Epidemiologic patterns of human Salmonella serotype diversity in the USA, 1996-2016.

Although researchers have described numerous risk factors for salmonellosis and for infection with specific common serotypes, the drivers of Salmonella serotype diversity among human populations remain poorly understood. In this retrospective observational study, we partition records of serotyped non-typhoidal Salmonella isolates from human clinical specimens reported to CDC national surveillance by demographic, geographic and seasonal characteristics and adapt sample-based rarefaction methods from the field of community ecology to study how Salmonella serotype diversity varied within and among these populations in the USA during 1996-2016. We observed substantially higher serotype richness in children <2 years old than in older children and adults and steadily increasing richness with age among older adults. Whereas seasonal and regional variation in serotype diversity was highest among infants and young children, variation by specimen source was highest in adults. Our findings suggest that the risk for infection from uncommon serotypes is associated with host and environmental factors, particularly among infants, young children and older adults. These populations may have a higher proportion of illness acquired through environmental transmission pathways than published source attribution models estimate.

Variable expression of O:61 in Salmonella group C2.

According to the Kauffmann-White scheme, 39 pairs of serovars in Salmonella serogroup C2 differ only by the minor antigen O:6(1). We characterized strains from 10 serovars representing five Salmonella serogroup C2 pairs. All strains demonstrated variable expression of O:6(1). These results indicate that these pairs are not distinct serovars.

A Salmonella locus that controls resistance to microbicidal proteins from phagocytic cells.

Facultative intracellular pathogens pose an important health problem because they circumvent a primary defense mechanism of the host: killing and degradation by professional phagocytic cells. A gene of the intracellular pathogen Salmonella typhimurium that is required for virulence and intracellular survival was identified and shown to have a role in resistance to defensins and possibly to other microbicidal mechanisms of the phagocyte. This gene may prove to be a regulatory element in the expression of virulence functions.

Evaluation of a Bead-Based Salmonella Molecular Serotyping Method for Salmonella Isolated from Food and Environmental Samples.

Salmonella is a leading cause of foodborne illness worldwide, and foods containing Salmonella (except raw meat and poultry products) are considered adulterated. Serotyping of Salmonella is an essential part of surveillance and investigation of outbreaks. This study evaluated a bead-based Salmonella molecular serotyping (SMS) method, which included the O-group 1, H-antigen, alternate target, and O-group 2 assays, compared with traditional serotyping. Salmonella was isolated from food, pet food, and environmental samples or were reference strains. A total of 572 isolates were analyzed by using two formats of the SMS method in comparison with traditional methods: 485 were analyzed by using Radix SMS (a custom user-mixed format), 218 were analyzed by using Luminex SMS (a commercial kit format), and 131 of the total isolates were analyzed by both formats for comparison. The SMS method was evaluated on the basis of the successful identification of antigens by the probes included in the method. The method identified 550 (96.2%) isolates as expected, 6 (1.0%) isolates were not identified as initially expected but were shown to be correctly identified by SMS after reanalysis by traditional serotyping, and 16 (2.8%) isolates not identified as expected possessed an antigen that should have been detected by the method but was not. Among the isolates considered correctly identified, 255 (44.6%) were identified to a single serovar, 44 (7.7%) required additional biochemical testing to differentiate variants or subspecies, and 251 (43.9%) were partially serotyped because probes for some antigens were not in the assay or had allelic variation for known serovars. Whole genome sequencing, SeqSero, and the Salmonella In Silico Typing Resource gave added confirmation for three isolates. Addition of the O-group 2 assay enabled the identification of 55 (9.6%) of 572 isolates. The SMS method could fully or partially serotype most isolates within a day. The SMS method should be a valuable tool when faster screening methods are needed, such as outbreaks and screening large numbers of environmental isolates.

Molecular phylogeny of the salmonellae: relationships among Salmonella species and subspecies determined from four housekeeping genes and evidence of lateral gene transfer events.

