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We conducted a comprehensive, multi-phase laboratory evaluation of the Tularemia BioThreat Alert® (BTA) test, a lateral flow assay (LFA) for the rapid detection of Francisella tularensis. The study, conducted at 2 sites, evaluated the limit of detection (LOD) of this assay using the virulent SchuS4 strain and the avirulent LVS strain of F. tularensis. In 6-phase evaluation (linear dynamic range and reproducibility, inclusivity, near-neighbor, environmental background, white powder, and environmental filter extract), 13 diverse strains of F. tularensis, 8 Francisella near neighbors, 61 environmental background organisms, 26 white powders, and a pooled aerosol extract were tested. In the 937 tests performed, the Tularemia BTA demonstrated an LOD of 107 to 108 cfu/mL, with a sensitivity of 100.00%, specificity of 98.08%, and accuracy of 98.84%. These performance data are important for accurate interpretation of qualitative results arising from screening suspicious white powders in the field.

We conducted a comprehensive, multiphase laboratory evaluation of the Plague BioThreat Alert® (BTA) test, a lateral flow immunoassay (LFA), for the rapid detection of Yersinia pestis. The study was conducted in 7 phases at 2 sites to assess the performance of the LFA. The limit of detection (LOD) was determined using both a virulent and avirulent strain of Y. pestis, CO99-3015 (105 CFU/ml) and A1122 (104 CFU/ml), respectively. In the other phases, 18 Y. pestis strains, 20 phylogenetic near-neighbor strains, 61 environmental background microorganisms, 26 white powders, and a pooled aerosol sample were also tested. A total of 1,110 LFA test results were obtained, and their analysis indicates that this LFA had a sensitivity of 97.65% and specificity of 96.57%. These performance data are important for accurate interpretation of qualitative results arising from testing suspicious white powders and aerosol samples in the field. Any positive specimen in this assay is considered presumptive positive and should be referred to the Centers for Disease Control and Prevention Laboratory Response Network for additional testing, confirmation, and characterization for an appropriate public health response.

Infections in immunocompromised patients that are caused by extensively drug-resistant (XDR) Acinetobacter baumannii strains have been increasingly reported worldwide. In particular, carbapenem-resistant A. baumannii strains are a prominent cause of health care-associated infections. Here, we report draft genome assemblies for two clinical XDR A. baumannii isolates obtained from hospitalized patients in Pakistan.

DNA-based monitoring of pathogens in aerosol samples requires extraction methods that provide high recovery of DNA. To identify a suitable method, we evaluated six DNA extraction methods for recovery of target-specific DNA from samples with four bacterial agents at low abundance (

Shigella spp. are the most common cause of dysentery in developing countries and the second leading cause of diarrheal deaths worldwide. Multidrug-resistant (MDR) Shigella spp. are a serious threat to global health. Herein, we report draft genome sequences for three MDR Shigella isolates from Pakistan, two Shigella flexneri isolates and one Shigella sonnei isolate.

Ricin, a heterodimeric toxin that is present in the seeds of the Ricinus communis plant, is the biothreat agent most frequently encountered by law enforcement agencies in the United States. Even in untrained hands, the easily obtainable seeds can yield a highly toxic product that has been used in various types of threats, including "white-powder" letters. Although the vast majority of these threats are hoaxes, an impediment to accurate hazard assessments by first responders is the unreliability of rapid detection assays for ricin, such as lateral flow assays (LFAs). One of the complicating factors associated with LFAs is the incorporation of antibodies of poor specificity that cross-react with near-neighbors or with plant lectins that are capable of nonspecifically cross-linking the capture and detector antibodies. Because of the compelling and critical need to promote the interests of public safety and public health, the Department of Homeland Security conducted a comprehensive laboratory evaluation study of a commercial LFA for the rapid detection of ricin. This study was conducted using comprehensive inclusivity and exclusivity panels of ricin and near-neighbor plant materials, along with panels of lectins and "white-powders," to determine the specificity, sensitivity, limits of detection, dynamic range, and repeatability of the assay for the specific intended use of evaluating suspicious white powders and environmental samples in the field.

The emergence and spread of colistin resistance among multidrug-resistant (MDR) Klebsiella pneumoniae represent a critical threat to global health. Here, we report the complete genome sequences of 10 MDR, colistin-susceptible and -resistant K. pneumoniae clinical isolates obtained in Pakistan between 2010 and 2013.

Anthrax has been a prevalent and fatal disease of grazing herbivorous animals such as cattle, sheep, goats, camels, antelopes, horses and bison and has sporadically claimed the lives of humans. Bacillus anthracis, the etiological agent of anthrax, is a non-motile Gram-positive, spore-forming, rod-shaped bacterium. The spores of B. anthracis, which are infectious for mammals, are highly resistant to a variety of environmental conditions, such as heat, cold, ultraviolet and ionizing radiation, pressure and chemical agents. There are four clinical forms of human anthrax based on the portal of entry of the spores, referred to as inhalational, cutaneous, gastrointestinal and injectional. The high mortality rate of untreated inhalational anthrax together with the ease with which spores can be aerosolized has made B. anthracis an attractive biological weapon and is considered by many to be a serious aerobiological threat for an intentional release. The 21st century has been marked by the 2001 anthrax incident in the United States. This incident led to unprecedented advances in anthrax diagnostics, anthrax vaccine development, detection of B. anthracis spores in environmental matrices, decontamination technology and strategies for B. anthracis contamination and anthrax incident waste management.

