scholarly journals Non-serotype 2 isolates from healthy pigs are a potential zoonotic reservoir of Streptococcus suis genetic diversity and antimicrobial resistance

2021 ◽  
Author(s):  
Nattinee Kittiwan ◽  
Jessica K Calland ◽  
Evangelos Mourkas ◽  
Matthew D Hitchings ◽  
Susan Murray ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Close Contact ◽  
Streptococcus Suis ◽  
Invasive Disease ◽  
Economic Losses ◽  
Swine Industry ◽  
Integrative And Conjugative Elements ◽  
Antimicrobial Resistance Genes

Streptococcus suis is a leading cause of bacterial meningitis in SE Asia, with frequent zoonotic transfer to humans associated with close contact with pigs. A small number of invasive lineages are responsible for endemic infection in the swine industry causing considerable global economic losses. A lack of surveillance and a rising trend in clinical treatment failure has raised concerns of growing antimicrobial resistance (AMR) among invasive S. suis. The source-sink dynamics between healthy and disease isolates is poorly understood and, in this study, we sample and sequence a collection of isolates predominantly from healthy pigs in Chiang Mai province, Northern Thailand. Pangenome comparisons with a selection of invasive serotype 2 isolates identified increased genetic diversity and more frequent AMR carriage in isolates from healthy pigs. Multiple antimicrobial resistance genes were identified conferring resistance to aminoglycosides, lincosamides, tetracycline and macrolides. All isolates were non-susceptinle to three or more different antimicrobial classes, and 75% of non-serotype 2 isolates were non-susceptible to 6 or more classes (compared to 37.5% of serotype 2 isolates). Antimicrobial resistance genes were found on integrative and conjugative elements (ICE) previously observed in other species, suggesting mobile gene pool which can be accessed by invasive disease isolates.

scholarly journals Streptococcus suis Research: Progress and Challenges

Pathogens ◽  
2020 ◽  
Vol 9 (9) ◽  
pp. 707 ◽  
Author(s):  
Mariela Segura
Keyword(s):  
Antimicrobial Resistance ◽  
Close Contact ◽  
Streptococcus Suis ◽  
Control Measures ◽  
Health Concern ◽  
Research Progress ◽  
Economic Losses ◽  
Swine Industry ◽  
Host Animal ◽  
Prophylactic Use

Streptococcus suis is considered among the top bacterial pathogens leading to important economic losses to the swine industry, with the incidence of disease increasing as the prophylactic use of antimicrobial is being vanished worldwide. S. suis is also a zoonotic agent afflicting people in close contact with infected pigs or pork meat. Besides, in some Asian countries, it is considered a major public health concern for the general population as well. Antimicrobial resistance is one of the most important global health challenges, and in the absence of preventive measures (such as effective vaccines), S. suis remains a risk for increased antimicrobial resistance and transmission of resistance genes to other bacteria beyond the host animal species. The studies in this Special Issue have evidenced the importance of swine population demographics and management on disease control, progress in molecular tools to better understand the epidemiology of S. suis infections in swine and humans, and the mechanisms involved in different aspects of the immuno-pathogenesis of the disease. The importance of reducing the prophylactic use of antimicrobials in livestock productions and the development of alternative control measures, including vaccination, are herein discussed.

scholarly journals Serotype distribution, antimicrobial susceptibility, antimicrobial resistance genes and virulence genes of Salmonella isolated from a pig slaughterhouse in Yangzhou, China

AMB Express ◽  
2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Quan Li ◽  
Jian Yin ◽  
Zheng Li ◽  
Zewei Li ◽  
Yuanzhao Du ◽  
...  
Keyword(s):  
Public Health ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Antimicrobial Susceptibility ◽  
Virulence Genes ◽  
Multidrug Resistant ◽  
Resistance Rate ◽  
Economic Losses ◽  
Production Chain ◽  
Antimicrobial Resistance Genes

AbstractSalmonella is an important food-borne pathogen associated with public health and high economic losses. To investigate the prevalence and the characteristics of Salmonella in a pig slaughterhouse in Yangzhou, a total of 80 Salmonella isolates were isolated from 459 (17.43%) samples in 2016–2017. S. Derby (35/80, 43.75%) was the most prevalent, followed by S. Rissen (16/80, 20.00%) and S. Newlands (11/80, 13.75%). The highest rates of susceptibility were observed to cefoxitin (80/80, 100.0%) and amikacin (80/80, 100.0%), followed by aztreonam (79/80, 98.75%) and nitrofurantoin (79/80, 98.75%). The highest resistance rate was detected for tetracycline (65/80, 81.25%), followed by ampicillin (60/80, 75.00%), bactrim (55/80, 68.75%), and sulfisoxazole (54/80, 67.50%). Overall, 91.25% (73/80) of the isolates were resistant to at least one antibiotic, while 71.25% (57/80) of the isolate strains were multidrug resistant in the antimicrobial susceptibility tested. In addition, 86.36% (19/22) of the 22 antimicrobial resistance genes in the isolates were identified. Our data indicated that the resistance to certain antimicrobials was significantly associated, in part, with antimicrobial resistance genes. Furthermore, 81.25% (65/80) isolates harbored the virulence gene of mogA, of which 2 Salmonella Typhimurium isolates carried the mogA, spvB and spvC virulence genes at the same time. The results showed that swine products in the slaughterhouse were contaminated with multidrug resistant Salmonella commonly, especially some isolates carry the spv virulence genes. The virulence genes might facilitate the dissemination of the resistance genes to consumers along the production chain, suggesting the importance of controlling Salmonella during slaughter for public health.

