Genomic Analysis of Emerging Florfenicol-Resistant Campylobacter coli Isolated from the Intestinal Cecal Contents of Cattle in the United States

Genomic Analysis of Emerging Florfenicol-Resistant Campylobacter coli Isolated from the Cecal Contents of Cattle in the United States

mSphere ◽

10.1128/msphere.00367-19 ◽

2019 ◽

Vol 4 (3) ◽

Author(s):

Shaohua Zhao ◽

Sampa Mukherjee ◽

Chih-Hao Hsu ◽

Shenia Young ◽

Cong Li ◽

...

Keyword(s):

United States ◽

Risk Assessment ◽

Antimicrobial Resistance ◽

The United States ◽

Mitigation Strategies ◽

Virulence Plasmid ◽

Campylobacter Coli ◽

Content Type ◽

Gram Positive Bacteria ◽

Antimicrobial Resistance Surveillance

ABSTRACT Genomic analyses were performed on florfenicol-resistant (FFNr) Campylobacter coli isolates recovered from cattle, and the cfr(C) gene-associated multidrug resistance (MDR) plasmid was characterized. Sixteen FFNr C. coli isolates recovered between 2013 and 2018 from beef cattle were sequenced using MiSeq. Genomes and plasmids were found to be closed for three of the isolates using the PacBio system. Single nucleotide polymorphisms (SNPs) across the genome and the structures of MDR plasmids were investigated. Conjugation experiments were performed to determine the transferability of cfr(C)-associated MDR plasmids. The spectrum of resistance encoded by the cfr(C) gene was further investigated by agar dilution antimicrobial susceptibility testing. All 16 FFNr isolates were MDR and exhibited coresistance to ciprofloxacin, nalidixic acid, clindamycin, and tetracycline. All isolates shared the same resistance genotype, carrying aph (3′)-III, hph, ΔaadE (truncated), blaOXA-61, cfr(C), and tet(O) genes plus a mutation of GyrA (T86I). The cfr(C), aph (3′)-III, hph, ΔaadE, and tet(O) genes were colocated on transferable MDR plasmids ranging in size from 48 to 50 kb. These plasmids showed high sequence homology with the pTet plasmid and carried several Campylobacter virulence genes, including virB2, virB4, virB5, VirB6, virB7, virB8, virb9, virB10, virB11, and virD4. The cfr(C) gene conferred resistance to florfenicol (8 to 32 μg/ml), clindamycin (512 to 1,024 μg/ml), linezolid (128 to 512 μg/ml), and tiamulin (1,024 μg/ml). Phylogenetic analysis showed SNP differences ranging from 11 to 2,248 SNPs among the 16 isolates. The results showed that the cfr(C) gene located in the conjugative pTet MDR/virulence plasmid is present in diverse strains, where it confers high levels of resistance to several antimicrobials, including linezolid, a critical drug for treating infections by Gram-positive bacteria in humans. This report highlights the power of genomic antimicrobial resistance surveillance to uncover the intricacies of transmissible coresistance and provides information that is needed for accurate risk assessment and mitigation strategies. IMPORTANCE Campylobacter is a leading cause of foodborne diarrheal illness worldwide, with more than one million cases each year in the United States alone. The global emergence of antimicrobial resistance in this pathogen has become a growing public health concern. Florfenicol-resistant (FFNr) Campylobacter has been very rare in the United States. In this study, we employed whole-genome sequencing to characterize 16 multidrug-resistant Campylobacter coli isolates recovered from cattle in the United States. A gene [cfr(C)] was found to be responsible for resistance not only to florfenicol but also to several other antimicrobials, including linezolid, a critical drug for treating infections by Gram-positive bacteria in humans. The results showed that cfr(C) is located in a conjugative pTet MDR/virulence plasmid. This report highlights the power of antimicrobial resistance surveillance to uncover the intricacies of transmissible coresistance and provides information that is needed for accurate risk assessment and mitigation strategies.

