26
|
Vasco K, Nohomovich B, Singh P, Venegas-Vargas C, Mosci RE, Rust S, Bartlett P, Norby B, Grooms D, Zhang L, Manning SD. Characterizing the Cattle Gut Microbiome in Farms with a High and Low Prevalence of Shiga Toxin Producing Escherichia coli. Microorganisms 2021; 9:microorganisms9081737. [PMID: 34442815 PMCID: PMC8399351 DOI: 10.3390/microorganisms9081737] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 08/06/2021] [Accepted: 08/12/2021] [Indexed: 12/20/2022] Open
Abstract
Cattle are the main reservoirs of Shiga toxin producing Escherichia coli (STEC), a major foodborne pathogen associated with acute enteric disease and hemolytic-uremic syndrome in humans. A total of 397 beef and dairy cattle from 5 farms were included in this study, of which 660 samples were collected for 16S rRNA gene sequencing. The microbiota of farms with a high-STEC prevalence (HSP) had greater richness compared to those of farms with a low-STEC prevalence (LSP). Longitudinal analyses showed STEC-shedders from LSP farms had higher microbiome diversity; meanwhile, changes in the microbiome composition in HSP farms were independent of the STEC shedding status. Most of the bacterial genera associated with STEC shedding in dairy farms were also correlated with differences in the percentage of forage in diet and risk factors of STEC carriage such as days in milk, number of lactations, and warm temperatures. Identifying factors that alter the gut microbiota and enable STEC colonization in livestock could lead to novel strategies to prevent fecal shedding and the subsequent transmission to humans.
Collapse
|
27
|
Avery TM, Boone RL, Lu J, Spicer SK, Guevara MA, Moore RE, Chambers SA, Manning SD, Dent L, Marshall D, Damo SM, Townsend SD, Gaddy JA. Analysis of Antimicrobial and Antibiofilm Activity of Human Milk Lactoferrin Compared to Bovine Lactoferrin against Multidrug Resistant and Susceptible Acinetobacter baumannii Clinical Isolates. ACS Infect Dis 2021; 7:2116-2126. [PMID: 34105954 DOI: 10.1021/acsinfecdis.1c00087] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Acinetobacter baumannii is an opportunistic bacterial pathogen that causes severe infections in immunocompromised patients. The emergence of multi- and pan-drug resistant strains of A. baumannii from clinical sources has confounded treatment and enhanced morbidity and mortality associated with these infections. One way that A. baumannii circumnavigates environmental and antimicrobial challenge is by forming tertiary architectural structures of cells known as biofilms. Biofilm-inhibiting molecules could be deployed as a potential chemotherapeutic strategy to inhibit or disrupt A. baumannii biofilms and mitigate adverse outcomes due to infection. Lactoferrin is an innate immune glycoprotein produced in high concentrations in both human and bovine milk which has previously been shown to have antibacterial and antibiofilm activities. We sought to test lactoferrin against a bank of clinical isolates of A. baumannii to determine changes in bacterial growth or biofilm formation. Our results indicate that human lactoferrin has slightly more potent antibacterial activities than bovine lactoferrin against certain strains of A. baumannii and that these effects are associated with anatomical site of isolation. Additionally, we have shown that both bovine and human lactoferrin can inhibit A. baumannii biofilm formation and that these effects are associated with anatomical site of isolation and whether the strain forms robust or weak biofilms.
Collapse
|
28
|
Rodrigues JA, Cha W, Mosci RE, Mukherjee S, Newton DW, Lephart P, Salimnia H, Khalife W, Rudrik JT, Manning SD. Epidemiologic Associations Vary Between Tetracycline and Fluoroquinolone Resistant Campylobacter jejuni Infections. Front Public Health 2021; 9:672473. [PMID: 34262891 PMCID: PMC8273344 DOI: 10.3389/fpubh.2021.672473] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Accepted: 05/27/2021] [Indexed: 11/13/2022] Open
Abstract
Campylobacter jejuni is the leading cause of bacterial gastroenteritis and antibiotic resistant C. jejuni are a serious threat to public health. Herein, we sought to evaluate trends in C. jejuni infections, quantify resistance frequencies, and identify epidemiological factors associated with infection. Campylobacter jejuni isolates (n = 214) were collected from patients via an active surveillance system at four metropolitan hospitals in Michigan between 2011 and 2014. The minimum inhibitory concentration for nine antibiotics was determined using microbroth dilution, while demographic and clinical data were used for the univariate and multivariate analyses. Over the 4-year period, a significant increase in the recovery of C. jejuni was observed (p ≤ 0.0001). Differences in infection rates were observed by hospital and several factors were linked to more severe disease. Patients residing in urban areas, for instance, were significantly more likely to be hospitalized than rural residents as were patients over 40 years of age and those self-identifying as non-White, highlighting potential disparities in disease outcomes. Among the 214 C. jejuni isolates, 135 (63.1%) were resistant to at least one antibiotic. Resistance was observed for all nine antibiotics tested yielding 11 distinct resistance phenotypes. Tetracycline resistance predominated (n = 120; 56.1%) followed by resistance to ciprofloxacin (n = 49; 22.9%), which increased from 15.6% in 2011 to 25.0% in 2014. Resistance to two antibiotic classes was observed in 38 (17.8%) isolates, while multidrug resistance, or resistance to three or more classes, was observed in four (1.9%). Notably, patients with ciprofloxacin resistant infections were more likely to report traveling in the past month (Odds Ratio (OR): 3.0; 95% confidence interval (CI): 1.37, 6.68) and international travel (OR: 9.8; 95% CI: 3.69, 26.09). Relative to patients with only tetracycline resistant infections, those with ciprofloxacin resistance were more likely to travel internationally, be hospitalized and have an infection during the fall or summer. Together, these findings show increasing rates of infection and resistance and highlight specific factors that impact both outcomes. Enhancing understanding of factors linked to C. jejuni resistance and more severe infections is critical for disease prevention, particularly since many clinical laboratories have switched to the use of culture-independent tests for the detection of Campylobacter.