The salmonellae are a diverse group of bacteria within the family Enterobacteriaceae that includes two species, Salmonella enterica and Salmonella bongori. In order to characterize the phylogenetic relationships of the species and subspecies of Salmonella, we analyzed four housekeeping genes, gapA, phoP, mdh and recA, comprising 3,459 bp of nucleotide sequence data for each isolate sequenced. Sixty-one isolates representing the most common serotypes of the seven subspecies of Salmonella enterica and six isolates of Salmonella bongori were included in this study. We present a robust phylogeny of the Salmonella species and subspecies that clearly defines the lineages comprising diphasic and monophasic subspecies. Evidence of intersubspecies lateral gene transfer of the housekeeping gene recA, which has not previously been reported, was obtained.

Properties of Bacillus subtilis 168 derivatives freed of their natural prophages.

An isogenic set of Bacillus subtilis 168 strains which are non-inducible for prophage PBSX and are cured of prophage SP beta has been constructed. By utilizing these strains, prophage SP beta has been shown to control the inducible DNA modification system which exists in this bacterium. However, neither the PBSX nor the SP beta prophages alter the ability of the bacterium to undergo genetic recombination, to repair damaged DNA or to sporulate. Prophageless B. subtilis would be a useful host for the phi 3T cloning vector, because of the absence of vector--prophage interactions.

Genes from the cyanobacterium Agmenellum quadruplicatum isolated by complementation: characterization and production of merodiploids.

The isolation of several biosynthetic genes from a cyanobacterium, Agmenellum quadruplicatum, by complementation of auxotrophic mutations in Escherichia coli, and their partial characterization, is described. Although our search for such genes has not been exhaustive, it appears that complementation of E. coli mutations may be of limited utility for the identification and/or isolation of cyanobacterial genes. Despite some overlap in the complementation abilities of these isolated cyanobacterial DNA fragments, the genes that we have studied in some detail are not located in operons. We have used mutagenized versions of these cyanobacterial DNA fragments to produce mutant phenotypes in the cyanobacterium, but clean auxotrophs were not obtained. Complementation of these mutant phenotypes can be obtained when the appropriate wild-type DNA fragment is introduced into the cyanobacterium on a shuttle vector. Recombination between two copies of a cyanobacterial gene occurs at high frequency in the cyanobacterium.

Rapid identification of Legionella pneumophila zinc metalloprotease using chromogenic detection.

Strains of Legionella spp. produce extracellular proteases than can be detected using synthetic chromogenic peptides. Chromogenic tri- and tetrapeptides show a high degree of sensitivity, specificity and reagent stability when linked to para-nitroaniline (pNA). For example, SucOMe-Arg-Pro-Tyr.pNa (S-2586) is specifically hydrolysed by proteases of Legionella pneumophila and some other Legionella species. A paper disc method to sample protease directly from agar plates has been used to evaluate chromogenic peptides as reagents for diagnostic purposes. Strains of Legionella spp., Pseudomonas spp. and Enterobacteriaceae were examined, together with a recombinant Escherichia coli strain containing the cloned 38 kDa zinc metalloprotease from L. pneumophila, S-2586 was hydrolysed by 282 out of 283 L. pneumophila strains, and by the recombinant E. coli. Two of the six strains representing other Legionella species, and 22 of the 50 strains from the Pseudomonas group were also positive. No reaction was seen with any of the Enterobacteriaceae strains. Although there was functional homology between proteases from several bacterial groups, the high prevalence of S 2586-hydrolysing proteases within L. pneumophila indicates a potential usefulness for phenotypic identification.

Campylobacter jejuni.

Campylobacter jejuni is the most frequently diagnosed bacterial cause of human gastroenteritis in the United States. The emergence of antimicrobial-resistant and, in particular, of fluoroquinolone-resistant C. jejuni infections in Europe and the United States, temporally associated with the approval of use of fluoroquinolones in veterinary medicine, is an important public health concern. Recent research has provided strong evidence for an association between Campylobacter infection and Guillain-Barr Syndrome (GBS), and Campylobacter is the most frequent antecedent infection in GBS. The consumption of undercooked poultry and cross-contamination of other foods with uncooked meat products are leading risk factors for human campylobacteriosis. Reinforcing hygienic practices at each link in the food chain, from producer to consumer, is critical in preventing the disease.

Resistance to antimicrobial chemotherapy: a prescription for research and action.

