Bacterial Respiratory Pathogens Research Articles

Accuracy of comprehensive PCR analysis of nasopharyngeal and oropharyngeal swabs for CT-scan-confirmed pneumonia in elderly patients: a prospective cohort study

ObjectivesWe aimed to assess the accuracy of PCR detection of viruses and bacteria on nasopharyngeal and oropharyngeal swabs (NPS) for the diagnosis of pneumonia in elderly individuals. MethodsWe included consecutive hospitalized elderly individuals suspected of having pneumonia. At inclusion, NPS were collected from all participants and tested by PCR for the presence of viral and bacterial respiratory pathogens (index test, defined as comprehensive molecular testing). Routine diagnostic tests (blood and sputum culture, urine antigen detection) were also performed. The reference standard was the presence of pneumonia on a low-dose CT scan as assessed by two independent expert radiologists. ResultsThe diagnosis of pneumonia was confirmed in 127 of 199 (64%) included patients (mean age 83 years, community-acquired pneumonia in 105 (83%)). A pathogen was identified by comprehensive molecular testing in 114 patients (57%) and by routine methods in 22 (11%). Comprehensive molecular testing was positive for viruses in 62 patients (31%) and for bacteria in 73 (37%). The sensitivity and specificity were 61% (95% CI 53%–69%) and 50% (95% CI 39%–61%) for comprehensive molecular testing, and 14% (95% CI 82%–21%) and 94% (95% CI 86%–98%) for routine testing, respectively. Positive likelihood ratio was 2.55 for routine methods and 1.23 for comprehensive molecular testing. ConclusionComprehensive molecular testing of NPS increases the number of pathogens detected compared with routine methods, but results are poorly predictive of the presence of pneumonia. Hence, comprehensive molecular testing is unlikely to impact clinical decision-making (NCT02467192). Clinical Trials RegistrationNCT02467192.

Intrinsic functional and structural connectivity of emotion regulation networks in obsessive-compulsive disorder

We aimed to assess the accuracy of PCR detection of viruses and bacteria on nasopharyngeal and oropharyngeal swabs (NPS) for the diagnosis of pneumonia in elderly individuals.We included consecutive hospitalized elderly individuals suspected of having pneumonia. At inclusion, NPS were collected from all participants and tested by PCR for the presence of viral and bacterial respiratory pathogens (index test, defined as comprehensive molecular testing). Routine diagnostic tests (blood and sputum culture, urine antigen detection) were also performed. The reference standard was the presence of pneumonia on a low-dose CT scan as assessed by two independent expert radiologists.The diagnosis of pneumonia was confirmed in 127 of 199 (64%) included patients (mean age 83 years, community-acquired pneumonia in 105 (83%)). A pathogen was identified by comprehensive molecular testing in 114 patients (57%) and by routine methods in 22 (11%). Comprehensive molecular testing was positive for viruses in 62 patients (31%) and for bacteria in 73 (37%). The sensitivity and specificity were 61% (95% CI 53%–69%) and 50% (95% CI 39%–61%) for comprehensive molecular testing, and 14% (95% CI 82%–21%) and 94% (95% CI 86%–98%) for routine testing, respectively. Positive likelihood ratio was 2.55 for routine methods and 1.23 for comprehensive molecular testing.Comprehensive molecular testing of NPS increases the number of pathogens detected compared with routine methods, but results are poorly predictive of the presence of pneumonia. Hence, comprehensive molecular testing is unlikely to impact clinical decision-making (NCT02467192).NCT02467192.

Diagnostic Utility of Real Time Multiplex PCR for Identification of Atypical Bacterial Respiratory Pathogens

Diagnostic Utility of Real Time Multiplex PCR for Identification of Atypical Bacterial Respiratory Pathogens

