In recent years, methicillin-resistant Staphylococcus aureus (MRSA) have become a truly global challenge. In addition to the long-known healthcare-associated clones, novel strains have also emerged outside of the hospital settings, in the community as well as in livestock. The emergence and spread of virulent clones expressing Panton-Valentine leukocidin (PVL) is an additional cause for concern. In order to provide an overview of pandemic, epidemic and sporadic strains, more than 3,000 clinical and veterinary isolates of MRSA mainly from Germany, the United Kingdom, Ireland, France, Malta, Abu Dhabi, Hong Kong, Australia, Trinidad & Tobago as well as some reference strains from the United States have been genotyped by DNA microarray analysis. This technique allowed the assignment of the MRSA isolates to 34 distinct lineages which can be clearly defined based on non-mobile genes. The results were in accordance with data from multilocus sequence typing. More than 100 different strains were distinguished based on affiliation to these lineages, SCCmec type and the presence or absence of PVL. These strains are described here mainly with regard to clinically relevant antimicrobial resistance- and virulence-associated markers, but also in relation to epidemiology and geographic distribution. The findings of the study show a high level of biodiversity among MRSA, especially among strains harbouring SCCmec IV and V elements. The data also indicate a high rate of genetic recombination in MRSA involving SCC elements, bacteriophages or other mobile genetic elements and large-scale chromosomal replacements.
Background Invasive pneumococcal disease remains an important health priority owing to increasing disease incidence caused by pneumococci expressing non-vaccine serotypes. We previously defined 621 Global Pneumococcal Sequence Clusters (GPSCs) by analysing 20 027 pneumococcal isolates collected worldwide and from previously published genomic data. In this study, we aimed to investigate the pneumococcal lineages behind the predominant serotypes, the mechanism of serotype replacement in disease, as well as the major pneumococcal lineages contributing to invasive pneumococcal disease in the post-vaccine era and their antibiotic resistant traits. Methods We whole-genome sequenced 3233 invasive pneumococcal disease isolates from laboratory-based surveillance programmes in Hong Kong (n=78), Israel (n=701), Malawi (n=226), South Africa (n=1351), The Gambia (n=203), and the USA (n=674). The genomes represented pneumococci from before and after pneumococcal conjugate vaccine (PCV) introductions and were from children younger than 3 years. We identified predominant serotypes by prevalence and their major contributing lineages in each country, and assessed any serotype replacement by comparing the incidence rate between the pre-PCV and PCV periods for Israel, South Africa, and the USA. We defined the status of a lineage as vaccine-type GPSC (≥50% 13-valent PCV [PCV13] serotypes) or non-vaccine-type GPSC (>50% non-PCV13 serotypes) on the basis of its initial serotype composition detected in the earliest vaccine period to measure their individual contribution toward serotype replacement in each country. Major pneumococcal lineages in the PCV period were identified by pooled incidence rate using a random effects model. Findings The five most prevalent serotypes in the PCV13 period varied between countries, with only serotypes 5, 12F, 15B/C, 19A, 33F, and 35B/D common to two or more countries. The five most prevalent serotypes in the PCV13 period varied between countries, with only serotypes 5, 12F, 15B/C, 19A, 33F, and 35B/D common to two or more countries. These serotypes were associated with more than one lineage, except for serotype 5 (GPSC8). Serotype replacement was mainly mediated by expansion of non-vaccine serotypes within vaccine-type GPSCs and, to a lesser extent, by increases in non-vaccine-type GPSCs. A globally spreading lineage, GPSC3, expressing invasive serotypes 8 in South Africa and 33F in the USA and Israel, was the most common lineage causing non-vaccine serotype invasive pneumococcal disease in the PCV13 period. We observed that same prevalent non-vaccine serotypes could be associated with distinctive lineages in different countries, which exhibited dissimilar antibiotic resistance profiles. In non-vaccine serotype isolates, we detected significant increases in the prevalence of resistance to penicillin (52 [21%] of 249 vs 169 [29%] of 575, p=0•0016) and erythromycin (three [1%] of 249 vs 65 [11%] of 575, p=0•0031) in the PCV13 period compared with the pre-PCV period. Interpretation Globally spreading line...
