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1.  Active Surveillance for Carbapenem-Resistant Enterobacteriaceae Using Stool Specimens Submitted for Testing for Clostridium difficile 
Active surveillance to identify asymptomatic carriers of carbapenem-resistant Enterobacteriaceae (CRE) is a recommended strategy for CRE control in healthcare facilities. Active surveillance using stool specimens tested for Clostridium difficile is a relatively low-cost strategy to detect CRE carriers. Further evaluation of this and other risk factor–based active surveillance strategies is warranted.
doi:10.1086/674391
PMCID: PMC3984911  PMID: 24334803
2.  Complete Nucleotide Sequence of a blaKPC-Harboring IncI2 Plasmid and Its Dissemination in New Jersey and New York Hospitals 
Antimicrobial Agents and Chemotherapy  2013;57(10):5019-5025.
Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae strains have spread worldwide and become a significant public health threat. blaKPC, the plasmid-borne KPC gene, was frequently identified on numerous transferable plasmids in different incompatibility replicon groups. Here we report the complete nucleotide sequence of a novel blaKPC-3-harboring IncI2 plasmid, pBK15692, isolated from a multidrug-resistant K. pneumoniae ST258 strain isolated from a New Jersey hospital in 2005. pBK15692 is 78 kb in length and carries a backbone that is similar to those of other IncI2 plasmids (pR721, pChi7122-3, pHN1122-1, and pSH146-65), including the genes encoding type IV pili and shufflon regions. Comparative genomics analysis of IncI2 plasmids reveals that they possess a conserved plasmid backbone but are divergent with respect to the integration sites of resistance genes. In pBK15692, the blaKPC-3-harboring Tn4401 was inserted into a Tn1331 element and formed a nested transposon. A PCR scheme was designed to detect the prevalence of IncI2 and pBK15692-like plasmids from a collection of clinical strains from six New Jersey and New York hospitals isolated between 2007 and 2011. IncI2 plasmids were found in 46.2% isolates from 318 clinical K. pneumoniae strains. Notably, 59 pBK15692-like plasmids (23%) have been identified in 256 KPC-bearing K. pneumoniae strains, and all carried KPC-3 and belong to the epidemic ST258 clone. Our study revealed that the prevalence of IncI2 plasmids has been considerably underestimated. Further studies are needed to understand the distribution of this plasmid group in other health care regions and decipher the association between IncI2 plasmids and blaKPC-3-bearing ST258 strains.
doi:10.1128/AAC.01397-13
PMCID: PMC3811408  PMID: 23896467
4.  Septic Shock Caused by Klebsiella pneumoniae Carbapenemase-Producing Enterobacter gergoviae in a Neutropenic Patient with Leukemia 
Journal of Clinical Microbiology  2013;51(8):2794-2796.
We present the first reported infection caused by Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacter gergoviae. The patient had leukemia and neutropenia and died of septic shock from KPC-producing E. gergoviae bacteremia. The emergence of KPCs in additional species of Enterobacteriaceae is alarming and may disproportionately affect patients with hematologic malignancies.
doi:10.1128/JCM.00004-13
PMCID: PMC3719649  PMID: 23761145
5.  Nosocomial Transmission of Extensively Drug-Resistant Tuberculosis in a Rural Hospital in South Africa 
Background. Extensively drug-resistant tuberculosis (XDR-tuberculosis) is a global public health threat, but few data exist elucidating factors driving this epidemic. The initial XDR-tuberculosis report from South Africa suggested transmission is an important factor, but detailed epidemiologic and molecular analyses were not available for further characterization.
Methods. We performed a retrospective, observational study among XDR-tuberculosis patients to identify hospital-associated epidemiologic links. We used spoligotyping, IS6110-based restriction fragment–length polymorphism analysis, and sequencing of resistance-determining regions to identify clusters. Social network analysis was used to construct transmission networks among genotypically clustered patients.
Results. Among 148 XDR-tuberculosis patients, 98% were infected with human immunodeficiency virus (HIV), and 59% had smear-positive tuberculosis. Nearly all (93%) were hospitalized while infectious with XDR-tuberculosis (median duration, 15 days; interquartile range: 10–25 days). Genotyping identified a predominant cluster comprising 96% of isolates. Epidemiologic links were identified for 82% of patients; social network analysis demonstrated multiple generations of transmission across a highly interconnected network.