964. Impact of Doxycycline as Malaria Prophylaxis on Risk of Influenza Like Illness Among International Travelers

BackgroundInternational travelers are often at risk for both influenza like illness (ILI) and malaria. Doxycycline is active against many pathogens causing ILI and is routinely used for malaria prophylaxis. We evaluated the incidence of and risk factors for ILI, and whether the choice of malaria prophylaxis was associated with ILI.MethodsTravMil is a prospective observational study enrolling subjects presenting to 6 military travel clinics. We analyzed pre- and post-travel surveys from travelers to regions outside of the continental United States, Western or Northern Europe, Canada, or New Zealand between July 2010 and August 2018. ILI was defined as subjective fever associated with either a sore throat or cough. Characteristics of trip and traveler and the use of malaria prophylaxis were analyzed to determine association with development of ILI. Poisson regression models with robust error variance were used to estimate relative risk of ILI.ResultsA total of 3,227 travelers were enrolled: 62.1% male, median age of 39 (IQR 27, 59), median travel duration 19 days (IQR 12, 49). 32% traveled to Africa, 40% to Asia, and 27% to the Caribbean, Mexico, and Central or South America. Military travel (46%) and vacation (40%) were most common reasons for travel. Twenty percent took doxycycline for malaria prophylaxis, 50% other prophylaxis (89% atovaquone–proguanil), and 30% took none. 8.7% developed ILI. Compared with those on no or other prophylaxis, doxycycline was associated with decreased risk of ILI [RR 0.65 (0.43–0.99), P = 0.046], as was military travel [RR 0.30 (0.21–0.43), P < 0.01]. Increased risk of ILI was associated with female gender [RR 1.57 (1.24–1.98), P < 0.01], travel to Asia [RR 1.37 (1.08–1.75), P = 0.01], cruises [RR 2.21 (1.73–2.83), P < 0.01], and longer duration of travel [RR 1.01 (1.00–1.01, P < 0.01].ConclusionThe use of doxycycline is associated with a decreased risk of ILI compared with taking no or other malaria prophylaxis. The reasons for this are unclear but may be related to anti-inflammatory effects, activity against bacterial respiratory pathogens, effects on disease transmission in closed populations (e.g., military deploying groups), or other unmeasured factors. With few proven strategies for decreasing ILI risk in travelers, these findings bear further investigation.Disclosures All authors: No reported disclosures.

1365. In Vitro Activity of Lefamulin (LEF) Against Bacterial Pathogens Causing Community-Acquired Bacterial Pneumonia (CABP): SENTRY Surveillance 2016 Results From Asia-Pacific (APAC) and Latin America (LA)

BackgroundLEF, a novel pleuromutilin antibiotic for IV and oral use, recently completed a phase 3 trial for the treatment of CABP in adults where it demonstrated noninferiority to moxifloxacin ± linezolid. LEF selectively inhibits bacterial translation. This study investigated the activity of LEF and comparators against contemporary bacterial respiratory pathogens collected from APAC and LA.MethodsUnique isolates were collected from patients with pneumonia/respiratory (n = 551), blood stream (n = 169), skin and soft tissue (n = 244), and other (n = 55) infections in seven countries in APAC (n = 587) and four countries in LA (n = 432). LEF and comparators were tested by CLSI broth microdilution methods, and susceptibility was determined using CLSI (2018) breakpoints.ResultsIn both APAC and LA, LEF showed potent in vitro activity against this collection of respiratory pathogens, with 100% of Streptococcus pneumoniae inhibited at ≤0.25 μg/mL. S. pneumoniae isolates were largely susceptible to moxifloxacin (98.2% APAC, 100.0% LA), amoxicillin/clavulanic acid (84.3% APAC, 89.4% LA), and ceftriaxone (85.2% APAC, 93.6% LA), but less susceptible to azithromycin (56.6% APAC, 68.1% LA) and penicillin (48.2% APAC, 67.0% LA). LEF was also active against Staphylococcus aureus with 99.6% of all isolates from both APAC and LA being inhibited at 0.25 µg/mL. 29.5% of methicillin-resistant S. aureus in APAC and 24.7% in LA showed particularly high resistance rates to erythromycin (59.3% APAC, 64.2% LA), moxifloxacin (49.4% APAC, 53.7% LA), and clindamycin (39.5% APAC, 59.7% LA). 98.2% and 97.9% of Haemophilus influenzae (in APAC and LA, respectively) were inhibited at LEF ≤2 μg/mL, and 100.0% of Moraxella catarrhalis were inhibited at LEF ≤0.12 μg/mL in both APAC and LA. Both organisms were largely susceptible to the comparators, except for ampicillin (49.1% and 74.5% susceptible among H. influenzae in APAC and LA, respectively) and trimethoprim/sulfamethoxazole (54.4% and 68.1% susceptible among H. influenzae) (figure). ConclusionIn APAC and LA, LEF was highly active against pathogens collected from CABP patients in 2016, and its activity was not affected by resistance to other antibiotic classes. These data support the ongoing development of LEF for the treatment of CABP.Disclosures S. Paukner, Nabriva: Employee and Shareholder, Salary. R. K. Flamm, Nabriva Therapeutics: Research Contractor, Research support. S. P. Gelone, Nabriva Therapeutics: Employee, Equity, Shareholder and Salary. Achaogen: Shareholder, Equity, Shareholder. H. S. Sader, Nabriva Therapeutics: Research Contractor, Research support.

