Identification of antimicrobial resistance-associated genes through whole genome sequencing of high and low MIC isolates of Mycoplasma bovis

AbstractAntimicrobial resistance (AMR) in Mycoplasma bovis has previously been associated with mutations within topoisomerases and ribosomal genes rather than specific resistance-conferring genes. This study used whole genome sequencing (WGS) to identify potential new AMR mechanisms. It was found that a 2019 clinical isolate with high MIC (2019-043682) had a new core genome multilocus sequencing (cgMLST) type (ST10-like) and 91% homology with the published genome of M. bovis PG45. Closely related to PG45, a 1982 isolate (1982-M6152) shared the same cgMLST type (ST17), 97.2% homology and similar low MIC results. Known and potential AMR-associated genetic events were identified through comparison with the published M. bovis PG45 genome. Isolate 2019-043682 had 507 genes with non-synonymous mutations (NSMs) and 67 genes disrupted. Isolate 1982-M6152 had 81 NSMs and 20 disruptions. Based on functional roles and known mechanisms of antimicrobials, a 55 gene subset was assessed for potential AMR mechanisms. Of these, 14 were previously identified from other bacteria as sites of AMR mutation, 41 shared similar functions to them, and 11 contained gene-disrupting mutations. This study indicated that M. bovis may obtain high AMR characteristics by mutating or disrupting other functional genes, in addition to topoisomerases and ribosomal genes.

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Identification of Antimicrobial Resistance-Associated Genes through Whole Genome Sequencing of Mycoplasma bovis Isolates with Different Antimicrobial Resistances

Pathogens ◽

10.3390/pathogens9070588 ◽

2020 ◽

Vol 9 (7) ◽

pp. 588 ◽

Cited By ~ 1

Author(s):

Lisa Ledger ◽

Jason Eidt ◽

Hugh Y. Cai

Keyword(s):

Antimicrobial Resistance ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Sequence Similarity ◽

Gene Mutations ◽

Ribosomal Gene ◽

Mycoplasma Bovis ◽

Whole Genome ◽

Multiple Sequence ◽

Synonymous Mutations

Antimicrobial resistance (AMR) in Mycoplasma bovis has been previously associated with topoisomerase and ribosomal gene mutations rather than specific resistance-conferring genes. Using whole genome sequencing (WGS) to identify potential new AMR mechanisms for M. bovis, it was found that a 2019 clinical isolate with high MIC (2019-043682) for fluoroquinolones, macrolides, lincosamides, pleuromutilins and tetracyclines had a new core genome multilocus sequencing (cgMLST) type (ST10-like) and 91% sequence similarity to the published genome of M. bovis PG45. Closely related to PG45, a 1982 isolate (1982-M6152) shared the same cgMLST type (ST17), 97.2% sequence similarity and low MIC results. Known and potential AMR- associated genetic events were identified through multiple sequence alignment of the three genomes. Isolate 2019-043682 had 507 genes with non-synonymous mutations (NSMs) and 67 genes disrupted. Isolate 1982-M6152 had 81 NSMs and 20 disruptions. Using functional roles and known mechanisms of antimicrobials, a 55 gene subset was assessed for AMR potential. Seventeen were previously identified from other bacteria as sites of AMR mutation, 38 shared similar functions to them, and 11 contained gene-disrupting mutations. This study indicated that M. bovis may obtain high AMR characteristics by mutating or disrupting other functional genes, in addition to topoisomerases and ribosomal genes.

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Enhancing the one health initiative by using whole genome sequencing to monitor antimicrobial resistance of animal pathogens: Vet-LIRN collaborative project with veterinary diagnostic laboratories in United States and Canada

BMC Veterinary Research ◽

10.1186/s12917-019-1864-2 ◽

2019 ◽

Vol 15 (1) ◽

Cited By ~ 5

Author(s):

Olgica Ceric ◽

Gregory H. Tyson ◽

Laura B. Goodman ◽

Patrick K. Mitchell ◽

Yan Zhang ◽

...

