Yaws is an endemic disease caused by Treponema pallidum subsp. pertenue (TPE) that primarily affects children in rural regions of the tropics. The endemic character of yaws infections and the expected exclusive reservoir of TPE in humans opened a new opportunity to start a yaws eradication campaign. We have developed a multi-locus sequence typing (MLST) scheme for TPE isolates combining the previously published (TP0548, TP0488) and new (TP0858) chromosomal loci, and we compared this typing scheme to the two previously published MLST schemes. We applied this scheme to TPE-containing clinical isolates obtained during a mass drug administration study performed in the Namatanai District of Papua New Guinea between June 2018 and December 2019. Of 1081 samples collected, 302 (28.5%) tested positive for TPE DNA, from which 255 (84.4%) were fully typed. The TPE PCR-positivity in swab samples was higher in younger patients, patients with single ulcers, first ulcer episodes, and with ulcer duration less than six months. Non-treponemal serological test positivity correlated better with PCR positivity compared to treponema-specific serological tests. The MLST revealed a low level of genetic diversity among infecting TPE isolates, represented by just three distinct genotypes (JE11, SE22, and TE13). Two previously used typing schemes revealed similar typing resolutions. Two new alleles (one in TP0858 and one in TP0136) were shown to arise by intragenomic recombination/deletion events. Compared to samples genotyped as JE11, the minor genotypes (TE13 and SE22) were more frequently detected in samples from patients with two or more ulcers and patients with higher values of specific TP serological tests. Moreover, the A2058G mutation in the 23S rRNA genes of three JE11 isolates was found, resulting in azithromycin resistance.
BACKGROUND: A novel Panton-Valentine leukocidin (PVL)-positive meticillin-resistant Staphylococcus aureus (MRSA) clonal complex (CC)5-MRSA-IVc ('Sri Lankan' clone) was recently described from Sri Lanka. Similar isolates caused a recent Irish hospital outbreak. AIM: To investigate the international dissemination and diversity of PVL-positive CC5-MRSA-IVc isolates from hospital and community settings using whole-genome sequencing (WGS). METHODS: Core-genome single nucleotide polymorphism (cgSNP) analysis, core-genome multi-locus sequence typing (cgMLST) and microarray-based detection of antimicrobial-resistance and virulence genes were used to investigate PVL-positive CC5-MRSA-IVc (N = 214 including 46 'Sri Lankan' clone) from hospital and community settings in 12 countries over 17 years. Comparators included 29 PVL-positive and 23 PVL-negative CC5/ST5-MRSA-I/II/IVa/IVc/IVg/V. RESULTS: Maximum-likelihood cgSNP analysis grouped 209/214 (97.7%) CC5-MRSA-IVc into Clade I; average of 110 cgSNPs between isolates. Clade III contained the five remaining CC5-MRSA-IVc; average of 92 cgSNPs between isolates. Clade II contained seven PVL-positive CC5-MRSA-IVa comparators, whereas the remaining 45 comparators formed an outlier group. Minimum-spanning cgMLST analysis revealed a comparably low average of 57 allelic differences between all CC5/ST5-MRSA-IVc. All 214 CC5/ST5-MRSA-IVc were identified as 'Sri Lankan' clone, predominantly spa type t002 (186/214) with low population diversity and harboured a similar range of virulence genes and variable antimicrobial-resistance genes. All 214 Sri Lankan clone isolates and Clade II comparators harboured a 9616-bp chromosomal PVL-encoding phage remnant, suggesting both arose from a PVL-positive meticillin-susceptible ancestor. Over half of Sri Lankan clone isolates were from infections (142/214), and where detailed metadata were available (168/214), most were community associated (85/168). CONCLUSIONS: Stable chromosomal retention of pvl may facilitate Sri-Lankan clone dissemination.