The emergence and dissemination of carbapenemases, bacterial enzymes able to inactivate most β-lactam antibiotics, in Enterobacteriaceae is of increasing concern. The concurrent spread of resistance against colistin, an antibiotic of last resort, further compounds this challenge further. Whole-genome sequencing (WGS) can play a significant role in the rapid and accurate detection/characterization of existing and emergent resistance determinants, an essential aspect of public health surveillance and response activities to combat the spread of antimicrobial resistant bacteria. In the current study, WGS data was used to characterize the genomic content of antimicrobial resistance genes, including those encoding carbapenemases, in 10 multidrug-resistant Klebsiella pneumoniae isolates from Pakistan. These clinical isolates represented five sequence types: ST11 (n = 3 isolates), ST14 (n = 3), ST15 (n = 1), ST101 (n = 2), and ST307 (n = 1). Resistance profiles against 25 clinically-relevant antimicrobials were determined by broth microdilution; resistant phenotypes were observed for at least 15 of the 25 antibiotics tested in all isolates except one. Specifically, 8/10 isolates were carbapenem-resistant and 7/10 isolates were colistin-resistant. The blaNDM-1 and blaOXA-48 carbapenemase genes were present in 7/10 and 5/10 isolates, respectively; including 2 isolates carrying both genes. No plasmid-mediated determinants for colistin resistance (e.g. mcr) were detected, but disruptions and mutations in chromosomal loci (i.e. mgrB and pmrB) previously reported to confer colistin resistance were observed. A blaOXA-48-carrying IncL/M-type plasmid was found in all blaOXA-48-positive isolates. The application of WGS to molecular epidemiology and surveillance studies, as exemplified here, will provide both a more complete understanding of the global distribution of MDR isolates and a robust surveillance tool useful for detecting emerging threats to public health.

To determine the aetiology of genital ulcer disease (GUD) and its association with HIV infection in the mining community of Carletonville, South Africa, from two cross sectional surveys of consecutive men presenting with genital lesions during October 1993 to January 1994 and July to November 1998.A multiplex polymerase chain reaction (M-PCR) assay combined with amplicon detection was used to identify DNA specific sequences of Treponema pallidum, herpes simplex virus (HSV), and Haemophilus ducreyi. A real time PCR assay was used to differentiate between HSV-1 and HSV-2.M-PCR detected T pallidum, HSV, and H ducreyi in 10.3%, 17.2%, and 69.4% of 232 GUD patients during 1993-4 and in 12.4%, 36.0%, and 50.5% of 186 GUD patients in 1998. The proportion of patients with more than one agent increased significantly from 7.3% (17/232) in 1993-4 to 16.7% (31/186) in 1998 (p0.01). HSV-2 was detected in a higher proportion of ulcer specimens from HIV infected patients than in specimens from HIV uninfected patients during both time periods (1993-4: 26.2% v 6.7%, p0.001; 1998: 42.1% v 29.6%, p0.09).Based on two cross sectional surveys, 4 years apart, chancroid remained the leading cause of GUD in men who presented at the STD clinic with genital ulcers in the mining community of Carletonville, South Africa. The relative prevalence of primary syphilis has remained low. However, HSV-2 has emerged as a more significant cause of GUD and the proportion of GUD patients infected with more than one agent also increased significantly. HSV-2 DNA was detected in a significantly higher proportion of ulcer specimens from HIV positive patients than from HIV negative patients. No association was found between HIV infection status and the relative prevalence of chancroid or syphilis.

We used radiotelemetry to study the movement of lake sturgeon Acipenser fulvescens in the Kettle River of east-central Minnesota. Our objectives were to determine whether the tracked fish were seasonal or year-round residents of the river and to determine their seasonal movements, responses to changes in discharge, and activity centers. We were also interested in the response of these fish to the removal of a hydroelectric dam that had blocked upstream movement of fish for 87 years. Eight fish received transmitter implants and were tracked for about 7 months, from October 1994 through May 1995. Three tagged fish were not identified or located thereafter, but the remaining five were tracked weekly from April 1995 to September 1996. Lake sturgeon did not move upstream of the former hydroelectric dam or downstream of the Kettle River's confluence with the St. Croix River but rather remained within this 20-mi reach, despite the absence of physical barriers at either end. We found that sturgeon moveme...

Baylisascaris procyonis, a roundworm infection of raccoons, is emerging as an important helminthic zoonosis, principally affecting young children. Raccoons have increasingly become peridomestic animals living in close proximity to human residences. When B. procyonis eggs are ingested by a host other than a raccoon, migration of larvae through tissue, termed larval migrans, ensues. This larval infection can invade the brain and eye, causing severe disease and death. The prevalence of B. procyonis infection in raccoons is often high, and infected animals can shed enormous numbers of eggs in their feces. These eggs can survive in the environment for extended periods of time, and the infectious dose of B. procyonis is relatively low. Therefore, the risk for human exposure and infection may be greater than is currently recognized.

High throughput sequencing (HTS) generates large amounts of high quality sequence data for microbial genomics. The value of HTS for microbial forensics is the speed at which evidence can be collected and the power to characterize microbial-related evidence to solve biocrimes and bioterrorist events. As HTS technologies continue to improve, they provide increasingly powerful sets of tools to support the entire field of microbial forensics. Accurate, credible results allow analysis and interpretation, significantly influencing the course and/or focus of an investigation, and can impact the response of the government to an attack having individual, political, economic or military consequences. Interpretation of the results of microbial forensic analyses relies on understanding the performance and limitations of HTS methods, including analytical processes, assays and data interpretation. The utility of HTS must be defined carefully within established operating conditions and tolerances. Validation is essential in the development and implementation of microbial forensics methods used for formulating investigative leads attribution. HTS strategies vary, requiring guiding principles for HTS system validation. Three initial aspects of HTS, irrespective of chemistry, instrumentation or software are: 1) sample preparation, 2) sequencing, and 3) data analysis. Criteria that should be considered for HTS validation for microbial forensics are presented here. Validation should be defined in terms of specific application and the criteria described here comprise a foundation for investigators to establish, validate and implement HTS as a tool in microbial forensics, enhancing public safety and national security. Published version

