Population Analysis of Daptomycin-non-Susceptible Methicillin-Resistant Staphylococcus aureus Reveals the Presence of Variants That Contribute to Daptomycin Resistance.

In this study, population analysis (PA) of methicillin-resistant Staphylococcus aureus (MRSA), before and after long-duration daptomycin (DAP) treatment, was used to detect subpopulations with different susceptibilities to DAP and to verify the changes in the number of resistant cells. Furthermore, we aimed to characterize the bacteriology of the variants present in the non-susceptible cell subpopulation. A DAP non-susceptible (NS) MRSA phenotype (D2) that emerged from a DAP- susceptible MRSA phenotype (D1) during treatment of an open wound, was used for testing. We performed bacteriological and genetic analyses of cryptic DAP-NS MRSA variants detected by PA to study the variants present in the resistant cell subpopulation. PA results suggest that MRSA adapted to survival in the presence of DAP are selected leading to reduced susceptibility. Within the cell population growing in media containing 2.0 mg/L of DAP, three variants with different pigment production and colony size were detected. Variant 3 was an orange colony due to enhanced production of staphyloxanthin. Our results revealed that the DAP minimum inhibitory concentration (MIC) value increased two-fold (4 mg/L) in variant 3, in which pigment production was most enhanced, compared to the parental strain D2. In conclusion, our results indicate that long-duration DAP treatment can lead to the emergence and increased proportion of DAP-NS subpopulations. Furthermore, slow-growing variants that can be detected only under antimicrobial selective pressure are present among DAP-NS cells, suggesting that these variants may also contribute to the development of DAP resistance.

Epigenetic effects of ceftriaxone-resistant Neisseria gonorrhoeae FC428 mosaic-like sequences found in PenA sequences unique to Neisseria subflava and related species.

OBJECTIVES: The aim of this study was to explore the origin of the PenA mosaic amino acid sequence in the ceftriaxone-resistant Neisseria gonorrhoeae FC428 clone. METHODS: The penA sequences of 27 Neisseria subflava pharyngeal isolates were determined by the Sanger method and penA sequences of 52 isolates from nine Neisseria species were obtained from the NCBI database. Comparative analysis of each PenA sequence was performed by multiple sequence alignment using ClustalW. In vitro resistance acquisition experiments were conducted to investigate the possibility of selection pressure by cefixime-induced amino acid substitution mutations in PenA. RESULTS: All N. subflava strains, including two with low susceptibility to expanded-spectrum cephalosporins (ESCs), possessed the majority of the PenA FC428 sequence. Furthermore, a number of strains, but not all, of closely related species of N. subflava showed similar results. PenA FC428 sequences were also found in some strains of distantly related species. No new mutations in the penA sequence were observed in colonies with increased MIC in in vitro resistance acquisition experiments. CONCLUSIONS: This study provides strong evidence that the FC428 PenA mosaic sequence originated from N. subflava and related species among oral commensal Neisseria species. The results of in vitro resistance acquisition experiments also suggested that one of the PenA FC428-like sequence gene polymorphisms resulted in the expression of ESC resistance. Furthermore, many of the PenA FC428 mosaic sequences were thought to be involved in the so-called epistasis effect that regulates the expression of resistance, without directly contributing to the resistance level itself.

The emergence of the ceftriaxone-resistant Neisseria gonorrhoeae FC428 clone by transfer of resistance from an oral Neisseria subflava reservoir of resistance.

BACKGROUND: The ceftriaxone-resistant Neisseria gonorrhoeae FC428 clone was first discovered in Japan in 2015. OBJECTIVES: We investigated the possibility of horizontal gene transfer from Neisseria subflava harbouring the mosaic-like PBP-2 in the emergence of the FC428 clone. We also analysed whether there were fitness costs associated with the sustained international dissemination of the clone. METHODS: Sequencing of the penA gene in ceftriaxone-resistant N. subflava strains was performed. For transformation experiments between donor N. subflava and ciprofloxacin-resistant wild-type penA N. gonorrhoeae recipient, the full-length PCR amplification product of the penA gene, including DUS regions, was used as the donor DNA. Biological fitness of the transformants was measured by growth competition assays. The impact of QRDR and mtrR mutations, which have been reported as compensatory mutations, on fitness was also assessed. RESULTS: The penA mosaic allele of the FC428 clone showed 100%, 91.8%, and 89.8% homology, respectively, with penA genes of three ceftriaxone-resistant N. subflava strains, No. 30, No. 9 and No. 14. Results were consistent with homologous recombination with the donated penA mosaic allele. In co-cultures with the parent strain, transformants showed comparable growth indicating that a gyrA mutation compensates for the fitness cost of mosaic penA alleles. CONCLUSIONS: Our findings support the hypothesis that the FC428 clone was generated by transformation of the mosaic penA allele from oropharyngeal N. subflava to N. gonorrhoeae. Furthermore, it suggests that mutations in the gyrA QRDR region compensate for fitness costs and contribute to the continued transmission of the FC428 clone.

