Salmonella Enteritidis emerged as a major egg-associated pathogen in the late 20th century. Epidemiologic data from England, Wales, and the United States indicate that S. Enteritidis filled the ecologic niche vacated by eradication of S. Gallinarum from poultry, leading to an epidemic increase in human infections. We tested this hypothesis by retrospective analysis of epidemiologic surveys in Germany and demonstrated that the number of human S. Enteritidis cases is inversely related to the prevalence of S. Gallinarum in poultry. Mathematical models combining epidemiology with population biology suggest that S. Gallinarum competitively excluded S. Enteritidis from poultry flocks early in the 20th century.

Whole-genome sequencing is transforming the study of pathogenic bacteria. Searches for single virulence genes can now be performed on a genomewide scale by a variety of computer and genetic techniques. These techniques are discussed to provide a perspective on the developing field of genomics.

The sequences of close to 30 microbial genomes have been completed during the past 5 years, and the sequences of more than 100 genomes should be completed in the next 2 to 4 years. Soon, completed microbial genome sequences will represent a collection of >200,000 predicted coding sequences. While analysis of a single genome provides tremendous biological insights on any given organism, comparative analysis of multiple genomes provides substantially more information on the physiology and evolution of microbial species and expands our ability to better assign putative function to predicted coding sequences.

Complete genomic sequences of microbial pathogens and hosts offer sophisticated new strategies for studying host-pathogen interactions. DNA microarrays exploit primary sequence data to measure transcript levels and detect sequence polymorphisms, for every gene, simultaneously. The design and construction of a DNA microarray for any given microbial genome are straightforward. By monitoring microbial gene expression, one can predict the functions of uncharacterized genes, probe the physiologic adaptations made under various environmental conditions, identify virulence-associated genes, and test the effects of drugs. Similarly, by using host gene microarrays, one can explore host response at the level of gene expression and provide a molecular description of the events that follow infection. Host profiling might also identify gene expression signatures unique for each pathogen, thus providing a novel tool for diagnosis, prognosis, and clinical management of infectious disease.

Several pathogens of humans and domestic animals depend on hematophagous arthropods to transmit them from one vertebrate reservoir host to another and maintain them in an environment. These pathogens use antigenic variation to prolong their circulation in the blood and thus increase the likelihood of transmission. By convergent evolution, bacterial and protozoal vector-borne pathogens have acquired similar genetic mechanisms for successful antigenic variation. Borrelia spp. and Anaplasma marginale (among bacteria) and African trypanosomes, Plasmodium falciparum, and Babesia bovis (among parasites) are examples of pathogens using these mechanisms. Antigenic variation poses a challenge in the development of vaccines against vector-borne pathogens.

Toxin synthesis by Shiga toxin-producing Escherichia coli (STEC) appears to be coregulated through induction of the integrated bacteriophage that encodes the toxin gene. Phage production is linked to induction of the bacterial SOS response, a ubiquitous response to DNA damage. SOS-inducing antimicrobial agents, particularly the quinolones, trimethoprim, and furazolidone, were shown to induce toxin gene expression in studies of their effects on a reporter STEC strain carrying a chromosome-based stx2::lacZ transcriptional fusion. At antimicrobial levels above those required to inhibit bacterial replication, these agents are potent inducers (up to 140-fold) of the transcription of type 2 Shiga toxin genes (stx2); therefore, they should be avoided in treating patients with potential or confirmed STEC infections. Other agents (20 studied) and incubation conditions produced significant but less striking effects on stx2 transcription; positive and negative influences were observed. SOS-mediated induction of toxin synthesis also provides a mechanism that could exacerbate STEC infections and increase dissemination of stx genes. These features and the use of SOS-inducing antibiotics in clinical practice and animal husbandry may account for the recent emergence of STEC disease.

We describe the isolation and characterization of a new Lassa virus strain imported into Germany by a traveler who had visited Ghana, Côte D'Ivoire, and Burkina Faso. This strain, designated "AV," originated from a region in West Africa where Lassa fever has not been reported. Viral S RNA isolated from the patient's serum was amplified and sequenced. A long-range reverse transcription polymerase chain reaction allowed amplification of the full-length (3.4 kb) S RNA. The coding sequences of strain AV differed from those of all known Lassa prototype strains (Josiah, Nigeria, and LP) by approximately 20%, mainly at third codon positions. Phylogenetically, strain AV appears to be most closely related to strain Josiah from Sierra Leone. Lassa viruses comprise a group of genetically highly diverse strains, which has implications for vaccine development. The new method for full-length S RNA amplification may facilitate identification and molecular analysis of new arenaviruses or arenavirus strains.

A nested polymerase chain reaction assay was used to determine the presence of Ehrlichia chaffeensis, E. canis, and E. ewingii DNA in blood samples of free-ranging coyotes from central and north-central Oklahoma. Of the 21 coyotes examined, 15 (71%) were positive for E. chaffeensis DNA; none was positive for E. canis or E. ewingii. Results suggest that E. chaffeensis infections are common in free-ranging coyotes in Oklahoma and that these wild canids could play a role in the epidemiology of human monocytotropic ehrlichiosis.