Collapse
|
29
|
Lu J, Francis JD, Guevara MA, Moore RE, Chambers SA, Doster RS, Eastman AJ, Rogers LM, Noble KN, Manning SD, Damo SM, Aronoff DM, Townsend SD, Gaddy JA. Front Cover: Antibacterial and Anti‐biofilm Activity of the Human Breast Milk Glycoprotein Lactoferrin against Group B
Streptococcus
(ChemBioChem 12/2021). Chembiochem 2021. [DOI: 10.1002/cbic.202100214] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
|
30
|
Lu J, Francis JD, Guevara MA, Moore RE, Chambers SA, Doster RS, Eastman AJ, Rogers LM, Noble KN, Manning SD, Damo SM, Aronoff DM, Townsend SD, Gaddy JA. Antibacterial and Anti-biofilm Activity of the Human Breast Milk Glycoprotein Lactoferrin against Group B Streptococcus. Chembiochem 2021; 22:2124-2133. [PMID: 33755306 DOI: 10.1002/cbic.202100016] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/15/2021] [Indexed: 12/14/2022]
Abstract
Group B Streptococcus (GBS) is an encapsulated Gram-positive human pathogen that causes invasive infections in pregnant hosts and neonates, as well as immunocompromised individuals. Colonization of the human host requires the ability to adhere to mucosal surfaces and circumnavigate the nutritional challenges and antimicrobial defenses associated with the innate immune response. Biofilm formation is a critical process to facilitate GBS survival and establishment of a replicative niche in the vertebrate host. Previous work has shown that the host responds to GBS infection by producing the innate antimicrobial glycoprotein lactoferrin, which has been implicated in repressing bacterial growth and biofilm formation. Additionally, lactoferrin is highly abundant in human breast milk and could serve a protective role against invasive microbial pathogens. This study demonstrates that human breast milk lactoferrin has antimicrobial and anti-biofilm activity against GBS and inhibits its adherence to human gestational membranes. Together, these results indicate that human milk lactoferrin could be used as a prebiotic chemotherapeutic strategy to limit the impact of bacterial adherence and biofilm formation on GBS-associated disease outcomes.
Collapse
|
31
|
Blankenship HM, Mosci RE, Dietrich S, Burgess E, Wholehan J, McWilliams K, Pietrzen K, Benko S, Gatesy T, Rudrik JT, Soehnlen M, Manning SD. Population structure and genetic diversity of non-O157 Shiga toxin-producing Escherichia coli (STEC) clinical isolates from Michigan. Sci Rep 2021; 11:4461. [PMID: 33627701 PMCID: PMC7904848 DOI: 10.1038/s41598-021-83775-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2020] [Accepted: 02/01/2021] [Indexed: 01/31/2023] Open
Abstract
Non-O157 STEC are increasingly linked to foodborne infections, yet little is known about the diversity and molecular epidemiology across locations. Herein, we used whole genome sequencing to examine genetic variation in 894 isolates collected from Michigan patients between 2001 and 2018. In all, 67 serotypes representing 69 multilocus sequence types were identified. Serotype diversity increased from an average of four (2001-2006) to 17 (2008-2018) serotypes per year. The top six serogroups reported nationally caused > 60% of infections in 16 of the 18 years; serogroups O111 and O45 were associated with hospitalization as were age ≥ 65 years, diarrhea with blood and female sex. Phylogenetic analyses of seven multilocus sequence typing (MLST) loci identified three clades as well as evidence of parallel evolution and recombination. Most (95.5%) isolates belonged to one clade, which could be further differentiated into seven subclades comprising isolates with varying virulence gene profiles and serotypes. No association was observed between specific clades and the epidemiological data, suggesting that serogroup- and serotype-specific associations are more important predictors of disease outcomes than lineages defined by MLST. Molecular epidemiological studies of non-O157 STEC are important to enhance understanding of circulating strain distributions and traits, genetic variation, and factors that may impact disease risk and severity.