Gene expression analysis in the potent bactericidal activity of sitafloxacin against Streptococcus pneumoniae.

We investigated the degree of expression of Streptococcus pneumoniae genes associated with bacteriolysis and cell death in relation to the rapid bactericidal activity of sitafloxacin. S. pneumoniae ATCC 49619 was added to brain heart infusion containing sitafloxacin and garenoxacin concentrations equivalent to the Cmax achieved with the usual single dose and 4 h post-Cmax concentration. RNA was extracted and cDNA was prepared using reverse transcriptase. Following RNA extraction and cDNA synthesis, quantitative PCR was performed to determine the amount of gene expression for 13 genes associated with cell death. Of the 13 genes analyzed, S. pneumoniae exposed for 10 min to a sitafloxacin concentration of 4 h post-Cmax showed 3.9 times increased expression of lytA compared to the control strain. Furthermore, we observed a slightly increased expression for cibA encoding a competence induced bacteriocin. Our study suggests that the induction of a lytic enzyme and bacteriocin may reflect gene expression in response to sitafloxacin accounting for part of its rapid bactericidal activity against S. pneumoniae.

Characterization of compensatory mutations associated with restoration of daptomycin-susceptibility in daptomycin non-susceptible methicillin-resistant Staphylococcus aureus and the role mprF mutations.

The objective of this study was to investigate the underlying mechanism explaining reversion of clinical DAP non-susceptible (NS) MRSA isolates to DAP-susceptible (S) by analysis of genomic and cell wall characteristics of clinical DAP-NS MRSA and DAP-S MRSA isolates as well as in vitro revertant DAP-S MRSA using whole genome sequencing (WGS) and analysis of biological properties. WGS of the 4 clinical DAP-NS MRSA revealed mprF mutations resulting in amino acid substitutions or deletion. These same amino acid substitutions and deletion were also observed in the 4 in vitro revertant DAP-S strains. While WGS identified the presence of the same mprF mutations in both the DAP-NS and in vitro DAP-S revertant strains, new mutations were also detected in other genes and intergenic regions of in vitro DAP-S revertant strains. Transmission electron microscopy to assess cell-wall (CW) thickness of 4 sets strains (pre- and post-DAP therapy isolates and in vitro DAP-S revertant) showed that 3 of the 4 isolates developed increased thickness of the CW after DAP therapy. After reversion to DAP susceptibility, CW thickness was decreased to the same level as DAP-S MRSA. Our results indicate that in vitro conversion of DAP-NS MRSA to DAP-S is independent of mprF gene mutations and may be partially explained by a change in CW thickness. However, as some strains showed no change in the CW, further studies are required to elucidate the different mechanisms of resistance to DAP, and factors for conversion of DAP-NS to DAP-S.

In vitro activity of various antibiotics against clinical strains of Legionella species isolated in Japan.