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Genomic Analysis of SARS-CoV-2 Variants of Concern Circulating in Hawai’i to Facilitate Public-Health Policies

10.21203/rs.3.rs-378702/v2 ◽

2021 ◽

Author(s):

David P Maison ◽

Sean B. Cleveland ◽

Vivek R Nerurkar

Keyword(s):

Public Health ◽

Phylogenetic Trees ◽

Genomic Analysis ◽

The United States ◽

Recent Common Ancestor ◽

Nucleotide Polymorphisms ◽

Multiple Sequence ◽

Consensus Sequences ◽

Most Recent Common Ancestor ◽

Global Initiative

Abstract Using genomics, bioinformatics and statistics, herein we demonstrate the effect of statewide and nationwide quarantine on the introduction of SARS-CoV-2 variants of concern (VOC) in Hawai’i. To define the origins of introduced VOC, we analyzed 260 VOC sequences from Hawai’i, and 301,646 VOC sequences worldwide, deposited in the GenBank and global initiative on sharing all influenza data (GISAID), and constructed phylogenetic trees. The trees define the most recent common ancestor as the origin. Further, the multiple sequence alignment used to generate the phylogenetic trees identified the consensus single nucleotide polymorphisms in the VOC genomes. These consensus sequences allow for VOC comparison and identification of mutations of interest in relation to viral immune evasion and host immune activation. Of note is the P71L substitution within the E protein, the protein sensed by TLR2 to produce cytokines, found in the B.1.351 VOC may diminish the efficacy of some vaccines. Based on the phylogenetic trees, the B.1.1.7, B.1.351, B.1.427, and B.1.429 VOC have been introduced in Hawai'i multiple times since December 2020 from several definable geographic regions. From the first worldwide report of VOC in GenBank and GISAID, to the first arrival of VOC in Hawai’i, averages 320 days with quarantine, and 132 days without quarantine. As such, the effect of quarantine is shown to significantly affect the time to arrival of VOC in Hawai’i, both during and following quarantine. Further, the collective 2020 quarantine of 43-states in the United States demonstrates a profound impact in delaying the arrival of VOC in states that did not practice quarantine, such as Utah. Our data demonstrates that at least 76% of all definable SARS-CoV-2 VOC have entered Hawai’i from California, with the B.1.351 variant in Hawai’i originating exclusively from the United Kingdom. These data provide a foundation for policy-makers and public-health officials to apply precision public health genomics to real-world policies such as mandatory screening and quarantine.

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Whole-Genome Sequencing of Gentamicin-Resistant Campylobacter coli Isolated from U.S. Retail Meats Reveals Novel Plasmid-Mediated Aminoglycoside Resistance Genes

Antimicrobial Agents and Chemotherapy ◽

10.1128/aac.00669-13 ◽

2013 ◽

Vol 57 (11) ◽

pp. 5398-5405 ◽

Cited By ~ 54

Author(s):

Yuansha Chen ◽

Sampa Mukherjee ◽

Maria Hoffmann ◽

Michael L Kotewicz ◽

Shenia Young ◽

...

Keyword(s):

Resistance Genes ◽

Antibiotic Resistance Genes ◽

The United States ◽

Campylobacter Coli ◽

Whole Genome ◽

Nucleotide Polymorphisms ◽

Aminoglycoside Resistance ◽

Content Type ◽

Retail Meats ◽

Gentamicin Resistance

ABSTRACTAminoglycoside resistance inCampylobacterhas been routinely monitored in the United States in clinical isolates since 1996 and in retail meats since 2002. Gentamicin resistance first appeared in a single human isolate ofCampylobacter coliin 2000 and in a single chicken meat isolate in 2007, after which it increased rapidly to account for 11.3% of human isolates and 12.5% of retail isolates in 2010. Pulsed-field gel electrophoresis analysis indicated that gentamicin-resistantC. coliisolates from retail meat were clonal. We sequenced the genomes of two strains of this clone using a next-generation sequencing technique in order to investigate the genetic basis for the resistance. The gaps of one strain were closed using optical mapping and Sanger sequencing, and this is the first completed genome ofC. coli. The two genomes are highly similar to each other. A self-transmissible plasmid carrying multiple antibiotic resistance genes was revealed within both genomes, carrying genes encoding resistance to gentamicin, kanamycin, streptomycin, streptothricin, and tetracycline. Bioinformatics analysis and experimental results showed that gentamicin resistance was due to a phosphotransferase gene,aph(2″)-Ig, not described previously. The phylogenetic relationship of this newly emerged clone to otherCampylobacterspp. was determined by whole-genome single nucleotide polymorphisms (SNPs), which showed that it clustered with the other poultry isolates and was separated from isolates from livestock.

