Retrospective Analysis to Optimize the Detection of MET Exon 14 Skipping Mutations in Non-Small Cell Lung Cancer.

Our study optimized METex14 skipping mutation detection by analyzing 223 Oncomine™ Focus Assay-positive cases using Pan Lung Cancer PCR Panel and reverse transcription (RT)-PCR. Among the 11 METex14 skipping mutation-positive cases (average read counts: 1390), 2 with Oncomine™ Focus Assay read counts of 2540 and 10,177 were positive on all platforms. Those with Oncomine™ Focus Assay read counts ranging from 179 to 612 tested negative elsewhere. Specimens with low ratios (average ratio: 0.12% for nine cases) may yield false-positive results. Our results suggested that monitoring read counts and ratios and validating the results with RT-PCR are crucial to prevent false positives.

Molecular Characteristics and Virulence Profile of Clinical Listeria monocytogenes Isolates in Northern Taiwan, 2009-2019.

Listeria monocytogenes is a critical foodborne pathogen that causes severe invasive and noninvasive diseases and is associated with high mortality. Information on the prevalence of L. monocytogenes infections in Taiwan is very limited. This study aimed to analyze the molecular epidemiological surveillance and virulence gene distribution of 176 human clinical L. monocytogenes isolates collected between 2009 and 2019 in northern Taiwan. Our results showed that the isolates belonged to 4 serogroups (IIa, IIb, IVb, and IIc), with most isolates in serogroups IIa (81/176, 46%) and IIb (71/176, 40.3%). Multilocus sequence typing analysis revealed 18 sequence types (STs) and 13 clonal complexes (CCs). Eighty-four percent of all isolates belonged to six STs: CC87-ST87 (40/176, 22.7%), CC19-ST378 (36/176, 19.9%), CC155-ST155 (28/176, 15.5%), CC1-ST710 (16/176, 8.8%), CC5-ST5 (16/176, 8.8%), and CC101-ST101 (11/176, 6.1%). Furthermore, our analysis showed the distributions of four Listeria pathogenicity islands (LIPI) among all isolates. LIPI-1 and LIPI-2 existed in all isolates, whereas LIPI-3 and LIPI-4 only existed in specific STs and CCs. LIPI-3 existed in the STs, CC1-ST710, CC3-ST3, CC288-ST295, and CC191-ST1458, whereas LIPI-4 could be found in the STs, CC87-ST87 and CC87-ST1459. Strains containing LIPI-3 and LIPI-4 are potentially hypervirulent; thus, 68/176 isolates (39.1%) collected in this study were potentially hypervirulent. Since L. monocytogenes infections are considered highly correlated with diet, molecular epidemiological surveillance of Listeria in food is important; continued surveillance will provide critical information to prevent foodborne diseases.

Molecular characterization of lugdunin inactivation mechanisms and their association with Staphylococcus lugdunensis genetic types.

BACKGROUND AND PURPOSE: Our previous studies showed that lugdunin activities are associated with Staphylococcus lugdunensis genotypes, and most isolates do not exhibit lugdunin activity. As a continuation of our previous analysis, we focused on the reasons for defects in lugdunin production in S. lugdunensis clinical isolates. METHODS: A comparative analysis of 36 S. lugdunensis whole genome sequencing data revealed three major mutation types, unknown deletion mechanism that caused most of lug operon genes lost, mobile genetic element (MGE) insertion, and nonsense mutations, which potentially damaged lugdunin production. A total of 152 S. lugdunensis clinical isolates belonging to lugdunin nonproducers were further examined for the above three mutation types. PCR products were sequenced to examine these variations. RESULTS: Forty-six of the 152 isolates were CRISPR-Cas IIC isolates, including 26 ST27, 14 ST4, and 6 ST29 isolates; further investigation confirmed that all of their lug operons had lost almost all lug operon genes except lugM. An IS256 insertion in lugA was identified in 16 isolates, and most isolates (15 over 16) belonged to ST3. In addition, three nonsense mutations caused by single nucleotide substitutions (an adenine deletion in lugB at the 361th and 1219th nucleotides and an adenine deletion in lugC at the 1612nd nucleotide) that were frequently observed among 36 S. lugdunensis whole genome sequencing data were further observed in our clinical isolates. These three nonsense mutations were frequently found in most of CRISPR-Cas IIIA strains, especially in ST6 isolates. CONCLUSION: Our findings suggest that the mechanisms affecting lugdunin production are associated with S. lugdunensis molecular types.

