Oral leukoplakia patient details and <i>Candida</i> species recovered.

a<p>Both of these patients with CL went on to develop squamous cell carcinoma at the lesional site within a two-year follow up period.</p><p>Abbreviations; CL, <i>Candida</i> leukoplakia; NCL, Non-<i>Candida</i> leukoplakia; SCC, squamous cell carcinoma; SC, semi-confluent growth (approx. 1000 cfu per swab or per ml oral wash); C, confluent (approx. 5000 cfu per swab or per ml oral wash); BM, buccal mucosa; TON, tongue, PAL, palate, AR, alveolar ridge; FM, floor of mouth; GIN, gingivae.</p

MLST DSTs, allelic profiles and ABC genotypes of <i>C. albicans</i> isolates recovered from OL patients and healthy oral carriers.

a<p>With regard to isolates recovered from CL and NCL patients, the numeral part of the isolate name refers to the corresponding patient numbers shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073738#pone-0073738-t001" target="_blank">Table 1</a>, column one (e.g. isolate CL10 was recovered from patient 10). Isolates CL12 and CL122 were recovered from two separate CL lesions in patient 12. CL and NCL isolates were recovered from lesional swabs, whereas OC isolates were recovered from oral rinse samples.</p>b<p>MLST clades defined according to Odds <i>et al</i>. <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073738#pone.0073738-Odds3" target="_blank">[17]</a>.</p>c<p>ABC genotypes were assigned based on the presence or absence of an intron in the 25S rRNA gene <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073738#pone.0073738-McCullough2" target="_blank">[14]</a>.</p>d<p>Two CL patients included in this study (patients 08 and 14, <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073738#pone-0073738-t001" target="_blank">Table 1</a>) developed squamous cell carcinoma at the lesional site within a two-year follow up period. Isolate CL14 (patient 14) and isolate CL08 (patient 8) belonged to ABC genotypes C and A, respectively.</p><p>Abbreviations: DST, diploid sequence type; CC, clonal complex; Htz, number of heterozygous sites; CL, <i>Candida</i> leukoplakia; NCL, non-<i>Candida</i> leukoplakia; OC, oral carriage; S, singleton.</p

UPGMA dendrogram depicting the genetic relatedness of all <i>C.</i><i>albicans</i> isolates subjected to MLST and ABC genotyping analysis in the present study.

<p>Individual isolates recovered from CL (n = 25) and NCL (n = 19) patients are indicated with the letters CL and OL in the isolate names, respectively. The numeral part of the isolate name refers to the corresponding patient numbers as shown in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073738#pone-0073738-t001" target="_blank">Table 1</a>, column 1. Isolates recovered from age and sex-matched healthy control patients (n = 34) by oral rinse are indicated using the letters OC in the isolate name. Hyphenated letters A, B or C following each isolate name indicate ABC genotypes. The scale bar indicates p- distance. Distinct MLST clades are indicated by separated square parenthesis to the right of the isolate names and labelled with previously designated clade numbers <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0073738#pone.0073738-Odds3" target="_blank">[17]</a>. Numbers at clade branches indicate bootstrap support levels, based on 1000 replications. Overall, the population analysis based on MLST suggests no clonal enrichment of <i>C. albicans</i> isolates recovered from CL or NCL lesions. Isolates recovered from CL patients are distributed among eight clades, isolates from NCL patients are distributed among eight clades and isolates from healthy carriers are distributed among nine clades, with clade 1 predominating in all three groups.</p

Distribution of ABC genotypes in isolates recovered from oral leukoplakia patients and healthy carriers.

a<p>The prevalence of genotype A and genotype C isolates differed significantly between the CL and OC groups (P<0.02).</p><p>Abbreviations: CL, <i>Candida</i> leukoplakia; NCL, non-<i>Candida</i> leukoplakia; OC, oral carriage.</p

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Novel primer and probe sequences and PCR conditions.