1353. In Vitro Activity of Lefamulin (LEF) Against Bacterial Pathogens Commonly Causing Community-Acquired Bacterial Pneumonia (CABP): 2016 SENTRY Data From the United States

BackgroundLEF, the first pleuromutilin antibiotic for IV and oral use in humans, is in Phase 3 clinical trials for the treatment of CABP in adults. In the first of these to be completed, LEF demonstrated noninferiority to moxifloxacin ± linezolid. LEF inhibits bacterial translation by binding the 50S ribosomal subunit at the A- and P-sites in the peptidyl transferase center. CABP is a leading cause of infectious diseases in the United States and increasing antibacterial resistance complicates its treatment. This study investigated the in vitro activity of LEF and comparators against a contemporary set of bacterial respiratory pathogens collected in the United States.MethodsIsolates (n = 1674, 1/patient) were collected from 32 medical centers in the United States as part of the SENTRY Surveillance Program. LEF and comparators were tested by CLSI broth microdilution methods, and susceptibility was determined using the CLSI (2018) breakpoints.ResultsLEF was the most active compound against Streptococcus pneumoniae (MIC50/90 of 0.12/0.12 µg/mL), and its activity was not affected by resistance to other antibiotic classes. S. pneumoniae isolates were susceptible to levofloxacin (99.1%) and ceftriaxone (97.7%), whereas only 53.9%, 63.9%, and 80.4% of isolates were susceptible to macrolides, penicillin (oral), and tetracycline, respectively. LEF also showed potent activity against Staphylococcus aureus (MIC50/90 of 0.06/0.12 µg/mL), including methicillin-resistant (MRSA) isolates (MIC50/90 of 0.06/0.12 µg/mL, 87.1% resistant to erythromycin), Haemophilus influenzae, (MIC50/90 of 0.5/1 µg/mL, 26.9% β-lactamase producing), and Moraxella catarrhalis (MIC50/90 0.06/0.06 µg/mL, 96.5% β-lactamase positive) (figure). ConclusionLEF displayed potent in vitro activity against a contemporary collection of respiratory pathogens from the United States. LEF was active regardless of resistance phenotype to other antibiotic classes including β-lactams, tetracyclines, or macrolides. These results further support the clinical development of lefamulin for the treatment of CABP or other respiratory tract infections.Disclosures S. Paukner, Nabriva: Employee and Shareholder, Salary. R. K. Flamm, Nabriva: Research Contractor, Research grant. S. P. Gelone, Nabriva Therapeutics: Employee, Equity, Shareholder and Salary. Achaogen: Shareholder, Equity, Shareholder. H. S. Sader, Nabriva Therapeutics: Research Contractor, Research support.