A molecular-based subtyping system for Treponema pallidum was used during an investigation of increasing syphilis in Maricopa County, Arizona. Genital ulcer or whole blood specimens from patients with syphilis were assayed by a polymerase chain reaction (PCR) amplification of a T. pallidum DNA polymerase I gene. Positive specimens were typed on the basis of PCR amplification of 2 variable genes. In all, 41 (93%) of 44 of ulcer specimens and 4 (27%) of 15 blood specimens yielded typeable T. pallidum DNA. Twenty-four (53%) of 45 specimens were subtype 14f; other subtypes identified included 4f, 4i, 5f, 12a, 12f, 14a, 14d, 14e, and 14i. Only 2 specimens were from epidemiologically linked patients. This investigation demonstrates that multiple subtypes of T. pallidum can be found in an area with high syphilis morbidity, although 1 subtype (14f) was predominant. Four typeable specimens were from blood, a newly identified specimen source for subtyping.

We used PCR assays to determine the etiology of genital ulcers in patients presenting to a sexually transmitted disease clinic in Dakar, Senegal, and evaluated the ability of two PCR tests ( groEL and recD ) and two serological tests (adsorption enzyme immunoassay [EIA] and lipooligosaccharide [LOS] EIA) to detect current Haemophilus ducreyi infection. We found that in this population, H. ducreyi , T. pallidum , and herpes simplex virus HSV DNA were detected in 56, 15, and 13% of 39 genital ulcer specimens, respectively, and H. ducreyi DNA was detected in 60% (3 of 5) of samples from ulcerated bubos. Among 40 consecutive patients with genital ulcer disease and with sufficient sample for both PCR assays, the recD and groEL H. ducreyi PCR assays were 83% concordant, with the recD PCR assay detecting six (15%) additional positive specimens and the groEL assay detecting one (3%) additional positive specimen. Compared to PCR, the adsorption EIA and LOS EIA tests had sensitivities of 71 and 59% and specificities of 57 and 90%, respectively, for the diagnosis of current H. ducreyi infection. While these differences in specificity could be due either to previous infection with H. ducreyi or to the detection of cross-reacting antibodies, only 6% of patients from a nearby family planning clinic gave a positive reaction in both the adsorption EIA and LOS EIA assays, indicating that cross-reacting antibodies are not prevalent among clinic attendees in this city. Our studies indicate that the adsorption EIA detects both current and past infection, while the LOS EIA assay is more specific for current infection with H. ducreyi in this population.

The iron-storage protein bacterioferritin (Bfr) from Neisseria gonorrhoeae strain F62 was identified in cell-free extracts and subsequently purified by column chromatography. Gonococcal Bfr had an estimated molecular mass of 400 kDa by gel filtration; however, analysis by SDS-PAGE revealed that it was composed of 18 kDa (BfrA) and 22 kDa (BfrB) subunits. DNA encoding BfrB was amplified by PCR using degenerate primers derived from the N-terminal amino acid sequence of BfrB and from a C-terminal amino acid sequence of Escherichia coli Bfr. The DNA sequence of bfrA was subsequently obtained by genome walking using single-specific-primer PCR. The two Bfr genes were located in tandem with an intervening gap of 27 bp. A potential Fur-binding sequence (12 of 19 bp identical to the consensus neisserial fur sequence) was located within the 5' flanking region of bfrA in front of a putative -35 hexamer. The homology between the DNA sequences of bfrA and bfrB was 55.7%; the deduced amino acid sequences of BfrA (154 residues) and BfrB (157 residues) showed 39.7% identity, and showed 41.3% and 56.1% identity, respectively, to E. coli Bfr. Expression of recombinant BfrA and BfrB in E. coli strain DH5alpha was detected on Western blots probed with polyclonal anti-E. coli Bfr antiserum. Most Bfrs are homopolymers with identical subunits; however, the evidence presented here suggests that gonococcal Bfr was composed of two similar but not identical subunits, both of which appear to be required for the formation of a functional Bfr. A Bfr-deficient mutant was constructed by inserting the omega fragment into the BfrB gene. The growth of the BfrB-deficient mutant in complex medium was reduced under iron-limited conditions. The BfrB-deficient mutant was also more sensitive to killing by H2O2 and paraquat than the isogenic parent strain. These results demonstrate that gonococcal Bfr plays an important role in iron storage and protection from iron-mediated oxidative stress.

To determine the etiology of genital ulcers and to assess the prevalence of human immunodeficiency virus (HIV) infection in ulcer patients in 10 US cities, ulcer and serum specimens were collected from approximately 50 ulcer patients at a sexually transmitted disease clinic in each city. Ulcer specimens were tested using a multiplex polymerase chain reaction assay to detect Haemophilus ducreyi, Treponema pallidum, and herpes simplex virus (HSV); sera were tested for antibody to HIV. H. ducreyi was detected in ulcer specimens from patients in Memphis (20% of specimens) and Chicago (12%). T. pallidum was detected in ulcer specimens from every city except Los Angeles (median, 9% of specimens; range, 0%-46%). HSV was detected in >/=50% of specimens from all cities except Memphis (42%). HIV seroprevalence in ulcer patients was 6% (range by city, 0%-18%). These data suggest that chancroid is prevalent in some US cities and that persons with genital ulcers should be a focus of HIV prevention activities.

