemistry in Japan.

Human papillomavirus (HPV) has emerged as a driving cause of head and neck cancer, but investigations outside the West are limited. A p16 immunohistochemistry is a commonly used biomarker for HPV cancers. We sought to investigate the pathology and rates of HPV head and neck oropharyngeal cancer in Japan via p16 immunohistochemistry at 2 institutions in Japan. Fifty-nine oropharyngeal specimens from 2 university hospitals in Japan were examined for morphology and p16 immunohistochemistry. The rate of p16 positivity was then determined, and the 2 groups were compared for differences in age, smoking history, gender, and stage of presentation and mortality. The rate of p16 positivity among the oropharyngeal specimens was 29.5%. There were important differences in the pathology compared to morphology usually seen in the US. The patients with p16+ cancer tended to be younger. There was no significant difference in smoking status. Patients with p16+ cancers trended toward better survival. There appears to be a geographical difference in HPV rates of oropharyngeal cancers with persistently lower rates in Asian countries when compared to Western Europe and the US. Conclusions about HPV head and neck squamous cell carcinoma (HNSCC) in Western countries may not be generalizable across the globe at this time.

The prevalence of human papillomavirus infections and associated risk factors in men-who-have-sex-with-men in Cape Town, South Africa.

BackgroundWe investigated the prevalence of human papillomavirus (HPV) infection and associated behavioural risk factors in men-who-have-sex-with-men (MSM) attending a clinical service in Cape Town, South Africa.MethodsMSM were enrolled at the Ivan Toms Centre for Men’s Health in Cape Town. A psychosocial and sexual behavioral risk questionnaire was completed for each participant and urine, oro-pharyngeal and anal swabs were collected for HPV testing using the Linear Array HPV Genotyping Test. Logistic regression analyses were performed to determine sexual risk factors associated with HPV infection at the three anatomical sites.ResultsThe median age of all 200 participants was 32 years (IQR 26-39.5), of which 31.0 % were black, 31.5 % mixed race/coloured and 35.5 % white. The majority of the participants (73.0 %) had completed high school, 42.0 % had a tertiary level qualification and 69.0 % were employed. HPV genotypes were detected in 72.8 % [95 % CI: 65.9–79.0 %], 11.5 % [95 % CI: 7.4–16.8 %] and 15.3 % [95 % CI: 10.5–21.2 %] of anal, oro-pharyngeal and urine specimens, respectively. Prevalence of high-risk (HR)-HPV types was 57.6 % [95 % CI: 50.3–64.7 %] in anal samples, 7.5 % [95 % CI: 4.3–12.1 %] in oro-pharyngeal samples and 7.9 % [95 % CI: 4.5–12.7 %] in urine, with HPV-16 being the most common HR-HPV type detected at all sites. HPV-6/11/16/18 was detected in 40.3 % [95 % CI: 33.3–47.6 %], 4.5 % [95 % CI: 2.1–8.4 %] and 3.2 % [95 % CI: 1.2–6.8 %] of anal, oro-pharyngeal and urine samples, respectively. Multiple HPV types were more common in the anal canal of MSM while single HPV types constituted the majority of HPV infections in the oropharynx and urine. Among the 88 MSM (44.0 %) that were HIV positive, 91.8 % [95 % CI: 83.8–96.6 %] had an anal HPV infection, 81.2 % [95 % CI: 71.2–88.8 %] had anal HR-HPV and 85.9 % [95 % CI: 76.6–92.5 %] had multiple anal HPV types. Having sex with men only, engaging in group sex in lifetime, living with HIV and practising receptive anal intercourse were the only factors independently associated with having any anal HPV infection.ConclusionsAnal HPV infections were common among MSM in Cape Town with the highest HPV burden among HIV co-infected MSM, men who have sex with men only and those that practiced receptive anal intercourse. Behavioural intervention strategies and the possible roll-out of HPV vaccines among all boys are urgently needed to address the high prevalence of HPV and HIV co-infections among MSM in South Africa.

Co-colonization by Streptococcus pneumoniae and Staphylococcus aureus in the throat during acute respiratory illnesses.