Lugdunin production and activity in Staphylococcus lugdunensis isolates are associated with its genotypes.

Lugdunin produced by Staphylococcus lugdunensis has been shown to have broad inhibitory activity against Gram-positive bacteria; however, lugdunin activity among S. lugdunensis isolates and its association with different agr, SCCmec, and sequence types remain unclear. We used matrix-assisted laser desorption ionization-time-of-flight mass spectrometry to identify S. lugdunensis and collected 202 S. lugdunensis samples for further assays. Agar spot tests were performed to characterize S. lugdunensis lugdunin production and activity. Multilocus sequence typing, SCCmec, and agr genotyping were performed on S. lugdunensis. In all, 91 Staphylococcus aureus strains with varying vancomycin susceptibilities were used to examine lugdunin activity in S. lugdunensis. In total, 48 S. lugdunensis strains (23.8%) were found to be oxacillin-resistant S. lugdunensis (ORSL), whereas 154 (76.2%) were classified as oxacillin-sensitive S. lugdunensis (OSSL). Moreover, 16 (33.3%) ORSL and 35 (22.7%) OSSL strains showed antibacterial activity against S. aureus. Our data showed that most lugdunin-producing ORSL strains (14/48, 29.2%) were of ST3-SCCmec V-agr II genotypes, whereas most lugdunin-producing OSSL strains (15/154, 9.7%) were of ST3-agr II, followed by ST1-agr I (10/154, 6.5%). Our data also revealed that lugdunin exhibited weak inhibitory activity against the VISA ST239 isolate. In addition, we observed that ST239 VSSA was more resistant to lugdunin than ST5, ST59, and ST45 VSSA. Taken together, our data pioneered the epidemiology of lugdunin production in S. lugdunensis isolates and revealed its association with genotypes. However, further molecular and bioinformatics investigations are needed to elucidate the regulatory mechanisms of lugdunin production and activity. IMPORTANCE Lugdunin is active against both methicillin-resistant Staphylococcus aureus and vancomycin-resistant enterococci by dissipating their membrane potential. However, the association of lugdunin activity with the genotypes of Staphylococcus lugdunensis has not been addressed. Here, we show the high prevalence of lugdunin-producing strains among ST1 (83.3%), ST2 (66.7%), and ST3 (53.3%) S. lugdunensis. Moreover, we identified the antibacterial activity of lugdunin-producing strains against VISA and hVISA. These results shed light on the potential application of lugdunin for the treatment of drug-resistant pathogens.

Clonal Spreading of ST42 Staphylococcus haemolyticus Strains Occurs Possibly Due to fusB and tetK Resistant Genes and Capsule-Related Genes.

Multi-drug resistant Staphylococcus haemolyticus is a frequent nosocomial invasive bacteremia pathogen in hospitals. Our previous analysis showed one of the predominant strains, ST42 originated from ST3, had only one multilocus sequence typing (MLST) variation among seven loci in SH1431; yet no significant differences in biofilm formation observed between ST42 and ST3, suggesting that other factors influence clonal lineage change. Whole genome sequencing was conducted on two isolates from ST42 and ST3 to find phenotypic and genotypic variations, and these variations were further validated in 140 clinical isolates. The fusidic acid- and tetracycline-resistant genes (fusB and tetK) were found only in CGMH-SH51 (ST42). Further investigation revealed consistent resistant genotypes in all isolates, with 46% and 70% of ST42 containing fusB and tetK, respectively. In contrast, only 23% and 4.2% ST3 contained these two genes, respectively. The phenotypic analysis also showed that ST42 isolates were highly resistant to fusidic acid (47%) and tetracycline (70%), compared with ST3 (23% and 4%, respectively). Along with drug-resistant genes, three capsule-related genes were found in higher percentage distributions in ST42 than in ST3 isolates. Our findings indicate that ST42 could become endemic in Taiwan, further constitutive surveillance is required to prevent the spread of this bacterium.

Characterization of oxacillin-resistant Staphylococcus lugdunensis isolated from sterile body fluids in a medical center in Taiwan: A 12-year longitudinal epidemiological study.

