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Background: Historically, antimicrobial resistance has been rare in US invasive meningococcal disease cases.Methods: Meningococcal isolates (n = 695) were collected through population-based surveillance, 2012-2016, and national surveillance, 2015-2016. Antimicrobial susceptibility was assessed by broth microdilution. Resistance mechanisms were characterized using whole-genome sequencing.Results: All isolates were susceptible to 6 antibiotics (cefotaxime, ceftriaxone, meropenem, rifampin, minocycline, and azithromycin). Approximately 25% were penicillin or ampicillin intermediate; among these, 79% contained mosaic penA gene mutations. Less than 1% of isolates were penicillin, ampicillin, ciprofloxacin, or levofloxacin resistant.Conclusions: Penicillin- and ampicillin-intermediate isolates were common, but resistance to clinically relevant antibiotics remained rare. [ABSTRACT FROM AUTHOR]

Our objectives were to evaluate the clinical efficacy of oral and intranasal administration of a commercial modified-live Salmonella Dublin vaccine in dairy calves and to determine the serologic response associated with these extralabel routes of administration. We conducted a randomized field trial with calves from a New York dairy farm following an outbreak of Salmonella Dublin. A total of 399 Holstein calves were allocated by pen to 3 treatment groups: oral vaccination, intranasal vaccination, and an unvaccinated control group. Administration of the vaccine through oral and intranasal routes did not have a significant effect on pneumonia incidence risk or weight gain; however, calves vaccinated orally and intranasally had lower mortality risk as compared with control calves. Among calves tested using a Salmonella Dublin ELISA, vaccination did not induce an increase in antibody production relative to control calves, indicating that oral and intranasal administration will not hinder diagnosis based on this assay. [ABSTRACT FROM AUTHOR]

The population size and geographic range of feral pigs in the United States are rapidly expanding. Nevertheless, the role of this invasive species in the ecology and transmission of zoonotic enteric pathogens is poorly understood. Our objectives were to describe the prevalence and diversity of Cryptosporidium and Giardia shedding among feral pigs throughout Texas and to identify risk factors for infection. Fecal samples were collected from feral pigs in Texas from February 2014 through May 2015. Cryptosporidium oocysts and Giardia cysts were detected using a direct immunofluorescence assay, and genotyping of positive samples was performed. The prevalence of Cryptosporidium shedding was 1.6% (6/370), and C. scrofarum and C. suis were identified. The prevalence of Giardia shedding was 4.3% (16/370), and assemblages A and E were identified. Cryptosporidium shedding was significantly more common among juvenile and subadult pigs than among adult pigs, but age group was not associated with Giardia shedding status. Feral pigs may serve as a source of Cryptosporidium and Giardia transmission to humans and livestock. [ABSTRACT FROM AUTHOR]

Background: For many putative Salmonella enterica subsp. enterica virulence genes, functional characterization across serovars has been limited. Cytolethal distending toxin B (CdtB) is an incompletely characterized virulence factor that is found not only in Salmonella enterica subsp. enfer/caserovar Typhi (Salmonella Typhi) and dozens of Gram negative bacterial pathogens, but also in non-typhoidal Salmonella (NTS) serovars. Methods: A comparative genomics approach was performed to characterize sequence conservation of the typhoid toxin (TT), encoded in the CdtB-islet, between Salmonella Typhi and NTS serovars. The cytotoxic activity of representative Salmonella enterica subsp. enterica serovars Javiana, Montevideo and Schwarzengrund strains and their respective isogenic cdtB mutants was determined in human intestinal epithelial Henle-407 cells by assessment of cell cycle progression of infected cells using fluorescence-activated cell sorting (FACS). Two-way analysis of variance (ANOVA) was used to determine whether cdtB deletion had a significant (p < 0.05) effect on the percentage of Henle-407 cells at each stage of the cell cycle. Results: Here we show that a CdtB-islet encoding the cytolethal distending toxin B (CdtB), pertussis-like toxin A (PltA), and pertussis-like toxin B (PltB) is present in a dozen NTS serovars and that these proteins have a high level of sequence conservation and each form monophyletic clades with corresponding Salmonella Typhi genes. Human epithelial Henle-407 cells infected with three representative CdtB-encoding NTS serovars displayed G2/M phase cell cycle arrest that was absent in cells infected with corresponding isogenic cdtB null mutants (p < 0.0001 for the factor AcdtB deletion). Conclusion: Our results show that CdtB encoded by NTS serovars has a genomic organization, amino acid sequence conservation and biological activity similar to the TT, and thus, may contribute to disease pathogenesis. [ABSTRACT FROM AUTHOR]

