The population structure, antimicrobial resistance, and pathogenicity of Streptococcus suis cps31

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.

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Comparative genomics of Staphylococcus epidermidis from prosthetic-joint infections and nares highlights genetic traits associated with antimicrobial resistance, not virulence

Microbial Genomics ◽

10.1099/mgen.0.000504 ◽

2021 ◽

Cited By ~ 1

Author(s):

Emeli Månsson ◽

Thor Bech Johannesen ◽

Åsa Nilsdotter-Augustinsson ◽

Bo Söderquist ◽

Marc Stegger

Keyword(s):

Population Structure ◽

Antimicrobial Resistance ◽

Staphylococcus Epidermidis ◽

Type Species ◽

Genetic Traits ◽

Content Type ◽

Link Type ◽

Joint Infections ◽

Prosthetic Joint ◽

Prosthetic Joint Infections

There is increased awareness of the worldwide spread of specific epidemic multidrug-resistant (MDR) lineages of the human commensal Staphylococcus epidermidis . Here, using bioinformatic analyses accounting for population structure, we determined genomic traits (genes, SNPs and k-mers) that distinguish S. epidermidis causing prosthetic-joint infections (PJIs) from commensal isolates from nares, by analysing whole-genome sequencing data from S. epidermidis from PJIs prospectively collected over 10 years in Sweden, and contemporary S. epidermidis from the nares of patients scheduled for arthroplasty surgery. Previously suggested virulence determinants and the presence of genes and mutations linked to antimicrobial resistance (AMR) were also investigated. Publicly available S. epidermidis sequences were used for international extrapolation and validation of findings. Our data show that S. epidermidis causing PJIs differed from nasal isolates not by virulence but by traits associated with resistance to compounds used in prevention of PJIs: β-lactams, aminoglycosides and chlorhexidine. Almost a quarter of the PJI isolates did not belong to any of the previously described major nosocomial lineages, but the AMR-related traits were also over-represented in these isolates, as well as in international S. epidermidis isolates originating from PJIs. Genes previously associated with virulence in S. epidermidis were over-represented in individual lineages, but failed to reach statistical significance when adjusted for population structure. Our findings suggest that the current strategies for prevention of PJIs select for nosocomial MDR S. epidermidis lineages that have arisen from horizontal gene transfer of AMR-related traits into multiple genetic backgrounds.

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Mass drug administration with azithromycin for trachoma elimination and the population structure of Streptococcus pneumoniae in the nasopharynx

10.1101/2020.04.01.20047266 ◽

2020 ◽

Author(s):

Rebecca A. Gladstone ◽

Ebrima Bojang ◽

John Hart ◽

Emma M Harding-Esch ◽

David Mabey ◽

...

Keyword(s):

Population Structure ◽

Streptococcus Pneumoniae ◽

Antimicrobial Resistance ◽

Drug Administration ◽

Mass Drug Administration ◽

Macrolide Resistance ◽

P Value ◽

Cross Sectional ◽

The Third ◽

Before And After

ABSTRACTBackgroundMass drug administration (MDA) with azithromycin for trachoma elimination reduces nasopharyngeal carriage of Streptococcus pneumoniae in the short term. We evaluated S. pneumoniae carried in the nasopharynx before and after a round of azithromycin MDA to determine whether MDA was associated with changes in pneumococcal population structure.MethodsWe analysed 514 pneumococcal isolates cultured from nasopharyngeal samples collected in Gambian villages that received MDA for trachoma elimination. The samples were collected during three cross-sectional surveys conducted before the third round of MDA (CSS-1) and at one (CSS-2) and six (CSS-3) months after MDA. Whole genome sequencing was conducted on randomly selected isolates. Bayesian Analysis of Population Structure (BAPS) was used to cluster related isolates by capturing variation in the core genome. Serotype and multi-locus sequence type were inferred from the genotype. The Antimicrobial Resistance Identification by Assembly (ARIBA) tool was used to identify macrolide resistance genes.ResultsTwenty-seven BAPS clusters were assigned. These consisted of 81 sequence types (STs), 15 of which were novel additions to pubMLST. Two BAPS clusters, BAPS20 (p-value<=0.016) and BAPS22 (p-value<=0.032) showed an increase in frequency at CSS-3 not associated with antimicrobial resistance. Macrolide resistance within BASP17 increased after treatment (p<0.05) and was carried on a mobile transposable element that also conferred resistance to tetracycline.ConclusionsLimited changes in pneumococcal population structure were observed after the third round of MDA suggesting treatment had little effect on the circulating lineages. An increase in macrolide resistance within one BAPS highlights the need for antimicrobial resistance surveillance in treated villages.

