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Multidrug resistance (MDR) represents a global threat to health. Here, we used whole genome sequencing to characterise Pseudomonas aeruginosa MDR clinical isolates from a hospital in Thailand. Using long-read sequence data we obtained complete sequences of two closely related megaplasmids (>420 kb) carrying large arrays of antibiotic resistance genes located in discrete, complex and dynamic resistance regions, and revealing evidence of extensive duplication and recombination events. A comprehensive pangenomic and phylogenomic analysis indicates that: 1) these large plasmids comprise an emerging family present in different members of the Pseudomonas genus, and associated with multiple sources (geographical, clinical or environmental); 2) the megaplasmids encode diverse niche-adaptive accessory traits, including multidrug resistance; 3) the accessory genome of the megaplasmid family is highly flexible and diverse. The history of the megaplasmid family, inferred from our analysis of the available database, suggests that members carrying multiple resistance genes date back to at least the 1970s. The emergence of multidrug resistance (MDR) in bacteria represents a global threat to human health. Here, Cazares et al. identify a family of MDR megaplasmids carrying large arrays of antibiotic resistance genes in Pseudomonas strains from various sources, including P. aeruginosa clinical isolates. [ABSTRACT FROM AUTHOR]

Background. Population-based estimates of the incidence of invasive pneumococcal disease are unavailable for Thailand and other countries in Southeast Asia. We estimated the incidence of pneumococcal bacteremia cases requiring hospitalization in rural Thailand. Methods. Blood cultures were performed on samples from hospitalized patients in 2 rural provinces where active, population-based surveillance of community-acquired pneumonia is conducted. Blood cultures were per- formed at clinician discretion and were encouraged for all patients with suspected pneumonia and all children aged <5 years with suspected sepsis. Pneumococcal antigen testing was performed on positive blood culture specimens that failed to grow organisms on subculture. Results. From May 2005 through June 2007, 23,853 blood culture specimens were collected overall, and 7319 were collected from children aged <5 years, which represented 66% and 47% of target patients, respectively. A total of 72 culture-confirmed pneumococcal bacteremia cases requiring hospitalization were identified. An additional 44 patients had media from positive blood cultures that yielded no growth on subculture but that had positive results of pneumococcal antigen testing. Of the 116 confirmed cases of bacteremia, 27 (23%) occurred in children aged <5 years; of these, 9 (33%) were confirmed by antigen testing only. The incidence of pneumococcal bacteremia cases requiring hospitalization among children aged <5 years had a range of 10.6-28.9 cases per 100,000 persons (incidence range if cases detected by antigen are excluded, 7.5-14.0 cases per 100,000 persons). Conclusions. Invasive pneumococcal disease is more common than was previously suspected in Thailand, even on the basis of estimates limited to hospitalized cases of bacteremia. These estimates, which are close to estimates of the incidence of hospitalized cases of pneumococcal bacteremia in the United States before introduction of pneumococcal conjugate vaccine, provide important data to guide public health care policy and to inform discussions about vaccine introduction in Thailand and the rest of Southeast Asia. [ABSTRACT FROM AUTHOR]

Background. Legionella species, Mycoplasma pneumoniae, and Chlamydia pneumoniae are recognized as important causes of pneumonia in high-income countries, but their significance in middle-income countries, such as Thailand, is unknown. Methods. Population-based surveillance identified inpatient 3489 cases of clinically-defined pneumonia in a rural Thai province for 1 year. Patients who had a chest radiograph performed (for 2059 cases of pneumonia) were enrolled in an etiology study (which included 755 cases of pneumonia among 738 patients). Paired serum, nasopharyngeal swab, and urine specimens were obtained for diagnostic immunologic and molecular tests. Patients aged !18 years were not systematically tested for Legionella species. We report a lower limit of incidence (observed incidence) and an upper limit extrapolated to persons not tested or not enrolled in the study. Results. The incidence of pneumonia due to Legionella longbeachae requiring hospitalization was 5-29 cases per 100,000 population. No case of Legionella pneumophila pneumonia was observed. The definite C. pneumoniae pneumonia incidence was 3-23 cases per 100,000 population; rates were highest among patients aged !1 year (18-166 cases per 100,000 population) and those aged 70 years (23-201 cases per 100,000 population). M. pneumoniae pneumonia had a similar age distribution, with an overall incidence of 6-44 cases per 100,000 population. These pathogens were associated with 15% of all cases of pneumonia. A nonsignificantly higher proportion of patients with pneumonia associated with L. longbeachae, compared with patients with pneumonia associated with M. pneumoniae or C. pneumoniae, required supplemental oxygen or mechanical ventilation (45% vs. 18%; P < .1). Among patients with atypical pneumonia, only 15% received antibiotics with activity against the associated pathogen. Conclusion. M. pneumoniae, C. pneumoniae, and L. longbeachae, but not L. pneumophila, are frequently associated with severe pneumonia in rural Thailand. Few patients receive a tibiotics that cover atypical pathogens. [ABSTRACT FROM AUTHOR]

Prior antibiotic use, contamination, limited blood volume, and processing delays reduce yield of blood cultures for detection of Streptococcus pneumoniae. We performed immunochromatographic testing (ICT) on broth from incubated blood culture bottles and real-time lytA polymerase chain reaction (PCR) on broth and whole blood and compared findings to blood culture in patients with suspected bacteremia. We selected 383 patients in Mali and 586 patients in Thailand based on their blood culture results: 75 and 31 were positive for pneumococcus, 100 and 162 were positive for other pathogens, and 208 and 403 were blood culture negative, respectively. ICT and PCR of blood culture broth were at least 87% sensitive and 97% specific compared with blood culture; whole blood PCR was 75-88% sensitive and 96-100% specific. Pneumococcal yields in children < 5 years of age increased from 2.9% to 10.7% in Mali with > 99% of additional cases detected by whole blood PCR, and from 0.07% to 5.1% in Thailand with two-thirds of additional cases identified by ICT. Compared with blood culture, ICT and lytA PCR on cultured broth were highly sensitive and specific but their ability to improve pneumococcal identification varied by site. Further studies of these tools are needed before widespread implementation., (© The American Society of Tropical Medicine and Hygiene.)

The incidence of pneumococcal pneumonia among adults is a key driver for the cost-effectiveness of pneumococcal conjugate vaccine used among children. We sought to obtain more accurate incidence estimates among adults by including results of pneumococcal urine antigen testing (UAT) from population-based pneumonia surveillance in two Thai provinces. Active surveillance from 2006 to 2011 identified acute lower respiratory infection (ALRI)-related hospital admissions. Adult cases of pneumococcal pneumonia were defined as hospitalized ALRI patients aged ≥ 18 years with isolation of Streptococcus pneumoniae from blood or with positive UAT. Among 39,525 adult ALRI patients, we identified 481 pneumococcal pneumonia cases (105 by blood culture, 376 by UAT only). Estimated incidence of pneumococcal pneumonia hospitalizations was 30.5 cases per 100,000 persons per year (2.2 and 28.3 cases per 100,000 persons per year by blood culture and UAT, respectively). Incidence varied between 22.7 in 2007 and 43.5 in 2010, and increased with age to over 150 per 100,000 persons per year among persons aged ≥ 70 years. Viral coinfections including influenza A/B, respiratory syncytial virus (RSV), and adenovirus occurred in 11% (44/409) of pneumococcal pneumonia cases tested. Use of UAT to identify cases of pneumococcal pneumonia among adults in rural Thailand substantially increases estimates of pneumococcal pneumonia burden, thereby informing cost-effectiveness analyses and vaccine policy decisions., (© The American Society of Tropical Medicine and Hygiene.)