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Genomic Analysis of SARS-CoV-2 Variants of Concern Circulating in Hawai’i to Facilitate Public-Health Policies

10.21203/rs.3.rs-378702/v3 ◽

2021 ◽

Author(s):

David P Maison ◽

Sean B. Cleveland ◽

Vivek R Nerurkar

Keyword(s):

Public Health ◽

Phylogenetic Trees ◽

Genomic Analysis ◽

The United States ◽

Recent Common Ancestor ◽

Nucleotide Polymorphisms ◽

Multiple Sequence ◽

Consensus Sequences ◽

Most Recent Common Ancestor ◽

Global Initiative

Abstract Using genomics, bioinformatics and statistics, herein we demonstrate the effect of statewide and nationwide quarantine on the introduction of SARS-CoV-2 variants of concern (VOC) in Hawai’i. To define the origins of introduced VOC, we analyzed 260 VOC sequences from Hawai’i, and 301,646 VOC sequences worldwide, deposited in the GenBank and global initiative on sharing all influenza data (GISAID), and constructed phylogenetic trees. The trees define the most recent common ancestor as the origin. Further, the multiple sequence alignment used to generate the phylogenetic trees identified the consensus single nucleotide polymorphisms in the VOC genomes. These consensus sequences allow for VOC comparison and identification of mutations of interest in relation to viral immune evasion and host immune activation. Of note is the P71L substitution within the E protein, the protein sensed by TLR2 to produce cytokines, found in the B.1.351 VOC may diminish the efficacy of some vaccines. Based on the phylogenetic trees, the B.1.1.7, B.1.351, B.1.427, and B.1.429 VOC have been introduced in Hawai'i multiple times since December 2020 from several definable geographic regions. From the first worldwide report of VOC in GenBank and GISAID, to the first arrival of VOC in Hawai’i, averages 320 days with quarantine, and 132 days without quarantine. As such, the effect of quarantine is shown to significantly affect the time to arrival of VOC in Hawai’i, both during and following quarantine. Further, the collective 2020 quarantine of 43-states in the United States demonstrates a profound impact in delaying the arrival of VOC in states that did not practice quarantine, such as Utah. Our data demonstrates that at least 76% of all definable SARS-CoV-2 VOC have entered Hawai’i from California, with the B.1.351 variant in Hawai’i originating exclusively from the United Kingdom. These data provide a foundation for policy-makers and public-health officials to apply precision public health genomics to real-world policies such as mandatory screening and quarantine.

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Synthesis and In Vitro Enzymatic Studies of New 3-Aryldiazenyl Indoles as Promising Helicobacter pylori IMPDH Inhibitors

Current Topics in Medicinal Chemistry ◽

10.2174/1568026619666190227212334 ◽

2019 ◽

Vol 19 (5) ◽

pp. 376-382 ◽

Cited By ~ 4

Author(s):

Sachin Jangra ◽

Gayathri Purushothaman ◽

Kapil Juvale ◽

Srimadhavi Ravi ◽

Aishwarya Menon ◽

...

Keyword(s):