BACKGROUND: In this study, our objective was to characterize Staphylococcus lugdunensis isolated from sterile body fluids (SBFs) in a medical center in Taiwan between 2009 and 2020. METHODS: We used MALDI-TOF MS, disk diffusion testing, agar dilution assay, SCCmec typing, and antibiotic resistance gene screening to identify and investigate the characteristics of oxacillin-resistant S. lugdunensis (ORSL). RESULTS: A total of 438 S. lugdunensis isolates were collected and 146 (33.3%) isolates were identified as ORSL. SCCmec type V was dominant (65.7%) in our ORSL isolates, followed by SCCmec type II (18.5%), and type IV (8.9%). After 2013, a slight increase in SCCmec types IV and V was revealed. Moreover, all ORSL isolates with type II and untypable SCCmec were highly resistant to oxacillin (MIC >32 µg/mL), compared to ORSL that had SCCmec types IV, V, and VT. All 146 ORSL isolates were resistant to penicillin and susceptible to teicoplanin and vancomycin. High resistance rates of ORSL to clindamycin (43.2%), erythromycin (43.2%), gentamicin (78.1%) and tetracycline (46.6%) was observed. Moreover, only two (1.4%) and six (4.1%) ORSL isolates were resistant to trimethoprim/sulfamethoxazole and ciprofloxacin, respectively. The erythromycin-resistant ORSL isolates mostly exhibited constitutive MLSB resistant phenotype (61/63, 96.8%) and contained either ermC alone (27/63, 42.9%) or a combination of ermC with ermA (28/63, 44.4%). CONCLUSION: Our present study showed a stable rate of ORSL from SBFs during 2009-2020. Moreover, teicoplanin, vancomycin, trimethoprim/sulfamethoxazole, and ciprofloxacin were shown to be highly efficient for the treatment of ORSL in vitro.

An lnu(A)-Carrying Multi-Resistance Plasmid Derived from Sequence Type 3 Methicillin-Resistant Staphylococcus lugdunensis May Contribute to Antimicrobial Resistance in Staphylococci.

Methicillin-resistant Staphylococcus lugdunensis (MRSL) strains showing resistance to several common antibiotics have been reported recently. Sequence type (ST) 3 MRSL carrying SCCmec types IV, V, or Vt is the major lineage associated with health care-associated infections. We aimed to investigate the distribution and dissemination of antimicrobial resistance determinants in this lineage. Two representative ST3-MRSL strains, CGMH-SL131 (SCCmec V) and CGMH-SL138 (SCCmec IV), were subjected to whole-genome sequencing. Detection of antibiotic resistance genes and screening of susceptibility patterns were performed for 30 ST3-MRSL and 16 ST6-MRSL strains via PCR and standard methods. Except for mecA and blaZ, antimicrobial resistance genes were located within two plasmids: a 28.6 kb lnu(A)-carrying plasmid (pCGMH_SL138) in CGMH-SL138 and a 26 kb plasmid carrying non-lnu(A) resistance genes (pCGMH_SL131) in CGMH-SL131. Both plasmids shared common genetic features with multiple copies of IS257 flanked by genes conferring resistance to aminoglycoside (aacA-aphD and aadD), TET (tetk), and cadmium (cadDX) and tolerance to chlorhexidine (qacA/R); however, only pCGMH_SL138 harbored lnu(A) that conferred resistance to lincomycin and rep13 that encodes a replication initiation protein. Unlike ST6-MRSL, none of the ST3-MRSL isolates contained the ermA gene. Instead, most isolates harbored lnu(A) (20/30, 66.7%), and several other resistance genes found on pCGMH_SL138. These isolates and transformants containing pCGMH_SL138 exhibited susceptibility to ERY and higher MICs for lincomycin and aforementioned antibiotics. A novel lnu(A)-carrying plasmid, pCGMH_SL138, that harbored a multiresistance gene cluster, was identified in ST3-MRSL strains and may contribute to the dissemination of antibiotic resistance in staphylococci.

Accurate detection of oxacillin-resistant Staphylococcus lugdunensis by use of agar dilution.

BACKGROUND/PURPOSE: Staphylococcus lugdunensis is a Gram-positive coagulase-negative bacterium and is recognized as a critical pathogenic species recently. Here, we aimed to evaluate the cefoxitin disk diffusion (CDD), oxacillin agar dilution (OAD), and mecA PCR for detecting oxacillin-resistant S. lugdunensis (ORSL) isolates. METHODS: Multilocus sequence typing (MLST) analysis was performed to determine the clonality of 117 S. lugdunensis isolates isolated between May 2009 and Jul 2014. CDD, OAD, and mecA PCR were used to identify oxacillin-resistant S. lugdunensis (ORSL). RESULTS: MLST results showed that the most common sequence type (ST) of our S. lugdunensis isolates was ST6 (35.9%) followed by ST3 (28.2%), ST27 (17.9%), and ST4 (6.8%). CDD and OAD showed that 39 and 43 isolates were ORSL, respectively. 4 ST3 CDD-susceptible S. lugdunensis (OSSL) isolates had MIC values ≥ 4 for oxacillin. mecA PCR results showed that 43 OAD-resistant S. lugdunensis and 3 OAD-susceptible ST27 S. lugdunensis had the mecA gene. Therefore, OAD was used as the gold standard to evaluate the performance of CDD and mecA PCR for identifying ORSL. The overall sensitivity, specificity, and accuracy of CCD for ORSL detection was 90.7%, 100%, and 96.8%, respectively. The sensitivity, specificity, and accuracy of mecA PCR for identifying ORSL was 100%, 95.9%, and 97.44%, respectively. CONCLUSION: Our results indicate that OAD shows higher accuracy for ORSL detection compared with CDD and mecA PCR.