scholarly journals Non-Penicillin-Susceptible Streptococcus suis Isolated from Humans

Pathogens ◽  
2021 ◽  
Vol 10 (9) ◽  
pp. 1178
Author(s):  
Nichari Bamphensin ◽  
Peechanika Chopjitt ◽  
Rujirat Hatrongjit ◽  
Parichart Boueroy ◽  
Nahuel Fittipaldi ◽  
...  
Keyword(s):  
Amino Acid ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Streptococcus Suis ◽  
Amino Acid Substitutions ◽  
Continuous Control ◽  
Antimicrobial Resistance Genes ◽  
Genes Encoding ◽  
Invasive Infections ◽  
Almost All

Streptococcus suis is a pathogen that causes invasive infections in humans and pigs. In this study, 448 S. suis isolates recovered from human infections in Thailand were characterized with regard to their antimicrobial susceptibility and antimicrobial resistance genes, including, for non-penicillin-susceptible isolates, sequence analyses of five genes encoding penicillin-binding proteins (pbp1a, pbp1b, pbp2a, pbp2b, and pbp2x). All 448 isolates were susceptible to cefepime and ceftriaxone, whereas 99.6%, 91.7%, and 72.9% of the isolates were susceptible to levofloxacin, penicillin, and chloramphenicol, respectively. Almost all isolates were resistant to tetracycline (98.2%), clindamycin (94%), erythromycin (92.4%), and azithromycin (82.6%). Genes tet(O) and ermB were the predominant resistance genes detected among macrolide- and tetracycline-resistant isolates. A total of 37 out of 448 isolates (8.2%) showed intermediately resistance to penicillin. Most of these isolates (59.5%) belonged to serotype 2-ST233. Comparison of the predicted translated sequences of five PBP proteins of a penicillin-susceptible isolate (strain P1/7) to the respective PBP sequences of ten non-penicillin-susceptible isolates revealed multiple amino acid substitutions. Isolates of CC221/234 showed highly variable amino acid substitutions in all PBP proteins. An ST104 isolate had a higher number of amino acid substitutions in PBP2X. Isolates belonging to CC233/379 had numerous substitutions in PBP2B and PBP2X. ST25 isolates exhibited fewer amino acid substitutions than isolates of other STs in all five PBPs. The antimicrobial resistance of S. suis is increasing worldwide; therefore, restrictions on antimicrobial use, continuous control, and the surveillance of this bacterium throughout the pork supply chain are crucial for ensuring public health and must be a priority concern.

scholarly journals Genes Encoding the Virulence and the Antimicrobial Resistance in Enterotoxigenic and Shiga-toxigenic E. coli Isolated from Diarrheic Calves

Toxins ◽  
2020 ◽  
Vol 12 (6) ◽  
pp. 383 ◽  
Author(s):  
Abdelazeem M. Algammal ◽  
Ali El-Kholy ◽  
Emad M. Riad ◽  
Hossam E. Mohamed ◽  
Mahmoud M. Elhaig ◽  
...  
Keyword(s):  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Virulence Genes ◽  
Antimicrobial Agents ◽  
Economic Losses ◽  
Shiga Toxins ◽  
E Coli ◽  
Calf Diarrhea ◽  
Antimicrobial Resistance Genes ◽  
Diarrheic Calves

