Pathogenic Microbiology Commons^™

Impact Of Probiotics On Black Soldier Fly Larvae Transmission Of Stenotrophomonas Maltophilia, Emily Marie Mclaughlin

Honors College

Stenotrophomonas maltophilia is an opportunistic pathogen which can cause a variety of infections, especially in immunocompromised individuals. It has recently been found that black soldier flies can act as carriers for S. maltophilia (Callegari et al., 2020). I have investigated how probiotics impact their vector capabilities. Black soldier fly larvae have been fed substrate spiked with S. maltophilia. After several days of feeding, the larvae were investigated by PCR and plating (Sveensson-Stadler et al., 2011). Two groups of larvae were fed with potatoes infected with S. maltophilia. Persistence of S. maltophilia was determined using PCR by taking samples …

Editorial: Pathogens, Pathobionts, And Autoimmunity, Linda A. Spatz, Gregg J. Silverman, Judith A. James

Publications and Research

No abstract provided.

Mara Repression Of Virulence Gene Hila In Salmonella, Alexandra King, Lauren Daugherty, Lon Chubiz Phd

Undergraduate Research Symposium

Salmonella is a bacteria most commonly known for causing the eponymous food-related illness. Due to their rapid reproduction rate and their ability to be propogated and maintained in a lab setting, they are commonly used in lab studies so that we can better understand how Salmonella causes disease in organisms that are more difficult to study. One area of interest is analyzing how Salmonella controls expression of the mechanisms that actually cause disease, called virulence traits, in response to the environment. In this study, antibiotic stress was used to analyze virulence gene expression. MarA is a gene that regulates ampicillin …

Higher Entropy Observed In Sars-Cov-2 Genomes From The First Covid-19 Wave In Pakistan, Najia Karim Ghanchi, Asghar Nasir, Kiran I. Masood, Syed Hani Abidi, Syed Faisal Mahmood, Akber Kanji, Safina Abdul Razzak, Waqasuddin Khan, Saba Shahid, Maliha Yameen, Ali Raza, Javaria Ashraf, Zeeshan Ansar Ahmed, Mohammad Buksh Dharejo, Nazneen Islam, Zahra Hasan, Rumina Hasan

Department of Pathology and Laboratory Medicine

Background: We investigated the genome diversity of SARS-CoV-2 associated with the early COVID-19 period to investigate evolution of the virus in Pakistan.
Materials and methods: We studied ninety SARS-CoV-2 strains isolated between March and October 2020. Whole genome sequences from our laboratory and available genomes were used to investigate phylogeny, genetic variantion and mutation rates of SARS-CoV-2 strains in Pakistan. Site specific entropy analysis compared mutation rates between strains isolated before and after June 2020.
Results: In March, strains belonging to L, S, V and GH clades were observed but by October, only L and GH strains were present. The …

Sterol Biosynthesis In Four Green Algae: A Bioinformatic Analysis Of The Ergosterol Versus Phytosterol Decision Point, Adam Voshall, Nakeirah T.M. Christie, Suzanne L. Rose, Maya Khasin, James L. Van Etten, Jennifer E. Markham, Wayne Riekhof, Kenneth Nickerson

Kenneth Nickerson Papers

Animals and fungi produce cholesterol and ergosterol, respectively, while plants produce the phytosterols stigmasterol, campesterol, and β-sitosterol in various combinations. The recent sequencing of many algal genomes allows the detailed reconstruction of the sterol metabolic pathways. Here, we characterized sterol synthesis in two sequenced Chlorella spp., the free-living C. sorokiniana, and symbiotic C. variabilis NC64A. Chlamydomonas reinhardtii was included as an internal control and Coccomyxa subellipsoidea as a plant-like outlier. We found that ergosterol was the major sterol produced by Chlorella spp. and C. reinhardtii, while C. subellipsoidea produced the three phytosterols found in plants. In silico analysis of the …

Telomeric And Sub-Telomeric Structure And Implications In Fungal Opportunistic Pathogens, Raffaella Diotti, Michelle Esposito, Chang Hui Shen