Helicobacter Pylori ◽

Bacterial Infections ◽

Immunosuppressive Drugs ◽

Multi Drug Resistance ◽

Metabolic Enzyme ◽

World Population ◽

Inhibitor Molecule ◽

Nucleotide Synthesis ◽

H Pylori

Background & Objective:Helicobacter pylori infection is one of the primary causes of peptic ulcer followed by gastric cancer in the world population. Due to increased occurrences of multi-drug resistance to the currently available antibiotics, there is an urgent need for a new class of drugs against H. pylori. Inosine 5′-monophosphate dehydrogenase (IMPDH), a metabolic enzyme plays a significant role in cell proliferation and cell growth. It catalyses guanine nucleotide synthesis. IMPDH enzyme has been exploited as a target for antiviral, anticancer and immunosuppressive drugs. Recently, bacterial IMPDH has been studied as a potential target for treating bacterial infections. Differences in the structural and kinetic parameters of the eukaryotic and prokaryotic IMPDH make it possible to target bacterial enzyme selectively.Methods:In the current work, we have synthesised and studied the effect of substituted 3-aryldiazenyl indoles on Helicobacter pylori IMPDH (HpIMPDH) activity. The synthesised molecules were examined for their inhibitory potential against recombinant HpIMPDH.Results:In this study, compounds 1 and 2 were found to be the most potent inhibitors amongst the database with IC50 of 0.8 ± 0.02µM and 1 ± 0.03 µM, respectively.Conclusion:When compared to the most potent known HpIMPDH inhibitor molecule C91, 1 was only four-fold less potent and can be a good lead for further development of selective and potent inhibitors of HpIMPDH.

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Comparative Genomic Analysis of 450 Strains of Salmonella enterica Isolated from Diseased Animals

Genes ◽

10.3390/genes11091025 ◽

2020 ◽

Vol 11 (9) ◽

pp. 1025

Author(s):

Shaohua Zhao ◽

Cong Li ◽

Chih-Hao Hsu ◽

Gregory H. Tyson ◽

Errol Strain ◽

...

Keyword(s):

Resistance Genes ◽

Bacterial Infections ◽

Genomic Analysis ◽

Heavy Metal Resistance ◽

Metal Resistance ◽

Comparative Genomic ◽

Salmonella Infections ◽

Antimicrobial Resistance Genes ◽

Salmonella Pathogenicity Islands ◽

Shed Light

Salmonella is a leading cause of bacterial infections in animals and humans. We sequenced a collection of 450 Salmonella strains from diseased animals to better understand the genetic makeup of their virulence and resistance features. The presence of Salmonella pathogenicity islands (SPIs) varied by serotype. S. Enteritidis carried the most SPIs (n = 15), while S. Mbandaka, S. Cerro, S. Meleagridis, and S. Havana carried the least (n = 10). S. Typhimurium, S. Choleraesuis, S. I 4,5,12:i:-, and S. Enteritidis each contained the spv operon on IncFII or IncFII-IncFIB hybrid plasmids. Two S. IIIa carried a spv operon with spvD deletion on the chromosome. Twelve plasmid types including 24 hybrid plasmids were identified. IncA/C was frequently associated with S. Newport (83%) and S. Agona (100%) from bovine, whereas IncFII (100%), IncFIB (100%), and IncQ1 (94%) were seen in S. Choleraesuis from swine. IncX (100%) was detected in all S. Kentucky from chicken. A total of 60 antimicrobial resistance genes (ARGs), four disinfectant resistances genes (DRGs) and 33 heavy metal resistance genes (HMRGs) were identified. The Salmonella strains from sick animals contained various SPIs, resistance genes and plasmid types based on the serotype and source of the isolates. Such complicated genomic structures shed light on the strain characteristics contributing to the severity of disease and treatment failures in Salmonella infections, including those causing illnesses in animals.

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307 A systems approach to understanding biosecurity decision-making

Journal of Animal Science ◽

10.1093/jas/skaa278.078 ◽

2020 ◽

Vol 98 (Supplement_4) ◽

pp. 43-43

Author(s):

Scott C Merrill ◽

Christopher Koliba ◽

Gabriela Bucini ◽

Eric Clark ◽

Luke Trinity ◽

...

Keyword(s):