Resolving Viral-Induced Secondary Bacterial Infection in COPD: A Concise Review

Chronic obstructive pulmonary disease (COPD) is a leading cause of disability and death world-wide, where chronic inflammation accelerates lung function decline. Pathological inflammation is worsened by chronic bacterial lung infections and susceptibility to recurrent acute exacerbations of COPD (AECOPD), typically caused by viral and/or bacterial respiratory pathogens. Despite ongoing efforts to reduce AECOPD rates with inhaled corticosteroids, COPD patients remain at heightened risk of developing serious lung infections/AECOPD, frequently leading to hospitalization and infection-dependent delirium. Here, we review emerging mechanisms into why COPD patients are susceptible to chronic bacterial infections and highlight dysregulated inflammation and production of reactive oxygen species (ROS) as central causes. This underlying chronic infection leaves COPD patients particularly vulnerable to acute viral infections, which further destabilize host immunity to bacteria. The pathogeneses of bacterial and viral exacerbations are significant as clinical symptoms are more severe and there is a marked increase in neutrophilic inflammation and tissue damage. AECOPD triggered by a bacterial and viral co-infection increases circulating levels of the systemic inflammatory marker, serum amyloid A (SAA). SAA is a functional agonist for formyl peptide receptor 2 (FPR2/ALX), where it promotes chemotaxis and survival of neutrophils. Excessive levels of SAA can antagonize the protective actions of FPR2/ALX that involve engagement of specialized pro-resolving mediators, such as resolvin-D1. We propose that the anti-microbial and anti-inflammatory actions of specialized pro-resolving mediators, such as resolvin-D1 should be harnessed for the treatment of AECOPD that are complicated by the co-pathogenesis of viruses and bacteria.

Phage Lysins for Fighting Bacterial Respiratory Infections: A New Generation of Antimicrobials.

Lower respiratory tract infections and tuberculosis are responsible for the death of about 4.5 million people each year and are the main causes of mortality in children under 5 years of age. Streptococcus pneumoniae is the most common bacterial pathogen associated with severe pneumonia, although other Gram-positive and Gram-negative bacteria are involved in respiratory infections as well. The ability of these pathogens to persist and produce infection under the appropriate conditions is also associated with their capacity to form biofilms in the respiratory mucous membranes. Adding to the difficulty of treating biofilm-forming bacteria with antibiotics, many of these strains are becoming multidrug resistant, and thus the alternative therapeutics available for combating this kind of infections are rapidly depleting. Given these concerns, it is urgent to consider other unconventional strategies and, in this regard, phage lysins represent an attractive resource to circumvent some of the current issues in infection treatment. When added exogenously, lysins break specific bonds of the peptidoglycan and have potent bactericidal effects against susceptible bacteria. These enzymes possess interesting features, including that they do not trigger an adverse immune response and raise of resistance is very unlikely. Although Gram-negative bacteria had been considered refractory to these compounds, strategies to overcome this drawback have been developed recently. In this review we describe the most relevant in vitro and in vivo results obtained to date with lysins against bacterial respiratory pathogens.

Severe Warm Autoimmune Hemolytic Anemia in a 7-Month-Old Infant Associated With a Mycoplasma Pneumoniae Infection.

A 7-month-old female infant had clinical and laboratory evidence of severe warm autoimmune hemolytic anemia. She also had clinical evidence of an upper respiratory tract infection with molecular detection of Mycoplasma pneumoniae. Although reticulocytopenic initially, she responded to red blood cell transfusion, steroids, and intravenous immunoglobulin and remains well today. With the increasing use of multiplex respiratory viral and bacterial pathogen detection systems, the rare association described in this report may prove to be more common than previously thought and may provide insight into the pathogenesis and clinical consequences of red blood cell autoantibodies.

Respiratory infections in yak (Bos grunniens): a pilot study on isolation and direct PCR diagnosis for pasteurellosis, mannheimiosis and histophilosis

Bovine respiratory disease (BRD) is a condition of severe pneumonia caused due to environmental stress followed by a multiple viral and bacterial pathogens.The present study aimed to detect the BRD agents such as Mannhaeimia haemolytica, Pasteurella multocida and Histophilus somni and IBR in yaks suffering from respiratory infections. For the study, 157 deep nasal and blood samples were collected from yak of Arunachal Pradesh and processed for isolation and PCR detection of respiratory bacterial pathogens such as M. haemolytica, P. multocida and H. somni and seroscreening of IBR. From 157 samples, one M. haemolytica and two H. somni isolates were recovered. This is the first report of H. somni and M. haemolytica isolation from yak nasal samples from India. In mPCR, 23 yak nasal samples (14.6%) amplified for M. haemolytica, two (1.2%) for P. multocida and six samples for H. somni (4.6%) by simplex PCR. Concurrence of H. somni and M. haemolytica in three samples, and M. haemolytica and P. multocida type B in two samples was also observed.Very high seroprevalence for IBR (37%) by Indirect ABELISA was recorded.The study concluded that highest number of samples were positive for M. haemolytica (14.6%) and emphasizes its role in respiratory infections along with high seroprevalence of IBR. It also reflected the diagnostic importance of mPCR/PCR in regions inaccessible for fresh sample collection and transportation as an alternate to isolation procedures.