Collapse
|
32
|
Boone RL, Whitehead B, Avery TM, Lu J, Francis JD, Guevara MA, Moore RE, Chambers SA, Doster RS, Manning SD, Townsend SD, Dent L, Marshall D, Gaddy JA, Damo SM. Analysis of virulence phenotypes and antibiotic resistance in clinical strains of Acinetobacter baumannii isolated in Nashville, Tennessee. BMC Microbiol 2021; 21:21. [PMID: 33422000 PMCID: PMC7796680 DOI: 10.1186/s12866-020-02082-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2020] [Accepted: 12/27/2020] [Indexed: 12/13/2022] Open
Abstract
BACKGROUND Acinetobacter baumannii is a gram-negative bacterium which causes opportunistic infections in immunocompromised hosts. Genome plasticity has given rise to a wide range of strain variation with respect to antimicrobial resistance profiles and expression of virulence factors which lead to altered phenotypes associated with pathogenesis. The purpose of this study was to analyze clinical strains of A. baumannii for phenotypic variation that might correlate with virulence phenotypes, antimicrobial resistance patterns, or strain isolation source. We hypothesized that individual strain virulence phenotypes might be associated with anatomical site of isolation or alterations in susceptibility to antimicrobial interventions. METHODOLOGY A cohort of 17 clinical isolates of A. baumannii isolated from diverse anatomical sites were evaluated to ascertain phenotypic patterns including biofilm formation, hemolysis, motility, and antimicrobial resistance. Antibiotic susceptibility/resistance to ampicillin-sulbactam, amikacin, ceftriaxone, ceftazidime, cefotaxime, ciprofloxacin, cefepime, gentamicin, levofloxacin, meropenem, piperacillin, trimethoprim-sulfamethoxazole, ticarcillin- K clavulanate, tetracyclin, and tobramycin was determined. RESULTS Antibiotic resistance was prevalent in many strains including resistance to ampicillin-sulbactam, amikacin, ceftriaxone, ceftazidime, cefotaxime, ciprofloxacin, cefepime, gentamicin, levofloxacin, meropenem, piperacillin, trimethoprim-sulfamethoxazole, ticarcillin- K clavulanate, tetracyclin, and tobramycin. All strains tested induced hemolysis on agar plate detection assays. Wound-isolated strains of A. baumannii exhibited higher motility than strains isolated from blood, urine or Foley catheter, or sputum/bronchial wash. A. baumannii strains isolated from patient blood samples formed significantly more biofilm than isolates from wounds, sputum or bronchial wash samples. An inverse relationship between motility and biofilm formation was observed in the cohort of 17 clinical isolates of A. baumannii tested in this study. Motility was also inversely correlated with induction of hemolysis. An inverse correlation was observed between hemolysis and resistance to ticarcillin-k clavulanate, meropenem, and piperacillin. An inverse correlation was also observed between motility and resistance to ampicillin-sulbactam, ceftriaxone, ceftoxamine, ceftazidime, ciprofloxacin, or levofloxacin. CONCLUSIONS Strain dependent variations in biofilm and motility are associated with anatomical site of isolation. Biofilm and hemolysis production both have an inverse association with motility in the cohort of strains utilized in this study, and motility and hemolysis were inversely correlated with resistance to numerous antibiotics.
Collapse
|
33
|
Rodrigues JA, Blankenship HM, Cha W, Mosci R, Manning SD. 1199. Phylogenomic analysis of Campylobacter jejuni isolated from gastroenteritis cases in Michigan. Open Forum Infect Dis 2020. [PMCID: PMC7776441 DOI: 10.1093/ofid/ofaa439.1384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Background C. jejuni is the leading cause of bacterial gastroenteritis worldwide. It has been classified as a serious antibiotic resistant threat, causing 13,000 hospitalizations and 120 deaths annually. Our goal was to describe the diversity of clinical C. jejuni using phylogenomics and classify resistance mechanisms. Methods Isolates were collected via sentinel surveillance at four hospitals, and demographic and clinical data were obtained. DNA was extracted and sequenced. Raw reads were processed with Trimmomatic and quality checked with FastQC. De novo genome assembly was performed in Spades. Assembled genomes were filtered for quality and completeness; samples of 1.4-2.1MB were annotated in Prokka followed by pangenome and phylogenetic analyses. Multilocus sequence typing loci and virulence and antibiotic resistance genes were extracted from each genome. Results Among the 214 C. jejuni isolates recovered, 86 unique sequence types (STs) were identified; five were novel STs with unique allele combinations. ST353 (8.3%: n=18), ST982 (7.4%: n=16), ST50 (5.1 %: n=11) and ST48 (5.1%: n=11) were the most prevalent STs identified, while the majority (50.1%: n=50) of STs were singletons. The pangenome analysis identified 8781, 615, and 1169 total, core, and shell core genes, respectively, which grouped the isolates into three major clades. Most isolates belonged to clade 1. A neighbor-net analysis detected significant recombination among all 86 STs (pairwise homoplasy index p=< 0.00001) and evidence of horizontal gene transfer across clades. The beta-lactamase gene, blaOXA-605, was the most common resistance gene identified (58.8%: n=125) followed by tet(O) (56.0%: n=121), which mediate resistance to beta-lactams and tetracyclines, respectively. Resistance phenotypes were confirmed using microbroth dilution. Conclusion: Together, these data demonstrate that the C. jejuni population is highly diverse and carries important resistance determinants. The phylogenomic analyses also provide insight into the evolution of this major foodborne pathogen. Future work will focus on identifying molecular and epidemiological factors associated with specific strain types and resistance and virulence profiles circulating in Michigan. Disclosures All Authors: No reported disclosures
Collapse
|
34
|
Guevara MA, Lu J, Moore RE, Chambers SA, Eastman AJ, Francis JD, Noble KN, Doster RS, Osteen KG, Damo SM, Manning SD, Aronoff DM, Halasa NB, Townsend SD, Gaddy JA. Vitamin D and Streptococci: The Interface of Nutrition, Host Immune Response, and Antimicrobial Activity in Response to Infection. ACS Infect Dis 2020; 6:3131-3140. [PMID: 33170652 DOI: 10.1021/acsinfecdis.0c00666] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Streptococcus species are common causes of human infection. These Gram-positive, encapsulated bacterial pathogens infect diverse anatomic spaces, leading to infections including skin and soft tissue infection, endocarditis, pneumonia, meningitis, sinusitis, otitis media, chorioamnionitis, sepsis, and even death. Risk for streptococcal infection is highest in low- and middle-income countries where micronutrient deficiency is common. Epidemiological data reveal that vitamin D deficiency is associated with enhanced risk of streptococcal infection and cognate disease outcomes. Additionally, vitamin D improves antibacterial defenses by stimulating innate immune processes such as phagocytosis and enhancing production of reactive oxygen species (oxidative burst) and antimicrobial peptides (including cathelicidin and lactoferrin), which are important for efficient killing of bacteria. This review presents the most recent published work that studies interactions between the micronutrient vitamin D, the host immune system, and pathogenic streptococci as well as comparisons with other relevant infection models.