Pneumonia due to either Streptococcus pneumoniae (Sp) or Staphylococcus aureus (Sa) accounts for most mortality after influenza and acute respiratory illness (ARI). Because carriage precedes infection, we estimated Sp and Sa carriage to examine the co-colonization dynamics between Sp, Sa and respiratory viruses in the presence of ARI in the oropharynx. We tested oropharyngeal specimens of community subjects (aged ⩾2 years) with ARI for the presence of influenza A and B, 11 other common respiratory viruses, Sp and Sa, using real-time PCR. A total of 338 participants reported 519 ARI episodes of which 119 (35%) carried Sp, 52 (13%) carried Sa and 25 (7%) carried both. Thirty-five subjects tested positive for influenza, of which 14 (40%) carried Sp and six (17%) carried Sa, significantly more than in the influenza-negative group (P = 0·03 and P = 0·04, respectively). In subjects infected by any virus compared to those with no virus, Sp carriage (39·2% vs. 27·9%, P = 0·03) but not Sa carriage (11·6% vs. 14%, P = 0·6) was more frequent. For children, when Sa was present, Sp carriage tended to be less frequent than expected given the presence of viral infection, but not significantly [observed relative risk 1·14, 95% confidence interval (CI) 0·4-3·1; with a relative excess risk due to interaction of -0·11]. Independent of age, Sp carriers were more likely to return that season with subsequent ARI (odds ratio 2·14, 95% CI 1·1-4·3, P = 0·03). Both Sp and Sa carriage rates in the oropharynx increase during influenza infection in children. However, no negative interaction between Sp and Sa was observed. Sp carriers are more likely to suffer subsequent ARI episodes than non-carriers.

Incidence and etiology of hospitalized acute respiratory infections in the Egyptian Delta.

IntroductionAcute Respiratory Infections (ARI) are responsible for nearly two million childhood deaths worldwide. A limited number of studies have been published on the epidemiology of viral respiratory pathogens in Egypt.MethodsA total of 6113 hospitalized patients >1 month of age with suspected ARI were enrolled between June 23, 2009 and December 31, 2013. Naso‐ and oropharyngeal specimens were collected and tested for influenza A and B, respiratory syncytial virus, human metapneumovirus, adenovirus, and parainfluenza viruses 1–3. Blood specimens from children 1–11 months were cultured and bacterial growth was identified by polymerase chain reaction. Results from a healthcare utilization survey on the proportion of persons seeking care for ARI was used to calculate adjusted ARI incidence rates in the surveillance population.ResultsThe proportion of patients with a viral pathogen detected decreased with age from 67% in patients age 1–11 months to 19% in patients ≥65 years of age. Influenza was the dominant viral pathogen detected in patients ≥1 year of age (13.9%). The highest incidence rates for hospitalized ARI were observed in children 1–11 months (1757.9–5537.5/100 000 population) and RSV was the most commonly detected pathogen in this age group.ConclusionIn this study population, influenza is the largest viral contributor to hospitalized ARIs and children 1–11 months of age experience a high rate of ARI hospitalizations. This study highlights a need for surveillance of additional viral pathogens and alternative detection methods for bacterial pathogens, which may reveal a substantial proportion of as yet unidentified etiologies in adults.

Effect of route of inoculation on replication of avian influenza virus (H9N2) and interferon gene expression in guinea fowl (Numida meleagridis)

The study was designed to investigate the replication of a re-assortant H9N2 avian influenza virus (AIV) and induction of the interferon (IFNγ) response after aerosol or intranasal inoculation with the virus in guinea fowl. To determine virus shedding pattern, oropharyngeal and cloacal swabs and tissue specimens of trachea, lungs, spleen and caecal tonsils were collected post-inoculation (pi).Infected guinea fowl showed mild clinical signs, while negative control guinea fowl remained healthy and active throughout the experiment irrespective of the inoculation route. However, the clinical signs were more prominent in guinea fowl infected through the aerosol route.Virus was detected in all oropharyngeal and cloacal swabs up to 7 d pi in guinea fowl from both inoculation groups. However, virus was detected more frequently and in higher titres in oropharyngeal swabs and specimens of trachea and lungs from the group exposed to aerosols than in the group given intranasal drops.In accordance with viral replication findings, expression of IFNγ was up-regulated on 1, 2 and 4 d pi to a significantly higher level in lung tissue specimens from the group exposed to virus aerosol than from controls treated with PBS intranasally. On the other hand, IFNγ was up-regulated above that of controls in lung tissue specimens from the group treated with intranasal drops of virus only on 4 d pi.These findings indicate that virus administered in aerosols was more efficient in infecting the lower respiratory tract and in inducing activity of the IFNγ gene than virus administered as intranasal drops. The results of this study suggest that virus aerosols cause more intense respiratory infection and increase the shedding of the H9N2 AIV in guinea fowl, highlighting the potential role of guinea fowl as a mixing bowl for transmission and maintenance of H9N2 AIV between poultry premises.