Publications and Research

Telomeres are long non-coding regions found at the ends of eukaryotic linear chromosomes. Although they have traditionally been associated with the protection of linear DNA ends to avoid gene losses during each round of DNA replication, recent studies have demonstrated that the role of these sequences and their adjacent regions go beyond just protecting chromosomal ends. Regions nearby to telomeric sequences have now been identified as having increased variability in the form of duplications and rearrangements that result in new functional abilities and biodiversity. Furthermore, unique fungal telomeric and chromatin structures have now extended clinical capabilities and understanding of pathogenicity …

Microbial Screening Reveals Oral Site-Specific Locations Of The Periodontal Pathogen Selenomonas Noxia, Jaydene Mcdaniel, Steven Mcdaniel, Beanca Jhanine Samiano, Matthew Marrujo, Karl Kingsley, Katherine M. Howard

Dental Medicine Faculty Publications

Introduction: Selenomonas noxia (SN) is an important periodontal pathogen, associated with gingivitis and periodontitis. Many studies have found associations between SN and indicators of poor health outcomes, such as smoking, low socioeconomic status and obesity. However, less is known about the prevalence of this organism and more specifically about other oral site-specific locations that may harbor this organism. Methods: Using an existing patient repository (n = 47) of DNA isolated from saliva and other oral sites (n = 235), including the dorsum of the tongue, lower lingual incisor, upper buccal molar and gingival crevicular fluid (GCF), molecular screening for SN …

Prevalence And Risk Factors Associated With Multi-Drug Resistant Organisms (Mdro) Carriage Among Pediatric Patients At The Time Of Admission In A Tertiary Care Hospital Of A Developing Country. A Cross-Sectional Study, Sonia Qureshi, Noshi Maria, Mohammad Zeeshan, Seema Irfan, Farah Naz Qamar

Department of Paediatrics and Child Health

Background: The rise of Multidrug-resistant organisms (MDROs) poses a considerable burden on the healthcare systems, particularly in low-middle income countries like Pakistan. There is a scarcity of data on the carriage of MDRO particularly in the pediatrics population therefore, we aimed to determine MDRO carriage in pediatric patients at the time of admission to a tertiary care hospital in Karachi, Pakistan, and to identify the risk factors associated with it.
Methods: A cross-sectional study conducted at the pediatric department of Aga Khan University Hospital (AKUH) from May to September 2019 on 347 children aged 1-18 years. For identification of MDRO …

Draft Genome Sequences Of 13 Vibrio Cholerae Strains From The Rio Grande Delta, Jeffrey W. Turner, Jorge Duran-Gonzalez, David A. Laughlin, Daniel Unterweger, David Silva, Boris Ermolinsky, Stefan Pukatzki, Daniele Provenzano

Publications and Research

Vibrio cholerae is the etiologic agent of cholera, an acute and often fatal diarrheal disease that affects millions globally. We report the draft genome sequences of 13 non-O1/O139 V. cholerae strains isolated from the Rio Grande Delta in Texas. These genomes will aid future analyses of environmental serovars.

Sickness Behaviors Across Vertebrate Taxa: Proximate And Ultimate Mechanisms, Patricia C. Lopes, Susannah S. French, Douglas C. Woodhams, Sandra A. Binning

Biology, Chemistry, and Environmental Sciences Faculty Articles and Research

There is nothing like a pandemic to get the world thinking about how infectious diseases affect individual behavior. In this respect, sick animals can behave in ways that are dramatically different from healthy animals: altered social interactions and changes to patterns of eating and drinking are all hallmarks of sickness. As a result, behavioral changes associated with inflammatory responses (i.e. sickness behaviors) have important implications for disease spread by affecting contacts with others and with common resources, including water and/or sleeping sites. In this Review, we summarize the behavioral modifications, including changes to thermoregulatory behaviors, known to occur in vertebrates …

Vignette 14: Eelgrass Wasting Disease, Olivia Graham, Morgan Eisenlord, Drew Harvell

