Stepwise pathogenic evolution of Mycobacterium abscessus.

Although almost all mycobacterial species are saprophytic environmental organisms, a few, such as Mycobacterium tuberculosis, have evolved to cause transmissible human infection. By analyzing the recent emergence and spread of the environmental organism M. abscessus through the global cystic fibrosis population, we have defined key, generalizable steps involved in the pathogenic evolution of mycobacteria. We show that epigenetic modifiers, acquired through horizontal gene transfer, cause saltational increases in the pathogenic potential of specific environmental clones. Allopatric parallel evolution during chronic lung infection then promotes rapid increases in virulence through mutations in a discrete gene network; these mutations enhance growth within macrophages but impair fomite survival. As a consequence, we observe constrained pathogenic evolution while person-to-person transmission remains indirect, but postulate accelerated pathogenic adaptation once direct transmission is possible, as observed for M. tuberculosis Our findings indicate how key interventions, such as early treatment and cross-infection control, might restrict the spread of existing mycobacterial pathogens and prevent new, emergent ones.

Healthcare-Associated Pneumonia and Hospital-Acquired Pneumonia: Bacterial Aetiology, Antibiotic Resistance and Treatment Outcomes: A Study From North India.

BACKGROUND: Data regarding the comparative profiling of HCAP and HAP from developing countries like India are scant. We set out to address the microbial aetiology, antibiotic resistance and treatment outcomes in patients with HCAP and HAP. METHODS: 318 consenting patients with HCAP (n = 165, aged 16-90 years; median 60 years; 97 males) or HAP (n = 153; aged 16-85 years; median 45 years; 92 males) presenting to a tertiary care hospital in North India from 2013 to 2015 were prospectively recruited for the study. Data on patient characteristics, microbial aetiology, APACHE II scores, treatment outcomes and mortality were studied. Clinical outcomes were compared with various possible predictors employing logistic regression analysis. RESULTS: Patients in HCAP had more comorbidity. Escherichia coli (30, 18%) and Acinetobacter baumannii (62, 41%) were the most commonly isolated bacteria in HCAP and HAP, respectively. Multidrug-resistant bacteria were isolated more frequently in HCAP, only because the incidence of extensively drug-resistant bacteria was markedly high in HAP (p = 0.00). The mean APACHE II score was lower in HCAP (17.55 ± 6.406, range 30) compared to HAP (19.74 ± 8.843, range 37; p = 0.013). The length of stay ≥ 5 days (p = 0.036) and in-hospital mortality was higher in HAP group (p = 0.002). The most reliable predictors of in-hospital mortality in HCAP and HAP were APACHE II score ≥ 17 (OR = 14, p = 0.00; HAP: OR = 10.8, p = 0.00), and septic shock (OR = 4.5, p = 0.00; HAP: OR = 6.9, p = 0.00). CONCLUSION: The patient characteristics in HCAP, treatment outcomes, bacterial aetiology, and a higher incidence of antibiotic-resistant bacteria, suggest that HCAP although not as severe as HAP, can be grouped as a separate third entity.

Bordetella bronchiseptica pneumonia: beware of the dog!

We report the case of a 35-year-old quadriplegic male with confirmed Bordetella bronchiseptica pneumonia, manifesting with acute hypoxic respiratory failure on a background of chronic hypercarbia requiring mechanical ventilation in intensive care.B. bronchiseptica are known to colonise the upper respiratory tracts of many mammals but are very rarely responsible for acute respiratory tract infections in humans.A review of the literature suggests preponderance for immunocompromised or immunoincompetent patients who have experienced environmental exposure to colonised animals. The disease pattern of B. bronchiseptica infection is non-uniform and while it is rarely described as a commensal or colonising organism, very few case reports describe severe respiratory infections.

The dynamics of the pulmonary microbiome during mechanical ventilation in the intensive care unit and the association with occurrence of pneumonia.