Enteroviruses and Rhinoviruses: Molecular Epidemiology of the Most Influenza-Like Illness Associated Viruses in Senegal.

Different viruses have been identified as etiologic agents of respiratory tract infections, including severe cases. Among these, human rhinoviruses (HRVs) and human enteroviruses (HEVs) are recognized as leading causes. The present study describes the molecular epidemiology of HRVs and HEVs in Senegal over a 3-year surveillance period. From January 2012 to December 2014, nasopharyngeal and oropharyngeal swabs specimen were collected from patients with influenza-like illness (ILI). A real-time reverse transcription polymerase chain reaction was performed for HRV and HEV detection using the RV16 kit. Two regions were targeted for the molecular characterization of RVs: 5' untranslated region (5'UTR) and viral protein 4/viral protein 2 (VP4/VP2) transition region. For enteroviruses (EVs) phylogeny, VP1 gene was targeted. A total of 4,194 samples were collected. Children up to 5 years accounted for 52.9%. Among them, 1,415 (33.7%) were positive for HRV, 857 (20.4%) for HEV, and 437 cases of dual infections HRV/HEV. HRVs and HEVs were identified significantly in children aged 5 years or less. Only cough and vomiting signs were observed with significant association with viral infection. Both viruses co-circulated all year long with a marked increase of activity during rainy and cold period. All HRV types circulate in Senegal. HRV-A and C groups were the most common. HEV serotyping identified coxsackie B viruses (CBV) only. VP1 region revealed different CBV (CBV1, CBV2, CBV3, CBV4, and CBV5), echoviruses, coxsackieviruses A4-like strains and a poliovirus 2. The results suggest strong year-round respiratory picornavirus activity in children up to 5 years of age. Molecular studies identified a wide variety of RVs along with diverse EVs in samples from patients with ILI.

Which influenza vaccine formulation should be used in Kenya? A comparison of influenza isolates from Kenya to vaccine strains, 2007–2013

IntroductionEvery year the World Health Organization (WHO) recommends which influenza virus strains should be included in a northern hemisphere (NH) and a southern hemisphere (SH) influenza vaccine. To determine the best vaccine formulation for Kenya, we compared influenza viruses collected in Kenya from April 2007 to May 2013 to WHO vaccine strains. MethodsWe collected nasopharyngeal and oropharyngeal (NP/OP) specimens from patients with respiratory illness, tested them for influenza, isolated influenza viruses from a proportion of positive specimens, tested the isolates for antigenic relatedness to vaccine strains, and determined the percentage match between circulating viruses and SH or NH influenza vaccine composition and schedule. ResultsDuring the six years, 7.336 of the 60,072 (12.2%) NP/OP specimens we collected were positive for influenza: 30,167 specimens were collected during the SH seasons and 3717 (12.3%) were positive for influenza; 2903 (78.1%) influenza A, 902 (24.2%) influenza B, and 88 (2.4%) influenza A and B positive specimens. We collected 30,131 specimens during the NH seasons and 3978 (13.2%) were positive for influenza; 3181 (80.0%) influenza A, 851 (21.4%) influenza B, and 54 (1.4%) influenza A and B positive specimens. Overall, 362/460 (78.7%) isolates from the SH seasons and 316/338 (93.5%) isolates from the NH seasons were matched to the SH and the NH vaccine strains, respectively (p<0.001). Overall, 53.6% and 46.4% SH and NH vaccines, respectively, matched circulating strains in terms of vaccine strains and timing. ConclusionIn six years of surveillance in Kenya, influenza circulated at nearly equal levels during the SH and the NH influenza seasons. Circulating viruses were matched to vaccine strains. The vaccine match decreased when both vaccine strains and timing were taken into consideration. Either vaccine formulation could be suitable for use in Kenya but the optimal timing for influenza vaccination needs to be determined.