From 1996 to 1999, 17 culture-documented systemic infections due to novel, atypical strains of Chryseobacterium meningosepticum occurred in two newborns and 15 immunocompromised patients in a medical center in Taiwan. All clinical isolates, which were initially misidentified as Aeromonassalmonicida by an automated bacterial identification system, were resistant to a number of antimicrobial agents. The isolates were characterized as atypical strains of C. meningosepticum by complete biochemical investigation, 16S rRNA gene sequence analysis, cellular fatty acid analysis, and random amplified polymorphic DNA fingerprinting (RAPD). This is the first report of a cluster of atypically variant strains of C. meningosepticum, which may be an emerging pathogen in newborns and the immunocompromised.

To establish the frequency of necrotizing funisitis in congenital syphilis, we conducted a prospective descriptive study of maternal syphilis in Bolivia by testing 1,559 women at delivery with rapid plasma reagin (RPR). We examined umbilical cords of 66 infants whose mothers had positive RPR and fluorescent treponemal antibody absorption tests. Histologic abnormalities were detected in 28 (42%) umbilical cords (seven [11%] had necrotizing funisitis with spirochetes; three [4%] had marked funisitis without necrosis; and 18 [27%] had mild funisitis), and 38 [58%] were normal. Of 22 umbilical cords of infants from mothers without syphilis (controls), only two (9%) showed mild funisitis; the others were normal. Testing umbilical cords by using immunohistochemistry is a research tool that can establish the frequency of funisitis due to Treponema pallidum infection.

We tested 46 fully vaccinated children in two day-care centers in Israel who were exposed to a fatal case of pertussis infection. Only two of five children who tested positive for Bordetella pertussis met the World Health Organization's case definition for pertussis. Vaccinated children may be asymptomatic reservoirs for infection.

We determined the prevalence of Shiga-toxin producing Escherichia coli (STEC) in diarrheal stool samples from Nebraska by three methods: cefixime-tellurite sorbitol MacConkey (CT-SMAC) culture, enterohemorrhagic E. coli (EHEC) enzyme immunoassay, and stx_1,2 polymerase chain reaction (PCR). Fourteen (4.2%) of 335 specimens were positive by at least one method (CT-SMAC culture [6 of 14], EHEC enzyme immunoassay [13 of 14], stx_1,2 PCR [14 of 14]). Six contained serogroup 0157, while non-0157 were as prevalent as 0157 serogroups.

To assess the rate of fecal vancomycin-resistant enterococci (VRE) colonization in Australia, we examined specimens from 1,085 healthy volunteers. VRE was cultured from 2 (0.2%) of 1,085 specimens; both were vanB Enterococcus faecium, identical by pulsed-field gel electrophoresis, but with a pattern rare in Melbourne hospitals.

Thirteen cases of falciparum malaria acquired by Europeans in the Dominican Republic occurred from June 1999 to February 2000. The cases were identified by the European Network on Imported Infectious Disease Surveillance (TropNetEurop).

We describe two cases of Mycobacterium microti infection causing pulmonary tuberculosis (TB) in HIV-seronegative immunocompetent patients in Germany. The isolates were identified as M. microti of the llama and vole types, according to spoligotype patterns. Our data demonstrate that M. microti can cause severe pulmonary TB in immunocompetent patients.

Four persons became ill with trichinellosis after eating meat from a wild boar hunted in Camargue, France. Nonencapsulated larvae of Trichinella pseudospiralis were detected in meat and muscle biopsy specimens. The diagnoses were confirmed by molecular typing. Surveillance for the emerging T. pseudospiralis should be expanded.

During the last decade, drug-resistant Mycobacterium tuberculosis (TB) strains have emerged, posing a major threat to global TB control efforts. The incidence of drug-resistant TB has increased in many parts of the world, not only in developing countries but also in industrialized countries, where the prevalence of drug-resistant TB had been low (1). The emergence of drug resistance during antituberculous therapy results mainly from inadequate therapy, i.e., improper prescription of treatment regimens, addition of single drugs to failing treatment regimens, and patient noncompliance. However, inconsistent drug-susceptibility patterns or delayed responses to TB therapy may also indicate exogenous reinfection with a strain resistant to multiple drugs or mixed infection with a sensitive and a multidrug-resistant TB strain. Such infections occur in immunocompromised and immunocompetent persons (2-7) and may be more common in areas with high prevalence of resistant TB.

Resistance of Streptococcus pneumoniae to antimicrobial drugs is increasing. To investigate the relationship between antimicrobial use and susceptibility of S. pneumoniae isolates at 24 U.S. medical centers, we obtained data on outpatient antimicrobial-drug use for the regions surrounding 23 of these centers. We found an association between decreased penicillin susceptibility and use of beta-lactam antimicrobial drugs.