RATIONALE: Ventilator-associated pneumonia (VAP) is the most common nosocomial infections in patients admitted to the ICU. The adapted island model predicts several changes in the respiratory microbiome during intubation and mechanical ventilation. OBJECTIVES: We hypothesised that mechanical ventilation and antibiotic administration decrease the diversity of the respiratory microbiome and that these changes are more profound in patients who develop VAP. METHODS: Intubated and mechanically ventilated ICU-patients were included. Tracheal aspirates were obtained three times a week. 16S rRNA gene sequencing with the Roche 454 platform was used to measure the composition of the respiratory microbiome. Associations were tested with linear mixed model analysis and principal coordinate analysis. MEASUREMENTS AND MAIN RESULTS: 111 tracheal aspirates were obtained from 35 patients; 11 had VAP, 18 did not have VAP. Six additional patients developed pneumonia within the first 48 hours after intubation. Duration of mechanical ventilation was associated with a decrease in α diversity (Shannon index; fixed-effect regression coefficient (ß): -0.03 (95% CI -0.05 to -0.005)), but the administration of antibiotic therapy was not (fixed-effect ß: 0.06; 95% CI -0.17 to 0.30). There was a significant difference in change of ß diversity between patients who developed VAP and control patients for Bray-Curtis distances (p=0.03) and for Manhattan distances (p=0.04). Burkholderia, Bacillales and, to a lesser extent, Pseudomonadales positively correlated with the change in ß diversity. CONCLUSION: Mechanical ventilation, but not antibiotic administration, was associated with changes in the respiratory microbiome. Dysbiosis of microbial communities in the respiratory tract was most profound in patients who developed VAP.

Emergence and Dissemination of ST131 Escherichia coli Isolates Among Patients with Hospital-Acquired Pneumonia in Asian Countries.

We investigated the molecular epidemiology and microbiological characteristics of 51 Escherichia coli isolates causing hospital-acquired pneumonia (HAP) in eight Asian areas. Sequence type 131 (ST131) was the most prevalent among E. coli isolates causing HAP, especially in South Korea, Thailand, and the Philippines. The current study showed that CTX-M-15-producing E. coli ST131 has emerged in and disseminated among patients with HAP in Asia. Our data suggest that this pandemic clone poses an important public health threat even in nosocomial infections.

Emergence and spread of a human-transmissible multidrug-resistant nontuberculous mycobacterium.

Lung infections with Mycobacterium abscessus, a species of multidrug-resistant nontuberculous mycobacteria, are emerging as an important global threat to individuals with cystic fibrosis (CF), in whom M. abscessus accelerates inflammatory lung damage, leading to increased morbidity and mortality. Previously, M. abscessus was thought to be independently acquired by susceptible individuals from the environment. However, using whole-genome analysis of a global collection of clinical isolates, we show that the majority of M. abscessus infections are acquired through transmission, potentially via fomites and aerosols, of recently emerged dominant circulating clones that have spread globally. We demonstrate that these clones are associated with worse clinical outcomes, show increased virulence in cell-based and mouse infection models, and thus represent an urgent international infection challenge.

Tracheal tube biofilm removal through a novel closed-suctioning system: an experimental study.

BACKGROUND: Tracheal tube biofilm develops during mechanical ventilation. We compared a novel closed-suctioning system vs standard closed-suctioning system in the prevention of tracheal tube biofilm. METHODS: Eighteen pigs, on mechanical ventilation for 76 h, with P. aeruginosa pneumonia were randomized to be tracheally suctioned via the KIMVENT* closed-suctioning system (control group) or a novel closed-suctioning system (treatment group), designed to remove tracheal tube biofilm through saline jets and an inflatable balloon. Upon autopsy, two tracheal tube hemi-sections were dissected for confocal and scanning electron microscopy. Biofilm area, maximal and minimal thickness were computed. Biofilm stage was assessed. RESULTS: Sixteen animals were included in the final analysis. In the treatment and control group, the mean (sd) pulmonary burden was 3.34 (1.28) and 4.17 (1.09) log cfu gr(-1), respectively (P=0.18). Tracheal tube P. aeruginosa colonization was 5.6 (4.9-6.3) and 6.2 (5.6-6.9) cfu ml(-1) (median and interquartile range) in the treatment and control group, respectively (P=0.23). In the treatment group, median biofilm area was 3.65 (3.22-4.21) log10 µm2 compared with 4.49 (4.27-4.52) log10 µm2 in the control group (P=0.031). In the treatment and control groups, the maximal biofilm thickness was 48.3 (26.7-71.2) µm (median and interquartile range) and 88.8 (43.8-125.7) µm, respectively. The minimal thickness in the treatment and control group was 0.6 (0-4.0) µm and 23.7 (5.3-27.8) µm (P=0.040) (P=0.017). Earlier stages of biofilm development were found in the treatment group (P<0.001). CONCLUSIONS: The novel CSS reduces biofilm accumulation within the tracheal tube. A clinical trial is required to confirm these findings and the impact on major outcomes.