Conclusions. The XDR-tuberculosis epidemic in Tugela Ferry, South Africa, has been highly clonal. However, the epidemic is not the result of a point-source outbreak; rather, a high degree of interconnectedness allowed multiple generations of nosocomial transmission. Similar to the outbreaks of multidrug-resistant tuberculosis in the 1990s, poor infection control, delayed diagnosis, and a high HIV prevalence facilitated transmission. Important lessons from those outbreaks must be applied to stem further expansion of this epidemic.
doi:10.1093/infdis/jis631
PMCID: PMC3523793  PMID: 23166374
tuberculosis; HIV; drug resistance; transmission; genotyping
6.  Characterization of Porin Expression in Klebsiella pneumoniae Carbapenemase (KPC)-Producing K. pneumoniae Identifies Isolates Most Susceptible to the Combination of Colistin and Carbapenems 
We characterized carbapenem resistance mechanisms among 12 Klebsiella pneumoniae carbapenemase (KPC)-producing K. pneumoniae (referred to here as KPC K. pneumoniae) clinical isolates and evaluated their effects on the activity of 2- and 3-drug combinations of colistin, doripenem, and ertapenem. All isolates were resistant to ertapenem and doripenem; 75% (9/12) were resistant to colistin. Isolates belonged to the ST258 clonal group and harbored blaKPC-2, blaSHV-12, and blaTEM-1. As determined by time-kill assays, doripenem (8 μg/ml) and ertapenem (2 μg/ml) were inactive against 92% (11/12) and 100% (12/12) of isolates, respectively. Colistin (2.5 μg/ml) exerted some activity (range, 0.39 to 2.5 log10) against 78% (7/9) of colistin-resistant isolates. Colistin-ertapenem, colistin-doripenem, and colistin-doripenem-ertapenem exhibited synergy against 42% (5/12), 50% (6/12), and 67% (8/12) of isolates, respectively. Expression of ompK35 and ompK36 porins correlated with each other (R2 = 0.80). Levels of porin expression did not correlate with colistin-doripenem or colistin-ertapenem synergy. However, synergy with colistin-doripenem-ertapenem was more likely against isolates with high porin expression than those with low expression (100% [8/8] versus 0% [0/4]; P = 0.002). Moreover, bactericidal activity (area under the bacterial killing curve) against isolates with high porin expression was greater for colistin-doripenem-ertapenem than colistin-doripenem or colistin-ertapenem (P ≤ 0.049). In conclusion, colistin-carbapenem combinations may provide optimal activity against KPC K. pneumoniae, including colistin-resistant isolates. Screening for porin expression may identify isolates that are most likely to respond to a triple combination of colistin-doripenem-ertapenem. In the future, molecular characterization of KPC K. pneumoniae isolates may be a practical tool for identifying effective combination regimens.
doi:10.1128/AAC.02411-12
PMCID: PMC3632930  PMID: 23459476
7.  Nasal Carriage as a Source of agr-Defective Staphylococcus aureus Bacteremia 
The Journal of Infectious Diseases  2012;206(8):1168-1177.
Inactivating mutations in the Staphylococcus aureus virulence regulator agr are associated with worse outcomes in bacteremic patients. However, whether agr dysfunction is primarily a cause or a consequence of early bacteremia is unknown. Analysis of 158 paired S. aureus clones from blood and nasal carriage sites in individual patients revealed that recovery of an agr-defective mutant from blood was usually predicted by the agr functionality of carriage isolates. Many agr-positive blood isolates produced low levels of hemolytic toxins, but levels were similar to those of colonizing strains within patients, suggesting that introduction into the blood did not select for mutations with minor functional effects. Evidently, the transition from commensalism to opportunism in S. aureus does not require full virulence in hospitalized patients. Furthermore, agr-defective mutants were found in uninfected nasal carriers in the same proportion as in carriers who develop bacteremia, suggesting low correlation between virulence and infectivity.
doi:10.1093/infdis/jis483
PMCID: PMC3448967  PMID: 22859823
8.  Staphylococcus aureus Nuclease Is an SaeRS-Dependent Virulence Factor 
Infection and Immunity  2013;81(4):1316-1324.