Keyword(s):

United States ◽

Antimicrobial Resistance ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

One Health ◽

Whole Genome ◽

Collaborative Project ◽

Health Initiative ◽

Animal Pathogens ◽

The One

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Whole genome sequencing analysis of multiple Salmonella serovars provides insights into phylogenetic relatedness, antimicrobial resistance, and virulence markers across humans, food animals and agriculture environmental sources

BMC Genomics ◽

10.1186/s12864-018-5137-4 ◽

2018 ◽

Vol 19 (1) ◽

Cited By ~ 27

Author(s):

Suchawan Pornsukarom ◽

Arnoud H M van Vliet ◽

Siddhartha Thakur

Keyword(s):

Antimicrobial Resistance ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Sequencing Analysis ◽

Phylogenetic Relatedness ◽

Virulence Markers ◽

Salmonella Serovars ◽

Food Animals

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Piglet Gut and in-Barn Manure from Farms on a Raised without Antibiotics Program Display Reduced Antimicrobial Resistance but an Increased Prevalence of Pathogens

Antibiotics ◽

10.3390/antibiotics10101152 ◽

2021 ◽

Vol 10 (10) ◽

pp. 1152

Author(s):

Samuel M. Chekabab ◽

John R. Lawrence ◽

Alvin C. Alvarado ◽

Bernardo Z. Predicala ◽

Darren R. Korber

Keyword(s):

Antimicrobial Resistance ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Whole Genome ◽

Fecal Samples ◽

Time Points ◽

Conventional Farms ◽

Production Practices ◽

On Farm ◽

The Impact

In response to new stringent regulations in Canada regarding the use of antibiotics in animal production, many farms have implemented practices to produce animals that are raised without antibiotics (RWA) from birth to slaughter. This study aims to assess the impact of RWA production practices on reducing the actual total on-farm use of antibiotics, the occurrence of pathogens, and the prevalence of antimicrobial resistance (AMR). A 28-month longitudinal surveillance of farms that adopted the RWA program and conventional farms using antibiotics in accordance with the new regulations (non-RWA) was conducted by collecting fecal samples from 6-week-old pigs and composite manure from the barn over six time points and applying whole-genome sequencing (WGS) to assess the prevalence of AMR genes as well as the abundance of pathogens. Analysis of in-barn drug use records confirmed the decreased consumption of antibiotics in RWA barns compared to non-RWA barns. WGS analyses revealed that RWA barns had reduced the frequency of AMR genes in piglet feces and in-barn manure. However, metagenomic analyses showed that RWA barns had a significant increase in the frequency of pathogenic Firmicutes in fecal samples and pathogenic Proteobacteria in barn manure samples.

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Wastewater-Based Epidemiology and Whole-Genome Sequencing for Community-Level Surveillance of SARS-CoV-2 in Selected Urban Communities of Davao City, Philippines: A Pilot Study

10.1101/2021.08.27.21262450 ◽

2021 ◽

Author(s):

Maria Catherine Bernolo Otero ◽

Lyre Anni E. Murao ◽

Mary Antoinette G. Limen ◽

Paul Lorenzo A. Gaite ◽

Michael G. Bacus ◽

...

Keyword(s):

Whole Genome Sequencing ◽

Genome Sequencing ◽

The Philippines ◽

Community Level ◽

Local Context ◽

Whole Genome ◽

Low Resource ◽

Synonymous Mutations ◽

Public Data ◽

Clinical Surveillance

Background: Over 50 countries have used Wastewater-Based Epidemiology (WBE) and whole-genome sequencing (WGS) for SARS-CoV-2 for monitoring COVID-19 cases. COVID-19 surveillance in the Philippines relies on clinical monitoring and contact tracing, with both having limited use in early detection or prediction of community outbreaks. Complementary public health surveillance methods that can provide community-level infection data faster and using lesser resources must be explored. Objectives: This study piloted and assessed WBE and WGS as approaches for COVID-19 surveillance in low-resource and low-sanitation communities in Davao City, Philippines. Methods: Weekly wastewater samples were collected from six barangay community sewer pipes or creeks from November to December 2020. Samples were concentrated using a PEG-NaCl precipitation method and analyzed by RT-PCR to detect the SARS-CoV-2 N, RdRP, and E genes. In addition, SARS-CoV-2 RNA-positive samples were subjected to WGS for genomic mutation surveillance. Public data from clinical surveillance were also reviewed to interpret WBE data. Results: Twenty-two of the 24 samples (91.7%) obtained from the six barangays tested positive for SARS-CoV-2 RNA. The cycle threshold (Ct) values were correlated with RNA concentration and attack rate. Thirty-two SARS-CoV-2 mutations were detected in WGS, including novel non-synonymous mutations or indels in seven SARS-CoV-2 genes and ten mutations previously reported in the Philippines. Discussion: SARS-CoV-2 RNA was detected in community wastewater from the six barangays of Davao City, even when the barangays were classified as having a low risk of COVID-19 transmission and no new cases were reported. Despite the fragmented genome sequences analyzed, our genomic surveillance in wastewater confirmed the presence of previously reported mutations while identifying mutations not yet registered in clinical surveillance. The local context of a community must be considered when planning to adopt WBE and WGS as complementary COVID-19 surveillance methodologies, especially in low-sanitation and low-resource settings. Keywords: COVID-19, Philippines, SARS-CoV-2, Wastewater-Based Epidemiology, Whole Genome Sequencing.

