The halophile Vibrio vulnificus is an etiologic agent of human mortality from seafood-borne infections. We applied whole-genome sequencing and comparative analysis to investigate the evolution of this pathogen. The genome of biotype 1 strain, V. vulnificus YJ016, was sequenced and includes two chromosomes of estimated 3377 kbp and 1857 kbp in size, and a plasmid of 48,508 bp. A super-integron (SI) was identified, and the SI region spans 139 kbp and contains 188 gene cassettes. In contrast to non-SI sequences, the captured gene cassettes are unique for any given Vibrio species and are highly variable among V. vulnificus strains. Multiple rearrangements were found when comparing the 5.3-Mbp V. vulnificus YJ016 genome and the 4.0-Mbp V. cholerae El Tor N16961 genome. The organization of gene clusters of capsular polysaccharide, iron metabolism, and RTX toxin showed distinct genetic features of V. vulnificus and V. cholerae. The content of the V. vulnificus genome contained gene duplications and evidence of horizontal transfer, allowing for genetic diversity and function in the marine environment. The genomic information obtained in this study can be applied to monitoring vibrio infections and identifying virulence genes in V. vulnificus.[Supplemental material is available online at www.genome.org and at http://genome.nhri.org.tw/vv/. The nucleotide sequence data from this study have been submitted to DDBJ/EMBL/GenBank under accession nos. BA000037, BA000038, and AP005352.]Vibrio vulnificus is an etiologic agent for severe human infection acquired through wounds or contaminated seafood. This organism is divided into three biotypes according to their different biochemical and biological properties (Linkous and Oliver 1999). Among them the biotype 1 strains are most frequently isolated from the clinical specimens. Opportunistic infection in susceptible individuals typically causes mortality within 24 to 48 h of the exposure. The bacterium is halophilic, and it is abundantly present in estuarine ecosystems throughout the world. Isolated incidents of V. vulnificus infection have been reported in the U.S.A., Europe, Korea, Taiwan (Park et al. 1991;Chuang et al. 1992;Dalsgaard et al. 1996;Hlady and Klontz 1996), and many other countries. According to CDC statistics, V. vulnificus is a major bacterial cause of mortality associated with food-borne diseases, and it results in the highest death rate of any causative agent (Todd 1989).V. vulnificus belongs to the ␥-group of Proteobacteria, and it shares morphological and biochemical characteristics with other human vibrio pathogens, including Vibrio cholerae and Vibrio parahaemolyticus. Bacteria of the Vibrionaceae family, which show a comma-shape microscopic appearance and a polar flagellum appendage, are mostly aquatic inhabitants that require NaCl for optimal growth. On the basis of clinical and epidemiology studies, diseases associated with V. vulnificus infection have been found to present in two patterns (Blake et al. 1979). In one, primary septicemia occurred in individ...

Klebsiella pneumoniae is an enteric pathogen causing community-acquired and hospital-acquired infections in humans. Epidemiological studies have revealed significant diversity in capsular polysaccharide (CPS) type and clinical manifestation of K. pneumoniae infection in different geographical areas of the world. We have sequenced the capsular polysaccharide synthesis (cps) region of seven clinical isolates and compared the sequences with the publicly available cps sequence data of five strains: NTUH-K2044 (K1 serotype), Chedid (K2 serotype), MGH78578 (K52 serotype), A1142 (K57 serotype) and A1517. Among all strains, six genes at the 59 end of the cps clusters that encode proteins for CPS transportation and processing at the bacterial surface are highly similar to each other. The central region of the cps gene clusters, which encodes proteins for polymerization and assembly of the CPS subunits, is highly divergent. Based on the collected sequence, we found that either the wbaP gene or the wcaJ gene exists in a given K. pneumoniae strain, suggesting that there is a major difference in the CPS biosynthesis pathway and that the K. pneumoniae strains can be classified into at least two distinct groups. All isolates contain gnd, encoding gluconate-6-phosphate dehydrogenase, at the 39 end of the cps gene clusters. The rmlBADC genes were found in CPS K9-positive, K14-positive and K52-positive strains, while manC and manB were found in K1, K2, K5, K14, K62 and two undefined strains. Our data indicate that, while overall genomic organization is similar between different pathogenic K. pneumoniae strains, the genetic variation of the sugar moiety and polysaccharide linkage generate the diversity in CPS molecules that could help evade host immune attack.