Collapse
|
35
|
Shiroda M, Manning SD. Lactobacillus strains vary in their ability to interact with human endometrial stromal cells. PLoS One 2020; 15:e0238993. [PMID: 32925983 PMCID: PMC7489503 DOI: 10.1371/journal.pone.0238993] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 08/27/2020] [Indexed: 12/17/2022] Open
Abstract
The placental membranes that surround the fetus during pregnancy were suggested to contain a low abundance microbiota. Specifically, abundance of Lactobacillus, a probiotic and dominant member of the microbiome of the lower reproductive tract, has been shown to correlate with healthy, term pregnancies. We therefore sought to assess the interactions between four different Lactobacillus strains with immortalized decidualized endometrial cells (dT-HESCs), which were used as a model to represent the outermost layer of the placental membranes. Notably, we demonstrated that all four Lactobacillus strains could associate with dT-HESCs in vitro. L. crispatus was significantly more successful (p < 0.00005), with 10.6% of bacteria attaching to the host cells compared to an average of 0.8% for the remaining three strains. The four strains also varied in their ability to form biofilms. Dependent on media type, L. reuteri 6475 formed the strongest biofilms in vitro. To examine the impact on immune responses, levels of total and phosphorylated protein p38, a member of the Mitogen Activated Protein Kinase (MAPK) pathway, were examined following Lactobacillus association with dT-HESCs. Total levels of p38 were reduced to an average of 44% that of the cells without Lactobacillus (p < 0.05). While a trend towards a reduction in phosphorylated p38 was observed, this difference was not significant (p > 0.05). In addition, association with Lactobacillus did not result in increased host cell death. Collectively, these data suggest that varying types of Lactobacillus can attach to the outermost cells of the placental membranes and that these interactions do not contribute to inflammatory responses or host cell death. To our knowledge this is the first in vitro study to support the ability of Lactobacillus to interact with placental cells, which is important when considering its use as a potential probiotic within the reproductive tract.
Collapse
|
36
|
Shiroda M, Aronoff DM, Gaddy JA, Manning SD. The impact of Lactobacillus on group B streptococcal interactions with cells of the extraplacental membranes. Microb Pathog 2020; 148:104463. [PMID: 32828901 DOI: 10.1016/j.micpath.2020.104463] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 08/12/2020] [Accepted: 08/18/2020] [Indexed: 01/27/2023]
Abstract
Group B Streptococcus (GBS) causes adverse pregnancy outcomes and neonatal disease. The recommended preventative measure is intrapartum antibiotic prophylaxis, which can prevent early onset neonatal disease but not chorioamnionitis, preterm labor, stillbirth, or late-onset disease. Novel prevention methods are therefore needed. Use of probiotics including Lactobacillus spp., has been suggested given that they are dominant members of the lower reproductive tract microbiome. Although Lactobacillus was shown to reduce recto-vaginal colonization of GBS, no studies have examined how Lactobacillus impacts GBS in the extraplacental membranes. Since Lactobacillus has been detected in the placental membranes, we sought to characterize GBS-Lactobacillus interactions in vitro using a colonizing and invasive GBS strain. While live Lactobacillus did not affect growth or biofilms in GBS, co-culture with L. gasseri led to a 224-fold increase in GBS association with decidualized human endometrial stromal cells for both GBS strains (p < 0.005). Increased association did not result in increased invasion (p > 0.05) or host cell death, though some GBS and Lactobacillus combinations contributed to a significant reduction in host cell death (p < 0.05). Since Lactobacillus secretes many inhibitory compounds, the effect of Lactobacillus supernatants on GBS was also examined. The supernatants inhibited GBS growth, biofilm formation and invasion of host cells, though strain dependent effects were observed. Notably, supernatant from L. reuteri 6475 broadly inhibited growth in 36 distinct GBS strains and inhibited GBS growth to an average of 46.6% of each GBS strain alone. Together, these data show that specific Lactobacillus strains and their secreted products have varying effects on GBS interactions with cells of the extraplacental membranes that could impact pathogenesis. Understanding these interactions could help guide new treatment options aimed at reducing GBS-associated maternal complications and disease.