Next-Generation Sequencing-Based HPV Genotyping Assay Validated in Formalin-Fixed, Paraffin-Embedded Oropharyngeal and Cervical Cancer Specimens.

Available clinical human papilloma virus (HPV) diagnostics for head and neck cancer have limited sensitivity and/or fail to define the HPV genotype. Common HPV genotyping assays are costly and labor intensive. We sought to develop a next-generation sequencing (NGS)-based HPV genotyping assay that was sensitive enough to work on formalin-fixed paraffin-embedded (FFPE) samples. We developed an ion torrent NGS HPV genotyping assay using barcoded HPV PCR broad-spectrum general primers 5(+)/6(+) (BSGP)5(+)/6(+). To validate genotype specificity and use in archived clinical FFPE tumor samples, we compared NGS HPV genotyping at 2 sequencing centers with typing by Roche Linear Array assay in 42 oropharyngeal and cervical cancer specimens representing 10 HPV genotypes, as well as HPV-negative cases. To demonstrate the detection of a broad range of HPV genotypes, we genotyped a cohort of 266 cervical cancers. A comparison of NGS genotyping of FFPE cancer specimens with genotyping by Linear Array showed concordant results in 34/37 samples (92%) at sequencing site 1 and 39/42 samples (93%) at sequencing site 2. Concordance between sites was 92%. Designed for use with 10 ng genomic DNA, the assay detected HPV using as little as 1.25 ng FFPE-derived genomic DNA. In 266 cervical cancer specimens, the NGS assay identified 20 different HPV genotypes, including all 13 carcinogenic genotypes. This novel NGS assay provides a sensitive and specific high-throughput method to detect and genotype HPV in a range of clinical specimens derived from FFPE with low per-sample cost.

Streptococcus pneumoniae and Haemophilus species colonization in health care workers: the launch of invasive infections?

BackgroundStreptococcus pneumoniae and Haemophilus influenzae are important human pathogens. The risk of airborne and droplet-transmitted respiratory tract infections in healthcare workers (HCW) is substantial. The aim of this study was to determine the extent of oropharyngeal colonization with S. pneumoniae and Haemophilus spp. their antibiogram and risk factors of colonization in HCW at a tertiary care center, Western Nepal.MethodsDuring 3 month period, 100 oropharyngeal swab specimens were collected from HCW of Manipal Teaching Hospital and 50 from non HCW from community. All the 150 specimens were screened for Haemophilus spp. and S. pneumoniae by standard techniques. Serotyping of H. influenzae type b was done by using specific antiserum. Antibiotic sensitivity patterns of isolates were determined by modified Kirby Bauer disc diffusion method. Association between the groups was analyzed using the Pearson χ2 test and Fisher exact test. A forward step logistic regression model was used to identify significant predictors for colonization.ResultSixty-five percent of HCW were colonized with S. pneumoniae and/or Haemophilus species compared to 32 % of non-HCW. Health care workers had odd ratio (OR) 3.946 [CI (1.916, 8.128)] times more tendency of colonization compared to non-HCW (P < 0.05). Pneumococcal colonization was observed high among smokers (81.5 %). Amongst HCW, post graduate resident doctors had higher rate of colonization (83.3 %) followed by interns (64.9 %), least being amongst the laboratory workers (58.3 %).ConclusionThe higher rate of colonization amongst HCW raises the possibility of occupational risk as well as horizontal spread of infections.

Bronchoscopy-guided antimicrobial therapy for cystic fibrosis.