Detection of Mycoplasma ovipneumoniae in Pneumonic Mountain Goat ( Oreamnos americanus) Kids.

We documented bronchopneumonia in seven mountain goat ( Oreamnos americanus) kid mortalities between 2011 and 2015 following a pneumonia epizootic in bighorn sheep ( Ovis canadensis) and sympatric mountain goats in the adjacent East Humboldt Range and Ruby Mountains in Elko County, Nevada, US. Gross and histologic lesions resembled those described in bighorn lambs following all-age epizootics, and Mycoplasma ovipneumoniae was detected with real-time PCR in the lower and upper respiratory tracts of all kids. Mannheimia haemolytica, with one isolate being leukotoxigenic, was cultured from the upper respiratory tract of five kids, and in one kid, a leukotoxigenic strain of Mannheimia glucosida was isolated from both upper and lower respiratory tracts. During this same period, 75 mountain goats within the two populations were marked and sampled for respiratory pathogens, and M. ovipneumoniae, leukotoxigenic Bibersteinia trehalosi, and Mannheimia haemolytica were identified. The M. ovipneumoniae recovered from the kid mortalities shared the same DNA sequence-based strain type detected in the adult goats and sympatric bighorn sheep during and after the 2009-10 pneumonia outbreak. Clinical signs in affected kids, as well as decreased annual kid recruitment, also resembled reports in bighorn lambs from some herds following all-age pneumonia-associated die-offs. Mycoplasma ovipneumoniae, Pasteurellaceae spp., and other respiratory bacterial pathogens should be considered as a cause of pneumonia with potential population-limiting effects in mountain goats.

The Eukaryotic Host Factor 14-3-3 Inactivates Adenylate Cyclase Toxins of Bordetella bronchiseptica and B.parapertussis, but Not B.pertussis.

ABSTRACTBordetella pertussis, Bordetella bronchiseptica, and Bordetella parapertussis share highly homologous virulence factors and commonly cause respiratory infections in mammals; however, their host specificities and disease severities differ, and the reasons for this remain largely unknown. Adenylate cyclase toxin (CyaA) is a homologous virulence factor that is thought to play crucial roles in Bordetella infections. We herein demonstrate that CyaAs function as virulence factors differently between B. bronchiseptica/B. parapertussis and B. pertussis. B. bronchiseptica CyaA bound to target cells, and its enzyme domain was translocated into the cytosol similarly to B. pertussis CyaA. The hemolytic activity of B. bronchiseptica CyaA on sheep erythrocytes was also preserved. However, in nucleated target cells, B. bronchiseptica CyaA was phosphorylated at Ser375, which constitutes a motif (RSXpSXP [pS is phosphoserine]) recognized by the host factor 14-3-3, resulting in the abrogation of adenylate cyclase activity. Consequently, the cytotoxic effects of B. bronchiseptica CyaA based on its enzyme activity were markedly attenuated. B. parapertussis CyaA carries the 14-3-3 motif, indicating that its intracellular enzyme activity is abrogated similarly to B. bronchiseptica CyaA; however, B. pertussis CyaA has Phe375 instead of Ser, and thus, was not affected by 14-3-3. In addition, B. pertussis CyaA impaired the barrier function of epithelial cells, whereas B. bronchiseptica CyaA did not. Rat infection experiments suggested that functional differences in CyaA are related to differences in pathogenicity between B. bronchiseptica/B. parapertussis and B. pertussis.

Respiratory Viruses and Atypical Bacteria Co-Infection in Children with Acute Respiratory Infection.