Collapse
|
37
|
Blankenship HM, Mosci RE, Phan Q, Fontana J, Rudrik JT, Manning SD. Genetic Diversity of Non-O157 Shiga Toxin-Producing Escherichia coli Recovered From Patients in Michigan and Connecticut. Front Microbiol 2020; 11:529. [PMID: 32300338 PMCID: PMC7145412 DOI: 10.3389/fmicb.2020.00529] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2019] [Accepted: 03/11/2020] [Indexed: 12/16/2022] Open
Abstract
Shiga toxin-producing Escherichia coli (STEC) are important foodborne pathogens and non-O157 serotypes have been gradually increasing in frequency. The non-O157 STEC population is diverse and is often characterized using serotyping and/or multilocus sequence typing (MLST). Although spacers within clustered regularly interspaced repeat (CRISPR) regions were shown to comprise horizontally acquired DNA elements, this region does not actively acquire spacers in STEC. Hence, it is useful for further characterizing non-O157 STEC and examining relationships between strains. Our study goal was to evaluate the genetic relatedness of 41 clinical non-O157 isolates identified in Michigan between 2001 and 2005 while comparing to 114 isolates from Connecticut during an overlapping time period. Whole genome sequencing (WGS) was performed, and sequences were extracted for serotyping, MLST and CRISPR analysis. Phylogenetic analysis of MLST and CRISPR data was performed using the Neighbor joining and unweighted pair group method with arithmetic mean (UPGMA) algorithms, respectively. In all, 29 serogroups were identified; eight were unique to Michigan and 13 to Connecticut. “Big-six” serogroup frequencies were similar by state (Michigan: 73.2%, Connecticut: 81.6%), though STEC O121 was not found in Michigan. The distribution of sequence types (STs) and CRISPR profiles was also similar across states. Interestingly, big-six serogroups such as O103 and O26, grouped into different STs located on distinct branches of the phylogeny, further confirming that serotyping alone is not adequate for evaluating strain relatedness. Comparatively, the CRISPR analysis identified 361 unique spacers that grouped into 80 different CRISPR profiles. CRISPR spacers 231 and 317 were isolated from 79.2% (n = 118) and 59.1% (n = 88) of strains, respectively, regardless of serogroup and ST. Spacer profiles clustered according to the MLST analysis, though some discrepancies were noted. Indeed, use of both MLST and CRISPR typing enhanced the discriminatory power when compared to the use of each tool separately. These data highlight the genetic diversity of clinical STEC from different locations and show that CRISPR profiling can be used alongside MLST to discriminate related strains. Use of targeted sequencing approaches are particularly helpful for sites without WGS capabilities and can help define which strains require additional characterization using more discriminatory methods.
Collapse
|
38
|
Chambers SA, Moore RE, Craft KM, Thomas HC, Das R, Manning SD, Codreanu SG, Sherrod SD, Aronoff DM, McLean JA, Gaddy JA, Townsend SD. A Solution to Antifolate Resistance in Group B Streptococcus: Untargeted Metabolomics Identifies Human Milk Oligosaccharide-Induced Perturbations That Result in Potentiation of Trimethoprim. mBio 2020; 11:e00076-20. [PMID: 32184236 PMCID: PMC7078465 DOI: 10.1128/mbio.00076-20] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Accepted: 01/30/2020] [Indexed: 01/21/2023] Open
Abstract
Adjuvants can be used to potentiate the function of antibiotics whose efficacy has been reduced by acquired or intrinsic resistance. In the present study, we discovered that human milk oligosaccharides (HMOs) sensitize strains of group B Streptococcus (GBS) to trimethoprim (TMP), an antibiotic to which GBS is intrinsically resistant. Reductions in the MIC of TMP reached as high as 512-fold across a diverse panel of isolates. To better understand HMOs' mechanism of action, we characterized the metabolic response of GBS to HMO treatment using ultrahigh-performance liquid chromatography-high-resolution tandem mass spectrometry (UPLC-HRMS/MS) analysis. These data showed that when challenged by HMOs, GBS undergoes significant perturbations in metabolic pathways related to the biosynthesis and incorporation of macromolecules involved in membrane construction. This study represents reports the metabolic characterization of a cell that is perturbed by HMOs.IMPORTANCE Group B Streptococcus is an important human pathogen that causes serious infections during pregnancy which can lead to chorioamnionitis, funisitis, premature rupture of gestational membranes, preterm birth, neonatal sepsis, and death. GBS is evolving antimicrobial resistance mechanisms, and the work presented in this paper provides evidence that prebiotics such as human milk oligosaccharides can act as adjuvants to restore the utility of antibiotics.
Collapse
|
39
|
Mukherjee S, Anderson CM, Mosci RE, Newton DW, Lephart P, Salimnia H, Khalife W, Rudrik JT, Manning SD. Increasing Frequencies of Antibiotic Resistant Non-typhoidal Salmonella Infections in Michigan and Risk Factors for Disease. Front Med (Lausanne) 2019; 6:250. [PMID: 31781566 PMCID: PMC6857118 DOI: 10.3389/fmed.2019.00250] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 10/17/2019] [Indexed: 11/13/2022] Open
Abstract
Non-typhoidal Salmonella (NTS) are important enteric pathogens causing over 1 million foodborne illnesses in the U.S. annually. The widespread emergence of antibiotic resistance in NTS isolates has limited the availability of antibiotics that can be used for therapy. Since Michigan is not part of the FoodNet surveillance system, few studies have quantified antibiotic resistance frequencies and identified risk factors for NTS infections in the state. We obtained 198 clinical NTS isolates via active surveillance at four Michigan hospitals from 2011 to 2014 for classification of serovars and susceptibility to 24 antibiotics using broth microdilution. The 198 isolates belonged to 35 different serovars with Enteritidis (36.9%) predominating followed by Typhimurium (19.5%) and Newport (9.7%), though the proportion of each varied by year, residence, and season. The number of Enteritidis and Typhimurium cases was higher in the summer, while Enteritidis cases were significantly more common among urban vs. rural residents. A total of 30 (15.2%) NTS isolates were resistant to ≥1 antibiotic and 15 (7.5%) were resistant to ≥3 antimicrobial classes; a significantly greater proportion of Typhimurium isolates were resistant compared to Enteritidis isolates and an increasing trend in the frequency of tetracycline resistance and multidrug resistance was observed over the 4-year period. Resistant infections were associated with longer hospital stays as the mean stay was 5.9 days for patients with resistant isolates relative to 4.0 days for patients infected with susceptible isolates. Multinomial logistic regression indicated that infection with serovars other than Enteritidis [Odds ratio (OR): 3.8, 95% confidence interval (CI): 1.23-11.82] as well as infection during the fall (OR: 3.0; 95% CI: 1.22-7.60) were independently associated with resistance. Together, these findings demonstrate the importance of surveillance, monitoring resistance frequencies, and identifying risk factors that can aid in the development of new prevention strategies.