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Differences in Neisseria gonorrhoeae population structure and antimicrobial resistance pattern between men who have sex with men and heterosexuals

Epidemiology and Infection ◽

10.1017/s095026881600234x ◽

2016 ◽

Vol 145 (2) ◽

pp. 379-385 ◽

Cited By ~ 7

Author(s):

J. SERRA-PLADEVALL ◽

M. J. BARBERÁ ◽

A. E. CALLARISA ◽

R. BARTOLOMÉ-COMAS ◽

A. ANDREU

Keyword(s):

Population Structure ◽

Antimicrobial Resistance ◽

Neisseria Gonorrhoeae ◽

Antimicrobial Susceptibility ◽

Sexual Practices ◽

Resistance Pattern ◽

High Prevalence ◽

Sex With Men ◽

Resistance Rates ◽

Sequence Types

SUMMARYThis study compared the antimicrobial susceptibility and genotypes of strains of Neisseria gonorrhoeae isolated from men who have sex with men (MSM) and from heterosexuals. One hundred and eleven strains were characterized from 107 patients, comprising 57 strains from 54 heterosexuals and 54 strains from 53 MSM. Antimicrobial resistance rates were higher in strains from heterosexual patients, with resistance to cefixime (P = 0·0159) and ciprofloxacin (P = 0·002) being significantly higher. Typing by N. gonorrhoeae multi-antigen sequence typing (NG-MAST) showed that the most prevalent sequence types (ST) and genogroups (G) respectively were ST2400, ST2992, and ST5793, and G1407, G2992, and G2400. A statistically significant association was observed for MSM and genogroups G2400 (P = 0·0005) and G2992 (P = 0·0488), and G1407 with heterosexuals (P = 0·0002). We conclude that in our region distinct populations of gonococci are circulating among subjects with different sexual practices, with their corresponding transmission patterns. Furthermore, the high prevalence of genotype G2400 in MSM, has not to our knowledge been previously described.

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Phylogenetic Characterization Reveals Prevalent Shigella flexneri ST100 Clone in Beijing, China, 2005 to 2018

mSphere ◽

10.1128/msphere.00161-20 ◽

2020 ◽

Vol 5 (4) ◽

Author(s):

Lang Yang ◽

Bing Lü ◽

Quanyi Wang ◽

Kaiying Wang ◽

Yanfeng Lin ◽

...

Keyword(s):

Population Structure ◽

Antimicrobial Resistance ◽

Bacillary Dysentery ◽

Shigella Flexneri ◽

Content Type ◽

Phylogenetic Characterization ◽

Local Expansion ◽

Resistance Determinants ◽

Genetic Features ◽

Beijing China

ABSTRACT Shigella flexneri is a major cause of bacillary dysentery in Beijing, China. The genetic features and population structure of locally circulating clones remained unclear. In this study, we sequenced the genomes of 93 S. flexneri isolates from patients in Beijing from 2005 to 2018. Phylogenetic analysis revealed a predominant lineage comprised of ST100 isolates that had acquired an extensive repertoire of antimicrobial resistance determinants. A rapid local expansion of the largest clade of this lineage began in 2008 and gradually resulted in the dominance of serotype 2a. Other clades showed substantial evidence of interregional spread from other areas of China. Another lineage consisting of ST18 isolates was also identified and appeared to have persisted locally for nearly 6 decades. These findings suggest that S. flexneri epidemics in Beijing were caused by both local expansion and interregional transmission. IMPORTANCE Beijing is the largest transportation hub in China, with a highly mobile population. Shigella flexneri is a major cause of bacillary dysentery in Beijing. However, little is known about the genetic features and population structure of locally circulating S. flexneri clones. Whole-genome sequencing of 93 S. flexneri isolates revealed that S. flexneri epidemics in Beijing were predominantly caused by an ST100 clone. Interregional spread, rapid local expansion, and acquirement of antimicrobial resistance determinants have cocontributed to the epidemics of this clone. Another ST18 clone was also identified and showed long-term colonization in Beijing. Our study provides comprehensive insights into the population structure and evolutionary history of S. flexneri in Beijing.

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Population Structure and Antimicrobial Resistance of Canine UropathogenicEscherichia coli

Journal of Clinical Microbiology ◽

10.1128/jcm.00788-18 ◽

2018 ◽

Vol 56 (9) ◽

Cited By ~ 12

Author(s):

Tessa E. LeCuyer ◽

Barbara A. Byrne ◽

Joshua B. Daniels ◽

Dubraska V. Diaz-Campos ◽

G. Kenitra Hammac ◽

...