Several prominent bacterial pathogens secrete nuclease (Nuc) enzymes that have an important role in combating the host immune response. Early studies of Staphylococcus aureus Nuc attributed its regulation to the agr quorum-sensing system. However, recent microarray data have indicated that nuc is under the control of the SaeRS two-component system, which is a major regulator of S. aureus virulence determinants. Here we report that the nuc gene is directly controlled by the SaeRS two-component system through reporter fusion, immunoblotting, Nuc activity measurements, promoter mapping, and binding studies, and additionally, we were unable identify a notable regulatory link to the agr system. The observed SaeRS-dependent regulation was conserved across a wide spectrum of representative S. aureus isolates. Moreover, with community-associated methicillin-resistant S. aureus (CA MRSA) in a mouse model of peritonitis, we observed in vivo expression of Nuc activity in an SaeRS-dependent manner and determined that Nuc is a virulence factor that is important for in vivo survival, confirming the enzyme's role as a contributor to invasive disease. Finally, natural polymorphisms were identified in the SaeRS proteins, one of which was linked to Nuc regulation in a CA MRSA USA300 endocarditis isolate. Altogether, our findings demonstrate that Nuc is an important S. aureus virulence factor and part of the SaeRS regulon.
doi:10.1128/IAI.01242-12
PMCID: PMC3639593  PMID: 23381999
9.  Complete Sequence of a blaKPC-2-Harboring IncFIIK1 Plasmid from a Klebsiella pneumoniae Sequence Type 258 Strain 
We report the nucleotide sequence of a novel blaKPC-2-harboring IncFIIK1 plasmid, pBK32179, isolated from a carbapenem-resistant Klebsiella pneumoniae ST258 strain from a New York City patient. pBK32179 is 165 kb long, consists of a large backbone of pKPN3-like plasmid, and carries an 18.5-kb blaKPC-2-containing element that is highly similar to plasmid pKpQIL. pBK32179-like plasmids were identified in 8.3% of strains in a collection of 96 K. pneumoniae isolates from hospitals in the New York City area.
doi:10.1128/AAC.02332-12
PMCID: PMC3591897  PMID: 23295924
10.  Genetic Variation among Panton-Valentine Leukocidin-Encoding Bacteriophages in Staphylococcus aureus Clonal Complex 30 Strains 
Journal of Clinical Microbiology  2013;51(3):914-919.
Clonal complex 30 (CC30), one of the major Staphylococcus aureus lineages, has caused extensive hospital-acquired and community-acquired infections worldwide. Recent comparative genomics studies have demonstrated that three CC30 clones—phage type 80/81, Southwest Pacific (SWP), and contemporary EMRSA-16 associated (Con) strains—shared a recent common ancestor more than 100 years ago. Panton-Valentine leukocidin (PVL), a bacteriophage encoded toxin that has been epidemiologically linked with community-associated methicillin-resistant S. aureus (CA-MRSA), has frequently been identified in CC30 clones, although the pvl gene variation and distribution of PVL-encoding phages are poorly understood. We determined here the distribution of PVL phages, PVL gene sequences, and chromosomal phage insertion sites in 52 S. aureus CC30 PVL-harboring isolates, collected from four continents over a 75-year period. Our results indicate that PVL phages with icosahedral heads, including Φ108PVL and ΦPVL, were mainly associated with phage 80/81 strains, whereas phages with elongated heads were predominantly found in SWP (ΦSa2958 and ΦTCH60) and Con (ΦSa2USA) strains. Nine single-nucleotide polymorphisms were identified in the lukSF-PV gene, with six isolates harboring the R variant that has been previously associated with CA-MRSA strains. Interestingly, all six R variant strains belonged to the same Con CC30 clone and carried a ΦSa2USA-like phage. Similar chromosomal phage insertion sites were also identified in all 52 PVL-harboring CC30 strains. These analyses provide important insights into the microepidemiology of PVL-harboring CC30 strains, while the discovery of ΦSa2USA-associated R variant strains sheds further light on the evolution of PVL-positive CA-MRSA.