Calf diarrhea is one of the considerable infectious diseases in calves, which results in tremendous economic losses globally. To determine the prevalence of Shiga-toxigenic E. coli (STEC) and Enterotoxigenic E. coli (ETEC) incriminated in calf diarrhea, with special reference to Shiga- toxins genes (stx1 and stx2) and enterotoxins genes (lt and sta) that govern their pathogenesis, as well as the virulence genes; eaeA (intimin) and f41(fimbrial adhesion), and the screening of their antibiogram and antimicrobial resistance genes; aadB, sul1, and bla-TEM, a total of 274 fecal samples were collected (April 2018–Feb 2019) from diarrheic calves at different farms in El-Sharqia Governorate, Egypt. The bacteriological examination revealed that the prevalence of E. coli in diarrheic calves was 28.8%. The serotyping of the isolated E. coli revealed 7 serogroups; O26, O128, O111, O125, O45, O119 and O91. Furthermore, the Congo red binding test was carried out, where 89.8% of the examined strains (n = 71) were positive. The antibiogram of the isolated strains was investigated; the majority of E. coli serotypes exhibit multidrug resistance (MDR) to four antimicrobial agents; neomycin, gentamycin, streptomycin, and amikacin. Polymerase chain reaction (PCR) was used to detect the prevalence of the virulence genes; stx1, stx2 lt, sta, f41 and eaeA, as well as the antimicrobial resistance genes; aadB, sul1, and bla-TEM. The prevalence of STEC was 20.2% (n = 16), while the prevalence of ETEC was 30.4% (n = 24). Briefly, the Shiga toxins genes; stx1 and stx2, are the most prevalent virulence genes associated with STEC, which are responsible for the pathogenesis of the disease and helped by the intimin gene (eaeA). In addition, the lt gene is the most prevalent enterotoxin gene accompanied by the ETEC strains, either alone or in combination with sta and/or f41 genes. The majority of pathogenic E. coli incriminated in calf diarrhea possesses the aadB resistance gene, followed by the sul1 gene. Enrofloxacin, florfenicol, amoxicillin-clavulanic acid, and ampicillin-sulbactam, are the most effective antimicrobial agents against the isolated STEC and ETEC strains.

scholarly journals Update on the Mechanisms of Antibiotic Resistance and the Mobile Resistome in the Emerging Zoonotic Pathogen Streptococcus suis

2021 ◽  
Vol 9 (8) ◽  
pp. 1765
Author(s):  
Manon Dechêne-Tempier ◽  
Corinne Marois-Créhan ◽  
Virginie Libante ◽  
Eric Jouy ◽  
Nathalie Leblond-Bourget ◽  
...  
Keyword(s):  
Antibiotic Resistance ◽  
Resistance Genes ◽  
Bacterial Species ◽  
Antibiotic Resistance Genes ◽  
Streptococcus Suis ◽  
Resistance Mechanisms ◽  
Economic Losses ◽  
Swine Production ◽  
Swine Industry ◽  
Zoonotic Pathogen

Streptococcus suis is a zoonotic pathogen causing important economic losses in swine production. The most commonly used antibiotics in swine industry are tetracyclines, beta-lactams, and macrolides. Resistance to these antibiotics has already been observed worldwide (reaching high rates for macrolides and tetracyclines) as well as resistance to aminoglycosides, fluoroquinolones, amphenicols, and glycopeptides. Most of the resistance mechanisms are encoded by antibiotic resistance genes, and a large part are carried by mobile genetic elements (MGEs) that can be transferred through horizontal gene transfer. This review provides an update of the resistance genes, their combination in multidrug isolates, and their localization on MGEs in S. suis. It also includes an overview of the contribution of biofilm to antimicrobial resistance in this bacterial species. The identification of resistance genes and study of their localization in S. suis as well as the environmental factors that can modulate their dissemination appear essential in order to decipher the role of this bacterium as a reservoir of antibiotic genes for other species.

scholarly journals Genomic analysis of diversity, population structure, virulence, and antimicrobial resistance inKlebsiella pneumoniae, an urgent threat to public health

2015 ◽  
Vol 112 (27) ◽  
pp. E3574-E3581 ◽  
Author(s):  
Kathryn E. Holt ◽  
Heiman Wertheim ◽  
Ruth N. Zadoks ◽  
Stephen Baker ◽  
Chris A. Whitehouse ◽  
...  
Keyword(s):  
Population Structure ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Genomic Analysis ◽  
Distinct Species ◽  
Invasive Disease ◽  
Multidrug Resistant ◽  
Human Infection ◽  
Whole Genome ◽  
Antimicrobial Resistance Genes

Klebsiella pneumoniaeis now recognized as an urgent threat to human health because of the emergence of multidrug-resistant strains associated with hospital outbreaks and hypervirulent strains associated with severe community-acquired infections.K.pneumoniaeis ubiquitous in the environment and can colonize and infect both plants and animals. However, little is known about the population structure ofK.pneumoniae, so it is difficult to recognize or understand the emergence of clinically important clones within this highly genetically diverse species. Here we present a detailed genomic framework forK.pneumoniaebased on whole-genome sequencing of more than 300 human and animal isolates spanning four continents. Our data provide genome-wide support for the splitting ofK.pneumoniaeinto three distinct species, KpI (K.pneumoniae), KpII (K.quasipneumoniae), and KpIII (K.variicola). Further, forK.pneumoniae(KpI), the entity most frequently associated with human infection, we show the existence of >150 deeply branching lineages including numerous multidrug-resistant or hypervirulent clones. We showK.pneumoniaehas a large accessory genome approaching 30,000 protein-coding genes, including a number of virulence functions that are significantly associated with invasive community-acquired disease in humans. In our dataset, antimicrobial resistance genes were common among human carriage isolates and hospital-acquired infections, which generally lacked the genes associated with invasive disease. The convergence of virulence and resistance genes potentially could lead to the emergence of untreatable invasiveK.pneumoniaeinfections; our data provide the whole-genome framework against which to track the emergence of such threats.