The activities of various antibiotics against 58 clinical isolates of Legionella species were evaluated using two methods, extracellular activity (minimum inhibitory concentration [MIC]) and intracellular activity. Susceptibility testing was performed using BSYEα agar. The minimum extracellular concentration inhibiting intracellular multiplication (MIEC) was determined using a human monocyte-derived cell line, THP-1. The most potent drugs in terms of MICs against clinical isolates were levofloxacin, garenoxacin, and rifampicin with MIC90 values of 0.015 µg/ml. The activities of ciprofloxacin, pazufloxacin, moxifloxacin, clarithromycin, and azithromycin were slightly higher than those of levofloxacin, garenoxacin, and rifampicin with an MIC90 of 0.03-0.06 µg/ml. Minocycline showed the highest activity, with an MIC90 of 1 µg/ml. No resistance against the antibiotics tested was detected. No difference was detected in the MIC distributions of the antibiotics tested between L. pneumophila serogroup 1 and L. pneumophila non-serogroup 1. The MIECs of ciprofloxacin, pazufloxacin, levofloxacin, moxifloxacin, garenoxacin, clarithromycin, and azithromycin were almost the same as their MICs, with MIEC90 values of 0.015-0.06 µg/ml, although the MIEC of minocycline was relatively lower and that of rifampicin was higher than their respective MICs. No difference was detected in the MIEC distributions of the antibiotics tested between L. pneumophila serogroup 1 and L. pneumophila non-serogroup 1. The ratios of MIEC:MIC for rifampicin (8) and pazufloxacin (2) were higher than those for levofloxacin (1), ciprofloxacin (1), moxifloxacin (1), garenoxacin (1), clarithromycin (1), and azithromycin (1). Our study showed that quinolones and macrolides had potent antimicrobial activity against both extracellular and intracellular Legionella species. The present data suggested the possible efficacy of these drugs in treatment of Legionella infections.

[Bacteriological Properties of Meropenem-resistant Escherichia coli Isolated from Seven Patients within a Month].

From April to May 2014, a total of seven cases of meropenem (MEPM)-resistant Escherichia coli were isolated from the sputum specimens in 7 different patients in a community hospital. The MICs of MEPM for isolates were 8 to 32 µg/mL, whereas the MICs of imipenem (IPM) were 0.5 µg/mL or 1 µg/mL. All of the isolates possessed the metallo ß-lactamase (MBL) IMP-6 gene, and were CTX-M-2 type extended-spectrum ß-lactamase (ESBL)-producers. Pulsed-field gel electrophoresis (PFGE) patterns for the isolates were identical. At the time of specimen collection, one patient had been hospitalized for a long time and the other six patients had been comparatively recently admitted to the hospital. Of the six patients, two had been staying in the same nursing facility before admission, whereas the remaining 4 patients had no relationship with each other because they had been in separate locations. Thus, these cases were not considered to be nosocomially-acquired infection. Our findings suggest that MBL-producing E. coli has been spreading widely in the community such as in local nursing facilities.

[Evaluation of the BD Phoenix ID Yeast System for the Species Identification of Clinical Yeast-Like Organisms].

Most fungi isolated from patients with deep-seated mycosis are yeast-like organisms such as Candida and Cryptococcus. As their respective susceptibilities to antifungal agents can vary depending on the species, rapid identification is important for the administration of appropriate antifungal therapy. The aim of this study was to evaluate the performance of a new automated identification panel, Phoenix Yeast ID (Becton, Dickinson Diagnostics, USA) as well as the time required for identification. The identification results of 106 isolates generated by this system were then compared with those of the API 20C AUX system (SYSMEX bioMérieux Co., Ltd. Japan). Among the 106 isolates, the identification agreement between the two yeast panels was 97/106 (91.5%). Of the 9 (8.5%) discrepant identifications, 5 identification using the Phoenix Yeast ID system and 1 identification using the API 20C AUX system agreed with the genotypic identification. Genotypic identification did not agree with the Phoenix Yeast ID or API 20C AUX findings for the remaining 3 discrepant identifications. Approximately 60% of the C. albicans, C. tropicalis, and C. parapsilosis isolates were identified within 4 hours. In total, about 90% of the 4 major Candida sp. (C. albicans, C. tropicalis and C. glabrata) were identified within 8 hours. In conclusion, the Phoenix Yeast ID findings agreed well with the API 20C AUX findings. Genotypic identification of the discrepant identifications confirmed most of the Phoenix Yeast ID panel identifications. As approximately 80% of the major Candida sp. could be identified within 8 hours using the Phoenix Yeast ID identification system, our results suggest that this system is a clinically useful addition to commercially available yeast identification panels. The Phoenix Yeast ID system showed excellent concordance with genotypic identification for the classification of organisms with discrepant API 20C AUX findings.

[Decreasing Susceptibility of MRSA to Daptomycin During the Course of Treatment].