Characterization of New Staphylococcus haemolyticus ST42 Populations in Northern Taiwan.

Introduction: Staphylococcus haemolyticus is an acquired opportunistic pathogen causing nosocomial infections. Our previous studies of S. haemolyticus showed a group of isolates that produced a significantly higher disease severity than the others. Further molecular typing showed that the sequence type (ST) 42 was the major clone among the isolates. The main aim of this study was to characterize ST42. Materials and Methods: Sixty-one and 36 isolates were collected from burn and nonburn patients, respectively. Molecular typing, antibiotic susceptibility assays, and phenotypic characterizations were performed. Results: Thirteen STs, including seven new STs, were established (ST42 to ST48). ST42 was prevalent in burn and nonburn patients, and all the pulsotype C isolates were ST42. Four of the novel STs originated from ST3, suggesting that these clonal lineages evolved locally. ST3 and ST42 showed a significant difference in clindamycin susceptibility; molecular typing showed only one MLST locus variation among seven loci in SH1431, which has been reportedly involved in the regulation of biofilm formation through Zn 2+ binding affinities. Conclusions: Seven novel S. haemolyticus STs were identified; phylogenetic analysis suggested the presence of locally evolved clonal lineages. The predominant ST42 showed weak biofilm formation abilities; other factors that cause the clonal lineage change still need further investigation.

Comparative Genomic Analyses Reveal Potential Factors Responsible for the ST6 Oxacillin-Resistant Staphylococcus lugdunensis Endemic in a Hospital.

Oxacillin-resistant Staphylococcus lugdunensis (ORSL) is considered a life-threatening isolate in healthcare settings. Among ORSL clones, ST6-SCCmec II strains are associated with an endemic spread in hospitals. We analyzed the complete genome of ORSL CGMH-SL118, a representative strain. Results revealed that this strain contained three MGEs (two prophages and one plasmid) other than the SCCmec II element, which showed remarkable differences in genome organization compared to the reference strains from NCBI. Eight multidrug-resistant genes were identified. All but blaZ were carried by MGEs, such as the SCCmec II element [mecA, ant (9)-Ia, and ermA] and the prophage φSPbeta [aac (6')-aph (2'), aph (3')-III, and ant (6)-Ia], indicating that MGEs carrying multidrug-resistant genes may be important for ST6 strains. The prophage φSPbeta contains sasX gene, which was responsible for the pathogenesis of Staphylococcus aureus. A phage-mediated resistant island containing fusB (SlRI fusB-118) was found near φSPbeta, which was highly homologous to type III SeRI fusB-5907 of Staphylococcus epidermidis. In contrast to previous studies, over 20% of ST6 isolates showed a fusidic acid-resistant phenotype, suggesting that phage-mediated intraspecies transmission of resistant islands may become an important issue for ST6 strains. Sixty-eight clinical isolates of ST6 Staphylococcus lugdunensis (50 OSSL, oxacillin-sensitive S. lugdunensis, and 18 ORSL, including CGMH-SL118) collected from various types of specimens in the hospital were studied. Among these isolates in this study, ORSL showed similar drug-resistant genes and phenotypes as CGMH-SL118. The comparative genomic analyses highlight the contribution of MGEs in the development and dissemination of antimicrobial resistance in ST6 strains, suggesting that resistance determinants and virulence factors encoded by MGEs provide a survival advantage for successful colonization and spread in healthcare settings.

Phylogenetic Distribution of CRISPR-Cas Systems in Staphylococcus lugdunensis.