Nosocomial salmonellosis continues to pose an important threat to veterinary medical teaching hospitals. The objectives of this study were to describe an outbreak of salmonellosis caused by Salmonella enterica serovar Oranienburg within our hospital and to highlight its unique features, which can be used to help mitigate or prevent nosocomial outbreaks in the future. We retrospectively analyzed data from patients that were fecal culture-positive for Salmonella Oranienburg between January 1, 2006, and June 1, 2011, including historical, clinical, and pulsed-field gel electrophoresis (PFGE) data. Salmonella Oranienburg was identified in 20 horses, five alpacas, and three cows during this time frame, with dates of admission spanning the period from August, 2006, through January, 2008. We consider most of these patients to have become infected through either nosocomial or on-farm transmission, as evidenced by molecular subtyping results and supportive epidemiologic data. Interpretation of PFGE results in this outbreak was challenging because of the identification of several closely related Salmonella Oranienburg subtypes. Furthermore, a high percentage of cases were fecal culture-positive for Salmonella Oranienburg within 24 h of admission. These patients initially appeared to represent new introductions of Salmonella into the hospital, but closer inspection of their medical records revealed epidemiologic links to the hospital following the index case. Cessation of this outbreak was observed following efforts to further heighten biosecurity efforts, with no known cases or positive environmental samples after January, 2008. This study demonstrates that a Salmonella-positive culture result within 24 h of admission does not exclude the hospital as the source of infection, and it underscores the important role played by veterinary medical teaching hospitals as nodes of Salmonella infection that can promote transmission outside of the hospital setting. [ABSTRACT FROM AUTHOR]

Background Within the last decade, Salmonella enterica subsp. enterica serovar Cerro (S. Cerro) has become one of the most common serovars isolated from cattle and dairy farm environments in the northeastern US. The fact that this serovar is commonly isolated from subclinically infected cattle and is rarely associated with human disease, despite its frequent isolation from cattle, has led to the hypothesis that this emerging serovar may be characterized by reduced virulence. We applied comparative and population genomic approaches to (i) characterize the evolution of this recently emerged serovar and to (ii) gain a better understanding of genomic features that could explain some of the unique epidemiological features associated with this serovar. Results In addition to generating a de novo draft genome for one Salmonella Cerro strain, we also generated whole genome sequence data for 26 additional S. Cerro isolates, including 16 from cattle operations in New York (NY) state, 2 from human clinical cases from NY in 2008, and 8 from diverse animal sources (7 from Washington state and 1 from Florida). All isolates sequenced in this study represent sequence type ST367. Population genomic analysis showed that isolates from the NY cattle operations form a well-supported clade within S. Cerro ST367 (designated here "NY bovine clade"), distinct from isolates from Washington state, Florida and the human clinical cases. A molecular clock analysis indicates that the most recent common ancestor of the NY bovine clade dates back to 1998, supporting the recent emergence of this clone. Comparative genomic analyses revealed several relevant genomic features of S. Cerro ST367, that may be responsible for reduced virulence of S. Cerro, including an insertion creating a premature stop codon in sopA. In addition, patterns of gene deletion in S. Cerro ST367 further support adaptation of this clone to a unique ecological or host related niche. Conclusions Our results indicate that the increase in prevalence of S. Cerro ST367 is caused by a highly clonal subpopulation and that S. Cerro ST367 is characterized by unique genomic deletions that may indicate adaptation to specific ecological niches and possibly reduced virulence in some hosts. [ABSTRACT FROM AUTHOR]

Dogs are a potential source of zoonotic Salmonella transmission. We had previously estimated the prevalence of Salmonella shedding among shelter dogs throughout Texas using a repeated cross‐sectional study design. Our current objectives were to fully characterize the Salmonella isolates and to assess their relatedness, using whole‐genome sequencing. Antimicrobial resistance (AMR) genes were detected in 4/27 (15%) of the isolates. The fosfomycin resistance gene fosA7 was identified in two isolates; to our knowledge, there are no published reports of this gene in canine Salmonella isolates. The biocide resistance gene qacEdelta1, conferring resistance to quaternary ammonium compounds, was detected in an isolate that had four additional AMR genes. The most frequently identified serotypes were Newport (6/27, 22%) and Javiana (4/27, 15%), both of which were widespread among animal shelters. For these serotypes, there was evidence of both transmission of Salmonella within the shelter environment and separate introductions of Salmonella into a shelter. Several canine Salmonella isolates were closely related to human clinical isolates (four canine isolates within 10 SNPs and six more within 20 SNPs), suggesting a shared pathogen population. Educational outreach programmes targeting animal shelter workers would be useful for optimizing knowledge of Salmonella and other canine‐associated zoonotic pathogens. [ABSTRACT FROM AUTHOR]