<p>Novel primer and probe sequences and PCR conditions.</p

The Emergence and Spread of Multiple Livestock-Associated Clonal Complex 398 Methicillin-Resistant and Methicillin-Susceptible <i>Staphylococcus aureus</i> Strains among Animals and Humans in the Republic of Ireland, 2010–2014

<div><p>Clonal complex (CC) 398 methicillin-resistant <i>Staphylococcus aureus</i> (MRSA) and methicillin-susceptible <i>S</i>. <i>aureus</i> (MSSA) are associated with carriage and infection among animals and humans but only a single case of CC398 MRSA has been reported in the Republic of Ireland (ROI). The present study investigated the molecular epidemiology of CC398 MRSA (<i>n</i> = 22) and MSSA (<i>n</i> = 10) from animals and humans in the ROI from 2010–2014. Isolates underwent antimicrobial susceptibility testing, <i>spa</i> typing, DNA microarray profiling and PCR for CC398-associated resistance genes. All MRSA underwent SCC<i>mec</i> IV or V subtyping. Four distinct CC398-MRSA incidents were identified from (i) a man in a nursing home (<i>spa</i> type t011-SCC<i>mec</i> IVa, immune evasion complex (IEC) negative), (ii) a horse and veterinarian who had recently travelled to Belgium (t011-IVa, IEC positive), (iii) pigs (<i>n</i> = 9) and farm workers (<i>n</i> = 9) on two farms, one which had been restocked with German gilts and the other which was a finisher farm (t034-V_T, IEC negative, 3/9 pigs; t011- V_T, IEC negative, 6/9 pigs & 9/9 farm workers), and (iv) a child who had worked on a pig farm in the UK (t034-V_T, IEC negative). Isolates also carried different combinations of multiple resistance genes including <i>erm</i>(A), <i>erm</i>(B), <i>tet</i>(K), <i>tet</i>(M) & <i>tet</i>(L), <i>fexA</i>, <i>spc</i>, <i>dfrG</i>, <i>dfrK aacA-aphD</i> and <i>aadD</i> further highlighting the presence of multiple CC398-MRSA strains. CC398 MSSA were recovered from pigs (<i>n</i> = 8) and humans (<i>n</i> = 2). CC398 MSSA transmission was identified among pigs but zoonotic transmission was not detected with animal and human isolates exhibiting clade-specific traits. This study highlights the importation and zoonotic spread of CC398 MRSA in the ROI and the spread of CC398 MSSA among pigs. Increased surveillance is warranted to prevent further CC398 MRSA importation and spread in a country that was considered CC398 MRSA free.</p></div

Image_1_Intra-Hospital, Inter-Hospital and Intercontinental Spread of ST78 MRSA From Two Neonatal Intensive Care Unit Outbreaks Established Using Whole-Genome Sequencing.PDF