Institute Publications

Rising seawater temperatures can increase the risk of disease outbreaks in many taxa. Pathogens are potentially the ultimate keystone species in that their small biomass can have massive impacts that ripple through ecosystems. Disease outbreaks can be particularly damaging when they affect ecosystem engineers, such as seagrasses. Outbreaks of wasting disease in seagrasses are one of a myriad of stressors associated with declining temperate and tropical seagrass meadows around the globe. Levels of eelgrass wasting disease are high in the San Juan Islands and Puget Sound. These increasing levels of disease are a threat to sustainability of eelgrass meadows, our …

Process Interventions For Improving The Microbiological Safety Of Low Moisture Food Ingredients, Tushar Verma

Department of Food Science and Technology: Dissertations, Theses, and Student Research

The recurrence of Salmonella in low moisture foods and the implementation of the FSMA rule requires a need to validate legacy and novel processing technologies. In this dissertation, a legacy thermal (extrusion), a novel thermal (radiofrequency (RF) heating), and a non-thermal (chlorine dioxide) technology, were evaluated as intervention technologies for Salmonella in low moisture foods. The twin-screw extruder was performed at different levels of screw speeds, temperatures, moisture contents, and fat contents to understand the impact of processing conditions on Salmonella inactivation in oat flour. At temperature >65°C, the Salmonella population was below the detection limit. At 55°C, Salmonella reduction …

Respiratory Pathogens In Patients With Acute Exacerbation Of Non-Cystic Fibrosis Bronchiectasis From A Developing Country, Shayan Shahid, Kausar Jabeen, Nousheen Iqbal, Joveria Farooqi, Muhammad Irfan

Medical College Documents

Bronchiectasis unrelated to cystic fibrosis (non-CF bronchiectasis) has become a major respiratory disease in developing nations. The dilated mucus filled airways promote bacterial overgrowth followed by chronic infection, bronchial inflammation, lung injury and re-infection Accurate pathogen identification and antimicrobial susceptibility allowing appropriate treatment, in turn, may break this vicious cycle. To study the spectrum and antimicrobial spectrum of pathogen yielded from respiratory specimens in adult patients with acute exacerbation of non-cystic fibrosis (CF) bronchiectasis. This cross-sectional study was performed at the pulmonology clinics of the Aga Khan University, Karachi, Pakistan from 2016-2019. Respiratory specimens were collected from adult patients with …

Molecular Surveillance Of Drug Resistance: Plasmodium Falciparum Artemisinin Resistance Single Nucleotide Polymorphisms In Kelch Protein Propeller (K13) Domain From Southern Pakistan, Najia Karim Ghanchi, Bushra Qurashi, Hadiqa Raees, Mohammad Asim Beg

Department of Pathology and Laboratory Medicine

Background: K13 propeller (k13) polymorphism are useful molecular markers for tracking the emergence and spread of artemisinin resistance in Plasmodium falciparum. Polymorphisms are reported from Cambodia with rapid invasion of the population and almost near fixation in south East Asia. The study describes single nucleotide polymorphisms in Kelch protein propeller domain of P. falciparum associated with artemisinin resistance from Southern Pakistan.
Methods: Two hundred and forty-nine samples were collected from patients with microscopy confirmed P. falciparum malaria attending Aga Khan University Hospital during September 2015-April 2018. DNA was isolated using the whole blood protocol for the QIAmp DNA Blood Kit. …

Pirnas As Modulators Of Disease Pathogenesis, Kayla J. Rayford, Ayorinde Cooley, Jelonia T. Rumph, Ashutosh Arun, Girish Rachakonda, Fernando Villalta, Maria F. Lima, Siddharth Pratap, Smita Misra, Pius N. Nde

Publications and Research

Advances in understanding disease pathogenesis correlates to modifications in gene expression within different tissues and organ systems. In depth knowledge about the dysregulation of gene expression profiles is fundamental to fully uncover mechanisms in disease development and changes in host homeostasis. The body of knowledge surrounding mammalian regulatory elements, specifically regulators of chromatin structure, transcriptional and translational activation, has considerably surged within the past decade. A set of key regulators whose function still needs to be fully elucidated are small non-coding RNAs (sncRNAs). Due to their broad range of unfolding functions in the regulation of gene expression during transcription and …

When The Pandemic Opts For The Lockdown: Secretion System Evolution In The Cholera Bacterium, Francis J. Santoriello, Stefan Pukatzki