Strains of Vibrio vulnificus, a marine bacterial species pathogenic for humans and eels, are divided into three biotypes, and those virulent for eels are classified as biotype 2. All biotype 2 strains possess one or more plasmids, which have been shown to harbor the biotype 2-specific DNA sequences. In this study we determined the DNA sequences of three biotype 2 plasmids: pR99 (68.4 kbp) in strain CECT4999 and pC4602-1 (56.6 kb) and pC4602-2 (66.9 kb) in strain CECT4602. Plasmid pC4602-2 showed 92% sequence identity with pR99. Curing of pR99 from strain CECT4999 resulted in loss of resistance to eel serum and virulence for eels but had no effect on the virulence for mice, an animal model, and resistance to human serum. Plasmids pC4602-2 and pR99 could be transferred to the plasmid-cured strain by conjugation in the presence of pC4602-1, which was self-transmissible, and acquisition of pC4602-2 restored the virulence of the cured strain for eels. Therefore, both pR99 and pC4602-2 were virulence plasmids for eels but not mice. A gene in pR99, which encoded a novel protein and had an equivalent in pC4602-2, was further shown to be essential, but not sufficient, for the resistance to eel serum and virulence for eels. There was evidence showing that pC4602-2 may form a cointegrate with pC4602-1. An investigation of six other biotype 2 strains for the presence of various plasmid markers revealed that they all harbored the virulence plasmid and four of them possessed the conjugal plasmid in addition.Vibrio vulnificus is a gram-negative bacterial species that is ubiquitous in marine environments. This organism causes infections that are characterized by severe wound infection and primary septicemia with high mortality in humans, particularly those with underlying diseases such as liver cirrhosis and hemochromatosis (33,40). It also causes systemic infections, called vibriosis, with high mortality in brackish-water-cultured eels (4, 16). This organism is considered an emerging pathogen, since cases in fish and human were first reported in 1976 and 1979, respectively (8, 34).Strains of V. vulnificus are divided into three biotypes, biotype 1 (BT1), BT2, and BT3, based on their differences in phenotypic traits, serological type, and host range (6, 7, 42). All three biotypes can cause sporadic cases of human diseases and have been shown to be virulent for the mouse, an animal model; however, only the BT2 strains produce epizootic or outbreaks of vibriosis, mainly in eels (4, 34). The lesions on the body of a V. vulnificus-infected eel, similar to those caused by Vibrio anguillarum, include external skin ulcer, hemorrhagic fins, protrusion of the rectum, and hemorrhages and inflammation of the internal organs (4). The BT2 strains are further subdivided into several serovars (6,16,22), among which serovar E is not only the most virulent and prevalent but also the only one isolated from sporadic human infections associated with handling of contaminated fish (1).The virulence mechanism of BT2 V. vulnificus strains in eels rem...

The genetic features of the antimicrobial resistance of a multidrug resistant Klebsiella pneumoniae strain harboring bla NDM-1 were investigated to increase our understanding of the evolution of NDM-1. The strain, KPX, came from a Taiwanese patient with a hospitalization history in New Delhi. Complete DNA sequencing was performed; and the genes responsible for antimicrobial resistance were systematically examined and isolated by library screening. KPX harbored two resistance plasmids, pKPX-1 and pKPX-2, which are 250-kb and 141-kb in size, respectively, with bla NDM-1 present on pKPX-1. The plasmid pKPX-1 contained genes associated with the IncR and IncF groups, while pKPX-2 belonged to the IncF family. Each plasmid carried multiple antimicrobial resistance genetic determinants. The gene responsible for resistance to carbapenems was found on pKPX-1 and that for resistance to aztreonam was found on pKPX-2. To our surprise, we discovered that bla NDM-1 exists on pKPX-1 as multiple copies in the form of tandem repeats. Amplification of bla NDM-1 was found to occur by duplication of an 8.6-kb unit, with the copy number of the repeat varying from colony to colony. This repeat sequence is identical to that of the pNDM-MAR except for two base substitutions. The copy number of bla NDM-1 of colonies under different conditions was assessed by Southern blotting and quantitative PCR. The bla NDM-1 sequence was maintained in the presence of the antimicrobial selection; however, removal of antimicrobial selection led to the emergence of susceptible bacterial populations with a reduced copy number or even the complete loss of the bla NDM-1 sequence. The dynamic nature of the NDM-1 sequence provides a strong argument for judicious use of the broad-spectrum antimicrobials in order to reduce the development and spread of antimicrobial resistance among pathogens.