The growing problem of resistance to antimicrobial chemotherapy was discussed by participants at the February 1995 workshop at Emory University on population biology, evolution, and control of infectious diseases. They discussed the nature and source of this problem and identified areas of research in which information is lacking for the development of programs to control of the emergence and spread of resistant bacteria. Particular attention was given to theoretical (mathematical modeling) and empirical studies of the within and between-host population biology (epidemiology) and the evolution of microbial resistance to chemotherapeutic agents. Suggestions were made about the kinds of models and data needed, and the procedures that could be employed to stem the ascent and dissemination of resistant bacteria. This article summarizes the observations and recommendations made at the 1995 meeting and in the correspondence between participants that followed. It concludes with an update on the theoretical and empirical research on the between- and within-host population biology and evolution of resistance to antimicrobial chemotherapy most of which has been done since that meeting.

DNA repair in B. subtilis: an inducible dimer specific W-reactivation system.

The W-reactivation system of Bacillus subtilis repairs pyrimidine dimers in bacteriophage DNA. This inducible repair system can be activated by treatment of the bacteria with UV, alkylating agents, cross-linking agents and gamma radiation. However, bacteriophage treated with agents other than those that cause pyrimidine dimers were not repaired by this unique form of W-reactivation. In contrast, the W-reactivation system of Escherichia coli repairs a variety of damages in the bacteriophage DNA.

Involvement of deoxyribonucleic acid polymerase III in W-reactivation in Bacillus subtilis.

6-(p-Hydroxyphenylazo)-uracil, a purine analog that is known to specifically inhibit deoxyribonucleic acid polymerase III in gram-positive organisms, inhibited W-reactivation in Bacillus subtilis. On the other hand, W-reactivation proceeded normally in the presence of 6-(p-hydroxyphenylazo)-uracil when a strain possessing a resistant deoxyribonucleic acid polymerase III was used as the host.

Chlamydia pneumoniae respiratory tract infection: the interpretation of high titres in the complement fixation test.

Sera from 5 acute respiratory disease patients from Northern Norway presenting with high chlamydia complement fixation (CF) titres, were analyzed for Chlamydia pneumoniae-specific IgG and IgM in a micro-immunofluorescence (micro-IF) test that included antigens from the prototype strain TW 183, and a Norwegian isolate, FML 10. The patients were confirmed to have had C. pneumoniae infection based on serologic findings. This establishes the clinical significance of early CF results in this geographical area. However, different micro-IF titres against the 2 C. pneumoniae isolates tested suggest antigenic variability among the species.

Use of polymerase chain reaction for detection of toxigenic Vibrio cholerae O1 strains from the Latin American cholera epidemic.

In January 1991, an outbreak of cholera started in Peru and spread throughout most of Latin America within 8 months. As of March 1992, over 450,000 cases and approximately 4,000 deaths have been reported to the Pan American Health Organization. The causative organism is toxigenic Vibrio cholerae O1 of the El Tor biotype and is distinct from the U.S. Gulf Coast strains. A polymerase chain reaction (PCR) that amplifies a 564-bp fragment of the cholera toxin A subunit gene (ctxA) was used to identify toxigenic V. cholerae O1 strains. A total of 150 V. cholerae O1 isolates were tested. They were of unknown toxin status, were associated with recent outbreaks, and were isolated from patients, food, and water. One hundred forty isolates were found to be toxigenic both by PCR and the routine diagnostic enzyme-linked immunosorbent assay. Thirty-eight known toxigenic strains isolated worldwide from 1921 to 1991 were also positive in the PCR. A collection of 18 nontoxigenic V. cholerae O1 strains, 35 Escherichia coli heat-labile-enterotoxin-I-producing strains, 26 Campylobacter strains, and 8 strains of Aeromonas hydrophila, previously reported to produce cholera toxin-like toxin, were all negative in the ctxA PCR. We conclude that this PCR is a diagnostic method that specifically detects toxin genes in V. cholerae O1 strains in a reference laboratory. It is more rapid and less cumbersome than other diagnostic methods for detection of toxicity in these strains.

DNA repair in Bacillus subtilis: excision repair capacity of competent cells.