Keyword(s):

Population Structure ◽

Antimicrobial Resistance ◽

Companion Animals ◽

Sequence Type ◽

Content Type ◽

E Coli ◽

Extraintestinal Disease ◽

Human Infections ◽

Sequence Types

ABSTRACTEscherichia coliis the most common cause of human and canine urinary tract infection (UTI). Clonal groups, often with high levels of antimicrobial resistance, are a major component of theE. colipopulation that causes human UTI. While little is known about the population structure ofE. colithat causes UTI in dogs, there is evidence that dogs and humans can share fecal strains ofE. coliand that human-associated strains can cause disease in dogs. In order to better characterize theE. colistrains that cause canine UTI, we analyzed 295E. coliisolates obtained from canine urine samples from five veterinary diagnostic laboratories and analyzed their multilocus sequence types, phenotypic and genotypic antimicrobial resistance profiles, and virulence-associated gene repertoires. Sequence type 372 (ST372), an infrequent human pathogen, was the predominant sequence type in dogs at all locations. Extended-spectrum β-lactamase-producing isolates withblaCTX-Mgenes were uncommon in canine isolates but when present were often associated with sequence types that have been described in human infections. This provides support for occasional cross-host-species sharing of strains that cause extraintestinal disease and highlights the importance of understanding the role of companion animals in the overall transmission patterns of extraintestinal pathogenicE. coli.

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Differences in the Population Structure of Invasive Streptococcus suis Strains Isolated from Pigs and from Humans in the Netherlands

PLoS ONE ◽

10.1371/journal.pone.0033854 ◽

2012 ◽

Vol 7 (5) ◽

pp. e33854 ◽

Cited By ~ 58

Author(s):

Constance Schultsz ◽

Ewout Jansen ◽

Wendy Keijzers ◽

Anja Rothkamp ◽

Birgitta Duim ◽

...

Keyword(s):

Population Structure ◽

The Netherlands ◽

Streptococcus Suis

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Five years of GenoTyphi: updates to the global Salmonella Typhi genotyping framework

10.1101/2021.04.28.441766 ◽

2021 ◽

Author(s):

Zoe A. Dyson ◽

Kathryn E. Holt

Keyword(s):

Population Structure ◽

Antimicrobial Resistance ◽

Typhoid Fever ◽

Salmonella Typhi ◽

Whole Genome Sequence ◽

Whole Genome ◽

Aetiological Agent ◽

Diverse Range ◽

Surveillance Studies ◽

Definition Of

AbstractIn 2016 a whole genome sequence (WGS) based genotyping framework (GenoTyphi) was developed providing a phylogenetically informative nomenclature for lineages of Salmonella Typhi, the aetiological agent of typhoid fever. Subsequent surveillance studies have revealed additional epidemiologically important subpopulations, necessitating the definition of new genotypes and extension of associated software to facilitate the detection of antimicrobial resistance (AMR) mutations. Analysis of 4,632 WGS provide an updated overview of the global S. Typhi population structure and genotyping framework, revealing the widespread nature of H58 (4.3.1) genotypes and the diverse range of genotypes carrying AMR mutations.

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Associations of Streptococcus suisSerotype 2 Ribotype Profiles with Clinical Disease and Antimicrobial Resistance

Journal of Clinical Microbiology ◽

10.1128/jcm.37.2.404-408.1999 ◽

1999 ◽

Vol 37 (2) ◽

pp. 404-408 ◽

Cited By ~ 12

Author(s):

S. R. Rasmussen ◽

F. M. Aarestrup ◽

N. E. Jensen ◽

S. E. Jorsal

Keyword(s):

Cluster Analysis ◽

Antimicrobial Resistance ◽

Clinical Signs ◽

Streptococcus Suis ◽

The Other ◽

Clinical Disease ◽

Resistance To Antibiotics

A total of 122 Streptococcus suis serotype 2 strains were characterized thoroughly by comparing clinical and pathological observations, ribotype profiles, and antimicrobial resistance. Twenty-one different ribotype profiles were found and compared by cluster analysis, resulting in the identification of three ribotype clusters. A total of 58% of all strains investigated were of two ribotypes belonging to different ribotype clusters. A remarkable relationship existed between the observed ribotype profiles and the clinical-pathological observations because strains of one of the two dominant ribotypes were almost exclusively isolated from pigs with meningitis, while strains of the other dominant ribotype were never associated with meningitis. This second ribotype was isolated only from pigs with pneumonia, endocarditis, pericarditis, or septicemia. Cluster analysis revealed that strains belonging to the same ribotype cluster as one of the dominant ribotypes came from pigs that showed clinical signs similar to those of pigs infected with strains with the respective dominant ribotype profiles. Furthermore, strains belonging to different ribotype clusters had totally different patterns of resistance to antibiotics because strains isolated from pigs with meningitis were resistant to sulfamethazoxazole and strains isolated from pigs with pneumonia, endocarditis, pericarditis, or septicemia were resistant to tetracycline.

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