Methicillin-resistant Staphylococcus aureus (MRSA) with decreased susceptibility to daptomycin (DAP) were isolated from 4 patients receiving DAP from November 2013 to May 2014. These patients were treated with DAP for more than 7 days in all the cases. The pulsed-field gel electrophoresis (PFGE) patterns for MRSA isolates recovered from each patient pre- and post-DAP therapy were identical. Sequencing of mprF detected 2 amino acid substitutions (T345I or L826F) in 2 of the isolates. These results suggest that in vivo MRSA was resistant to DAP during DAP therapy. Furthermore, the MICs for DAP can vary by±1 dilution depending on the susceptibility test. When testing DAP susceptibility, there is a need to monitor reproducibility using different susceptibility tests, including the CLSI method.

Distribution of Staphylococcus aureus carriage among healthcare workers in a Japanese convalescent and rehabilitation hospital.

Earlobes, nasal cavities, and fingers of 145 healthcare workers in convalescent and rehabilitation hospital (60 nurses and 85 rehabilitation healthcare workers) were sampled. Of the 3 sites sampled, Staphylococcus aureus was detected in one or more sites in 25 nurses and 27 rehabilitation workers. S. aureus was detected in all 3 sites in 2 (8.0%) nurses and 2 (7.4%) rehabilitation workers, and the S. aureus isolates in each case showed related PFGE pattern. S. aureus was detected in both the fingers and nasal cavities of 5 (18.5%) of the rehabilitation healthcare workers; in all 5 cases, the PFGE patterns of the S. aureus isolates from each site belonged to same cluster based on PFGE. Of the 2 cases in which methicillinresistant S. aureus (MRSA) was recovered from earlobes, fingers, and nasal cavities, in both cases, MRSA isolates from the 3 sites were the same clone according to PFGE analysis and SCCmec type IV. As S. aureus was detected in pierced earlobes of nurses, hand hygiene must be practiced after touching pierced earlobes and before patient contact. The same S. aureus clone in the nasal cavity and earlobes indicates that the route of transmission is through the fingers.

Antimicrobial susceptibility of commensal Neisseria spp. in parents and their children in Belgium: a cross-sectional survey.

BACKGROUND: commensal Neisseria species are part of the oropharyngeal microbiome and play an important role in nitrate reduction and protecting against colonization by pathogenic bacteria. They do, however, also serve as a reservoir of antimicrobial resistance. Little is known about the prevalence of these species in the general population, how this varies by age and how antimicrobial susceptibility varies between species. METHODS: we assessed the prevalence and antimicrobial susceptibility of commensal Neisseria species in the parents (n = 38) and children (n = 50) of 35 families in Belgium. RESULTS: various commensal Neisseria (n = 5) could be isolated from the participants. Most abundant were N. subflava and N. mucosa. Neisseria subflava was detected in 77 of 88 (87.5%) individuals and N. mucosa in 64 of 88 (72.7%). Neisseria mucosa was more prevalent in children [41/50 (82%)] than parents [23/38 (60.5%); P < .05], while N. bacilliformis was more prevalent in parents [7/36 (19.4%)] than children [2/50 (4%); P < .05]. Neisseria bacilliformis had high ceftriaxone minimum inhibitory concentrations (MICs; median MIC 0.5 mg/l; IQR 0.38-0.75). The ceftriaxone MICs of all Neisseria isolates were higher in the parents than in the children. This could be explained by a higher prevalence of N. bacilliformis in the parents. INTERPRETATION: the N. bacilliformis isolates had uniformly high ceftriaxone MICs which warrant further investigation.

Molecular characteristics and antimicrobial susceptibility of penicillinase-producing Neisseria gonorrhoeae isolates in Fukuoka, Japan, 1996-2018.

