Significance: Klebsiella pneumoniae is rapidly becoming untreatable using last-line antibiotics. It is especially problematic in hospitals, where it causes a range of acute infections. To approach controlling such a bacterium, we first must define what it is and how it varies genetically. Here we have determined the DNA sequence of K . pneumoniae isolates from around the world and present a detailed analysis of these data. We show that there is a wide spectrum of diversity, including variation within shared sequences and gain and loss of whole genes. Using this detailed blueprint, we show that there is an unrecognized association between the possession of specific gene profiles associated with virulence and antibiotic resistance and the differing disease outcomes seen for K . pneumoniae .

No detailed reports regarding extended-spectrum β-lactamase (ESBL)-producing Enterobacteriaceae are currently available from Indonesia, the fourth most populous country in the world. A survey was carried out to investigate the molecular epidemiology and genetic characteristics of clinical ESBL-producing Escherichia coli and Klebsiella pneumoniae isolates originating from the Dr. Soetomo Academic Hospital in Surabaya, Indonesia, over a 4 month period (January to April 2005). ESBLs were characterized by isoelectric focusing and PCR assays. Clonality of the isolates was assessed by PFGE and repetitive-sequence-based PCR (rep-PCR). Phylogenetic grouping was performed among CTX-M-15-producing E. coli. In total, 73 consecutive non-duplicate ESBL-positive E. coli and 72 K. pneumoniae strains were isolated. The bla_CTX-M-15 gene was found to be highly prevalent (69/73 strains, 94.5%) among the 73 ESBL-positive E. coli isolates. The gene was detected in both clonal and non-clonal isolates, as defined by PFGE and rep-PCR. Sixteen CTX-M-15-positive E. coli could be assigned to a single rep-PCR type and phylogenetic group B2 and belonged to the well-known O25b-ST131 clone. Among the 72 ESBL-positive K. pneumoniae isolates, bla_CTX-M-15 was again the most prevalent ESBL (40/72, 55.6%). Several SHV-type enzymes were also frequently detected: SHV-5 (n = 28); SHV-12 (n = 13); and SHV-2 (n = 6). TEM-type ESBLs were not detected in any of the isolates. Indonesia is another developing country affected by the emergence and spread of bacterial strains harbouring ESBL genes, including the CTX-M-15-producing B2-E. coli O25b-ST131 clone.

Enterobacteriaceae are important pathogens of both nosocomial and community-acquired infections. In particular, strains with broad-spectrum beta-lactamases increasingly cause problems in health care settings. Rapid and reliable typing systems are key tools to identify transmission, so that targeted infection control measures can be taken. In this study, we evaluated the performance of Raman spectroscopic analysis (RA) for the typing of multiresistant Escherichia coli and Klebsiella pneumoniae isolates using the SpectraCell RA bacterial strain analyzer (River Diagnostics). Analysis of 96 unrelated isolates revealed that RA generated highly reproducible spectra and exhibited a discriminatory power that is comparable to pulsed-field gel electrophoresis. Furthermore, adequate results were obtained for three collections of clinical isolates. RA was able to discriminate outbreak-related isolates from isolates that were not involved in an outbreak or transmission. Furthermore, it was found that the RA approach recognized clones, irrespective of the extended-spectrum β-lactamase type. It can be concluded that RA is a suitable typing technique for E. coli and K. pneumoniae isolates. Combining high reproducibility, speed, and ease-of-use, this technique may play an important role in monitoring the epidemiology of these important nosocomial species.

Few data on the molecular characteristics and epidemiology of Staphylococcus aureus from Indonesia are available. The purpose of the present study was to define S. aureus reservoirs in both the Indonesian community and hospital using a collection of 329 nasal carriage isolates obtained during a survey of 3,995 healthy individuals and patients from Java, Indonesia. Only one strain (0.3%) was identified as methicillin-resistant S. aureus by mecA gene PCR. The Panton-Valentine leukocidin (PVL) genes were detected in 35 methicillin-sensitive S. aureus strains (10.6%). Molecular typing by pulsed-field gel electrophoresis of the 329 isolates showed extensive genetic diversity among both PVL-positive and PVL-negative strains. In Surabaya, Indonesia, however, a cluster was identified that was strongly associated with the presence of the PVL locus ( P < 0.0001). As determined by high-throughput amplified fragment length polymorphism, PVL-positive strains occurred throughout all major AFLP clusters (I to IV). Multilocus sequence typing of a subset of isolates showed that most PVL-positive strains belonged to sequence type (ST) 188, while most PVL-negative isolates belonged to ST45. The high prevalence of PVL-positive S. aureus strains in certain regions of Indonesia is of concern since these strains may cause severe infections in the community and in hospitals.