Clustered regularly interspaced short palindromic repeats (CRISPRs) and CRISPR-associated (Cas) genes (CRISPR-Cas) are present in many bacterial genomes with functions beyond adaptive immunity. We aimed to characterize the CRISPR-Cas system in the pathogenic Gram-positive bacterium Staphylococcus lugdunensis and determine its association with sequence types (STs) determined by multilocus sequence typing (MLST) and oxacillin susceptibility. Primers were designed to detect and sequence types IIIA and IIC CRISPR-Cas in 199 S. lugdunensis isolates. MLST and oxacillin susceptibility tests were also performed on the isolates. We found that 84 S. lugdunensis isolates had type IIIA CRISPR-Cas, while 46 had type IIC. The results showed a strong association between STs and CRISPR-Cas types. The ST1, ST6, ST12, and ST15 isolates had type IIIA CRISPR-Cas systems, and the ST4, ST27, and ST29 isolates had type IIC CRISPR-Cas. Interestingly, of 83 isolates containing type IIIA CRISPR-Cas, 17 (20.5%) were oxacillin-resistant S. lugdunensis (ORSL), and all of these ORSL isolates belonged to ST6 cluster 1. Moreover, spacers 23 and 21 were found in 16 and 17 ORSL isolates, respectively. In contrast, all 46 isolates with type IIC CRISPR-Cas were susceptible to oxacillin. Our results showed that 41.3% of CRISPR-Cas IIIA spacers were homologous to plasmids and 20.2% were homologous to phages. However, in type IIC CRISPR-Cas, 11.8% and 39.9% of spacers showed sequence homology with plasmids and phages, respectively. In conclusion, we found that the distribution and composition of the CRISPR-Cas system in S. lugdunensis was associated with STs and oxacillin susceptibility. IMPORTANCE CRISPR-Cas systems have been characterized as playing several biological roles in many bacterial genomes. Moreover, CRISPR-Cas systems are useful for epidemiological, diagnostic, and evolutionary studies of pathogenic bacteria. However, the characteristics of CRISPR-Cas systems in Staphylococcus lugdunensis have been rarely reported. In this study, we revealed that type IIIA CRISPR-Cas was dominant in S. lugdunensis isolates, followed by type IIC CRISPR-Cas. Moreover, the composition of CRISPR-Cas spacers was strongly associated with multilocus sequence typing and oxacillin susceptibility of S. lugdunensis. These results advance our understanding of the evolution of CRISPR-Cas systems; however, the biological functions of CRISPR-Cas systems in S. lugdunensis remain to be further characterized.

Molecular Epidemiological Survey of Staphylococcus lugdunensis Isolates With Variable Number of Repeats in the von Willebrand Factor-Binding Protein Gene.

The von Willebrand factor binding protein in Staphylococcus lugdunensis (vWbl) comprises four major regions: the signal peptide (S), the non-repetitive (A) region, the repeat (R) region, and the wall-associated (W) region. Previous studies have demonstrated that the R region contains 10 copies of repeating sequences; however, we reveal that the copy number of repeats in the vWbl gene varies among different S. lugdunensis isolates. In this study, an epidemiological surveillance was conducted to determine whether the copy number of repeats in vWbl in different isolates of S. lugdunensis correlates with their infectivity. The number of repeats was estimated in a total of 212 isolates, consisting of 162 isolates of oxacillin-sensitive S. lugdunensis (OSSL) and 50 isolates of oxacillin-resistant S. lugdunensis (ORSL). Our data showed that 72.5% (116/162) of OSSL isolates contained 9 (25, 15.4%), 12 (43, 26.5%), or 13 (48, 29.6%) repeats, and 90% (45/50) of ORSL isolates had 9 (32, 64%) or 13 (13, 26%) repeats. In addition, 89.6% (26 of 29) of the sequence type (ST)27 strain had 12 repeats, and 86.8% (13 of 15) of the ST4 strain had 14 repeats. Twenty-seven of the 28 isolates with nine repeats were of the staphylococcal cassette chromosome mec (SCCmec) V or Vt type and belonged to ST3, and all isolates with 13 repeats were of SCCmec II type and belonged to ST6. All isolates with nine repeats had a stop codon at the 18th codon of the third repeat, suggesting that these isolates coded for nonfunctional vWbl. Further, western blot analysis confirmed that all strains translated vWbl, and only vWbl proteins coded by genes with nine repeats were exported outside the cell. These results suggest that number of vWbl repeats in S. lugdunensis have clonal specificities and may correlate with potential pathogenicity.

Clustered Regularly Interspaced Short Palindromic Repeat Analysis of Clonal Complex 17 Serotype III Group B Streptococcus Strains Causing Neonatal Invasive Diseases.