Asymptomatic oropharyngeal carriage of Neisseria meningitidis peaks in adolescence and young adulthood. Following a meningococcal disease outbreak at a U.S. college, we profiled the oropharyngeal microbiomes of 158 students to identify associations between bacterial community composition and meningococcal carriage or risk factors for carriage, including male gender, smoking, and frequent social mixing. Metagenomic shotgun sequencing identified 268 bacterial taxa at the genus or species level, with Streptococcus, Veillonella, and Rothia species being most abundant. Microbiome composition showed weak associations with meningococcal carriage and risk factors for carriage. N. meningitidis abundance was positively correlated with that of Fusobacterium nucleatum, consistent with hypothesized propionic acid cross-feeding. Additional species had positive abundance correlations with N. meningitidis, including Aggregatibacter aphrophilus, Campylobacter rectus, Catonella morbi, Haemophilus haemolyticus, and Parvimonas micra. N. meningitidis abundance was negatively correlated with unidentified Veillonella species. Several of these species are commonly found in dental plaque, while N. meningitidis is primarily found in the pharynx, suggesting that ecological interactions extend throughout the oral cavity. Although risk factors for meningococcal carriage do not strongly impact most bacterial species in the oropharynx, variation in the upper respiratory tract microbiome may create conditions that are more or less favorable for N. meningitidis carriage. [ABSTRACT FROM AUTHOR]

There are few epidemiologic studies on the shedding of Campylobacter among dogs in the United States, despite the potential public health implications. Our objectives were to estimate the prevalence of faecal Campylobacter shedding among Texas shelter dogs as detected by culture methods and to characterize the isolates by species and antimicrobial susceptibility. Using a cross‐sectional study design, faecal samples were collected from 185 dogs in six animal shelters throughout Texas between May and December 2014. Four culture methods were used to isolate Campylobacter from samples, and isolates were characterized. The prevalence of Campylobacter shedding was 45.4% (84/185; 95% CI, 38.1%–52.9%). Of 294 isolates from the 84 positive dogs, 26 (8.8%) isolates from seven dogs were identified as Campylobacter jejuni. Two of the isolates from one dog demonstrated resistance to ciprofloxacin and nalidixic acid. Direct plating on mCCDA‐CAT agar without enrichment identified the highest number of positive dogs (62%; 52/84). Incidence of ciprofloxacin‐resistant Campylobacter infections among humans has increased over the last several years. Canine shedding of Campylobacter is a potential source of zoonotic transmission. [ABSTRACT FROM AUTHOR]

Wild birds may play an important role in maintaining and transmitting Salmonella. Their ability to travel large distances and their proximity to human habitations could make them a vehicle for bridging Salmonella from wild and domestic animals to humans. To determine the potential public health risk presented by urban birds, we investigated the prevalence of Salmonella among great-tailed grackles ( Quiscalus mexicanus) and other cohabiting urban bird species. Fecal samples were collected from 114 birds communally roosting in parking lots of retail locations in Brazos County, Texas, from February through July of 2015. Great-tailed grackles and European starlings ( Sturnus vulgaris) were the predominant species sampled. Standard bacteriologic culture methods were used to isolate Salmonella from samples, and isolates were characterized by serotyping and antimicrobial susceptibility testing. Overall, 1.8% (2/114) of samples were confirmed positive for Salmonella. Both positive birds were great-tailed grackles sampled in June, yielding a 2.6% (2/76) apparent prevalence among this species. Isolates were serotyped as Salmonella Typhimurium and found to be pan-susceptible based on the National Antimicrobial Resistance Monitoring System (NARMS) panel of antimicrobial agents. The occurrence of Salmonella in great-tailed grackles represents a potential threat to public health, particularly considering their population size and tendency to congregate near human establishments such as grocery stores. [ABSTRACT FROM AUTHOR]