- MeSH
- Exotoxins genetics MeSH
- Leukocidins genetics MeSH
- Humans MeSH
- Methicillin-Resistant Staphylococcus aureus * MeSH
- Methicillin MeSH
- Microbial Sensitivity Tests MeSH
- Multilocus Sequence Typing MeSH
- Hospitals MeSH
- Staphylococcal Infections * epidemiology MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
AIM: To investigate the epidemiology of Clostridioides difficile infection (CDI) in Slovakian hospitals after the emergence of ribotype 176 (027-like) in 2016. METHODS: Between 2018 and 2019, European Centre for Disease Control and Prevention CDI surveillance protocol v2.3 was applied to 14 hospitals, with additional data collected on recent antimicrobial use and the characterization of C. difficile isolates. RESULTS: The mean hospital incidence of CDI was 4.1 cases per 10,000 patient bed-days. One hundred and five (27.6%) in-hospital deaths were reported among the 381 cases. Antimicrobial treatment within the previous 4 weeks was recorded in 90.5% (333/368) of cases. Ribotype (RT)176 was detected in 50% (n=185/370, 14 hospitals) and RT001 was detected in 34.6% (n=128/370,13/14 hospitals) of cases with RT data. Overall, 86% (n=318/370) of isolates were resistant to moxifloxacin by Thr82Ile in GyrA (99.7%). Multi-locus variable tandem repeat analysis showed clonal relatedness of predominant RTs within and between hospitals. Seven of 14 sequenced RT176 isolates and five of 13 RT001 isolates showed between zero and three allelic differences by whole-genome multi-locus sequence typing. The majority of sequenced isolates (24/27) carried the erm(B) gene and 16/27 also carried the aac(6')-aph(2'') gene with the corresponding antimicrobial susceptibility phenotypes. Nine RT176 strains carried the cfr(E)gene and one RT001 strain carried the cfr(C) gene, but without linezolid resistance. CONCLUSIONS: The newly-predominant RT176 and endemic RT001 are driving the epidemiology of CDI in Slovakia. In addition to fluoroquinolones, the use of macrolide-lincosamide-streptogramin B antibiotics can represent another driving force for the spread of these epidemic lineages. In C. difficile, linezolid resistance should be confirmed phenotypically in strains with detected cfr gene(s).
- MeSH
- Anti-Bacterial Agents pharmacology therapeutic use MeSH
- Clostridioides difficile * genetics MeSH
- Clostridioides genetics MeSH
- Fluoroquinolones pharmacology MeSH
- Clostridium Infections * epidemiology drug therapy MeSH
- Humans MeSH
- Linezolid MeSH
- Macrolides MeSH
- Microbial Sensitivity Tests MeSH
- Multilocus Sequence Typing MeSH
- Ribotyping MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Geographicals
- Slovakia MeSH
Závěrečná zpráva o řešení grantu Agentury pro zdravotnický výzkum MZ ČR
nestr.
Cílem projektu je vyvinutí molekulární surveillance invazivního pneumokokového onemocnění v České republice, zhodnocení účinnosti aktuální vakcinační strategie a doporučení její aktualizace. Vytčené cíle budou dosaženy těmito postupy: sběr kmenů S. pneumoniae izolovaných od nemocných s invazivním pneumokokovým onemocněním v období 2017-2020; implementace molekulární identifikace a typizace (mPCR, rt-PCR) S. pneumoniae přímo z klinických vzorků u pacientů kultivačně negativních; molekulární charakterizace MLST (multilokusová sekvenační typizace), MLVA (multilokusová analýza tandemových repetic) a WGS (sekvenace celého genomu) vybraných kmenů S. pneumoniae izolovaných od nemocných s invazivním pneumokokovým onemocněním v období 2007-2020; analýza molekulárních charakteristik S. pneumoniae izolovaných od nemocných s invazivním pneumokokovým onemocněním v období před a po zavedení pneumokokové konjugované vakcíny do očkovacího schématu malých dětí; zhodnocení účinnosti aktuální vakcinační strategie a doporučení její aktualizace.; The aim is the development of molecular surveillance of invasive pneumococcal disease in the Czech Republic, the assessment of current vaccination strategy effectiveness and recommendations for strategy updating. The following steps will be used: collection of S. pneumoniae strains isolated from patients with invasive pneumococcal disease in the period from 2017-2020; implementation of molecular typing (mPCR, rt-PCR) of S. pneumoniae directly from clinical specimens of culture-negative patients; molecular characterization by MLST (Multi Locus Sequence Typing), MLVA (Multi Locus Variable Analysis), WGS (Whole Genome Sequencing) of selected S. pneumoniae strains isolated from patients with invasive pneumococcal disease in the period 2007-2020; analysis of molecular characteristics of S. pneumoniae strains isolated from patients with invasive pneumococcal disease in the periods before and after introduction of pneumococcal conjugated vaccine into the immunization programme for young children; assessment of current vaccination strategy effectiveness and recommendations for its updating.