Early diagnosis and treatment of lower respiratory tract infections are the mainstay of management of lung disease in cystic fibrosis. When sputum samples are unavailable, treatment relies mainly on cultures from oropharyngeal specimens; however, there are concerns regarding the sensitivity of these to identify lower respiratory organisms.Bronchoscopy and related procedures (including bronchoalveolar lavage) though invasive, allow the collection of lower respiratory specimens from non-sputum producers. Cultures of bronchoscopic specimens provide a higher yield of organisms compared to those from oropharyngeal specimens. Regular use of bronchoscopy and related procedures may help in a more accurate diagnosis of lower respiratory tract infections and guide the selection of antimicrobials, which may lead to clinical benefits.This is an update of a previous review. To evaluate the use of bronchoscopy-guided antimicrobial therapy in the management of lung infection in adults and children with cystic fibrosis. We searched the Cochrane Cystic Fibrosis Trials Register, compiled from electronic database searches and handsearching of journals and conference abstract books. We also searched two registries of ongoing studies and the reference lists of relevant articles and reviews.Date of latest search: 28 August 2015. We included randomized controlled studies including people of any age with cystic fibrosis, comparing outcomes following therapies guided by the results of bronchoscopy (and related procedures) with outcomes following therapies guided by the results of any other type of sampling (including cultures from sputum, throat swab and cough swab). Two review authors independently selected studies, assessed their risk of bias and extracted data. We contacted study investigators for further information. The search identified nine studies, but only one study with data from 157 participants (170 people were enrolled) was eligible for inclusion in the review. This study compared outcomes following therapy directed by bronchoalveolar lavage for pulmonary exacerbations during the first five years of life with standard treatment based on clinical features and oropharyngeal cultures. The study enrolled infants with CF who were under six months of age and diagnosed through newborn screening and followed them until they were five years old.We considered this study to have a low risk of bias; however, the statistical power to detect a significant difference in the prevalence of Pseudomonas aeruginosa was limited due to the prevalence (of Pseudomonas aeruginosa isolation in bronchoalveolar lavage samples at five years age) being much lower in both the groups compared to that which was expected and which was used for the power calculation. The sample size was adequate to detect a difference in high-resolution computed tomography scoring. The quality of evidence for the key parameters was graded as moderate except high-resolution computed tomography scoring and cost of care analysis, which were graded as high quality.At five years of age, there was no clear benefit of bronchoalveolar lavage-directed therapy on lung function z scores or nutritional parameters. Evaluation of total and component high-resolution computed tomography scores showed no significant difference in evidence of structural lung disease in the two groups.In addition, this study did not show any difference between the number of isolates of Pseudomonas aeruginosa per child per year diagnosed in the bronchoalveolar lavage-directed therapy group compared to the standard therapy group. The eradication rate following one or two courses of eradication treatment was comparable in the two groups, as were the number of pulmonary exacerbations. However, the number of hospitalizations was significantly higher in the bronchoalveolar lavage-directed therapy group, but the mean duration of hospitalizations was significantly less compared to the standard therapy group.Mild adverse events were reported in a proportion of participants, but these were generally well-tolerated. The most common adverse event reported was transient worsening of cough after 29% of procedures. Significant clinical deterioration was documented during or within 24 hours of bronchoalveolar lavage in 4.8% of procedures. This review, limited to a single, well designed randomized-controlled study, shows no clear evidence to support the routine use of bronchoalveolar lavage for the diagnosis and management of pulmonary infection in pre-school children with cystic fibrosis compared to the standard practice of providing treatment based on results of oropharyngeal culture and clinical symptoms. No evidence was available for adult and adolescent populations.

Epidemiological and virological characterization of influenza A virus subtype H1N1 at tertiary-care hospital, Ahmedabad

Background: In April 2009, a new strain of influenza virus, A H1N1, started to spread in various parts of the world, and the first case was reported on May 16, 2009.[1] The associated morbidity and mortality have made it a major health burden. In this study, we have investigated samples of patients with suspected influenza-like illnesses (ILIs) received at civil hospital, Ahmedabad, from January 1, 2015 to March 15, 2015. Objective: To study the epidemiologic and virologic profiles of patients found positive for influenza A H1N1 at a tertiary-care hospital. Materials and Methods: Nasopharyngeal and oropharyngeal swab specimens from patients presenting with ILI were received and subjected to real time RT-PCR (rRT-PCR) for detection and characterization of swine influenza and other seasonal influenza. Result: Of the 6,197 specimens tested, 3,242 and 866 yielded swine H1N1 and seasonal influenza virus, respectively. Most specimens were received from children aged

A Cross Sectional Analysis of Gonococcal and Chlamydial Infections among Men-Who-Have-Sex-with-Men in Cape Town, South Africa.