Decision Making ◽

Negative Impact ◽

Risk Mitigation ◽

African Swine Fever Virus ◽

The United States ◽

Mitigation Strategies ◽

Communication Strategy ◽

Livestock Industry ◽

Diarrhea Virus ◽

Operational Level

Abstract Disease and its consequences result in social and economic impacts to the US animal livestock industry, ranging from losses in human capital to economic costs in excess of a billion dollars annually. Impacts would dramatically escalate if a devastating disease like Foot and Mouth Disease or African Swine Fever virus were to emerge in the United States. Investing in preventative biosecurity can reduce the likelihood of disease incursions and their negative impact on our livestock industry, yet uncertainty persists with regards to developing an effective biosecurity structure and culture. Here we show the implications of human behavior and decision making for biosecurity effectiveness, from the operational level to the owner/managerial level and finally to the systems level. For example, adjustments to risk messaging strategies could double worker compliance with biosecurity practices at the operational level. The improvement of our risk communication strategy may increase willingness to invest in biosecurity. Furthermore, the adaptation of policies could nudge behavior so that we observe a short disease outbreak followed by a quick eradication instead of a pandemic. Our research shows how the emergence of now-endemic diseases, such as Porcine Epidemic Diarrhea virus, cannot be adequately modeled without the use of a human behavioral component. Focusing solely on any one sector or level of the livestock system is not sufficient to predict emergent disease patterns and their social and economic impact on livestock industries. These results provide insight toward developing more effective risk mitigation strategies and ways to nudge behavior toward more disease resilient systems.

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652. Comparison of fosfomycin (FOF) activity and prevalence of subpopulations between Escherichia coli (EC) and Klebsiella pneumoniae (KP) during susceptibility testing

Open Forum Infectious Diseases ◽

10.1093/ofid/ofaa439.846 ◽

2020 ◽

Vol 7 (Supplement_1) ◽

pp. S384-S384

Author(s):

Jadyn C Anderson ◽

Amanda R Krueger ◽

Elizabeth C Smith ◽

Morgan L Bixby ◽

Hunter V Brigman ◽

...

Keyword(s):

Clinical Efficacy ◽

Inhibitory Concentration ◽

Panel Member ◽

Colony Growth ◽

The United States ◽

Research Support ◽

Review Panel ◽

Agreement Rate ◽

Future Studies ◽

Agar Dilution

Abstract Background In the United States, interpretive criteria for FOF are established only for EC, yet those criteria are often extrapolated to KP. Recent studies have highlighted both inferior clinical outcomes after FOF treatment and difficulties in interpretation of inner colony subpopulations, the presence of which may affect clinical efficacy. We sought to compare FOF activity against EC and KP and to determine the prevalence of inner colony subpopulations following disk diffusion (DD) testing of the two species. Methods A convenience collection of 73 KP and 42 EC isolates from 3 U.S. institutions were included. Minimal inhibitory concentration (MIC) testing was performed in duplicate on separate days using agar dilution (AD) and DD as recommended by the Clinical and Laboratory Standards Institute guidelines, with application of EC susceptibility (≤ 64mg/L) breakpoints. The frequency and counts of inner colonies observed during DD testing was calculated, and colonies were subcultured for use in future studies. Results MIC50/90 values were 1/16 mg/L and 32/256 mg/L for EC and KP respectively. All EC isolates were considered susceptible and therefore categorical agreement was 100%. The majority of KP isolates were considered susceptible (83.6% with AD and 86.3% with DD) and categorical agreement between the methods was 84.9%. Inner colonies were observed during DD testing in 88.1% of EC isolates and 80.8% of KP isolates during at least one replicate, with 47.6% of EC isolates and 39.7% of KP isolates showing inner colony growth during both DD test replicates. More than 10 inner colonies were observed in 50% of EC isolates compared to 12.3% of KP isolates. Conclusion KP isolates demonstrated considerably higher FOF MIC values compared to EC, as evidenced by MIC50/90 values 4-5 dilutions higher than those for EC. The categorical agreement rate was higher among EC than KP, highlighting concerns regarding the practice of extrapolating FOF susceptibility breakpoints for EC to KP. The high frequency of inner colonies observed in DD for both species necessitates further studies to determine best practices for interpreting their relevance, fitness, and resistance in order to identify potential impacts to clinical efficacy of FOF. Disclosures Elizabeth B. Hirsch, PharmD, Merck (Grant/Research Support)Nabriva Therapeutics (Advisor or Review Panel member)

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PSV-13 Genetic parameters and quantitative trait loci for heat stress related traits in sheep

Journal of Animal Science ◽

10.1093/jas/skaa054.289 ◽

2020 ◽

Vol 98 (Supplement_3) ◽

pp. 163-164

Author(s):

Devin R Jacobs ◽

Claudia E Silvera-Rojas ◽

Jennifer M Bormann ◽

Terry A Gipson ◽

Arthur L Goetsch ◽

...