Epidemiology of Coxiella burnetii infection in Africa: a OneHealth systematic review.

BACKGROUND: Q fever is a common cause of febrile illness and community-acquired pneumonia in resource-limited settings. Coxiella burnetii, the causative pathogen, is transmitted among varied host species, but the epidemiology of the organism in Africa is poorly understood. We conducted a systematic review of C. burnetii epidemiology in Africa from a "One Health" perspective to synthesize the published data and identify knowledge gaps. METHODS/PRINCIPAL FINDINGS: We searched nine databases to identify articles relevant to four key aspects of C. burnetii epidemiology in human and animal populations in Africa: infection prevalence; disease incidence; transmission risk factors; and infection control efforts. We identified 929 unique articles, 100 of which remained after full-text review. Of these, 41 articles describing 51 studies qualified for data extraction. Animal seroprevalence studies revealed infection by C. burnetii (≤13%) among cattle except for studies in Western and Middle Africa (18-55%). Small ruminant seroprevalence ranged from 11-33%. Human seroprevalence was <8% with the exception of studies among children and in Egypt (10-32%). Close contact with camels and rural residence were associated with increased seropositivity among humans. C. burnetii infection has been associated with livestock abortion. In human cohort studies, Q fever accounted for 2-9% of febrile illness hospitalizations and 1-3% of infective endocarditis cases. We found no studies of disease incidence estimates or disease control efforts. CONCLUSIONS/SIGNIFICANCE: C. burnetii infection is detected in humans and in a wide range of animal species across Africa, but seroprevalence varies widely by species and location. Risk factors underlying this variability are poorly understood as is the role of C. burnetii in livestock abortion. Q fever consistently accounts for a notable proportion of undifferentiated human febrile illness and infective endocarditis in cohort studies, but incidence estimates are lacking. C. burnetii presents a real yet underappreciated threat to human and animal health throughout Africa.

Atypical pneumonia.

PURPOSE OF REVIEW: We present the key advances in the infections that clinicians conventionally associate with atypical pneumonia: legionellosis, Mycoplasma pneumonia, Chlamydophila species pneumonia and Q fever. RECENT FINDINGS: There have been significant developments in molecular diagnosis to include Mycoplasma pneumoniae and Chlamydophila pneumoniae in multiplex PCR of respiratory specimens. There are diagnostic challenges in distinguishing carriage from infection, which is recognized in C. pneumoniae and now also evident in M. pneumoniae. Macrolide-resistant M. pneumoniae has emerged in Asia. There are new antimicrobials on the horizon in the ketolide class with activity against typical and atypical pathogens and useful empirical agents. SUMMARY: There are few advances in our knowledge of the epidemiology of atypical pathogens or the effectiveness of antimicrobial therapy--empirical or pathogen specific. However, if molecular testing becomes widely implemented, there will be an increased understanding of the epidemiology and presentation of atypical pneumonia and a shift to more targeted antimicrobial therapy.

Validation of a scoring tool to predict drug-resistant pathogens in hospitalised pneumonia patients.