Group B Streptococcus (GBS) is an important pathogen of neonatal infections, and the clonal complex (CC)-17/serotype III GBS strain has emerged as the dominant strain. The clinical manifestations of CC17/III GBS sepsis may vary greatly but have not been well-investigated. A total of 103 CC17/III GBS isolates that caused neonatal invasive diseases were studied using a new approach based on clustered regularly interspaced short palindromic repeats (CRISPR) loci and restriction fragment length polymorphism (RFLP) analyses. All spacers of CRISPR loci were sequenced and analyzed with the clinical presentations. After CRISPR-RFLP analyses, a total of 11 different patterns were observed among the 103 CRISPR-positive GBS isolates. GBS isolates with the same RFLP patterns were found to have highly comparable spacer contents. Comparative sequence analysis of the CRISPR1 spacer content revealed that it is highly diverse and consistent with the dynamics of this system. A total of 29 of 43 (67.4%) spacers displayed homology to reported phage and plasmid DNA sequences. In addition, all CC17/III GBS isolates could be categorized into three subgroups based on the CRISPR-RFLP patterns and eBURST analysis. The CC17/III GBS isolates with a specific CRISPR-RFLP pattern were more significantly associated with occurrences of severe sepsis (57.1% vs. 29.3%, p = 0.012) and meningitis (50.0% vs. 20.8%, p = 0.009) than GBS isolates with RFLP lengths between 1000 and 1300 bp. Whole-genome sequencing was also performed to verify the differences between CC17/III GBS isolates with different CRISPR-RFLP patterns. We concluded that the CRISPR-RFLP analysis is potentially applicable to categorizing CC17/III GBS isolates, and a specific CRISPR-RFLP pattern could be used as a new biomarker to predict meningitis and illness severity after further verification.

Genomic Characterization of Serotype III/ST-17 Group B Streptococcus Strains with Antimicrobial Resistance Using Whole Genome Sequencing.

Background: Antibiotic-resistant type III/ST-17 Streptococcus agalactiae (group B Streptococcus, GBS) strain is predominant in neonatal invasive GBS diseases. We aimed to investigate the antibiotic resistance profiles and genetic characteristics of type III/ST-17 GBS strains. Methods: A total of 681 non-duplicate GBS isolates were typed (MLST, capsular types) and their antibiotic resistances were performed. Several molecular methods (WGS, PCR, sequencing and sequence analysis) were used to determine the genetic context of antibiotic resistant genes and pili genes. Results: The antibiotic resistant rates were significantly higher in type Ib (90.1%) and type III (71.1%) GBS isolates. WGS revealed that the loss of PI-1 genes and absence of ISSag5 was found in antibiotic-resistant III/ST-17 GBS isolates, which is replaced by a ~75-kb integrative and conjugative element, ICESag37, comprising multiple antibiotic resistance and virulence genes. Among 190 serotype III GBS isolates, the most common pilus island was PI-2b (58.4%) alone, which was found in 81.3% of the III/ST-17 GBS isolates. Loss of PI-1 and ISSag5 was significantly associated with antibiotic resistance (95.5% vs. 27.8%, p < 0.001). The presence of ICESag37 was found in 83.6% of all III/ST-17 GBS isolates and 99.1% (105/106) of the antibiotic-resistant III/ST-17 GBS isolates. Conclusions: Loss of PI-1 and ISSag5, which is replaced by ICESag37 carrying multiple antibiotic resistance genes, accounts for the high antibiotic resistance rate in III/ST-17 GBS isolates. The emerging clonal expansion of this hypervirulent strain with antibiotic resistance after acquisition of ICESag37 highlights the urgent need for continuous surveillance of GBS infections.

Protein Biomarker Discovery for Methicillin-Sensitive, Heterogeneous Vancomycin-Intermediate and Vancomycin-Intermediate Staphylococcus aureus Strains Using Label-Free Data-Independent Acquisition Proteomics.

Rapid identification of methicillin-sensitive Staphylococcus aureus (MSSA), heterogeneous vancomycin-intermediate S. aureus (hVISA), and vancomycin-intermediate S. aureus (VISA) is important for accurate treatment, timely intervention, and prevention of outbreaks. Here, 90 S. aureus isolates were analyzed for protein biomarker discovery, including MSSA, vancomycin-susceptible S. aureus (VSSA), hVISA, and VISA strains. Label-free data-independent acquisition proteomics was used to identify protein biomarkers that allow for discrimination among MSSA, hVISA, and VISA strains. There were 8786 nonredundant peptides identified, corresponding to 418 different annotated nonredundant proteins. Two VISA protein biomarkers, two hVISA protein biomarkers, and one MSSA protein biomarker with high sensitivities and specificities were discovered and verified. Data are available via MassIVE with identifier MSV000085776.