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Serotype Diversity and Antimicrobial Resistance amongSalmonella entericaIsolates from Patients at an Equine Referral Hospital

Applied and Environmental Microbiology ◽

10.1128/aem.02829-17 ◽

2018 ◽

Vol 84 (13) ◽

pp. e02829-17 ◽

Cited By ~ 3

Author(s):

I. M. Leon ◽

S. D. Lawhon ◽

K. N. Norman ◽

D. S. Threadgill ◽

N. Ohta ◽

...

Keyword(s):

Antimicrobial Resistance ◽

Whole Genome Sequencing ◽

Genome Sequencing ◽

Salmonella Enterica ◽

Referral Hospital ◽

Whole Genome ◽

Content Type ◽

Genes Encoding ◽

Life Threatening ◽

Common Serotypes

ABSTRACTAlthoughSalmonella entericacan produce life-threatening colitis in horses, certain serotypes are more commonly associated with clinical disease. Our aim was to evaluate the proportional morbidity attributed to different serotypes, as well as the phenotypic and genotypic antimicrobial resistance (AMR) ofSalmonellaisolates from patients at an equine referral hospital in the southern United States. A total of 255Salmonellaisolates was obtained from clinical samples of patients admitted to the hospital between 2007 and 2015. Phenotypic resistance to 14 antibiotics surveilled by the U.S. National Antimicrobial Resistance Monitoring System was determined using a commercially available panel. Whole-genome sequencing was used to identify serotypes and genotypic AMR. The most common serotypes wereSalmonella entericaserotype Newport (18%),Salmonella entericaserotype Anatum (15.2%), andSalmonella entericaserotype Braenderup (11.8%). Most (n= 219) of the isolates were pansusceptible, while 25 were multidrug resistant (≥3 antimicrobial classes). Genes encoding beta-lactam resistance, such asblaCMY-2,blaSHV-12,blaCTX-M-27, andblaTEM-1B, were detected. TheqnrB2 andaac(6′)-Ib-crgenes were present in isolates with reduced susceptibility to ciprofloxacin. Genes encoding resistance to gentamicin (aph(3′)-Ia,aac(6′)-IIc), streptomycin (strA andstrB), sulfonamides (sul1), trimethoprim (dfrA), phenicols (catA), tetracyclines [tet(A) andtet(E)], and macrolides [ere(A)] were also identified. The main predicted incompatibility plasmid type was I1 (10%). Core genome-based analyses revealed phylogenetic associations between isolates of common serotypes. The presence of AMRSalmonellain equine patients increases the risk of unsuccessful treatment and causes concern for potential zoonotic transmission to attending veterinary personnel, animal caretakers, and horse owners. Understanding the epidemiology ofSalmonellain horses admitted to referral hospitals is important for the prevention, control, and treatment of salmonellosis.IMPORTANCEIn horses, salmonellosis is a leading cause of life-threatening colitis. At veterinary teaching hospitals, nosocomial outbreaks can increase the risk of zoonotic transmission, lead to restrictions on admissions, impact hospital reputation, and interrupt educational activities. The antimicrobials most often used in horses are included in the 5th revision of the World Health Organization's list of critically important antimicrobials for human medicine. Recent studies have demonstrated a trend of increasing bacterial resistance to drugs commonly used to treatSalmonellainfections. In this study, we identify temporal trends in the distribution ofSalmonellaserotypes and their mechanisms of antimicrobial resistance; furthermore, we are able to determine the likely origin of several temporal clusters of infection by using whole-genome sequencing. These data can be used to focus strategies to better contain the dissemination and enhance the mitigation ofSalmonellainfections and to provide evidence-based policies and guidelines to steward antimicrobial use in veterinary medicine.

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