Publications and Research

Vibrio cholerae, the causative agent of the diarrheal disease cholera, is a microbe capable of inhabiting two different ecosystems: chitinous surfaces in brackish, estuarine waters and the epithelial lining of the human gastrointestinal tract. V. cholerae defends against competitive microorganisms with a contact-dependent, contractile killing machine called the type VI secretion system (T6SS) in each of these niches. The T6SS resembles an inverted T4 bacteriophage tail and is used to deliver toxic effector proteins into neighboring cells. Pandemic strains of V. cholerae encode a unique set of T6SS effector proteins, which may play a role in pathogenesis or pandemic …

Pandemic Vibrio Cholerae Shuts Down Site-Specific Recombination To Retain An Interbacterial Defence Mechanism, Francis J. Santoriello, Lina Michel, Daniel Unterweger, Stefan Pukatzki

Publications and Research

Vibrio cholerae is an aquatic microbe that can be divided into three subtypes: harmless environmental strains, localised pathogenic strains, and pandemic strains causing global cholera outbreaks. Each type has a contact-dependent type VI secretion system (T6SS) that kills neighbouring competitors by translocating unique toxic effector proteins. Pandemic isolates possess identical effectors, indicating that T6SS effectors may affect pandemicity. Here, we show that one of the T6SS gene clusters (Aux3) exists in two states: a mobile, prophage-like element in a small subset of environmental strains, and a truncated Aux3 unique to and conserved in pandemic isolates. Environmental Aux3 can be readily …

Aspergillus Niger Decreases Bioavailability Of Arsenic(V) Via Biotransformation Of Manganese Oxide Into Biogenic Oxalate Minerals, Bence Farkas, Marek Kolenčík, Miroslav Hain, Edmund Dobročka, Gabriela Kratošová, Marek Bujdoš, Huan Feng, Yang Deng, Qian Yu, Ramakanth Illa, B. Ratna Sunil, Hyunjung Kim, Peter Matúš, Martin Urík

Department of Earth and Environmental Studies Faculty Scholarship and Creative Works

The aim of this work was to evaluate the transformation of manganese oxide (hausmannite) by microscopic filamentous fungus Aspergillus niger and the effects of the transformation on mobility and bioavailability of arsenic. Our results showed that the A. niger strain CBS 140837 greatly affected the stability of hausmannite and induced its transformation into biogenic crystals of manganese oxalates—falottaite and lindbergite. The transformation was enabled by fungal acidolysis of hausmannite and subsequent release of manganese ions into the culture medium. While almost 45% of manganese was bioextracted, the arsenic content in manganese precipitates increased throughout the 25-day static cultivation of fungus. …

Carbapenem-Resistant Enterobacteriaceae (Cre): Epidemiology, Duration Of Carriage, And Progression To Infection In A Large Healthcare System In Miami, Fl, Adriana Jimenez

FIU Electronic Theses and Dissertations

Carbapenem-resistant Enterobacteriaceae (CRE) are multidrug-resistant organisms (MDRO) considered by the CDC as an urgent public health threat that is spreading globally. Little is known about the epidemiology of CRE in Miami, FL. The purpose of this dissertation was to 1) Evaluate trends in the epidemiology of CRE among patients admitted to the acute care facilities of the largest healthcare system in Miami, FL between 2012 and 2016, 2) Identify factors associated with progressing to infection among patients colonized with carbapenemase-producing Enterobacteriaceae (CPE), and 3) Determine the duration of CPE carriage and factors associated with long-term carriage in our cohort.

A …

Investigating Microbial And Host Factors That Modulate Severity Of Clostridioides Difficile Associated Disease, Armando Lerma

Department of Food Science and Technology: Dissertations, Theses, and Student Research

Clostridioides difficile is recognized as one of the most important pathogens in hospital and community healthcare settings. The clinical outcome of infection of toxigenic C. difficile infection (CDI) ranges from asymptomatic colonization to fulminant pseudomembranous colitis and death. In recent studies, it has been suggested that a high proportion of nosocomial CDI cases are transmitted from asymptomatic carriers which might be acting as infection reservoirs. Understanding what causes the different responses to infection could lead to the development of novel prevention and treatment strategies. Although several explanations have been proposed to explain variations in susceptibility, understanding of the exact mechanisms …