- MeSH
- Outcome Assessment, Health Care MeSH
- Molecular Epidemiology MeSH
- Multilocus Sequence Typing MeSH
- Pneumococcal Infections epidemiology microbiology prevention & control MeSH
- Polymerase Chain Reaction MeSH
- Whole Genome Sequencing MeSH
- Practice Guidelines as Topic MeSH
- Streptococcus pneumoniae isolation & purification MeSH
- Population Surveillance MeSH
- Tandem Repeat Sequences MeSH
- Vaccination MeSH
- Geographicals
- Czech Republic MeSH
- Conspectus
- Patologie. Klinická medicína
- NML Fields
- molekulární biologie, molekulární medicína
- epidemiologie
- preventivní medicína
- NML Publication type
- závěrečné zprávy o řešení grantu AZV MZ ČR
Cíl práce: Cílem studie bylo určit genetickou rozmanitost humánních izolátů získaných v letech 2016–2020 z klinických laboratoří z různých lokalit České republiky (ČR) s ohledem na možné epidemické souvislosti a virulenci Listeria monocytogenes za využití dat celogenomového sekvenování. Metody: Ve studii byl použit soubor 102 humánních izolátů L. monocytogenes, u kterých byl určen sérotyp sklíčkovou aglutinací v kombinaci s multiplex PCR sérotypizací. Retrospektivně bylo provedeno celogenomové sekvenování a na základě získaných dat byla posouzena klonální příbuznost testovaných kmenů a přítomnost genů virulence pomocí softwaru Ridom SeqSphere+. Výsledky: V období let 2016–2020 bylo celkem charakterizováno 102 humánních izolátů L. monocytogenes, což činí 65 % ze všech hlášených případů listerióz registrovaných ve sledovaném období v ČR v systémech ISIN/EPIDAT. Dominantní zastoupení měl sérotyp 1/2a (57 %), následoval sérotyp 4b (30 %) a jen ojediněle byly detekovány kmeny sérotypu 1/2b (12 %) a 1/2c (1 %). Na základě analýzy celogenomových dat byly kmeny zařazeny k 26 klonálním komplexům a 27 sekvenačním typům. Porovnáním cgMLST (core genome Multi-Locus Sequence Typing) byly detekovány čtyři klastry o více jak třech kmenech vykazující vysokou příbuznost (rozdíly do 10 alel) s možnou epidemickou souvislostí. U všech kmenů byla potvrzena přítomnost klíčových genů virulence. Pouze u tří kmenů (sérotypu 1/2a, 1/2b a 1/2c) byla detekována bodová mutace v genu inlA spojovaná s expresí zkráceného proteinu internalinu A, který je zapojený do mechanismu přestupu L. monocytogenes intestinální bariérou. Závěr: Molekulární epidemiologie založená na celogenomovém sekvenování představuje účinný nástroj ke studiu populační struktury kmenů L. monocytogenes. V této studii byla zjištěna vysoká heterogenita humánních kmenů L. monocytogenes, zejména u v České republice dominantního sérotypu 1/2a. Bylo identifikováno několik klastrů s možnou epidemickou souvislostí, jejichž výskyt bude dále sledován.