Keyword(s):

Heat Stress ◽

Quantitative Trait Loci ◽

Rectal Temperature ◽

Quantitative Trait ◽

Fixed Effects ◽

Univariate Analysis ◽

Average Daily Gain ◽

The United States ◽

Nucleotide Polymorphisms ◽

Trait Loci

Abstract Greater selection emphasis has been placed on efficiency than on fitness in livestock populations over the last several decades. Heat stress is a concern in production systems due to the negative effects on production, reproduction, and immunity. The objective of the study was to estimate variance components and identify quantitative trait loci (QTL) for heat stress related traits in sheep. A total of 125 Dorper, Katahdin, and St. Croix ewes originating from four regions of the United States were selected for the experiment. Animals were separated into four trials due to facility limitations. Data were collected for each trial over four consecutive two-week periods in an environmentally controlled facility with targeted heat load index (HLI) for daytime/nighttime of 70/70, 85/77, 90/77, and 95/81. Body weight was collected three times per week and rectal temperature was collected weekly. Black globe temperature and humidity were measured every 15 minutes. Animals were genotyped using the Illumina OvineSNP50 BeadChip. After quality control, 49,396 effective single nucleotide polymorphisms were included in the univariate analysis performed with the BLUPF90 suite of programs. Fixed effects in the models included region of origin, breed, trial, and age as a covariate. Traits analyzed included rectal temperature at 95 HLI (RT95), feed intake at 95 HLI (FI95), and average daily gain for the period for HLI between 90 and 95 (ADG). Heritabilities for RT95, FI95, and ADG were 0.35, 0.10, and 0.10, respectively. Largest effect QTL were identified on chromosomes 23, 9, and 6 for RT95, chromosomes 9, 2, and 20 for FI95, and chromosomes 6, 1, and 5 for ADG. Many of the regions identified have also been associated with weight and carcass traits in other studies, but few had obvious connections to the heat stress related response. In conclusion, results suggest selection could improve heat tolerance in sheep.

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COVID-TRACK: world and USA SARS-COV-2 testing and COVID-19 tracking

BioData Mining ◽

10.1186/s13040-021-00233-2 ◽

2021 ◽

Vol 14 (1) ◽

Author(s):

Ye Emma Zohner ◽

Jeffrey S. Morris

Keyword(s):

Web Application ◽

The United States ◽

Mitigation Strategies ◽

Time Lags ◽

Policy Makers ◽

Major Health ◽

Dynamic Representation ◽

Graphical Displays ◽

The Usa ◽

User Friendly

Abstract Background The COVID-19 pandemic has caused major health and socio-economic disruptions worldwide. Accurate investigation of emerging data is crucial to inform policy makers as they construct viral mitigation strategies. Complications such as variable testing rates and time lags in counting cases, hospitalizations and deaths make it challenging to accurately track and identify true infectious surges from available data, and requires a multi-modal approach that simultaneously considers testing, incidence, hospitalizations, and deaths. Although many websites and applications report a subset of these data, none of them provide graphical displays capable of comparing different states or countries on all these measures as well as various useful quantities derived from them. Here we introduce a freely available dynamic representation tool, COVID-TRACK, that allows the user to simultaneously assess time trends in these measures and compare various states or countries, equipping them with a tool to investigate the potential effects of the different mitigation strategies and timelines used by various jurisdictions. Findings COVID-TRACK is a Python based web-application that provides a platform for tracking testing, incidence, hospitalizations, and deaths related to COVID-19 along with various derived quantities. Our application makes the comparison across states in the USA and countries in the world easy to explore, with useful transformation options including per capita, log scale, and/or moving averages. We illustrate its use by assessing various viral trends in the USA and Europe. Conclusion The COVID-TRACK web-application is a user-friendly analytical tool to compare data and trends related to the COVID-19 pandemic across areas in the United States and worldwide. Our tracking tool provides a unique platform where trends can be monitored across geographical areas in the coming months to watch how the pandemic waxes and wanes over time at different locations around the USA and the globe.

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