BACKGROUND:Acute respiratory infections (ARI) are one of the prevalent pediatric diseases. Coinfections of respiratory viruses and atypical bacterial respiratory pathogens are common.AIM:This study aimed to determine the prevalence of co-infection between respiratory pathogens including viruses, bacteria and atypical bacteria in a sample of Egyptian children presenting with symptoms of acute respiratory tract infection.METHODS:This one-year prospective cohort study conducted in Abo El Rish Pediatric Hospital, Cairo University over one year included children presenting with symptoms of acute respiratory infection. Enrolled children were subjected to nasopharyngeal swabs or throat swabs and then processed to detect viral, bacterial and atypical bacterial causative agents by culture), retrotranscription polymerase, Monoplex polymerase chain reaction (PCR) and Multiplex PCR.RESULTS:Viral etiological agents were detected in 20 cases (20.8%), while 76 patients (79.2%) had no definite viral aetiology. The most abundant virus detected was Rhinovirus in 36 (27.3%), followed by 21 (15.9%) were positive for RSV, 12 (9.1%) were positive for HMPV, 6 (4.5%) were positive for adenovirus and 3 (2.3%) were positive for influenza B. For Atypical bacterial causes Mycoplasma were positive for 9 (6.8%) cases and one case was positive for Bordetella parapertussis. Viral and atypical bacteria Co infection were detected in 14 (10.6%) of cases.CONCLUSION:These results suggest that coinfection with bacteria or atypical bacteria in children with acute respiratory tract infection is common and this co-infection can induce serious illness. The multiplex reverse-transcriptase polymerase chain reaction should become an essential tool for epidemiological studies and can fill the gap between clinical presentation and definitive diagnosis.

Staphylococcus aureus Biofilm Growth on Cystic Fibrosis Airway Epithelial Cells Is Enhanced during Respiratory Syncytial Virus Coinfection.

Staphylococcus aureus is a major cause of chronic respiratory infection in patients with cystic fibrosis (CF). We recently showed that Pseudomonas aeruginosa exhibits enhanced biofilm formation during respiratory syncytial virus (RSV) coinfection on human CF airway epithelial cells (AECs). The impact of respiratory viruses on other bacterial pathogens during polymicrobial infections in CF remains largely unknown. To investigate if S.aureus biofilm growth in the CF airways is impacted by virus coinfection, we evaluated S.aureus growth on CF AECs. Initial studies showed an increase in S.aureus growth over 24h, and microscopy revealed biofilm-like clusters of bacteria on CF AECs. Biofilm growth was enhanced when CF AECs were coinfected with RSV, and this observation was confirmed with S.aureus CF clinical isolates. Apical conditioned medium from RSV-infected cells promoted S.aureus biofilms in the absence of the host epithelium, suggesting that a secreted factor produced during virus infection benefits S.aureus biofilms. Exogenous iron addition did not significantly alter biofilm formation, suggesting that it is not likely the secreted factor. We further characterized S.aureus-RSV coinfection in our model using dual host-pathogen RNA sequencing, allowing us to observe specific contributions of S.aureus and RSV to the host response during coinfection. Using the dual host-pathogen RNA sequencing approach, we observed increased availability of nutrients from the host and upregulation of S.aureus genes involved in growth, protein translation and export, and amino acid metabolism during RSV coinfection.IMPORTANCE The airways of individuals with cystic fibrosis (CF) are commonly chronically infected, and Staphylococcus aureus is the dominant bacterial respiratory pathogen in CF children. CF patients also experience frequent respiratory virus infections, and it has been hypothesized that virus coinfection increases the severity of S.aureus lung infections in CF. We investigated the relationship between S.aureus and the CF airway epithelium and observed that coinfection with respiratory syncytial virus (RSV) enhances S.aureus biofilm growth. However, iron, which was previously found to be a significant factor influencing Pseudomonas aeruginosa biofilms during virus coinfection, plays a minor role in S.aureus coinfections. Transcriptomic analyses provided new insight into how bacterial and viral pathogens alter host defense and suggest potential pathways by which dampening of host responses to one pathogen may favor persistence of another in the CF airways, highlighting complex interactions occurring between bacteria, viruses, and the host during polymicrobial infections.

High frequency of Haemophilus influenzae associated with respiratory tract infections among Malaysian Hajj pilgrims.