Study aim: To determine the genetic diversity of human isolates of Listeria monocytogenes obtained in 2016–2020 from clinical laboratories in various locations of the Czech Republic with a focus on their possible epidemic links and virulence using whole genome sequencing data. Methods: A total of 102 human L. monocytogenes isolates, serotyped by slide agglutination in combination with multiplex PCR serotyping, were used in this study. Whole genome sequencing was performed retrospectively, and based on the obtained data, the clonal relatedness of the tested strains and the presence of virulence genes were assessed using the Ridom SeqSphere+ software. Results: In 2016-2020, 102 human isolates of L. monocytogenes were characterized, which represented 65% of all cases of listeriosis reported to the ISIN/EPIDAT systems in the Czech Republic in the monitored period. Serotype 1/2a (57%) was dominant, followed by serotype 4b (30%). Strains of serotype 1/2b (12%) and 1/2c (1%) were rarely detected. Based on the analysis of whole genome sequencing data, the strains were assigned to 26 clonal complexes and 27 sequence types. The cgMLST (core genome Multi-Locus Sequence Typing) analysis revealed four clusters of more than three strains, showing high relatedness (differences up to 10 alleles) with a possible epidemic link. The presence of all key virulence genes was confirmed in all strains. Only three strains (of serotypes 1/2a, 1/2b, and 1/2c) carried a point mutation in the inlA gene responsible for the expression of truncated internalin A protein, which is involved in the mechanism of intestinal barrier crossing by L. monocytogenes. Conclusion: Molecular epidemiology based on whole genome sequencing is an effective tool to study the population structure of L. monocytogenes strains. This study found high heterogeneity of human L. monocytogenes strains, especially for serotype 1/2a, dominant in the Czech Republic. Several clusters with a possible epidemic link have been identified, and their occurrence will be further monitored.
Investigating genetically-structured diversity in pathogen populations over time is important to better understand disease maintenance and spread. Herd-level surveillance of Mycobacterium bovis genotypes (multi-locus VNTR analysis types, MLVA types) from all culture-confirmed bovine tuberculosis (TB) herd cases was undertaken in Northern Ireland (NI), generating an unparalleled, longitudinal, population-level 14-year survey for this pathogen. Across this population, 295 genetically-distinct M. bovis MLVA types were identified in the 19,717 M. bovis isolates surveyed. Of these, the most frequent was MLVA type 002 (23.0%); 151 MLVA types were represented more than once, in groups ranging from 2 to 4438 isolates. Only 23 MLVA types were isolated in all 14 years. Investigating inter-annual frequency of M. bovis MLVA types, examples of statistically-significant expansions (MLVA types 002, 004, 006, 009 and 027), contractions (MLVA types 001, 007 and 011) and maintenance (MLVA types 003 and 005) were disclosed, during a period of fluctuating bovine TB herd-level incidence at the NI scale. The fixed period frequency distribution of MLVA types remained highly right-skewed. Novel VNTR copy number variant MLVA types (N = 242; an average of 17 per annum) were identified throughout the survey. The MLVA type distribution in the landscape was not random; MLVA types showed statistically-significant geographical localization and strong spatial associations with Divisional Veterinary Office (DVO) regions. There was also evidence of differential risk of particular MLVA types across breeds (Holstein/Friesian vs. other), age-class, and sex and some evidence of an association between the number of animals testing positive for bovine TB during the disclosing test and particular MLVA types, although there was substantial variation.