In 1994, an apparent outbreak of atypical genital ulcers was noted by clinicians at the sexually transmitted disease clinic in Jackson, Mississippi. Of 143 patients with ulcers tested with a multiplex polymerase chain reaction (PCR) assay, 56 (39%) were positive for Haemophilus ducreyi, 44 (31%) for herpes simplex virus, and 27 (19%) for Treponema pallidum; 12 (8%) were positive for > 1 organism. Of 136 patients tested for human immunodeficiency virus (HIV) by serology, 14 (10%) were HIV-seropositive, compared with none of 200 patients without ulcers (P < .001). HIV-1 DNA was detected by PCR in ulcers of 6 (50%) of 12 HIV-positive patients. Multivariate analysis indicated that men with chancroid were significantly more likely than male patients without ulcers to report sex with a crack cocaine user, exchange of money or drugs for sex, and multiple sex partners. The strong association between genital ulcers and HIV infection in this population highlights the urgency of preventing genital ulcers in the southern United States.

A multiplex polymerase chain reaction (M-PCR) assay that simultaneously detects the three major causes of genital ulcer disease (GUD), Haemophilus ducreyi, Treponema pallidum, and herpes simplex virus, was used to evaluate swab specimens for 38 sequential patients with GUD at a Thai sexually transmitted disease clinic. Subjects received clinical diagnoses and syndromic treatment. Swab specimens for H. ducreyi cultures and M-PCR were obtained. No H. ducreyi cultures were positive. Of 38 M-PCR specimens, 31 (81.6%) were positive for HSV, 1 (2.3%) for both HSV and T. pallidum, and none for H. ducreyi or T. pallidum alone; 6 (15.8%) were negative for all 3 pathogens. Clinical diagnoses corresponded poorly to M-PCR findings; none of 5 suspected cases of chancroid were positive by M-PCR and none of 1 for syphilis, but 21 of 24 suspected herpes lesions were confirmed by M-PCR. Human immunodeficiency virus infection status was known for 24 of 38 subjects; 11 (45.8%) were seropositive, and all 11 had HSV by M-PCR. HSV appeared to be the most common pathogen overall.

The performance of two EIAs (adsorption EIA and lipooligosaccharide [LOS] EIA) that detect antibodies to Haemophilus ducreyi was evaluated with serum specimens obtained from 163 patients (96 with genital ulcer disease [GUD]). Paired serum specimens (initial and follow-up) were obtained from 52 of the GUD patients. By use of initial serum specimens from 82 GUD patients whose etiologic agents for their ulcers had been identified, the adsorption EIA had a sensitivity and specificity for chancroid of 53% and 71%, while the LOS EIA had a sensitivity and specificity of 48% and 89%, respectively. Sensitivity and specificity of the adsorption EIA increased to 78% and 84%, respectively, when the results of follow-up serum specimens were used to calculate optimal performance. The proportion of patients testing positive for H. ducreyi who had anti-H. ducreyi IgG antibodies, as determined by adsorption EIA, increased with the duration of infection, thus limiting the role of EIAs in the diagnosis of chancroid.

Made available in DSpace on 2013-08-12T19:20:42Z (GMT). No. of bitstreams: 0 Previous issue date: 2012-07-01 Made available in DSpace on 2013-09-30T19:21:28Z (GMT). No. of bitstreams: 0 Previous issue date: 2012-07-01 Submitted by Vitor Silverio Rodrigues (vitorsrodrigues@reitoria.unesp.br) on 2014-05-20T15:33:31Z No. of bitstreams: 0 Made available in DSpace on 2014-05-20T15:33:31Z (GMT). No. of bitstreams: 0 Previous issue date: 2012-07-01 Evogene Ltd. ACME-HARDESTY Oleochemicals Castor (Ricinus communis L.) is one of the oldest cultivated crops, but currently it represents only 0.15% of the vegetable oil produced in the world. Castor oil is of continuing importance to the global specialty chemical industry because it is the only commercial source of a hydroxylated fatty acid. Castor also has tremendous future potential as an industrial oilseed crop because of its high seed oil content (more than 480 g kg(-1)), unique fatty acid composition (900 g kg(-1) of ricinoleic acid), potentially high oil yields (1250-2500 L ha(-1)), and ability to be grown under drought and saline conditions. The scientific literature on castor has been generated by a relatively small global community of researchers over the past century. Much of this work was published in dozens of languages in journals that are not easily accessible to the scientific community. This review was conducted to provide a compilation of the most relevant historic research information and define the tremendous future potential of castor. The article was prepared by a group of 22 scientists from 16 institutions and eight countries. Topics discussed in this review include: (i) germplasm, genetics, breeding, biotic stresses, genome sequencing, and biotechnology; (ii) agronomic production practices, diseases, and abiotic stresses; (iii) management and reduction of toxins for the use of castor meal as both an animal feed and an organic fertilizer; (iv) future industrial uses of castor including renewable fuels; (v) world production, consumption, and prices; and (vi) potential and challenges for increased castor production. Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA) Algodao, BR-58428095 Campina Grande, PB, Brazil Texas Tech Univ, Dep Plant & Soil Sci, Lubbock, TX 79409 USA Universidade Federal do Ceará (UFC), Dep Zootecnia, BR-60021970 Fortaleza, Ceara, Brazil Univ Pisa, Pisa, Italy ARS, USDA, Western Reg Res Ctr, Albany, CA 94710 USA Univ Windsor, Windsor, on N9B 3P4, Canada Zibo Acad Agr Sci, Zibo, Shandong, Peoples R China Directorate Oilseed Res, Hyderabad 500030, Andhra Pradesh, India Univ Estadual Norte Fluminense, BR-28013600 Campos Dos Goytacazes, RJ, Brazil Oil World, Hamburg, Germany Texas A&M Univ, College Stn, TX 77843 USA ARS, USDA, PGRCU, Griffin, GA 30223 USA Ctr Dis Control & Prevent, Atlanta, GA 30333 USA Univ Estadual Paulista, BR-18610307 Botucatu, SP, Brazil Corpo La Selva, Rio Negro, Antioquia, Colombia Synthet Genom Inc, La Jolla, CA 92037 USA Univ Estadual Paulista, BR-18610307 Botucatu, SP, Brazil