Evaluation Of Semi-Quantitative Compared To Quantitative Cultures Of Tracheal Aspirates For The Yield Of Culturable Respiratory Pathogens - A Cross-Sectional Study, Salima Rattani, Joveria Farooqi, Ghazala Jabeen, Saeeda Chandio, Qaiser Kash, Aijaz Khan, Kauser Jabeen

Department of Pathology and Laboratory Medicine

Background: Diagnosis of lower respiratory tract infections (LRTI) depends on the presence of clinical, radiological and microbiological findings. Endotracheal suction aspirate (ETSA) is the commonest respiratory sample sent for culture from intubated patients. Very few studies have compared quantitative and semi-quantitative processing of ETSA cultures for LRTI diagnosis. We determined the diagnostic accuracy of quantitative and semi-quantitative ETSA culture for LRTI diagnosis, agreement between the quantitative and semi quantitative culture techniques and the yield of respiratory pathogens with both methods.
Methods: This was a cross-sectional study conducted at the Aga Khan University clinical laboratory, Karachi, Pakistan. One hundred and seventy-eight …

How Does Molecular Biology Help To Identify Plant Disease?, Madina Akramova

English Language Institute

This study examines a process of plant disease diagnostics in light of a particular method of molecular biology - polymerase chain reaction.

Repression Of Tick Microrna-133 Induces Organic Anion Transporting Polypeptide Expression Critical For Anaplasma Phagocytophilumsurvival In The Vector And Transmission To The Vertebrate Host, Ellango Ramasamy, Vikas Taank, John F. Anderson, Hameeda Sultana, Girish Neelakanta

Biological Sciences Faculty Publications

The microRNAs (miRNAs) are important regulators of gene expression. In this study, we provide evidence for the first time to show that rickettsial pathogen Anaplasma phagocytophilum infection results in the down-regulation of tick microRNA-133 (miR-133), to induce Ixodes scapularis organic anion transporting polypeptide (isoatp4056) gene expression critical for this bacterial survival in the vector and for its transmission to the vertebrate host. Transfection studies with recombinant constructs containing transcriptional fusions confirmed binding of miR-133 to isoatp4056 mRNA. Treatment with miR-133 inhibitor resulted in increased bacterial burden and isoatp4056 expression in ticks and tick cells. In contrast, treatment with …

Plant Defensin Antibacterial Mode Of Action Against Pseudomonas Species, Andrew E. Sathoff, Shawn Lewenza, Deborah A. Samac

Faculty Research & Publications

Background: Though many plant defensins exhibit antibacterial activity, little is known about their antibacterial mode of action (MOA). Antimicrobial peptides with a characterized MOA induce the expression of multiple bacterial outer membrane modifications, which are required for resistance to these membrane-targeting peptides. Mini-Tn5- lux mutant strains of Pseudomonas aeruginosa with Tn insertions disrupting outer membrane protective modifications were assessed for sensitivity against plant defensin peptides. These transcriptional lux reporter strains were also evaluated for lux gene expression in response to sublethal plant defensin exposure. Also, a plant pathogen, Pseudomonas syringae pv. syringae was modified through transposon mutagenesis to …

Contributions Of Gyra And Parc Mutations And Qnrs2 Acquisition To Ciprofloxacin Resistance In Aeromonas Veronii Hm21, Daniel J. Silverstein

Honors Scholar Theses

In recent years, ciprofloxacin resistant (CpR) Aeromonas veronii and A. hydrophila strains have been isolated from the wounds of patients receiving leech therapy. Genome comparisons of these CpR isolates revealed the presence of chromosomal mutations in gyrA and parC as well as the gain of qnrS2 on either a large, 34 kb, conjugatable, low-copy plasmid, pAv42, or on a small, 6.8 kb, high-copy plasmid, pAh1471. The minimum inhibitory concentration, MIC, for Cp of these clinical isolates ranged from 1 to ≥32 µg/mL and some harbored a qnrS2 containing plasmid. We wanted to assess the contributions of these factors in an …