- MeSH
- Breeding MeSH
- Genotyping Techniques veterinary MeSH
- Longitudinal Studies MeSH
- Minisatellite Repeats * MeSH
- Multilocus Sequence Typing veterinary MeSH
- Mycobacterium bovis classification genetics growth & development isolation & purification MeSH
- Risk Factors MeSH
- Cattle MeSH
- Population Surveillance MeSH
- Tuberculosis, Bovine diagnosis epidemiology MeSH
- DNA Copy Number Variations MeSH
- Animals MeSH
- Check Tag
- Male MeSH
- Cattle MeSH
- Female MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Northern Ireland MeSH
BACKGROUND: Nivolumab is a human monoclonal antibody against programmed cell death receptor-1 (PD-1) able to rescue quiescent tumor infiltrating cytotoxic T lymphocytes (CTLs) restoring their ability to kill target cells expressing specific tumor antigen-derived epitope peptides bound to homologue human leukocyte antigen (HLA) molecules. Nivolumab is currently an active but expensive therapeutic agent for metastatic non-small cell lung cancer (mNSCLC), producing, in some cases, immune-related adverse events (irAEs). At the present, no reliable biomarkers have been validated to predict either treatment response or adverse events in treated patients. METHODS: We performed a retrospective multi-institutional analysis including 119 patients with mNSCLC who received PD-1 blockade since November 2015 to investigate the predictive role of germinal class I HLA and DRB1 genotype. We investigated the correlation among patients' outcome and irAEs frequency with specific HLA A, B, C and DRB1 alleles by reverse sequence-specific oligonucleotide (SSO) DNA typing. RESULTS: A poor outcome in patients negative for the expression of two most frequent HLA-A alleles was detected (HLA: HLA-A*01 and or A*02; progression-free survival (PFS): 7.5 (2.8 to 12.2) vs 15.9 (0 to 39.2) months, p=0.01). In particular, HLA-A*01-positive patients showed a prolonged PFS of 22.6 (10.2 to 35.0) and overall survival (OS) of 30.8 (7.7 to 53.9) months, respectively. We also reported that HLA-A and DRB1 locus heterozygosis (het) were correlated to a worse OS if we considered het in the locus A; in reverse, long survival was correlated to het in DRB1. CONCLUSIONS: This study demonstrate that class I and II HLA allele characterization to define tumor immunogenicity has relevant implications in predicting nivolumab efficacy in mNSCLC and provide the rationale for further prospective trials of cancer immunotherapy.
- MeSH
- Alleles MeSH
- Survival Analysis MeSH
- HLA Antigens metabolism MeSH
- Immune Checkpoint Inhibitors pharmacology therapeutic use MeSH
- Humans MeSH
- Lung Neoplasms genetics mortality MeSH
- Carcinoma, Non-Small-Cell Lung genetics mortality MeSH
- Retrospective Studies MeSH
- Aged MeSH
- Treatment Outcome MeSH
- Germ-Line Mutation genetics MeSH
- Check Tag
- Humans MeSH
- Male MeSH
- Aged MeSH
- Female MeSH
- Publication type
- Journal Article MeSH
- Multicenter Study MeSH
- Research Support, Non-U.S. Gov't MeSH
We evaluated the prevalence and epidemiology of extended-spectrum beta-lactamase (ESBL)-producing Escherichia coli isolates in pigs during production cycle on a Czech farm with the history of previous use of ceftiofur. ESBL-producing E. coli isolates were obtained from rectal swabs from pigs of different age groups (suckling piglets, weaned piglets, growers and sows). Collected samples were directly cultivated on MacConkey agar with cefotaxime (2 mg l-1 ), whereas intestinal swabs of slaughtered pigs and surface swabs from pig carcasses were also pre-enriched in buffered peptone water without antimicrobials before the cultivation. Clonal relationship of selected isolates was determined by XbaI pulse-field gel electrophoresis and multi-locus sequence typing. The transferability of plasmids carrying blaCTX-M genes was tested by conjugation experiments. From all examined samples, 141 (43·7%, n = 323) were positive for ESBL-producing E. coli. All ESBL-producing isolates showed resistance to multiple antimicrobials and were positive for blaCTX-M genes. The blaCTX-M-1 was carried by conjugative IncN/ST1 plasmids (c. 40-45 kb) while the blaCTX-M-15 was located on conjugative F plasmids with F:18:A5:B1 formula (c. 165 kb). This study demonstrated the persistence of CTX-M-positive E. coli isolates 2 months after banner of ceftiofur usage and indicated possible risk of transmission of these isolates to humans via the food chain.