Overcrowding during the annual Hajj pilgrimage has been known to increase the risk of infectious diseases transmission. Despite the high prevalence of respiratory illness among Malaysian Hajj pilgrims, knowledge about the etiologic pathogens is yet very limited. Thus, this study aimed to determine the spectrum of bacterial respiratory pathogens among the Hajj pilgrims returning to Malaysia in year 2016. Expectorated sputum specimens were collected from the Hajj pilgrims with symptomatic respiratory tract infections (RTIs). Subsequently, the bacterial pathogens were identified using the standard bacteriological culture method and Vitek II system. This study indicated that 255 (87.33%) out of 292 cultured sputa were positive with at least one potential pathogenic bacteria. Out of 345 total bacterial isolates, 60% (n=207) were Haemophilus influenzae, which was associated with both single bacterium infection (132/173, 76.3%) and multiple bacterial infections (75/82, 91.5%). The other bacterial isolates included; Klebsiella pneumoniae (n=37, 10.7%), Moraxella catarrhalis (n=27, 7.8%), Haemophilus parainfluenzae (n=25, 7.2%), Streptococcus group G (n=18, 5.2%), Klebsiella spesies (n=16, 4.6%), Streptococcus pneumoniae (n=11, 3.2%) and few other organisms. High frequency of H. influenzae was isolated from Malaysian Hajj pilgrims, especially those with respiratory symptoms. Further study should evaluate the actual pathogenicity of the organism and the interactions between the respiratory microbiota towards developing effective prevention strategies of RTIs among the local pilgrims.

Ecology and diversity in upper respiratory tract microbial population structures from a cross-sectional community swabbing study.

Respiratory tract infections (RTIs) are responsible for over 2.8 million deaths per year worldwide with pathobiont carriage a required precursor to infection. We sought to determine carriage epidemiology for both bacterial and viral respiratory pathogens as part of a large population-based cross-sectional carriage study. Nose self-swab samples were collected in two separate time-points, May to August 2012 (late spring/summer) and February to April 2013 (winter/early spring). The presence of six bacterial species: S. pneumoniae, H. influenzae, M. catarrhalis, S. aureus, P. aeruginosa and N. meningitidis in addition to respiratory syncytial virus, influenza viruses A and B, rhinovirus/enterovirus, coronavirus, parainfluenza viruses 1-3 and adenovirus was determined using culture and PCR methods.Results/Key findings. Carriage was shown to vary with age, recent RTI and the presence of other species. Spatial structures of microbial communities were more disordered in the 0-4 age group and those with recent RTI. Species frequency distributions were flatter than random expectation in young individuals (X2=20.42, P=0.002), indicating spatial clumping of species consistent with facilitative relationships. Deviations from a neutral model of ecological niches were observed in summer samples and from older individuals but not in the winter or younger individuals (0-4 years), suggesting the presence of seasonal and age-dependent niche processes in respiratory community assembly. The application of epidemiological methods and ecological theory to respiratory tract samples has yielded novel insights into the factors that drive microbial community composition.

A Survey of Bacterial Respiratory Pathogens in Native and Introduced Mountain Goats ( Oreamnos americanus).

In contrast to broad range expansion through translocations, many mountain goat ( Oreamnos americanus) populations have shown signs of decline. Recent documentation of pneumonia in mountain goats highlights their susceptibility to bacterial pathogens typically associated with bighorn sheep ( Ovis canadensis) epizootics. Respiratory pathogen communities of mountain goats are poorly characterized yet have important implications for management and conservation of both species. We characterized resident pathogen communities across a range of mountain goat populations as an initial step to inform management efforts. Between 2010 and 2017, we sampled 98 individuals within three regions of the Greater Yellowstone Area (GYA), with a smaller sampling effort in southeast Alaska, US. Within the GYA, we detected Mycoplasma ovipneumoniae in two regions and we found at least two Pasteurellaceae species in animals from all regions. Mannheimia haemolytica was the only pathogen that we detected in southeast Alaska. Given the difficult sampling conditions, limited sample size, and imperfect detection, our failure to detect specific pathogens should be interpreted with caution. Nonetheless, respiratory pathogens within the GYA may be an important, yet underappreciated, cause of mountain goat mortality. Moreover, because of the strong niche overlap of bighorn sheep and mountain goats, interspecific transmission is an important concern for managers restoring or introducing mountain ungulates within sympatric ranges.