OBJECTIVES: The objective of this study was to investigate the molecular characteristics and antimicrobial susceptibility of penicillinase-producing Neisseria gonorrhoeae (PPNG) isolates collected in Fukuoka, Japan, from 1996-2018. METHODS: Antimicrobial susceptibility to seven antibiotics was determined by the agar dilution method. Molecular characteristics were determined by Sanger sequencing of the blaTEM allele, plasmid typing and N. gonorrhoeae multiantigen sequence typing (NG-MAST). Furthermore, full sequences of the penA gene, encoding penicillin-binding protein 2 (PBP2), of PPNG isolates with reduced susceptibility to cefixime were analysed. RESULTS: Among 50 PPNG isolates, 17 and 33 were collected during 1996-2006 and 2007-2018, respectively. In 1996-2006, blaTEM-1 in African plasmid was most frequent (64.7%), followed by blaTEM-1 in Asian plasmid (29.4%) and blaTEM-135 in Toronto/Rio plasmid (5.9%). In 2007-2018, blaTEM-135 in Toronto/Rio plasmid was predominant (54.5%), followed by blaTEM-1 in African plasmid (36.4%) and blaTEM-135 in Asian plasmid (6.1%). Among isolates with the blaTEM-135-carrying Toronto/Rio plasmid in 2007-2018, a novel genogroup G15576 was predominant (66.7%). Isolates with the TEM-135 ß-lactamase were more resistant to ciprofloxacin but were more susceptible to ceftriaxone and tetracycline than isolates with TEM-1. Seven PPNG isolates less susceptible to cefixime possessed the plasmidic blaTEM-1 allele and had mosaic or non-mosaic alterations within PBP2. CONCLUSION: The proportion of PPNG with the blaTEM135-carrying Toronto/Rio plasmid increased during the last 12 years. The increase in PPNG carrying the blaTEM-135 allele is of particular concern as it is considered a possible direct precursor of an extended-spectrum ß-lactamase (ESBL).

Does sub-culturing of positive MRSA blood cultures affect vancomycin MICs?

Introduction. Empirical vancomycin (VAN) treatment failure for methicillin-resistant Staphylococcus aureus (MRSA) bacteraemia, with significantly higher mortality, has been reported for MRSA strains with reduced VAN susceptibility.Aim. Our goal was to study the effect of sub-culture on VAN minimum inhibitory concentration (MIC) values compared to direct susceptibility of MRSA-positive blood cultures.Methodology. Using 19 MRSA-positive blood cultures and 19 seeded MRSA-positive blood cultures, we compared the VAN MICs from direct susceptibility testing of MRSA-positive blood cultures and MRSA sub-cultured from positive blood cultures.Results. In comparing direct VAN MICs from MRSA-positive blood cultures and standard agar dilution, nearly half of the MICs from agar dilution were lower, with one sample decreasing from 1.5 to 0.75 µg ml-1. Furthermore, in seeded blood cultures, 80 % or more showed lower values from standard agar dilution compared to direct VAN MICs.Conclusion. Our results reveal a trend towards lower MICs after positive blood culture isolates are sub-cultured. Some clinical failures among MRSA infections treated with VAN may result from this phenomenon.

Antimicrobial resistance and molecular characterisation of Neisseria gonorrhoeae isolates in Fukuoka, Japan, 1996-2016.

OBJECTIVES: Antimicrobial resistance and molecular characteristics of Neisseria gonorrhoeae isolates obtained from 1996-2005 (n=200) and 2008-2016 (n=200) in Fukuoka, Japan, were examined. METHODS: MICs were determined by agar dilution. Sequence types (STs) were examined using N. gonorrhoeae multiantigen sequence typing (NG-MAST). Sequencing of major extended-spectrum cephalosporin (ESC) resistance determinants (penA, mtrR and ponA) was performed. RESULTS: Increases in the proportion of gonococci with decreased susceptibility or resistance to cefixime (from 18.0% in 1996-2005 to 46.0% in 2008-2016) and ceftriaxone (from 2.5% to 4.0%) were observed. Gonococcal isolates also showed increased resistance to ciprofloxacin and azithromycin. The four most prevalent NG-MAST STs with a multidrug-resistant phenotype were ST2958 (n=18), ST1407 (n=14), ST6798 (n=12) and ST4015 (n=10). The number of isolates belonging to these four STs rose between the first and second period. Among the 54 isolates belonging to the four major STs, 42 (77.8%) contained a penA mosaic allele and 12 (22.2%) contained a penA non-mosaic allele. The sequence pattern types in the 42 isolates with a penA mosaic allele included type X (64.3%), type XXXIV (33.3%) and a novel pattern type (2.4%). In contrast, all 12 isolates with the penA non-mosaic allele included the sequence pattern type V. CONCLUSION: Neisseria gonorrhoeae isolates with decreased susceptibility or resistance to ESC have increased over the years. Four major STs with a multidrug-resistant phenotype were identified. These isolates contained a penA mosaic allele or a non-mosaic allele.