- MeSH
- beta-Lactamases genetics metabolism MeSH
- Escherichia coli enzymology genetics isolation & purification MeSH
- Farms MeSH
- Escherichia coli Infections microbiology physiopathology veterinary MeSH
- Humans MeSH
- Multilocus Sequence Typing MeSH
- Swine Diseases microbiology physiopathology MeSH
- Plasmids genetics metabolism MeSH
- Swine growth & development microbiology MeSH
- Escherichia coli Proteins genetics metabolism MeSH
- Animals MeSH
- Check Tag
- Humans MeSH
- Animals MeSH
- Publication type
- Journal Article MeSH
- Geographicals
- Czech Republic MeSH
Parasites of the genus Leishmania (Kinetoplastida: Trypanosomatidae) cause widespread and devastating human diseases. Visceral leishmaniasis due to Leishmania donovani is endemic in Ethiopia where it has also been responsible for major epidemics. The presence of hybrid genotypes has been widely reported in surveys of natural populations, genetic variation reported in a number of Leishmania species, and the extant capacity for genetic exchange demonstrated in laboratory experiments. However, patterns of recombination and the evolutionary history of admixture that produced these hybrid populations remain unclear. Here, we use whole-genome sequence data to investigate Ethiopian L. donovani isolates previously characterized as hybrids by microsatellite and multi-locus sequencing. To date there is only one previous study on a natural population of Leishmania hybrids based on whole-genome sequences. We propose that these hybrids originate from recombination between two different lineages of Ethiopian L. donovani occurring in the same region. Patterns of inheritance are more complex than previously reported with multiple, apparently independent, origins from similar parents that include backcrossing with parental types. Analysis indicates that hybrids are representative of at least three different histories. Furthermore, isolates were highly polysomic at the level of chromosomes with differences between parasites recovered from a recrudescent infection from a previously treated individual. The results demonstrate that recombination is a significant feature of natural populations and contributes to the growing body of data that shows how recombination, and gene flow, shape natural populations of Leishmania.
- MeSH
- Chimera * MeSH
- Genotype MeSH
- Leishmania donovani genetics MeSH
- Leishmaniasis, Visceral parasitology MeSH
- Humans MeSH
- Recombination, Genetic MeSH
- Whole Genome Sequencing MeSH
- Check Tag
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Ethiopia MeSH
BACKGROUND: Treponema pallidum subspecies pallidum (TPA) and subsp. endemicum (TEN) are the causative agents of syphilis and bejel, respectively. TEN shows similar clinical manifestations and is morphologically and serologically indistinguishable from TPA. Recently, bejel was found outside of its assumed endemic areas. Using molecular typing we aimed to discover bejel and characterize circulating TPA types among syphilis cases with Surinamese, Antillean and Dutch ethnicity in Amsterdam. METHODS: DNA was extracted from 137 ulcer swabs, which tested positive in the in-house diagnostic PCR targeting the polA gene. Samples were collected between 2006 and 2018 from Surinamese, Antillean and Dutch patients attending the Amsterdam STI clinic. Multilocus sequence typing was performed by partial sequence analysis of the tp0136, tp0548 and tp0705 genes. In addition, the 23S rRNA loci were analyzed for A2058G and A2059G macrolide resistance mutations. RESULTS: We found 17 distinct allelic profiles in 103/137 (75%) fully typed samples, which were all TPA and none TEN. Of the strains, 82.5% were SS14-like and 17.5% Nichols-like. The prevalence of Nichols-like strains found in this study is relatively high compared to nearby countries. The most prevalent types were 1.3.1 (42%) and 1.1.1 (19%), in concordance with similar TPA typing studies. The majority of the TPA types found were unique per country. New allelic types (7) and profiles (10) were found. The successfully sequenced 23S rRNA loci from 123/137 (90%) samples showed the presence of 79% A2058G and 2% A2059G mutations. CONCLUSIONS: No TEN was found in the samples from different ethnicities residing in Amsterdam, the Netherlands, so no misdiagnoses occurred. Bejel has thus not (yet) spread as a sexually transmitted disease in the Netherlands. The strain diversity found in this study reflects the local male STI clinic population which is a diverse, mixed group.
- MeSH
- Alleles MeSH
- Genes, Bacterial * MeSH
- Adult MeSH
- Ethnicity statistics & numerical data MeSH
- Humans MeSH
- Syphilis epidemiology ethnology microbiology MeSH
- DNA Barcoding, Taxonomic MeSH
- Treponema pallidum classification genetics pathogenicity MeSH
- Check Tag
- Adult MeSH
- Humans MeSH
- Publication type
- Journal Article MeSH
- Research Support, Non-U.S. Gov't MeSH
- Geographicals
- Netherlands Antilles MeSH
- Netherlands MeSH
- Suriname MeSH