The bacterial genus Listeria contains both saprotrophic and facultative pathogenic species. A small genome size has been suggested to be associated with the loss of pathogenic potential of L. welshimeri and L. seeligeri. In this paper we present data on the genome of L. monocytogenes strain FSL J1-208, a representative of phylogenetic lineage IV. Although this strain was isolated from a clinical case in a caprine host and has no decreased invasiveness in human intestinal epithelial cells, our analyses show that this strain has one of the smallest Listeria chromosomes reported to date (2.78 Mb). The chromosome contains 2,772 protein-coding genes, including well-characterized virulence-associated genes, such as inlA, inlB, and inlC and the full prfA gene cluster. The small genome size is mainly caused by the absence of prophages in the genome of L. monocytogenes FSL J1-208, and further analyses showed that the total size of prophage-related regions is highly correlated to chromosome size in the genus Listeria. L. monocytogenes FSL J1-208 carries a unique type of plasmid of approximately 80 kbp that does not carry genes annotated as being involved in resistance to antibiotics or heavy metals. The accessory genes in this plasmid belong to the internalin family, a family of virulence-associated proteins, and therefore this is the first report of a potential virulence plasmid in the genus Listeria. [ABSTRACT FROM AUTHOR]

Background: We conducted a Neisseria meningitidis (Nm) carriage study among men who have sex with men (MSM) to explore possible sexual transmission.Methods: We paired information on patient characteristics with oropharyngeal, rectal, and urethral Nm culture results to assess associations with Nm carriage among 706 MSM at New York City sexual health clinics. The Nm isolates were characterized by whole genome sequencing.Results: Twenty-three percent (163 of 706) of MSM were Nm carriers. Oropharyngeal carriage was 22.6% (159 of 703), rectal 0.9% (6 of 695), and urethral 0.4% (3 of 696). Oropharyngeal carriage was associated with the following recent (past 30 days) exposures: 3 or more men kissed (adjusted relative risk [aRR], 1.38; 95% confidence interval [CI], 1.03-1.86), performing oral sex (aRR, 1.81; 95% CI, 1.04-3.18), and antibiotic use (aRR, 0.33; 95% CI, 0.19-0.57). Sixteen clonal complexes were identified; 27% belonged to invasive lineages.Conclusions: Our findings suggest that oral sex and the number of recent kissing partners contribute to Nm carriage in MSM. [ABSTRACT FROM AUTHOR]

Background: Haemophilus influenzae (Hi) can cause invasive diseases such as meningitis, pneumonia, or sepsis. Typeable Hi includes six serotypes (a through f), each expressing a unique capsular polysaccharide. The capsule, encoded by the genes within the capsule locus, is a major virulence factor of typeable Hi. Non-typeable (NTHi) does not express capsule and is associated with invasive and non-invasive diseases. Methods: A total of 395 typeable and 293 NTHi isolates were characterized by whole genome sequencing (WGS). Phylogenetic analysis and multilocus sequence typing were used to characterize the overall genetic diversity. Pair-wise comparisons were used to evaluate the capsule loci. A WGS serotyping method was developed to predict the Hi serotype. WGS serotyping results were compared to slide agglutination (SAST) or real-time PCR (rt-PCR) serotyping. Results: Isolates of each Hi serotype clustered into one or two subclades, with each subclade being associated with a distinct sequence type (ST). NTHi isolates were genetically diverse, with seven subclades and 125 STs being detected. Regions I and III of the capsule locus were conserved among the six serotypes (≥82% nucleotide identity). In contrast, genes in Region II were less conserved, with only six gene pairs from all serotypes showing ≥56% nucleotide identity. The WGS serotyping method was 99.9% concordant with SAST and 100% concordant with rt-PCR in determining the Hi serotype. Conclusions: Genomic analysis revealed a higher degree of genetic diversity among NTHi compared to typeable Hi. The WGS serotyping method accurately predicted the Hi capsule type and can serve as an alternative method for Hi serotyping. [ABSTRACT FROM AUTHOR]