<p>From 2009 to 2011 [transmission period (TP) 1] and 2014 to 2017 (TP2), two outbreaks involving community-associated clonal complex (CC) 88-MRSA spa types t186 and t786, respectively, occurred in the Neonatal Intensive Care Unit (NICU) of an Irish hospital (H1). This study investigated the relatedness of these isolates, their relationship to other CC88 MRSA from Ireland and their likely geographic origin, using whole-genome sequencing (WGS). All 28 CC88-MRSA isolates identified at the Irish National MRSA Reference Laboratory between 2009 and 2017 were investigated including 20 H1 patient isolates, two H1 isolates recovered from a single healthcare worker (HCW) 2 years apart, three patient isolates from a second hospital (H2) and one patient isolate from each of three different hospitals (H3, H4, and H5). All isolates underwent DNA microarray profiling. Thirteen international isolates with similar microarray profiles to at least one Irish isolate were selected from an extensive global database. All isolates underwent Illumina MiSeq WGS. The majority of Irish isolates (25/28; all H1 isolates, two H2 isolates and the H3 isolate) were identified as ST78-MRSA-IVa and formed a large cluster, exhibiting 1–71 pairwise allelic differences, in a whole-genome MLST-based minimum spanning tree (MST) involving all Irish isolates. A H1/H2, H1/H3, and H1 HCW/patient isolate pair each exhibited one allelic difference. The TP2 isolates were characterised by a different spa type and the loss of hsdS. The three remaining Irish isolates (from H2, H4, and H5) were identified as ST88-MRSA-IVa and dispersed at the opposite end of the MST, exhibiting 81–211 pairwise allelic differences. Core-genome MLST and sequence-based plasmid analysis revealed the recent shared ancestry of Irish and Australian ST78-MRSA-IVa, and of Irish and French/Egyptian ST88-MRSA-IVa. This study revealed the homogeneity of isolates recovered during two NICU outbreaks (despite spa type and hsdS carriage variances), HCW involvement in the outbreak transmission chain and the strain's spread to two other Irish hospitals. The outbreak strain, CC88/ST78-MRSA-IVa, was likely imported from Australia, where it is prevalent. CC88/ST88-MRSA-IVa was also identified in Irish hospitals and was likely imported from Africa, where it is predominant, and/or a country with a large population of African descent.</p

Detection of <i>mecC-</i>Positive <i>Staphylococcus aureus</i> (CC130-MRSA-XI) in Diseased European Hedgehogs (<i>Erinaceus europaeus</i>) in Sweden

<div><p>Recently, a novel <i>mec</i> gene conferring beta-lactam resistance in <i>Staphylococcus aureus</i> has been discovered. This gene, <i>mecC</i>, is situated on a SCC<i>mec</i> XI element that has to date been identified in clonal complexes 49, 130, 425, 599 and 1943. Some of the currently known isolates have been identified from animals. This, and observations of <i>mecA</i> alleles that do not confer beta-lactam resistance, indicate that <i>mec</i> genes might have a reservoir in <i>Staphylococcus</i> species from animals. Thus it is important also to screen wildlife isolates for <i>mec</i> genes. Here, we describe <i>mecC</i>-positive <i>Staphylococcus aureus</i> (ST130-MRSA-XI) and the lesions related to the infection in two diseased free-ranging European hedgehogs (<i>Erinaceus europaeus</i>). One was found dead in 2003 in central Sweden, and suffered from <i>S. aureus</i> septicaemia. The other one, found on the island of Gotland in the Baltic Sea in 2011, showed a severe dermatitis and was euthanised. ST130-MRSA-XI isolates were isolated from lesions from both hedgehogs and were essentially identical to previously described isolates from humans. Both isolates carried the complete SCC<i>mec</i> XI element. They lacked the <i>lukF-PV/lukS-PV</i> and <i>lukM/lukF-P83</i> genes, but harboured a gene for an exfoliative toxin homologue previously described from <i>Staphylococcus hyicus</i>, <i>Staphylococcus pseudintermedius</i> and other <i>S. aureus</i> of the CC130 lineage. To the best of our knowledge, these are the first reported cases of CC130-MRSA-XI in hedgehogs. Given that one of the samples was taken as early as 2003, this was the earliest detection of this strain and of <i>mecC</i> in Sweden. This and several other recent observations suggest that CC130 might be a zoonotic lineage of <i>S. aureus</i> and that SCC<i>mec</i> XI/<i>mecC</i> may have originated from animal pathogens.</p></div

Epidemiological, phenotypic and genotypic characteristics of CC398 methicillin-resistant and methicillin-susceptible <i>S</i>. <i>aureus</i> (MRSA and MSSA) identified in the Republic of Ireland among animals and humans.

<p>Epidemiological, phenotypic and genotypic characteristics of CC398 methicillin-resistant and methicillin-susceptible <i>S</i>. <i>aureus</i> (MRSA and MSSA) identified in the Republic of Ireland among animals and humans.</p