doi:10.1128/JCM.03015-12
PMCID: PMC3592069  PMID: 23284024
11.  Complete Nucleotide Sequences of blaKPC-4- and blaKPC-5-Harboring IncN and IncX Plasmids from Klebsiella pneumoniae Strains Isolated in New Jersey 
Klebsiella pneumoniae carbapenemase (KPC)-producing Enterobacteriaceae have emerged as major nosocomial pathogens. blaKPC, commonly located on Tn4401, is found in Gram-negative bacterial strains, with the two most common variants, blaKPC-2 and blaKPC-3, identified in plasmids with diverse genetic backgrounds. In this study, we examined blaKPC-4- and blaKPC-5-bearing plasmids recovered from two K. pneumoniae strains, which were isolated from a single New Jersey hospital in 2005 and 2006, respectively. IncN plasmid pBK31551 is 84 kb in length and harbors blaKPC-4, blaTEM-1, qnrB2, aac(3)-Ib, aph(3′)-I, qacF, qacEΔ1, sul1, and dfrA14, which confer resistance to β-lactams, quinolones, aminoglycosides, quaternary ammonium compounds, and co-trimoxazole. The conserved regions within pBK31551 are similar to those of other IncN plasmids. Surprisingly, analysis of the Tn4401 sequence revealed a large IS110- and Tn6901-carrying element (8.3 kb) inserted into the istA gene, encoding glyoxalase/bleomycin resistance, alcohol dehydrogenase, and S-formylglutathione hydrolase. Plasmid pBK31567 is 47 kb in length and harbors blaKPC-5, dfrA5, qacEΔ1, and sul1. pBK31567 belongs to a novel IncX subgroup (IncX5) and possesses a highly syntenic plasmid backbone like other IncX plasmids; however, sequence similarity at the nucleotide level is divergent. The blaKPC-5 gene is carried on a Tn4401 element and differs from the genetic environment of blaKPC-5 described in Pseudomonas aeruginosa strain P28 from Puerto Rico. This study underscores the genetic diversity of multidrug-resistant plasmids involved in the spread of blaKPC genes and highlights the mobility and plasticity of Tn4401. Comparative genomic analysis provides new insights into the evolution and dissemination of KPC plasmids belonging to different incompatibility groups.
doi:10.1128/AAC.01648-12
PMCID: PMC3535970  PMID: 23114770
12.  Distinct Clinical and Epidemiological Features of Tuberculosis in New York City Caused by the RDRio Mycobacterium tuberculosis Sublineage 
Infection, Genetics and Evolution  2011;12(4):664-670.
Background
Genetic tracking of Mycobacterium tuberculosis is a cornerstone of tuberculosis (TB) control programs. The RDRio M. tuberculosis sublineage was previously associated with TB in Brazil. We investigated 3847 M. tuberculosis isolates and registry data from New York City (NYC) (2001–2005) to: 1) affirm the position of RDRio strains within the M. tuberculosis phylogenetic structure, 2) determine its prevalence, and 3) define transmission, demographic, and clinical characteristics associated with RDRio TB.
Methods
Isolates classified as RDRio or non-RDRio M. tuberculosis by multiplex PCR were further classified as clustered (≥2 isolates) or unique based primarily upon IS6110-RFLP patterns and lineage-specific cluster proportions were calculated. The secondary case rate of RDRio was compared with other prevalent M. tuberculosis lineages. Genotype data were merged with the data from the NYC TB Registry to assess demographic and clinical characteristics.
Results
RDRio strains were found to: 1) be restricted to the Latin American-Mediterranean family, 2) cause approximately 8% of TB cases in NYC, and 3) be associated with heightened transmission as shown by: i) a higher cluster proportion compared to other prevalent lineages, ii) a higher secondary case rate, and iii) cases in children. Furthermore, RDRio strains were significantly associated with US-born Black or Hispanic race, birth in Latin American and Caribbean countries, and isoniazid resistance.
Conclusions
The RDRio genotype is a single M. tuberculosis strain population that is emerging in NYC. The findings suggest that expanded RDRio case and exposure identification could be of benefit due to its association with heightened transmission.
doi:10.1016/j.meegid.2011.07.018
PMCID: PMC3290718  PMID: 21835266
tuberculosis; lineage; epidemiology; transmission; RDRio
13.  Telavancin in Therapy of Experimental Aortic Valve Endocarditis in Rabbits Due to Daptomycin-Nonsusceptible Methicillin-Resistant Staphylococcus aureus 
Antimicrobial Agents and Chemotherapy  2012;56(11):5528-5533.