The pathogenic Neisseria and most commensal Neisseria species produce an iron-binding protein (Fbp) when grown under iron-limited conditions. In the current study, we confirmed the presence of Fbp, as well as DNA sequences homologous to the gonococcal fbp, in strains of N. gonorrhoeae, N. meningitidis, N. cinerea, N. lactamica, N. subflava, N. kochii and N. polysaccharea. The fbp genes from these strains were amplified by the polymerase chain reaction, digested with StuI or RsaI, and the restriction patterns examined. The patterns for the gonococcal and meningococcal fbp were virtually identical; however, variations were observed in the fbp sequences of the commensal Neisseria species. N. flavescens, N. mucosa, N. sicca, N. ovis and Branhamella catarrhalis, did not produce Fbp as detected by sodium dodecyl sulfate-polyacrylamide gel electrophoresis and reactivity with an Fbp specific monoclonal antibody, nor did they hybridize to an fbp-specific DNA probe.

Alphaviruses exist throughout the world and commonly cause natural encephalitis outbreaks among horses and humans. Generally, this disease is fatal in horses but only incapacitating in humans. Nevertheless, Venezuelan equine encephalitis virus (VEEV) was weaponized by the pre-1992 Soviet and pre-1969 United States biological warfare programs. Largely for this reason, alphaviruses are classified by the Centers for Disease Control and Prevention as Category B threat agents, or of second highest priority with respect to public health and national security. However, their potential as biothreat agents remains unclear as it would be technically difficult to weaponize and disperse them. Keywords: Togaviridae; alphavirus; category B agent; Eastern equine encephalomyelitis virus; EEEV; Venezuelan equine encephalitis virus; VEEV; Western equine encephalomyelitis virus; WEEV; encephalitis

The ferric iron-binding protein (Fbp) expressed by pathogenic Neisseria spp. has been proposed to play a central role in the high-affinity acquisition of iron from human transferrin. The results of this investigation provide evidence that Fbp participates in this process as a functional analogue of a Gram-negative periplasmic-binding protein component, which operates as a part of a general active transport process for the receptor-mediated, high-affinity transport of iron from human transferrin. Known properties of Fbp are correlated with those of other well-characterized periplasmic-binding proteins, including structural features and the reversible binding of ligand. Predictive of a periplasmic-binding protein, which functions in the high-affinity acquisition of iron, is that Fbp is a transient participant in the process of iron acquisition from human transferrin. Evidence for this is demonstrated by results of pulse-chase experiments. Taken together, the data described here and elsewhere suggest that pathogenic Neisseria spp. use a periplasmic-binding protein-mediated active transport mechanism for the acquisition of iron from human transferrin.

Communication between research laboratories within a given field is often an important key to rapid successes within that field. We propose that consensus standards may be a useful tool to help facilitate such communication by providing a “common language” for laboratories that utilize similar methodologies within a field. The existence of consensus standards is well known in other fields, and through this commentary we hope to (i) introduce the concept of consensus standards to investigators in the field of microbial pathogenesis/host response who may not be familiar with them and (ii) provoke thought and discussion by others in the field regarding the possible usefulness of additional consensus standards for their own work.

Antimicrobial resistance is a major global health issue that restricts treatment options for many bacterial infections. Although biothreat agents such as Bacillus anthracis, Burkholderia mallei, B. pseudomallei, Francisella tularensis and Yersinia pestis are usually susceptible to the recommended antimicrobial agents, there are naturally-occurring resistance mechanisms reported in several of these species, and the potential for release of genetically-engineered strains cannot be ruled out.

The ability of Haemophilus ducreyi, the causative agent of chancroid, to grow in subcutaneous chambers implanted in mice was studied. All seven H. ducreyi strains tested were able to maintain a long-term infection in ICR mice; one mouse remained infected with strain Hd175 for more than 4 months. Growth curves obtained following the removal of chamber fluid at various time points from infected mice demonstrated that H. ducreyi was growing during the course of the infection. In addition, all three mouse strains tested (ICR, CBA and BALB/c) were able to maintain long-term H. ducreyi infections. This model will be valuable in studying the effects of in vivo growth on the antigenic composition of H. ducreyi as well as for the identification of virulence factors.

Intraspecies genotypic heterogeneity among Haemophilus ducreyi isolates was examined by using genomic fingerprints with rRNA from Escherichia coli as a probe. DNA from 44 isolates of H. ducreyi was digested by restriction endonuclease HincII or HindIII, separated by agarose gel electrophoresis, transferred to nylon membranes, and hybridized with 32P-labeled 16S and 23S rRNA. HincII digests yielded four hybridization patterns (ribotypes), whereas HindIII digests yielded eight ribotypes. Four HincII and five HindIII ribotypes were observed among 14 H. ducreyi isolates collected within a period of 1 month in Kenya, where chancroid is endemic. In contrast, one HincII and two HindIII ribotypes were observed among 28 isolates collected during the Orange County, Calif., chancroid epidemic that occurred in 1981 and 1982. The plasmid content, in conjunction with ribotyping, provided additional differentiation among some isolates of H. ducreyi. This study demonstrates that ribotyping of H. ducreyi may be used to study the epidemiology of chancroid.