SignificanceUSA300 is a hypervirulent, community-acquired, multidrug-resistant Staphylococcus aureus clone that started to spread in the United States around 17 years ago. Many studies detected it also in South America, Europe, and the Asia-Pacific region. In this study, we show that USA300 is also circulating in sub-Saharan Africa. Locating the temporal and spatial origin of clonal lineages is important with respect to epidemiology and molecular evolution of pathogens. We show that USA300 evolved from a less virulent and less resistant ancestor circulating in Central Europe around 160 years ago. Constant surveillance of pathogen transmission routes is vital to prevent and control potential outbreaks. Whole genome sequencing proved to be a useful tool for epidemiological surveillance.
In 2006, the first isolate of KPC-2-producing Pseudomonas aeruginosa in the world was identified in Colombia. Recently, similar strains have been reported in Puerto Rico. We now report KPC-2-producing P. aeruginosa in Trinidad and Tobago. Surveillance for similar strains is warranted, considering their wide geographic spread and known association with mobile genetic elements. CASE REPORTA 63-year-old male patient was admitted to a hospital in Mount Hope, Trinidad and Tobago, with hematuria, dysuria, fever, and chills. He had no history of travel abroad. Four months prior to his presentation, he had a left hip fracture caused by a fall and was hospitalized at another regional hospital for 10 weeks without any surgical intervention but with conservative care. He had remained bedridden since the fracture.Upon physical examination, he appeared chronically ill, was stuporous, febrile (38°C), severely pale, and dehydrated, had bedsores on the buttocks and sacral area, and had a urinary catheter. He had swelling of the left thigh, which was tender and warm to the touch, with subcutaneous emphysema.Blood and urine specimens were submitted for culture. Radiological investigations of the pelvis and legs revealed a fracture of the neck of the left femur, with subcutaneous emphysema and fluid collection along the lateral compartment of the thigh, extending to the inguinal region, hip joint, and left lower abdominal wall.He was given gentamicin, ceftazidime, and metronidazole. A fasciotomy was performed, revealing gas gangrene. Two liters of greenish yellow pus from the anterior compartment of the left thigh, extending to the left lower abdomen, was drained. This pus was cultured.Blood and urine cultures were negative. However, the culture of the pus from surgery yielded Pseudomonas aeruginosa. Antimicrobial susceptibility testing using the MicroScan WalkAway 96 SI system (Siemens) revealed that the isolate was resistant to all tested antimicrobials, including gentamicin, ceftazidime, ciprofloxacin, and carbapenems. Meropenem monotherapy was given despite in vitro resistance, while efforts were made to procure polymyxin B or colistin; unfortunately, these efforts were unsuccessful, and the patient died 10 days postadmission.The P. aeruginosa isolate was sent to the International Center for Medical Research and Training, Cali, Colombia, where the MIC was determined using the Clinical and Laboratory Standards Institute (CLSI)-approved broth microdilution method (2). Ertapenem, imipenem, and meropenem MICs were Ͼ128 g/ml. This isolate was also resistant to ceftazidime (MIC, 128 g/ml), cefepime (MIC, Ͼ128 g/ml), aztreonam (MIC, Ͼ128 g/ml), piperacillin-tazobactam (MICs, Ͼ256 and 4 g/ml), and ciprofloxacin (MIC, Ͼ8 g/ml) and remained susceptible only to polymyxin B (MIC, 2 g/ml).A three-dimensional test to screen for carbapenemases was performed as reported previously (10) with some modifications. This test uses a carbapenem-susceptible organism as an indicator for carbapenemases in a cellular extract. To detect the carbapenemase...
It has been shown previously that high rates of methicillin- and mupirocin-resistant Staphylococcus aureus exist in the Caribbean islands of Trinidad and Tobago, as well as a high prevalence of Panton-Valentine leukocidin-positive S. aureus. Beyond these studies, limited typing data have been published. In order to obtain insight into the population structure not only of MRSA but also of methicillin-susceptible S. aureus, 294 clinical isolates collected in 2012/2013 were typed by microarray hybridisation. A total of 15.31% of the tested isolates were MRSA and 50.00% were PVL-positive. The most common MSSA strains were PVL-positive CC8-MSSA (20.41% of all isolates tested), PVL-positive CC152-MSSA (9.52%) and PVL-positive CC30-MSSA (8.84%) while the most common MRSA were ST239-MRSA-III&SCCmer (9.18%) and ST8-MRSA-IV, “USA300” (5.78%). 2.38% of characterised isolates belonged to distinct strains likely to be related to “Staphylococcus argenteus” lineages. The population structure of S. aureus isolates suggests an importation of strains from Africa, endemicity of PVL-positive MSSA (mainly CC8) and of ST239-MRSA-III, and a recent emergence of the PVL-positive CC8-MRSA-IV strain “USA300”.
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