Investigation Of Rapid Diagnostic Tests For Characterization Of Mycobacterium Avium Complex (Mac) From Various Isolates And Identification Of Virulence Factors Of Porcine Reproductive And Respiratory Syndrome Virus (Prrsv) In Vitro, Claudia Antonika

UCARE Research Products

Chapter 1

Mycobacterium avium complex (MAC) has become one of the major problems in public health and livestock. Members of MAC, such as M. avium subsp paratuberculosis (MAP) and M. avium subsp hominissuis (MAH), are responsible for many opportunistic infections and the loss of livestock. MAP is economically significant to the beef and dairy industries because it is the etiologic agent of Johnes’s disease, a chronic and fatal enteritis in ruminants. Tracing the infection sources of MAC could be difficult since it infects many types of hosts in the natural environment. Furthermore, there is less information known about MAP pathogenicity …

Microbiota Accessible Carbohydrates And Susceptibility To Clostridioides Difficile Infection, Keegan Schuchart, Jennifer Auchtung, Thomas Auchtung

UCARE Research Products

This experiment looked into the effects of dietary microbiota accessible carbohydrates (MACs)on the composition of human GI microbe colonies and their susceptibility to pathogen infection. Three different concentrations of MAC ingrained media were tested in mini bioreactor arrays, treated with antibiotics, infected with Clostridioides difficile, then allowed to recover. Microbe community was examined for strain composition and diversity before and after the antibiotic treatment and Clostridioides difficile infection. After the initial mini bioreactor run, individual isolates were investigated in their ability to respond to specific MACs Arabinoglactina, Inulin, and Soluble starch at experimental concentrations.

Biological Sex Influences Susceptibility To Acinetobacter Baumannii Pneumonia In Mice, Sílvia Pires, Adeline Peignier, Jeremy Seto, Davida S. Smyth, Dane Parker

Publications and Research

Acinetobacter baumannii (A. baumannii) is an extremely versatile multidrug-resistant pathogen with a very high mortality rate; therefore, it has become crucial to understand the host response during its infection. Given the importance of mice for modeling infection and their role in preclinical drug development, equal emphasis should be placed on the use of both sexes. Through our studies using a murine model of acute pneumonia with A. baumannii, we observed that female mice were more susceptible to infection. Likewise, treatment of male mice with estradiol increased their susceptibility to infection. Analysis of the airway compartment revealed enhanced inflammation and reduced …

Histidine-Triad Hydrolases Provide Resistance To Peptide-Nucleotide Antibiotics., Eldar Yagmurov, Darya Tsibulskaya, Alexey Livenskyi, Marina Serebryakova, Yury I Wolf, Sergei Borukhov, Konstantin Severinov, Svetlana Dubiley

Rowan-Virtua School of Osteopathic Medicine Faculty Scholarship

The Escherichia coli microcin C (McC) and related compounds are potent Trojan horse peptide-nucleotide antibiotics. The peptide part facilitates transport into sensitive cells. Inside the cell, the peptide part is degraded by nonspecific peptidases releasing an aspartamide-adenylate containing a phosphoramide bond. This nonhydrolyzable compound inhibits aspartyl-tRNA synthetase. In addition to the efficient export of McC outside the producing cells, special mechanisms have evolved to avoid self-toxicity caused by the degradation of the peptide part inside the producers. Here, we report that histidine-triad (HIT) hydrolases encoded in biosynthetic clusters of some McC homologs or by standalone genes confer resistance to McC-like …

Fungicide Sensitivity Of Sclerotinia Sclerotiorum Isolates Selected From Five Different States That Use Different Fungicide Treatments, Cristian Wulkop Gil

UCARE Research Products

Sclerotinia sclerotiorum is a plant pathogenic fungus that causes a disease called white mold that can infect more than 450 plant species including soybeans, dry beans, green beans, canola, and sunflower. This pathogen is capable of up to $252M in losses every year (U.S. Canola Association, 2014). Fungicides are widely used in developed agricultural systems to control disease. However, resistance to the most effective fungicides has emerged and spread in pathogen populations and there have been multiple reports of S. sclerotiorum isolates becoming resistant to certain fungicides. Since different fields in different states use different fungicide treatments on plants and …