Meningococcal disease is a rare, but serious, bacterial infection that progresses rapidly and can be life-threatening, even with prompt antibiotic treatment. Men who have sex with men (MSM) have previously been reported to be at increased risk for meningococcal disease compared with other men, and recent outbreaks of serogroup C meningococcal disease among MSM have occurred (1). However, the epidemiology of meningococcal disease among MSM in the United States is not well described, in part, because information about MSM has not historically been collected as part of routine meningococcal disease surveillance. To better characterize and identify risk factors for meningococcal disease in general, supplementary data and isolates have been collected since 2015 through enhanced meningococcal disease surveillance activities. During 2015-2016, 271 cases of meningococcal disease in men aged ≥18 years were reported to the National Notifiable Diseases Surveillance System (NNDSS) in 45 states participating in this enhanced surveillance. Forty-eight (17.7%) cases were in men identified as MSM, including 17 (37.8%) with human immunodeficiency virus (HIV) infection. Among MSM, 39 (84.8%) cases were caused by Neisseria meningitidis serogroup C, whereas this serogroup was responsible for only 16.4% of cases among men who were not known to be MSM (non-MSM). Despite improvements in surveillance, MSM likely remain underascertained among men with meningococcal disease. Improved surveillance data are needed to understand the prevalence of and risk for meningococcal disease among MSM and inform policy and prevention strategies. Vaccination with quadrivalent meningococcal conjugate (MenACWY) vaccine is recommended for the control of meningococcal disease outbreaks caused by serogroups A, C, W, or Y, including during outbreaks among MSM; in addition, all persons aged ≥2 months with HIV infection should receive MenACWY vaccine because of the increased risk for meningococcal disease. [ABSTRACT FROM AUTHOR]

The genetic diversity represented by >2,500 different Salmonella serovars provides a yet largely uncharacterized reservoir of mobile elements that can contribute to the frequent emergence of new pathogenic strains of this important zoonotic pathogen. Currently, our understanding of Salmonella mobile elements is skewed by the fact that most studies have focused on highly virulent or common serovars. To gain a more global picture of mobile elements in Salmonella, we used prediction algorithms to screen for mobile elements in 16 sequenced Salmonella genomes representing serovars for which no prior genome scale mobile element data were available. From these results, selected mobile elements underwent further analyses in the form of validation studies, comparative analyses, and PCR-based population screens. Through this analysis we identified a novel plasmid that has two cointegrated replicons (IncI1-IncFIB); this plasmid type was found in four genomes representing different Salmonella serovars and contained a virulence gene array that had not been previously identified. A Salmonella Montevideo isolate contained an IncHI and an IncN2 plasmid, which both encoded antimicrobial resistance genes. We also identified two novel genomic islands (SGI2 and SGI3), and 42 prophages with mosaic architecture, seven of them harboring known virulence genes. Finally, we identified a novel integrative conjugative element (ICE) encoding a type IVb pilus operon in three non-typhoidal Salmonella serovars. Our analyses not only identified a considerable number of mobile elements that have not been previously reported in Salmonella, but also found evidence that these elements facilitate transfer of genes that were previously thought to be limited in their distribution among Salmonella serovars. The abundance of mobile elements encoding pathogenic properties may facilitate the emergence of strains with novel combinations of pathogenic traits. [ABSTRACT FROM AUTHOR]

In this study, we report a whole-genome single nucleotide polymorphism (SNP)-based evolutionary approach to study the epidemiology of a multistate outbreak of Salmonella enterica subsp. enterica serovar Montevideo. This outbreak included 272 cases that occurred in 44 states between July 2009 and April 2010. A case-control study linked the consumption of salami made with contaminated black and red pepper to the outbreak. We sequenced, on the SOLiD System, 47 isolates with XbaI PFGE pattern JIXX01.0011, a common pulsed-field gel electrophoresis (PFGE) pattern associated with isolates from the outbreak. These isolates represented 20 isolates collected from human sources during the period of the outbreak and 27 control isolates collected from human, food, animal, and environmental sources before the outbreak. Based on 253 high-confidence SNPs, we were able to reconstruct a tip-dated molecular clock phylogeny of the isolates and to assign four human isolates to the actual outbreak. We developed an SNP typing assay to rapidly discriminate between outbreak-related cases and non-outbreak-related cases and tested this assay on an extended panel of 112 isolates. These results suggest that only a very small percentage of the human isolates with the outbreak PFGE pattern and obtained during the outbreak period could be attributed to the actual pepper-related outbreak (20%), while the majority (80%) of the putative cases represented background cases. This study demonstrates that next-generation-based SNP typing provides the resolution and accuracy needed for outbreak investigations of food-borne pathogens that cannot be distinguished by currently used subtyping methods. [ABSTRACT FROM AUTHOR]