Molecular Epidemiological Survey of Prophages in MRSA Isolates in Taiwan.

INTRODUCTION: The prevalence of methicillin-resistant Staphylococcus aureus (MRSA) type SCCmec IV or V is increasing in Taiwan. It has been suggested that the surface protein SasX is responsible for their transmission. However, the sasX gene was not detected in our SCCmec IV or V isolates. Since sasX was originally found in S. epidermidis and believed to be transferred to S. aureus by a prophage, studies were conducted to detect and type this prophage in our clinical isolates. MATERIALS AND METHODS: A total of 1192 MRSA isolates collected from 2006 to 2014 were examined. Multiplex PCRs were performed to determine SCCmec, sasX, and prophage types. RESULTS: The prevalence of SCCmec IV and V isolates was increased in recent years (from 2006 to 2014). The sasX gene was present in most SCCmec III isolates but was absent in SCCmec IV or V isolates. The Sa5 prophage was found only in SCCmec IV and SCCmec V (or Vt) isolates, and the Sa6 prophage was mainly present in SCCmec III isolates. MRSA isolates harboring prophage combinations Sa1, Sa2, and Sa3; Sa2 and Sa3; Sa2, Sa3, and Sa7; or Sa2 and Sa7 were mainly of SCCmec II, and those that harbored prophage combinations Sa3 and Sa6; Sa3, Sa6, and Sa7; or Sa3 and Sa7 were mostly of SCCmec III. The numbers of SCCmec II isolates containing prophages Sa2, Sa3, and Sa7 and those of SCCmec III isolates containing prophages Sa3 and Sa6 or Sa3, Sa6, and Sa7 were decreased from 2010 to 2014. The number of SCCmec IV isolates with prophage Sa3 or prophages Sa3 and Sa5 was decreased, but that of those with prophage Sa6 or prophages Sa2 and Sa3 was increased from 2010 to 2014. CONCLUSION: The sasX gene was found to play no role in clonal selection of MRSA. The finding that different SCCmec types of MRSA harbored different types of prophages suggests that these prophages may affect the survival and clonal expansion of certain types of MRSA.

Rapid identification of invasive fungal species using sensitive universal primers-based PCR and restriction endonuclease digestions coupled with high-resolution melting analysis.

BACKGOUND: Conventional diagnosis of invasive fungal disease from blood cultures is often notoriously delayed and inadequately sensitive. We aimed to develop a universal primers-based polymerase chain reaction (PCR) assay and restriction fragment length polymorphisms (RFLP) for rapid identification of invasive fungal disease (IFD). METHODS: We evaluated 16 clinical fungal species using a combination of PCR assays with 3 different restriction endonucleases targeting various internal transcribed spacer (ITS) regions and high resolution melting analysis (HRMA). Serial samples from 75 patients suspected to have IFD were analyzed for clinical verification. RESULTS: We have designed a universal PCR capable of amplifying a portion of the 18S rRNA gene of 16 clinically important fungal species. The restriction patterns of most PCR products generated by EcoRI or double digested by ClaI and AvaI were different, except Aspergillus niger and Aspergillus flavus had a similar pattern, and Aspergillus fumigatus and Aspergillus terreus had a similar pattern. All these species had a unique melting curve shape using the HRMA. Both HRMA and universal PCR had adequate sensitivity, and all sixteen reference fungal species can be clearly distinguished by the universal PCR-RFLP-HRMA assay. With a reference library of 176 clinically relevant fungal strains, and 75 clinical samples from patients with suspicious IFD were tested, our assay identified 100% and 61.1% of isolates from the reference library and clinical samples, respectively. CONCLUSIONS: Universal PCR and RFLP coupled with HRMA could be a highly discriminative and useful molecular diagnostic that could enhance the current diagnostic, treatment, and surveillance methods of invasive fungal disease.

Characterization of a novel, type II staphylococcal cassette chromosome mec element from an endemic oxacillin-resistant Staphylococcus lugdunensis clone in a hospital setting.