Patients on maintenance hemodialysis are particularly prone to opportunistic infections because of their increased exposure to antibiotics, frequent vascular access, and altered cellular immunity. This case report discusses a 63-year-old African American patient on maintenance hemodialysis who presented with acute painful swelling of her left knee and fever. She was diagnosed to have septic arthritis, candidemia, and arteriovenous (AV) graft infection caused by Candida albicans. The management included removal of the infected AV graft, intravenous fluconazole, and arthrotomy with lavage. The Candida infection subsided, but the patient continued to have knee swelling because of chronic synovitis. We believe that this is the first case of acute Candida septic arthritis in a patient with end-stage renal disease, where hematogenous spread was proven by positive C. albicans cultures from the blood, AV graft, and synovial fluid.

Alphaviruses are classified by the Centers for Disease Control and Prevention as Category B agents, or of second highest priority with respect to public health and national security. The viruses exist throughout the world, and natural outbreaks among horses and humans are common. Generally, this disease is fatal in horses but only incapacitating in humans. Western equine encephalitis (WEE) virus has been researched and developed as a biological weapon by state-level programs in the past. Its potential as a terrorist threat agent remains unclear. Keywords: alphavirus; category B agent; Eastern equine encephalomyelitis; EEE; VEE; Venezuelan equine encephalitis; WEE; Western equine encephalomyelitis

Publisher Summary Epidemiology is the study of the distribution and determinants of health-related states or events in specied populations and the application of this study to control health problems. It reflects that diseases are not randomly distributed in the population and that individuals have certain characteristics that predispose to, or protect against, a variety of different diseases. Disease is the result of an epidemiological triad, where disease results from the interaction of: the human host, an infectious agent or toxin, and the environment that promotes the exposure. This chapter focuses on the use of epidemiology to identify the source of diseases caused by microorganisms or toxins. Microorganisms are very efficient at infecting humans, using a number of different strategies and mechanisms. The deliberate dissemination of a biological agent by many of these mechanisms presents the latest challenge to public health. It requires a careful epidemiologic investigation to determine whether an outbreak of infectious disease is because of the intentional release of an agent, or is naturally occurring. A number of molecular techniques have been developed for sub typing bacteria, viruses, fungi, and protozoa, which will facilitate this investigation as well as identify clusters of related microorganisms.

Because of their asymptomatic nature and nonspecific symptoms, laboratory tests are often required to diagnose a sexually transmitted infection. Over the past few years, there have been advances in technology, such as the development of nucleic acid amplification assays, which have improved our ability to diagnose infections caused by Chlamydia trachomatis. The finding that nucleic acid amplification tests can detect more infected individuals and are useful in screening low prevalence populations, has led to the development of strategies designed to reduce the cost of these assays without significantly impacting their sensitivity. The development of new tests for the diagnosis of syphilis has gained momentum from the report of a synthetic VDRL antigen, which will result in better nontreponemal antibody tests for syphilis. In spite of the completion of the genome sequence of Treponema pallidum and its annotation, we are still unable to cultivate this microorganism in vitro. However, the molecular revolution has resulted in the development of PCR assays for detecting Treponema pallidum in various types of clinical specimens, and to the production of recombinant antigens for use in tests that detect treponemal-specific antibodies. Further research will improve the availability of low cost, sensitive tests for the diagnosis of sexually transmitted infections. The English version of this paper is available too at: http://www.insp.mx/salud/index.html

Genital ulcers are typically caused by one of three organisms, Haemophilus ducreyi, Treponema pallidum, or herpes simplex virus, which cause chancroid, syphilis, and genital herpes, respectively. Although traditionally these diseases have been differentiated by their clinical presentation, there is considerable overlap in their clinical manifestations (1).

Molecular diagnostic tests are more sensitive and, in many cases, more specific than conventional laboratory methods for the detection of sexually transmitted infections. Here, we review recently developed molecular methods for the diagnosis and subtyping of the most common sexually transmitted infections: infections caused by Chlamydia trachomatis, Neisseria gonorrhoeae, human papillomavirus, Trichomonas vaginalis, and the agents of genital ulcer disease (Haemophilus ducreyi, herpes simplex virus, Treponema pallidum, and Calymmatobacterium granulomatis). We also provide an overview of the laboratory diagnostic tests and clinical specimens to use when infection with these agents is suspected.

While genital ulcers are a risk factor in HIV infection, the association of specific agents of genital ulcer disease (GUD) with HIV infection may vary.To determine the etiology of GUD in HIV-infected and HIV-uninfected men attending sexually transmitted disease (STD) clinics in Durban, Johannesburg, and Cape Town, South Africa, and the association of previous and current sexually transmitted infections with HIV infection in men with ulcerative and nonulcerative STDs.A cross-sectional study of 558 men with genital ulcers and 602 men with urethritis.Patients with GUD were more likely to be infected with HIV than patients with urethritis (39.4% versus 21.4%, Por =0.001). Herpes simplex virus 2 (HSV-2) was the most common agent identified in ulcer specimens (35.9%), and was detected in a significantly higher proportion of ulcer specimens from HIV-infected patients than in specimens from HIV-uninfected patients (47.4% versus 28.2%, Por =0.001). Patients infected with HIV-1 were significantly more likely to have HSV-2 infection, as measured by the presence of the antibody to glycoprotein G-2, than patients not infected with HIV (63.1% versus 38.5%, Por =0.001). Patients infected with HIV-1 were also significantly more likely to have initial HSV-2 infection than HIV-uninfected patients with GUD (50.0% versus 31.6%, P = 0.007). Haemophilus ducreyi was detected in 31.7% of ulcer specimens; prevalence did not vary by HIV-infection status. Treponema pallidum DNA was detected significantly less frequently in ulcer specimens from patients infected with HIV than in specimens from patients not infected with HIV (10.2% versus 26%, Por =0.001); no association was found between HIV-infection status and fluorescent treponemal antibody absorption test seroreactivity, even when men with M-PCR-positive syphilis lesions were excluded from the analyses.The authors found that HSV-2 is a more common etiology of GUD than has been suggested by previous studies conducted in South Africa; serologic evidence of HSV-2 infection and current cases of genital herpes are strongly associated with HIV infection among men who present to STD clinics with GUD or urethritis.