BACKGROUND: Health care-associated pneumonia (HCAP) affects a heterogeneous group of patients in frequent contact with health care systems. However, HCAP criteria poorly predict infection with drug-resistant (DR) pathogens. OBJECTIVE: To validate our previously reported risk-scoring model (predictive of DR pathogen infection) in patients admitted to hospital with pneumonia. DESIGN: We evaluated 580 patients admitted with culture-positive bacterial pneumonia. We identified risk factors, evaluated the risk-scoring model's capacity to predict infection by DR pathogens and compared the model's diagnostic accuracy with that of current HCAP criteria. RESULTS: DR pathogens were observed in 227/580 patients (39.1%). Of 269 HCAP patients, 153 (56.9%) were infected with DR pathogens. Overtreatment was more common in HCAP than in community-acquired pneumonia (58.7% vs. 41.2%, P < 0.001). Recent hospitalisation, admission from a long-term care facility, recent antibiotic treatment and tube feeding were independently associated with DR pathogens. For pathogen prediction, the risk-scoring model showed better diagnostic accuracy than HCAP criteria (area under receiver operating-characteristic curve = 0.723 vs. 0.673, P < 0.001). CONCLUSION: According to current HCAP criteria, half of the HCAP patients were treated unnecessarily with broad-spectrum antibiotics. Risk scoring by stratifying risk factors could improve the identification of patients likely to be infected with DR pathogens.

Effects of isolation rooms on the prevalence of hospital acquired pneumonia in a respiratory ICU.

BACKGROUND: The incidence of hospital acquired pneumonia (HAP) varies according to the type of intensive care units (ICUs). AIM: The aims of this study were to determine the frequency of hospital acquired pneumonia (HAP) and the effect of isolation rooms on the frequency of pneumonia in the ICU. MATERIALS AND METHODS: The present investigation was carried out between January 2004 and July 2008. The ICU, which was 4-bed ward-type between January 2004 and February 2006 (1st period), was reconfigured as isolated rooms with only 2 beds each after March 2006 (2nd period). 153 and 379 patients were followed up in the ICU in the 1st and 2nd periods, respectively. Blood, sputum, and deep tracheal aspiration cultures were used for the isolation of the causative agents. RESULTS: No significant difference was detected between the general characteristics of patients. HAP developed in 101 patients (19%). The prevalence of HAP was 22.9% in the 1st period and 17.4% in the 2nd period. During the 1st and 2nd periods, the HAP infection densities were 22.2 and 16.1/1000 patient-days and the ventilator-associated pneumonia densities were 48.1 and 37.6/1000 ventilator-days, respectively. Eighty-six percent of HAP was ventilator-associated pneumonia (VAP). CONCLUSIONS: Isolation rooms in the ICU may be an effective strategy to control and decrease the rate of pneumonia in the ICU in addition to other preventive strategies.

Rhodococcus equi pneumonia in the foal--part 1: pathogenesis and epidemiology.

Rhodococcus equi pneumonia is a worldwide infectious disease of major concern to the equine breeding industry. The disease typically manifests in foals as pyogranulomatous bronchopneumonia, resulting in significant morbidity and mortality. Inhalation of aerosolised virulent R. equi from the environment and intracellular replication within alveolar macrophages are essential components of the pathogenesis of R. equi pneumonia in the foal. Recently documented evidence of airborne transmission between foals indicates the potential for an alternative contagious route of disease transmission. In the first of this two-part review, the complexity of the host, pathogen and environmental interactions that underpin R. equi pneumonia will be discussed through an exploration of current understanding of the epidemiology and pathogenesis of R. equi pneumonia in the foal.

Nursing-home-acquired pneumonia in Germany: an 8-year prospective multicentre study.