scholarly journals Culture-Independent Genotyping, Virulence and Antimicrobial Resistance Gene Identification of Staphylococcus aureus from Orthopaedic Implant-Associated Infections

2021 ◽  
Vol 9 (4) ◽  
pp. 707
Author(s):  
J. Christopher Noone ◽  
Fabienne Antunes Ferreira ◽  
Hege Vangstein Aamot
Keyword(s):  
Staphylococcus Aureus ◽  
Antimicrobial Resistance ◽  
Resistance Genes ◽  
Virulence Gene ◽  
Orthopaedic Implant ◽  
Metagenomic Sequencing ◽  
Gene Detection ◽  
Shotgun Metagenomic Sequencing ◽  
Antimicrobial Resistance Genes ◽  
Culture Independent

Our culture-independent nanopore shotgun metagenomic sequencing protocol on biopsies has the potential for same-day diagnostics of orthopaedic implant-associated infections (OIAI). As OIAI are frequently caused by Staphylococcus aureus, we included S. aureus genotyping and virulence gene detection to exploit the protocol to its fullest. The aim was to evaluate S. aureus genotyping, virulence and antimicrobial resistance genes detection using the shotgun metagenomic sequencing protocol. This proof of concept study included six patients with S. aureus-associated OIAI at Akershus University Hospital, Norway. Five tissue biopsies from each patient were divided in two: (1) conventional microbiological diagnostics and genotyping, and whole genome sequencing (WGS) of S. aureus isolates; (2) shotgun metagenomic sequencing of DNA from the biopsies. Consensus sequences were analysed using spaTyper, MLST, VirulenceFinder, and ResFinder from the Center for Genomic Epidemiology (CGE). MLST was also compared using krocus. All spa-types, one CGE and four krocus MLST results matched Sanger sequencing results. Virulence gene detection matched between WGS and shotgun metagenomic sequencing. ResFinder results corresponded to resistance phenotype. S. aureus spa-typing, and identification of virulence and antimicrobial resistance genes are possible using our shotgun metagenomics protocol. MLST requires further optimization. The protocol has potential application to other species and infection types.

scholarly journals Whole genome-based characterisation of antimicrobial resistance and genetic diversity in Campylobacter jejuni and Campylobacter coli from ruminants

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Medelin Ocejo ◽  
Beatriz Oporto ◽  
José Luis Lavín ◽  
Ana Hurtado
Keyword(s):  
Genetic Diversity ◽  
Antimicrobial Resistance ◽  
Campylobacter Jejuni ◽  
Resistance Genes ◽  
Campylobacter Coli ◽  
Whole Genome ◽  
Northern Spain ◽  
Sequence Alignments ◽  
Phenotypic Data ◽  
Wide Range

AbstractCampylobacter, a leading cause of gastroenteritis in humans, asymptomatically colonises the intestinal tract of a wide range of animals.Although antimicrobial treatment is restricted to severe cases, the increase of antimicrobial resistance (AMR) is a concern. Considering the significant contribution of ruminants as reservoirs of resistant Campylobacter, Illumina whole-genome sequencing was used to characterise the mechanisms of AMR in Campylobacter jejuni and Campylobacter coli recovered from beef cattle, dairy cattle, and sheep in northern Spain. Genome analysis showed extensive genetic diversity that clearly separated both species. Resistance genotypes were identified by screening assembled sequences with BLASTn and ABRicate, and additional sequence alignments were performed to search for frameshift mutations and gene modifications. A high correlation was observed between phenotypic resistance to a given antimicrobial and the presence of the corresponding known resistance genes. Detailed sequence analysis allowed us to detect the recently described mosaic tet(O/M/O) gene in one C. coli, describe possible new alleles of blaOXA-61-like genes, and decipher the genetic context of aminoglycoside resistance genes, as well as the plasmid/chromosomal location of the different AMR genes and their implication for resistance spread. Updated resistance gene databases and detailed analysis of the matched open reading frames are needed to avoid errors when using WGS-based analysis pipelines for AMR detection in the absence of phenotypic data.

Sign in / Sign up

Export Citation Format

Share Document