Ulcer material from consecutive patients attending clinics in Antananarivo, Madagascar, was tested using multiplex polymerase chain reaction (M-PCR) to detect Treponema pallidum, Haemophilus ducreyi, and herpes simplex virus. Sera were tested for syphilis and for IgG and IgM antibodies to Chlamydia trachomatis by microimmunofluorescence testing (MIF). By M-PCR, 33% of 196 patients had chancroid, 29% had syphilitic ulcers, and 10% had genital herpes; 32% of the ulcer specimens were M-PCR negative. Compared with M-PCR, syphilis serology was 72% sensitive and 83% specific. The sensitivity of clinical diagnosis of syphilis, chancroid, and genital herpes was 93%, 53%, and 0% and specificity was 20%, 52%, and 99%, respectively. Less schooling was associated with increased prevalence of syphilitic ulcers (P=.001). Sixteen patients (8%) were clinically diagnosed with lymphogranuloma venereum (LGV); 1 plausible case of LGV was found by MIF. In Madagascar, primary care of genital ulcers should include syndromic treatment for syphilis and chancroid.

Individuals presenting consecutively with genital ulcers in Kingston, Jamaica, underwent serological testing for human immunodeficiency virus (HIV) infection, chlamydial infection, and syphilis. Ulcer material was analyzed by multiplex polymerase chain reaction (M-PCR) analysis. DNA from herpes simplex virus (HSV), Haemophilus ducreyi, and Treponema pallidum was detected in 158 (52.0%), 72 (23.7%), and 31 (10.2%) of 304 ulcer specimens. Of the 304 subjects, 67 (22%) were HIV-seropositive and 64 (21%) were T. pallidum-seroreactive. Granuloma inguinale was clinically diagnosed in nine (13.4%) of 67 ulcers negative by M-PCR analysis and in 12 (5.1%) of 237 ulcers positive by M-PCR analysis (P = .03). Lymphogranuloma venereum was clinically diagnosed in eight patients. Compared with M-PCR analysis, the sensitivity and specificity of a clinical diagnosis of syphilis, herpes, and chancroid were 67.7%, 53.8%, and 75% and 91.2%, 83.6%, and 75.4%, respectively. Reactive syphilis serology was 74% sensitive and 85% specific compared with M-PCR analysis. Reported contact with a prostitute in the preceding 3 months was associated with chancroid (P = .009), reactive syphilis serology (P = .011), and HIV infection (P = .007). The relatively poor accuracy of clinical and locally available laboratory diagnoses pleads for syndromic management of genital ulcers in Jamaica. Prevention efforts should be intensified.

Chancroid, a sexually transmitted disease caused by Haemophilus ducreyi, is one of the most common genital ulcer diseases in developing countries. In the United States, while less common, the disease has been associated with outbreaks in inner cities, particularly among persons who engage in sex for drugs or money. Two outbreaks of chancroid were recently studied in the United States, one in New Orleans (from 1990 to 1992) and one in Jackson, Mississippi (from 1994 to 1995). By use of ribotyping, plasmid content, and antibiotic susceptibility, the chancroid cases in New Orleans were found to be due to a limited number of strains, consistent with a limited introduction of H. ducreyi into this community. The H. ducreyi isolates from New Orleans and Jackson had different ribotype patterns, suggesting that the two outbreaks were probably not linked.

Transmission of Chlamydia trachomatis and Neisseria gonorrhoeae among infected men and their female sex partners was examined using a design enhancing the likelihood that spread was directed from men to women. Chlamydia culture-negative specimens were examined using DNA amplification tests. Infection rates in women exposed to male sex partners with Chlamydia only were 65% (20/31) and with gonorrhea only were 73% (33/45). Infection of women by either agent was not influenced by the number of sexual exposures to or coinfection in men. There was a 98% (40/41) concordance of N. gonorrhoeae isolates among partners by auxotype and serovar. Chlamydia isolates were serotyped using ELISA and immunofluorescence testing and confirmed by nested polymerase chain reaction: 50% (6/12) of men and 57% (8/14) of women yielded mixed serovars. Sixty-four percent of pairs (9/14) were infected with identical serovars and an additional 28% shared at least one serovar. Multiple serovars of C. trachomatis, but not of N. gonorrhoeae, were common in sex partners and exchanged frequently.