BackgroundMen-who-have-sex-with-men (MSM) are at high risk of HIV and sexually transmitted infection (STI) transmission. Asymptomatic STIs are common in MSM and remain undiagnosed and untreated where syndromic management is advocated. Untreated STIs could be contributing to high HIV rates. This study investigated symptomatic (SSTI) and asymptomatic STIs (ASTIs) in MSM in Cape Town.MethodsMSM, 18 years and above, were enrolled into this study. Participants underwent clinical and microbiological screening for STIs. Urine, oro-pharyngeal and anal swab specimens were collected for STI analysis, and blood for HIV and syphilis screening. A psychosocial and sexual questionnaire was completed. STI specimens were analysed for Neisseria gonorrhoeae (NG) and Chlamydia trachomatis (CT) infection.Results200 MSM were recruited with a median age of 32 years (IQR 26–39.5). Their median number of sex partners within the last year was 5 (IQR 2–20). 155/200 (78%) reported only male sex partners while 45/200 (23%) reported sex with men and women. 77/200 (39%) reported transactional sex. At enrolment, 88/200 (44%) were HIV positive and 8/112 (7%) initially HIV-negative participants seroconverted during the study. Overall, 47/200 (24%) screened positive for either NG or CT. There were 32 MSM (16%) infected with NG and 7 (3.5%) of these men had NG infections at two anatomical sites (39 NG positive results in total). Likewise, there were 23 MSM (12%) infected with CT and all these men had infections at only one site. Eight of the 47 men (17%) were infected with both NG and CT. ASTI was more common than SSTI irrespective of anatomical site, 38 /200 (19%) versus 9/200 (5%) respectively (p<0.001). The anus was most commonly affected, followed by the oro-pharynx and then urethra. Asymptomatic infection was associated with transgender identity (OR 4.09 CI 1.60–5.62), ≥5 male sex partners in the last year (OR 2.50 CI 1.16–5.62) and transactional sex (OR 2.33 CI 1.13–4.79) but not with HIV infection.ConclusionsAsymptomatic STI was common and would not have been detected using a syndromic management approach. Although molecular screening for NG/CT is costly, in our study only four MSM needed to be screened to detect one case. This supports dual NG/CT molecular screening for MSM, which, in the case of confirmed NG infections, may trigger further culture-based investigations to determine gonococcal antimicrobial susceptibility in the current era of multi-drug resistant gonorrhoea.

The upper respiratory tract microbiome of hospitalised patients with community-acquired pneumonia of unknown aetiology: a pilot study.

The composition of the upper respiratory tract microbiome may play an important role in the development of lower respiratory tract infections. Here, we characterised the microbiome of the nasopharynx and oropharynx of hospitalised patients with community-acquired pneumonia (CAP) with unknown aetiology in an attempt to obtain insight into the aetiology of CAP. A random sample of 10 patients hospitalised with CAP previously enrolled in a separate clinical trial (ClinicalTrials.gov registry, Study ID: NCT01248715) in which a complete microbiological workup was not able to define an aetiology were analysed in this pilot study. This larger trial (n = 1,221) enrolled patients from 9 adult hospitals in Louisville, Kentucky, USA. Nasopharyngeal and oropharyngeal swabs were obtained for metagenomic analysis. Polymerase chain reaction (PCR) for Streptococcus pneumoniae was performed in all patients. One patient had a distinct nasophararyngeal microbiome consisting largely of Haemophilus influenzae. This was the only patient with a negative PCR for S. pneumoniae in both nasophararyngeal and oropharyngeal specimens. Overall, substantial differences were found between nasophararyngeal and oropharyngeal microbiomes. The upper respiratory tract microbiome of only one patient suggested H. influenzae as a probable aetiology of CAP. Although this was a pilot study of only 10 patients, the presence of S. pneumoniae in the upper respiratory tract of the other 9 patients warrants further investigation.