Collapse
|
40
|
Richards VP, Velsko IM, Alam MT, Zadoks RN, Manning SD, Pavinski Bitar PD, Hassler HB, Crestani C, Springer GH, Probert BM, Town CD, Stanhope MJ. Population Gene Introgression and High Genome Plasticity for the Zoonotic Pathogen Streptococcus agalactiae. Mol Biol Evol 2019; 36:2572-2590. [PMID: 31350563 PMCID: PMC6805230 DOI: 10.1093/molbev/msz169] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Revised: 04/04/2019] [Accepted: 07/18/2019] [Indexed: 01/06/2023] Open
Abstract
The influence that bacterial adaptation (or niche partitioning) within species has on gene spillover and transmission among bacterial populations occupying different niches is not well understood. Streptococcus agalactiae is an important bacterial pathogen that has a taxonomically diverse host range making it an excellent model system to study these processes. Here, we analyze a global set of 901 genome sequences from nine diverse host species to advance our understanding of these processes. Bayesian clustering analysis delineated 12 major populations that closely aligned with niches. Comparative genomics revealed extensive gene gain/loss among populations and a large pan genome of 9,527 genes, which remained open and was strongly partitioned among niches. As a result, the biochemical characteristics of 11 populations were highly distinctive (significantly enriched). Positive selection was detected and biochemical characteristics of the dispensable genes under selection were enriched in ten populations. Despite the strong gene partitioning, phylogenomics detected gene spillover. In particular, tetracycline resistance (which likely evolved in the human-associated population) from humans to bovine, canines, seals, and fish, demonstrating how a gene selected in one host can ultimately be transmitted into another, and biased transmission from humans to bovines was confirmed with a Bayesian migration analysis. Our findings show high bacterial genome plasticity acting in balance with selection pressure from distinct functional requirements of niches that is associated with an extensive and highly partitioned dispensable genome, likely facilitating continued and expansive adaptation.
Collapse
|
41
|
Flaherty RA, Borges EC, Sutton JA, Aronoff DM, Gaddy JA, Petroff MG, Manning SD. Genetically distinct Group B Streptococcus strains induce varying macrophage cytokine responses. PLoS One 2019; 14:e0222910. [PMID: 31536604 PMCID: PMC6752832 DOI: 10.1371/journal.pone.0222910] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2019] [Accepted: 09/10/2019] [Indexed: 12/18/2022] Open
Abstract
Group B Streptococcus (GBS) is an opportunistic pathogen that causes preterm birth and neonatal disease. Although GBS is known to exhibit vast diversity in virulence across strains, the mechanisms of GBS-associated pathogenesis are incompletely understood. We hypothesized that GBS strains of different genotypes would vary in their ability to elicit host inflammatory responses, and that strains associated with neonatal disease would induce different cytokine profiles than those associated with colonization. Using a multiplexed, antibody-based protein detection array, we found that production of a discrete number of inflammatory mediators by THP-1 macrophage-like cells was universally induced in response to challenge with each of five genetically distinct GBS isolates, while other responses appeared to be strain-specific. Key array responses were validated by ELISA using the initial five strains as well as ten additional strains with distinct genotypic and phenotypic characteristics. Interestingly, IL-6 was significantly elevated following infection with neonatal infection-associated sequence type (ST)-17 strains and among strains possessing capsule (cps) type III. Significant differences in production of IL1-β, IL-10 and MCP-2 were also identified across STs and cps types. These data support our hypothesis and suggest that unique host innate immune responses reflect strain-specific differences in virulence across GBS isolates. Such data might inform the development of improved diagnostic or prognostic strategies against invasive GBS infections.
Collapse
|
42
|
Ayala OD, Doster RS, Manning SD, O’Brien CM, Aronoff DM, Gaddy JA, Mahadevan-Jansen A. Raman microspectroscopy differentiates perinatal pathogens on ex vivo infected human fetal membrane tissues. JOURNAL OF BIOPHOTONICS 2019; 12:e201800449. [PMID: 31162821 PMCID: PMC6902120 DOI: 10.1002/jbio.201800449] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2018] [Revised: 02/28/2019] [Accepted: 06/02/2019] [Indexed: 06/01/2023]
Abstract
Streptococcus agalactiae, also known as Group B Streptococcus (GBS), is a major cause of chorioamnionitis and neonatal sepsis. This study evaluates Raman spectroscopy (RS) to identify spectral characteristics of infection and differentiate GBS from Escherichia coli and Staphylococcus aureus during ex vivo infection of human fetal membrane tissues. Unique spectral features were identified from colonies grown on agar and infected fetal membrane tissues. Multinomial logistic regression analysis accurately identified GBS infected tissues with 100.0% sensitivity and 88.9% specificity. Together, these findings support further investigation into the use of RS as an emerging microbiologic diagnostic tool and intrapartum screening test for GBS carriage.