BACKGROUND: Staphylococcus lugdunensis is a significant pathogen that causes community-acquired and nosocomial infections. The high prevalence of oxacillin-resistant S. lugdunensis (ORSL) is of major concern. Resistance to ß-lactams is caused by acquisition of the staphylococcal cassette chromosome mec (SCCmec) element. The cassette is highly diverse, both structurally and genetically, among CoNS. Isolates carrying SCCmec II-ST6 are the major persistent clones in hospitals. OBJECTIVES: To investigate the structure and evolutionary origin of a novel type II SCCmec element in an endemic ST6 S. lugdunensis clone. METHODS: The structure of the SCCmec II element carried by ST6 strain CGMH-SL118 was determined by WGS and compared with those reported previously. RESULTS: A novel 39 kb SCCmec element, SCCmecCGMH-SL118, with a unique mosaic structure comprising 41 ORFs integrated into the 3' end of the rlmH gene, was observed. Some regions of SCCmecCGMH-SL118 were homologous to SCCmec IIa of the prototype MRSA strain N315. The structure of SCCmecCGMH-SL118 was similar to that of SCCmec IIb of the MRSA strain, JCSC3063, mainly lacking the aminoglycoside resistance determinant pUB110 in the J3 region but containing the insertion sequence IS256 in the J2 region. Notably, SCCmecCGMH-SL118 deletions in the J1 region compared with SCCmec types IIa and IIb, and a high homology to SCCmec elements of Staphylococcus aureus JCSC4610 and Staphylococcus haemolyticus strain 621 were found. CONCLUSIONS: The genetic diversity of the type II SCCmec element in ORSL suggests that CoNS is a potential reservoir for interspecies transfer of SCCmec to S. aureus in hospitals.

Molecular Characteristics and Antimicrobial Resistance of Group B Streptococcus Strains Causing Invasive Disease in Neonates and Adults.

We aimed to analyze the molecular characteristics, clonality and antimicrobial resistance profiles of group B streptococcus (GBS) isolates collected in Taiwan from invasive diseases and carriage. Multilocus sequence typing (MLST) was used to assess the genetic diversity of 225 GBS strains from neonates and adults with invasive GBS diseases. 100 GBS strains collected from colonized pregnant women during the same period were compared, and all strains were characterized for one of nine capsule genotypes. We also determined the susceptibilities of all GBS isolates to various antimicrobial agents. The most frequently identified serotypes that caused invasive disease in neonates were III (60.6%) and Ia (17.3%), whereas type VI (32.7%), Ib (19.4%), and V (19.4%) were the most common to cause invasive disease in adults. Serotype VI was the leading type that colonized pregnant women (35.0%). Twenty-six sequence types (STs) were identified, and 90.5% of GBS strains were represented by 6 STs. ST-17 and ST-1 were more prevalent in invasive diseases in neonates and adults, respectively. The majority of serotype III and VI isolates belonged to clonal complex (CC)-17 and CC-1, respectively. ST-17 strains were more likely to cause meningitis and late-onset disease than other strains. In addition, ST-12 and ST-17 GBS strains showed the highest rate of resistance to erythromycin and clindamycin (range: 75.8-100%). In conclusion, CC-17/type III and CC-1/type VI are the most important invasive pathogens in infants and non-pregnant adults in Taiwan, respectively. GBS genotypes vary between different age groups and geographical areas and should be considered during GBS vaccine development.

Identification of a proteomic biomarker associated with invasive ST1, serotype VI Group B Streptococcus by MALDI-TOF MS.

BACKGROUND: Group B Streptococcus (GBS) is an important invasive pathogen in neonates, pregnant women and the elderly. Serotype VI GBS, which has been rarely reported globally, has emerged as a significant pathogen in Asia. However, traditional serologic latex agglutination (LA) methods may fail to type isolates that lack of or low expression of CPS. METHODS: A total of 104 GBS strains were analyzed by MALDI-TOF MS. Multiplex PCR and multilocus sequence typing (MLST) were also performed to confirm their strains. The protein markers were purified with gel electrophoresis and LC-column, followed by identification with nanoLC-MS/MS analysis. RESULTS: Protein peak of 6251-Da was appeared in most (20/24, 92%) serotypes VI (94% ST-1 or single locus variant of ST-1), and protein peak of 6891-Da was appeared in most serotypes III (15/18, 83%) and Ib (19/23, 83%) strains. The protein peak of 6251-Da and 6891-Da were identified as CsbD family protein and UPF0337 protein gbs0600, respectively. CONCLUSIONS: The protein peak of 6251 Da may play a role of emergence of ST-1 clone, serotype VI GBS in central Taiwan and could be useful in rapid identifying invasive serotype VI from III isolates, which is hardly achieved by LA.