OBJECTIVE: To determine differences in aetiologies, initial antimicrobial treatment choices and outcomes in patients with nursing-home-acquired pneumonia (NHAP) compared with patients with community-acquired pneumonia (CAP), which is a controversial issue. METHODS: Data from the prospective multicentre Competence Network for Community-acquired pneumonia (CAPNETZ) database were analysed for hospitalised patients aged ≥65 years with CAP or NHAP. Potential differences in baseline characteristics, comorbidities, physical examination findings, severity at presentation, initial laboratory investigations, blood gases, microbial investigations, aetiologies, antimicrobial treatment and outcomes were determined between the two groups. RESULTS: Patients with NHAP presented with more severe pneumonia as assessed by CRB-65 (confusion, respiratory rate, blood pressure, 65 years and older) score than patients with CAP but received the same frequency of mechanical ventilation and less antimicrobial combination treatment. There were no clinically relevant differences in aetiology, with Streptococcus pneumoniae the most important pathogen in both groups, and potential multidrug-resistant pathogens were very rare (<5%). Only Staphylococcus aureus was more frequent in the NHAP group (n=12, 2.3% of the total population, 3.1% of those with microbial sampling compared with 0.7% and 0.8% in the CAP group, respectively). Short-term and long-term mortality in the NHAP group was higher than in the CAP group for patients aged ≥65 years (26.6% vs 7.2% and 43.8% vs 14.6%, respectively). However, there was no association between excess mortality and potential multidrug-resistant pathogens. CONCLUSIONS: Excess mortality in patients with NHAP cannot be attributed to a different microbial pattern but appears to result from increased comorbidities, and consequently, pneumonia is frequently considered and managed as a terminal event.

The 2007­2010 Q fever epidemic in The Netherlands: characteristics of notified acute Q fever patients and the association with dairy goat farming.

We describe the Q fever epidemic in the Netherlands with emphasis on the epidemiological characteristics of acute Q fever patients and the association with veterinary factors. Data from 3264 notifications for acute Q fever in the period from 2007 through 2009 were analysed. The patients most affected were men, smokers and persons aged 40­60 years. Pneumonia was the most common clinical presentation (62% in 2007 and 2008). Only 3.2% of the patients were working in the agriculture sector and 0.5% in the meat-processing industry including abattoirs. Dairy goat farms with Coxiella burnetii-induced abortion waves were mainly located in the same area where human cases occurred. Airborne transmission of contaminated dust particles from commercial dairy goat farms in densely populated areas has probably caused this epidemic. In 2010, there was a sharp decline in the number of notified cases following the implementation of control measures on dairy goat and sheep farms such as vaccination, hygiene measures and culling of pregnant animals on infected farms. In combination with a rise in the human population with antibodies against C. burnetii, these have most likely ended the outbreak. Development of chronic Q fever in infected patients remains an important problem for years to come.

Profile of bacterial pneumonia during Hajj.

BACKGROUND & OBJECTIVES: The congregation of a large number of people during Hajj seasons from different parts of the world in overcrowded conditions within a confined area for a long period of time presents many public health challenges and health risks. One of the main health problems of the crowding is ease transmission of pneumonia by air droplets. This study was aimed to determine the most common causes of bacterial pneumonia during the 2005 Hajj season and to relate the findings with clinical conditions. METHODS: A total of 141 patients with suspected pneumonia from the three main tertiary care hospitals in Makkah, Saudi Arabia, were investigated during Hajj season, 2005. Sputum and serum samples were collected and investigated for the possible presence of typical or atypical causative agents. RESULTS: Of the 141 clinically suspected pneumonia cases, 76 (53.9%) were confirmed positive by microbiological tests. More than 94 per cent of the confirmed cases were in the age group >50 yr, and 56.6 per cent of the cases were men. The most frequent isolates were Candida albicans (28.7%) and Pseudomonas aeruginosa (21.8%), followed by Legionella pneumophila (14.9%) and Klabsiella pneumoniae (9.2%). More than one causative pathogens were isolated in 15 patients (16.3%), and 55 per cent of patients were diabetic. INTERPRETATION & CONCLUSIONS: Clinicians should be aware that typical pneumonia treatment regimens may not work well during the Hajj season due to the wide variety of isolated organisms. This necessitates taking a sputum sample before starting treatment for identification and sensitivity testing. Special precautions need to be taken for >50 yr old patients.