Collapse
|
43
|
Gendrin C, Vornhagen J, Armistead B, Singh P, Whidbey C, Merillat S, Knupp D, Parker R, Rogers LM, Quach P, Iyer LM, Aravind L, Manning SD, Aronoff DM, Rajagopal L. A Nonhemolytic Group B Streptococcus Strain Exhibits Hypervirulence. J Infect Dis 2019; 217:983-987. [PMID: 29244079 DOI: 10.1093/infdis/jix646] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 12/11/2017] [Indexed: 11/13/2022] Open
Abstract
Group B streptococci (GBS) are Gram-positive bacteria that are a leading cause of neonatal infections. Most invasive isolates are β-hemolytic, and hemolytic activity is critical for GBS virulence. Although nonhemolytic GBS strains are occasionally isolated, they are often thought to be virulence attenuated. In this study, we show that a nonhemolytic GBS strain (GB37) isolated from a septic neonate exhibits hypervirulence. Substitution of tryptophan to leucine (W297L) in the sensor histidine kinase CovS results in constitutive kinase signaling, leading to decreased hemolysis and increased activity of the GBS hyaluronidase, HylB. These results describe how nonpigmented and nonhemolytic GBS strains can exhibit hypervirulence.
Collapse
|
44
|
Sutton JA, Rogers LM, Dixon B, Kirk L, Doster R, Algood HM, Gaddy JA, Flaherty R, Manning SD, Aronoff DM. Protein kinase D mediates inflammatory responses of human placental macrophages to Group B Streptococcus. Am J Reprod Immunol 2019; 81:e13075. [PMID: 30582878 PMCID: PMC6459189 DOI: 10.1111/aji.13075] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Revised: 12/11/2018] [Accepted: 12/18/2018] [Indexed: 01/22/2023] Open
Abstract
PROBLEM During pregnancy, Group B Streptococcus (GBS) can infect fetal membranes to cause chorioamnionitis, resulting in adverse pregnancy outcomes. Macrophages are the primary resident phagocyte in extraplacental membranes. Protein kinase D (PKD) was recently implicated in mediating pro-inflammatory macrophage responses to GBS outside of the reproductive system. This work aimed to characterize the human placental macrophage inflammatory response to GBS and address the extent to which PKD mediates such effects. METHOD Primary human placental macrophages were infected with GBS in the presence or absence of a specific, small molecule PKD inhibitor, CRT 0066101. Macrophage phenotypes were characterized by evaluating gene expression, cytokine release, assembly of the NLRP3 inflammasome, and NFκB activation. RESULTS GBS evoked a strong inflammatory phenotype characterized by the release of inflammatory cytokines (TNFα, IL-1β, IL-6 (P ≤ 0.05), NLRP3 inflammasome assembly (P ≤ 0.0005), and NFκB activation (P ≤ 0.05). Pharmacological inhibition of PKD suppressed these responses, newly implicating a role for PKD in mediating immune responses of primary human placental macrophages to GBS. CONCLUSION PKD plays a critical role in mediating placental macrophage inflammatory activation in response to GBS infection.
Collapse
|
45
|
Korir ML, Flaherty RA, Rogers LM, Gaddy JA, Aronoff DM, Manning SD. Investigation of the Role That NADH Peroxidase Plays in Oxidative Stress Survival in Group B Streptococcus. Front Microbiol 2018; 9:2786. [PMID: 30515142 PMCID: PMC6255910 DOI: 10.3389/fmicb.2018.02786] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2018] [Accepted: 10/30/2018] [Indexed: 02/02/2023] Open
Abstract
Macrophages play an important role in defending the host against infections by engulfing pathogens and containing them inside the phagosome, which consists of a harsh microbicidal environment. However, many pathogens have developed mechanisms to survive inside macrophages despite this challenge. Group B Streptococcus (GBS), a leading cause of sepsis and meningitis in neonates, is one such pathogen that survives inside macrophages by withstanding phagosomal stress. Although a few key intracellular survival factors have been identified, the mechanisms by which GBS detoxifies the phagosome are poorly defined. Transcriptional analysis during survival inside macrophages revealed strong upregulation of a putative NADH peroxidase (npx) at 1 and 24 h post-infection. A deletion mutant of npx (Δnpx) was more susceptible to killing by a complex in vitro model of multiple phagosomal biochemical/oxidant stressors or by hydrogen peroxide alone. Moreover, compared to an isogenic wild type GBS strain, the Δnpx strain demonstrated impaired survival inside human macrophages and a reduced capacity to blunt macrophage reactive oxygen species (ROS) production. It is therefore likely that Npx plays a role in survival against ROS production in the macrophage. A more thorough understanding of how GBS evades the immune system through survival inside macrophages will aid in development of new therapeutic measures.