Distinct bacterial metacommunities inhabit the upper and lower respiratory tracts of healthy feedlot cattle and those diagnosed with bronchopneumonia

Specific nasopharyngeal bacterial communities can provide colonization resistance against respiratory pathogens in cattle. However, the role of bacterial communities of the lower airways in respiratory health remains largely unknown. Therefore, our objective was to compare nasopharyngeal and tracheal bacterial communities between healthy feedlot cattle and those with bronchopneumonia (BP). Deep nasal swabs and trans-tracheal aspiration samples were collected from steers with (n = 60) and without (n = 60) BP at 4 feedlots in Western Canada. After DNA extraction, 16S rRNA gene (V4) was amplified and sequenced. Alpha-diversity analysis revealed a lower bacterial diversity in the nasopharynx and trachea of steers with BP compared to healthy pen-mates. Bacterial communities present within the airways clustered into 4 distinct metacommunities that were associated with sampling locations and health status. Metacommunity 1, enriched with Mycoplasma bovis, Mannheimia haemolytica and Pasteurella multocida, was dominant in the nasopharynx and trachea of steers with BP. In contrast, metacommunity 3, enriched with Mycoplasma dispar, Lactococcus lactis and Lactobacillus casei, was mostly present in the trachea of healthy steers. Metacommunity 4, enriched with Corynebacterium, Jeotgalicoccus, Psychrobacter and Planomicrobium, was present in the nasopharynx only. Metacommunity 2, enriched with Histophilus somni, Moraxella and L. lactis, was present in both healthy and sick steers, but was primarily detected in one feedlot. We concluded that distinct bacterial metacommunities inhabited the nasopharynx and trachea of healthy feedlot cattle and those with BP. Because L. lactis and L. casei can inhibit M. haemolytica growth in vitro, their presence in healthy steers may have provided colonization resistance against bacterial respiratory pathogens.

Multidrug resistant Mannheimia haemolytica isolated from high-risk beef stocker cattle after antimicrobial metaphylaxis and treatment for bovine respiratory disease

Antimicrobial resistance (AMR) in bacterial respiratory pathogens in high-risk stocker cattle has been poorly characterized. The objective of this study was to describe the prevalence of multidrug resistant (MDR; resistance to > 3 antimicrobial classes) respiratory pathogens in 50 conventionally managed stocker cattle over 21 days after arrival. Cattle received tildipirosin metaphylaxis on day 0 and were eligible to receive up to 3 additional antimicrobials for bovine respiratory disease (BRD): florfenicol, ceftiofur and enrofloxacin. Nasopharyngeal swabs were collected on days 0, 7, 14, and 21 for bacterial culture and antimicrobial susceptibility testing using disc diffusion and broth microdilution. Mannheimia haemolytica was isolated from 5 of 48, 27 of 50, 44 of 50, and 40 of 50 cattle on days 0, 7, 14, and 21, respectively. One of 5, 27 of 27, 43 of 44, and 40 of 40 M. haemolytica were MDR on days 0, 7, 14, and 21, respectively. Pasteurella multocida was isolated from 6 of 48 cattle on day 0 and none were MDR; no other pathogens were isolated. Twenty-four cattle required at least one BRD treatment; M. haemolytica was isolated before treatment from 13 of 24 cattle; all were MDR. One hundred-eighteen M. haemolytica isolates were subjected to pulsed-field gel electrophoresis (PFGE); multiple genotypes were identified. Whole genome sequencing of 33 isolates revealed 14 known AMR genes. Multidrug resistant M. haemolytica can be highly prevalent and genetically diverse in stocker cattle; additional research is necessary to determine factors that influence prevalence and the impact on cattle health.

Early use of Antibiotics for at Risk CHildren with InfluEnza (ARCHIE): protocol for a double-blind, randomised, placebo-controlled trial

IntroductionInfluenza and influenza-like illness (ILI) create considerable burden on healthcare resources each winter. Children with pre-existing conditions such as asthma, diabetes mellitus and cerebral palsy are among those at greatest...