P07.11 Whole genome sequencing characterisation of a unique neisseria strain generating a positive result with the cobas® ct/ng test

<h3>Introduction</h3> <i>Neisseria gonorrhoeae</i> (NG) cause sexually transmitted bacterial infections. The Roche cobas^® CT/NG Test is a qualitative Nucleic Acid Amplification test (NAAT) utilising a dual-target approach to detect sequences within the direct repeat (DR-9) region of the NG genome. To date, clinical performance data show excellent sensitivity and specificity for urogenital specimens. The test is validated for endocervical swabs, vaginal swabs and urine specimens. <h3>Methods</h3> One clinical case report¹ describes a positive test result for an oropharyngeal swab, an off-label specimen type for the cobas^® CT/NG Test. This interesting Neisseria sample was subject to analysis as part of Roche’s Global Surveillance Program. The isolate was tested by culture, phenotyping, whole cell MALDI-TOF MS and molecular methods such as 16S rDNA based typing and whole genome sequencing. <h3>Results</h3> Whole genome sequencing resulted in a complete genome assembly supporting phylogenetic analysis. Sequencing data assembled into a 2,882,113bp contig and genome closure, which identified the sample as a Neisseria commensal species clustering in the same clade with both N. sicca and N. macacae. One partial assay specific DR-9 target region was identified within the genome of this commensal strain in the context of a phage like motif, which can facilitate genomic exchange of DNA fragments between <i>N. gonorrhoeae</i> and commensal strains. BLAST searches for the prophage/DR9 genetic signature of this newly characterised Neisseria strain revealed no matches to sequences in the public domain, suggesting that this strain is rare. Based on the sequence information of the prophage/DR9 genetic signature oropharyngeal swab specimens determined to be positive by the cobas^® CT/NG Test are currently being evaluated for the presence of this sequence motif. <h3>Conclusion</h3> The cobas^® CT/NG Test on the cobas 4800 system is a reliable molecular method for detection of Chlamydia and Gonorrhoeae from genital specimens. <h3>Disclosure of interest</h3> Authors of the abstract are employees of Roche Molecular Systems. <h3>Reference</h3> Upton A, Bromhead C, Whiley DM. <i>Neisseria gonorrhoeae</i> false-positive result obtained from a pharyngeal swab by using the Roche cobas 4800 CT/NG assay in New Zealand in 2012. <i>J Clin Microbiol</i>. 2013;<b>51</b>:1609–10

Effect of interactions with humans on behaviour, mucosal immunity and upper respiratory disease of shelter cats rated as contented on arrival

Sustained positive affect may decrease vulnerability to upper respiratory infections in cats admitted to a shelter. Incidence of upper respiratory infections was examined in cats rated as Content upon admission to an animal shelter when provided with or without treatment to sustain contentment. Ninety-six cats rated as Content upon admission were provided with either human interaction, including petting, playing, and grooming, in four 10min sessions/d for 10 days or were exposed to a control treatment of a human standing in front of the cage with eyes averted for the same period. Changes in emotional state and mucosal immune responses were measured daily in treated and control groups. Infectious status was determined upon admission and on days 4 and 10 using combined conjunctival and oropharyngeal swab specimens tested by quantitative real-time PCR for feline herpes virus type 1, feline calicivirus, Mycoplasma felis, Chlamydophila felis, and Bordetella bronchiseptica. The onset of upper respiratory disease (URD) was determined by veterinary staff based on clinical signs, including ocular or nasal discharge. Treated cats were more likely to remain Content (Incident Rate Ratio [IRR]:1.13, Confidence Interval: 0.98-1.30, P <0.0001) and less likely to be rated as Anxious or Frustrated than Control cats over a 10 day period (IRR: 0.61, 95% CI: 0.42-0.88, P =0.007). Feline secretory IgA (S-IgA) quantified in faeces by ELISA techniques, was greater for Treated than Control cats (1451 Vs 846μg/g). Within the Treatment group, S-IgA was greater for cats that sustained Contentment throughout the study period compared to cats that became Anxious or Frustrated (1846 Vs 1394μg/g). An increasing proportion of Control than Treated cats shed pathogens over time (Control 22%, 36%, 61%; Treated 35%, 26%, 32% on d 1, 4 and 10, respectively; P =0.006). Control cats were more likely to develop URD than Treated cats (HR 2.9, CI: 1.30-6.67, P =0.01). Cats that responded positively to Treatment had a lower incidence of URD than negative responders (P =0.02). We conclude that the provision of human interaction treatments to shelter cats can facilitate sustained contentment, enhance secretion of S-IgA, and reduce incidence of URD.