Competent Bacillus subtilis were investigated for their ability to support the repair of UV-irradiated bacteriophage and bacteriophage DNA. UV-irradiated bacteriophage DNA cannot be repaired to the same level as UV-irradiated bacteriophage, suggesting a deficiency in the ability of competent cells to repair UV damage. However, competent cells were as repair proficient as noncompetent cells in their ability to repair irradiated bacteriophage in marker rescue experiments. The increased sensitivity of irradiated DNA is shown to be due to the inability of excision repair to function on transfecting DNA in competent bacteria. Furthermore, competent cells show no evidence of possessing an inducible BsuR restriction system to complement their inducible BsuR modification enzyme.

Mutants of Salmonella typhimurium that cannot survive within the macrophage are avirulent.

Salmonella typhimurium is a facultative intracellular pathogen capable of surviving within phagocytic cells of the reticuloendothelial system. To identify the genes important for intracellular survival, 9516 independent Tn10 insertional mutations were isolated in a virulent strain of S. typhimurium. By using an in vitro assay for survival within macrophages, 83 Tn10 mutants have been identified that have a diminished capacity for intracellular survival (designated MS or macrophage survival mutants). All of the MS mutants are less virulent than the parent strain in vivo, demonstrating that, for Salmonella, survival within the macrophage is essential for virulence. Thirty-seven of the MS mutants have been characterized as to their phenotype, including several mutations that confer sensitivity to specific microbiocidal mechanisms of the macrophage.

Salmonella bacteriuria: an increasing entity in elderly women in the United States.

Salmonellosis is a major cause of gastroenteritis in the United States and can lead to septicaemia, and other extra-intestinal illness including urinary tract infections (UTIs). To examine trends in Salmonella bacteriuria in the United States, surveillance data from the National Salmonella Surveillance System from 1980 to the end of 1999 were reviewed. Overall, 17442 urinary Salmonella isolates were reported, representing 2% of all Salmonella isolates from a known source. This proportion increased from 2% during 1980--1984 to 4% during 1995--1999. The median age of persons from whom these isolates came was 51 years; 12,176 (70 %) were women. Compared to the last national survey conducted between 1968 and 1979, the rate of Salmonella bacteriuria increased among women, from 2.0 per million persons in 1980 to 3.7 in 1999; the highest rate occurring in women > or = 70 years. National reporting of Salmonella bacteriuria increased in absolute incidence and as a proportion of all Salmonella, especially in elderly women and may represent an increase in the incidence of Salmonella UTIs. Better understanding of the uropathogenicity of Salmonella serotypes may further clarify the mechanisms of Salmonella UTIs.

Characterization of nonmotile variants of Escherichia coli O157 and other serotypes by using an antiflagellin monoclonal antibody.

An antiflagellin monoclonal antibody (15D8) was used to detect the presence of flagella in nonmotile variants of several pathogenic Escherichia coli serotypes. Of the 48 isolates examined, 15 reacted with monoclonal antibody 15D8 and were culturally confirmed to be motile. Of the 38 clinical strains designated O157:NM or O157:H-, 7 were antibody reactive and motile and agglutinated with anti-H7 sera.

Use of the beta-lactamase inhibitor clavulanic acid in the isolation of auxotrophic mutants of Bacillus licheniformis.

The isolation of auxotrophic mutants of Bacillus licheniformis, a microbe containing constitutive beta-lactamase activity, was found to be facilitated by the addition of clavulanic acid and cefotaxime during enrichment.

Detection of Chlamydia pneumoniae in clinical specimens by polymerase chain reaction using nested primers.

A nested primers strategy was used to develop a two-step PCR test for the direct species-specific detection of the 16s rRNA gene of Chlamydia pneumoniae. This test was applied to 58 nasopharyngeal or oropharyngeal swab specimens collected from patients in studies of community-acquired pneumonia and in a local outbreak of respiratory disease. Twelve patients (21%) showed evidence of Chlamydia pneumoniae infection in serological tests (7/56; 13%), culture (8/58; 14%) or PCR (10/58; 17%). Nested PCR but not single-step PCR was found to be as sensitive as culture or serology for detection of infection with this organism. In summary, nested PCR can be useful in direct testing of clinical specimens for Chlamydia pneumoniae, making additional DNA purification steps unnecessary.