Collapse
|
46
|
Rogers LM, Gaddy JA, Manning SD, Aronoff DM. Variation in Macrophage Phagocytosis of Streptococcus agalactiae Does Not Reflect Bacterial Capsular Serotype, Multilocus Sequence Type or Association with Invasive Infection. Pathog Immun 2018. [PMID: 29930990 PMCID: PMC6007880 DOI: 10.20411/pai.v3i1.233] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Background: Group B Streptococcus(GBS) is an encapsulated Gram-positive coccus that is an important cause of infections in adults with chronic medical conditions, pregnant women, and neonates. GBS causes a range of clinical syndromes, from asymptomatic colonization to deep-seated invasive and highly lethal infections. Macrophages are important sentinels of innate immunity, protecting host tissues from infection when bacteria advance beyond cutaneous or mucosal barriers. We hypothesized that the capacity for macrophages to phagocytose unopsonized GBS would vary across distinct clinical strains, and such differences would reflect serotype diversity.Methods: A high-throughput screen using the phorbol ester-differentiated THP-1 macrophage-like human cell line was used to quantify phagocytosis of a diverse group of 35 different human clinical isolates of GBS representing a wide variety of capsular serotypes. Validation studies were conducted using human primary phagocytes.Results: Phagocytosis of GBS differed widely across clinical isolates but this was not related to capsular serotype, genetic sequence type, pilus type, or clinical source of the GBS isolate (colonizing or invasive strain).Conclusions: Structural and/or biochemical differences among diverse GBS strains are reflected in a diverse capacity for macrophages to ingest them through non-opsonic phagocytosis. Mechanisms explaining these differences are not clear.Keywords: Neonatal sepsis; innate immunity; macrophages; Gram-positive bacteria; diabetes
Collapse
|
47
|
Mukherjee S, Mosci RE, Anderson CM, Snyder BA, Collins J, Rudrik JT, Manning SD. Antimicrobial Drug-Resistant Shiga Toxin-Producing Escherichia coli Infections, Michigan, USA. Emerg Infect Dis 2018; 23:1609-1611. [PMID: 28820370 PMCID: PMC5572870 DOI: 10.3201/eid2309.170523] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
High frequencies of antimicrobial drug resistance were observed in O157 and non-O157 Shiga toxin–producing E. coli strains recovered from patients in Michigan during 2010–2014. Resistance was more common in non-O157 strains and independently associated with hospitalization, indicating that resistance could contribute to more severe disease outcomes.
Collapse
|
48
|
Cha W, Fratamico PM, Ruth LE, Bowman AS, Nolting JM, Manning SD, Funk JA. Prevalence and characteristics of Shiga toxin-producing Escherichia coli in finishing pigs: Implications on public health. Int J Food Microbiol 2018; 264:8-15. [DOI: 10.1016/j.ijfoodmicro.2017.10.017] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2017] [Revised: 10/11/2017] [Accepted: 10/12/2017] [Indexed: 10/18/2022]
|
49
|
Mukherjee S, Mosci R, Anderson C, Snyder B, Collins J, Rudrik J, Manning SD. Frequency of Antimicrobial Resistance in Shiga Toxin-Producing Escherichia coli (STEC) and Non-Typhoidal Salmonella (NTS) Clinical Infections and Association with Epidemiological Factors. Open Forum Infect Dis 2017. [PMCID: PMC5630854 DOI: 10.1093/ofid/ofx163.893] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Abstract
Background
STEC and NTS are leading causes of foodborne infections in the US. Monitoring resistance in these pathogens is essential to understand the distribution of resistance profiles and because of the high likelihood of horizontal transfer of resistance genes to other pathogens. Data involving resistance in clinical STEC and NTS isolates from Michigan is lacking.
Methods
Clinical STEC (n = 353) and NTS (n = 148) isolates from the MDHHS (2010–2014) were examined for resistance using disk diffusion, E-test or broth microdilution. Case information and epidemiological data for STEC isolates was extracted and associations with resistant infections were determined using chi square tests in SAS 9.3 and EpiInfo™ 7.
Results
Overall, 31 (8.8%, n = 353) STEC isolates were resistant to at least one antibiotic; high frequencies of resistance were observed for ampicillin (7.4%) and trimethoprim-sulfamethoxazole (4.0%). Resistance to ciprofloxacin (0.28%) and all three drug classes (0.28%) was less common. Preliminary results indicate that O157 resistance to ampicillin (4.8%) and trimethoprim-sulfamethoxazole (3.4%) was higher in Michigan compared with national frequencies (ampicillin = 2.7%, trimethoprim-sulfamethoxazole= 1.5%). Higher resistance frequencies were also observed in counties with high (11.3%) vs. low (7.7%) antibiotic prescription rates. For NTS, 23 (15.5%) isolates were resistant to ≥1 antibiotic. Resistance varied by serotype with high frequencies in Typhimurium (20%, n = 20), Newport (17.6%, n = 17) and Enteritidis (4.8%, n = 42); 11 (7.4%) NTS isolates were resistant to ≥3 antimicrobial classes.
Conclusion
Continuous monitoring of resistance in clinical STEC and NTS is warranted due to their importance as food pathogens. The identification of risk factors for resistance is crucial to develop alternative prevention practices to reduce the health burden of resistant infections in Michigan, which is not part of the FoodNet surveillance network.
Disclosures
All authors: No reported disclosures.
Collapse
|
50
|
Mukherjee S, Mosci RE, Anderson CM, Snyder BA, Collins J, Rudrik JT, Manning SD. Antimicrobial Drug–Resistant Shiga Toxin–Producing Escherichia coli Infections, Michigan, USA. Emerg Infect Dis 2017. [DOI: 10.3201/eid2309.17-0523] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
|