Background and objectives Epidemiologic studies on syphilis have been hampered by the fact that strains of Treponema pallidum subspecies pallidum (T. pallidum), the causative agent of this disease, cannot be differentiated by either protein-based or deoxyribonucleic acid-based methods. Syphilis is endemic in many developing countries and is common in some industrialized nations. In addition, the disease has been shown to increase the risk of infection with the human immunodeficiency virus. Goal To develop a molecular subtyping method for T. pallidum. Study design Two genes exhibiting intrastrain variability were identified as potential targets for strain differentiation: the acidic repeat protein (arp) gene, which contains a variable number of 60 base pair repeats, and a member of the treponema pallidum repeat (tpr) gene family. Polymerase chain reaction amplification and restriction endonuclease digestion of polymerase chain reaction products from laboratory strains and clinical specimens were used to develop a molecular subtyping scheme for T. pallidum. Results Determining the number of repeats in the arp gene by polymerase chain reaction resulted in 12 different subtypes among the 63 isolates that were studied. Among those, most (54.2%) had arp genes with 14 repeats. The other 11 subtypes had arp genes with 7 to 21 repeats, each accounting for 2% to 14% of the isolates. Polymerase chain reaction amplification of a member of the tpr gene family from a subset of 46 isolates followed by digestion of the polymerase chain reaction product with MseI resulted in seven restriction fragment length polymorphism patterns designated a to g. Strains with 14 repeats could be grouped into five restriction fragment length polymorphism subtypes. By combining the two systems we observed 16 subtypes among 46 isolates examined. This typing system is stable, reproducible, and easy to perform. In addition, the use of the ABI Genetic Analyzer for the determination of fragment size and banding patterns makes the results unbiased. Conclusion This is the first molecular subtyping system that distinguishes among clinical isolates of T. pallidum.

In this study, we have mapped the promoter region of the Neisseria gonorrhoeae ferric iron binding protein-encoding gene fbpA, determined the start point of transcription, and examined the accumulation of fbpA mRNA Primer extension analysis of the fbpA promoter region indicated a single transcriptional start site located 51 bp upstream of the ATG translational start site. Northern blot analysis with a 200-bp fbpA structural gene probe detected one transcript of 1.0 kb in RNAs extracted from gonococcal cultures grown under iron-restricted conditions; the 1.0-kb transcript was observed to accumulate at a steady rate throughout the growth cycle. In comparison, in cultures grown under iron-sufficient conditions, the intensity of the 1.0-kb transcript was reduced considerably. Isolation of total RNA from rifampin-treated cells indicated that the half-life of the 1.0-kb fbpA transcript in cells grown under iron-restricted conditions was 1.2 +/- 0.2 min, while that of the 1.0-kb fbpA transcript obtained from cultures grown under iron-sufficient conditions was 0.5 +/- 0.1 min. Taken together, our results indicate that the fbpA promoter is regulated by iron and that transcription and translation of FbpA are closely linked.

A multiplex polymerase chain reaction (M-PCR) assay for Haemophilus ducreyi, Treponema pallidum, and herpes simplex virus (HSV) was compared with clinical and standard laboratory methods for the diagnosis of genital ulcer disease (GUD) in 105 patients; 36% were human immunodeficiency virus (HIV)-seropositive. Chancroid (80%), syphilis (8%), and genital herpes (8%) were the most frequent diagnoses. H. ducreyi and HSV were isolated from ulcers of 43% and 18% of patients, respectively; in 35%, all cultures were negative and the laboratory diagnosis indeterminate. M-PCR detected H. ducreyi, T. pallidum, and HSV in 56%, 23%, and 26% of patients, respectively; (no definitive diagnosis, 6%). The proportion of patients with more than one agent was 4% by culture and 17% by M-PCR (P = .002). Resolved sensitivities of M-PCR for H. ducreyi and HSV cultures were 95% and 93%, respectively. The sensitivities of H. ducreyi and HSV cultures were 75% and 60%, respectively. HSV, detected in 47% of specimens from HIV-infected versus 16% from HIV-uninfected patients (P < .001), may be emerging as a more frequent cause of GUD.

Haemophilus ducreyi is a fastidious gram-negative bacillus that causes the sexually transmitted infection chancroid. Chancroid is a major genital ulcerative disease in Africa, Southeast Asia, the Caribbean, and Latin America and is of increasing concern in the United States. Genital ulcerative disease and chancroid in particular have been associated with facilitating the transmission of human immunodeficiency virus. The diagnosis of chancroid based on the clinical appearance of the genital lesion or on the isolation of H. ducreyi on selective medium is relatively insensitive. However, recent advances in nonculture diagnostic tests have enhanced our ability to diagnose chancroid. There has been renewed interest in understanding the pathogenesis of H. ducreyi. In vitro and in vivo models have been developed to help identify important virulence determinants. Through the use of biochemical and molecular techniques, macromolecular components that may be important in virulence have been identified.

Resistance of Neisseria gonorrhoeae to structurally diverse hydrophobic agents (HAs) has been associated with missense or deletion mutations in the mtrR (m ultiple transferable r esistance R egulator) gene of laboratory-derived strains but their prevalence in clinical isolates was heretofore unknown. Since faecal lipids provide strong selective pressure for the emergence of variants resistant to HAs (HAR), the nucleotide sequence of the mtrR gene from rectal isolates of N. gonorrhoeae, which displayed different levels of HAR, was determined. Compared to the mtrR gene possessed by the HA-sensitive strain FA19, each clinical isolate contained mutations in the coding and/or promoter regions of their mtrR gene. A missense mutation in codon 45 (Gly-45 to Asp) was the most common mutation found in the strains studied and impacted the structure of the helix-turn-helix domain of the MtrR protein thought to be important in DNA-binding activity. Two clinical isolates bearing a missense mutation in codon 45 also contained a single basepair deletion in a 13 bp inverted sequence positioned within the mtrR promoter region. Introduction of mtrR sequences amplified from the clinical isolates into strain FA19 revealed that acquisition of the single basepair deletion was correlated with high level HAR while mutations in the mtrR-coding region provided for an intermediate level of HAR.