A number of cases of both methicillin-susceptible Staphylococcus aureus (MSSA) and methicillin-resistant S. aureus (MRSA) strains that have developed daptomycin resistance (DAP-R) have been reported. Telavancin (TLV) is a lipoglycopeptide agent with a dual mechanism of activity (cell wall synthesis inhibition plus depolarization of the bacterial cell membrane). Five recent daptomycin-susceptible (DAP-S)/DAP-R MRSA isogenic strain pairs were evaluated for in vitro TLV susceptibility. All five DAP-R strains (DAP MICs ranging from 2 to 4 μg/ml) were susceptible to TLV (MICs of ≤0.38 μg/ml). In vitro time-kill analyses also revealed that several TLV concentrations (1-, 2-, and 4-fold MICs) caused rapid killing against the DAP-R strains. Moreover, for 3 of 5 DAP-R strains (REF2145, A215, and B2.0), supra-MICs of TLV were effective at preventing regrowth at 24 h of incubation. Further, the combination of TLV plus oxacillin (at 0.25× or 0.50× MIC for each agent) increased killing of DAP-R MRSA strains REF2145 and A215 at 24 h (∼2-log and 5-log reductions versus TLV and oxacillin alone, respectively). Finally, using a rabbit model of aortic valve endocarditis caused by DAP-R strain REF2145, TLV therapy produced a mean reduction of >4.5 log10 CFU/g in vegetations, kidneys, and spleen compared to untreated or DAP-treated rabbits. Moreover, TLV-treated rabbits had a significantly higher percentage of sterile tissue cultures (87% in vegetations and 100% in kidney and spleen) than all other treatment groups (P < 0.0001). Together, these results demonstrate that TLV has potent bactericidal activity in vitro and in vivo against DAP-R MRSA isolates.
doi:10.1128/AAC.00922-12
PMCID: PMC3486568  PMID: 22890759
14.  Coagulases as Determinants of Protective Immune Responses against Staphylococcus aureus 
Infection and Immunity  2012;80(10):3389-3398.
During infection, Staphylococcus aureus secretes two coagulases (Coa and von Willebrand factor binding protein [vWbp]), which, following an association with host prothrombin and fibrinogen, form fibrin clots and enable the establishment of staphylococcal disease. Within the genomes of different S. aureus isolates, coagulase gene sequences are variable, and this has been exploited for a classification of types. We show here that antibodies directed against the variable prothrombin binding portion of coagulases confer type-specific immunity through the neutralization of S. aureus clotting activity and protection from staphylococcal disease in mice. By combining variable portions of coagulases from North American isolates into hybrid Coa and vWbp proteins, a subunit vaccine that provided protection against challenge with different coagulase-type S. aureus strains in mice was derived.
doi:10.1128/IAI.00562-12
PMCID: PMC3457572  PMID: 22825443
15.  Epidemiologic Consequences of Microvariation in Mycobacterium tuberculosis 
The Journal of Infectious Diseases  2012;205(6):964-974.
Background. Evidence from genotype-phenotype studies suggests that genetic diversity in pathogens have clinically relevant manifestations that can impact outcome of infection and epidemiologic success. We studied 5 closely related Mycobacterium tuberculosis strains that collectively caused extensive disease (n = 862), particularly among US-born tuberculosis patients.
Methods. Representative isolates were selected using population-based genotyping data from New York City and New Jersey. Growth and cytokine/chemokine response were measured in infected human monocytes. Survival was determined in aerosol-infected guinea pigs.
Results. Multiple genotyping methods and phylogenetically informative synonymous single nucleotide polymorphisms showed that all strains were related by descent. In axenic culture, all strains grew similarly. However, infection of monocytes revealed 2 growth phenotypes, slower (doubling ∼55 hours) and faster (∼25 hours). The faster growing strains elicited more tumor necrosis factor α and interleukin 1β than the slower growing strains, even after heat killing, and caused accelerated death of infected guinea pigs (∼9 weeks vs 24 weeks) associated with increased lung inflammation/pathology. Epidemiologically, the faster growing strains were associated with human immunodeficiency virus and more limited in spread, possibly related to their inherent ability to induce a strong protective innate immune response in immune competent hosts.
Conclusions. Natural variation, with detectable phenotypic changes, among closely related clinical isolates of M. tuberculosis may alter epidemiologic patterns in human populations.
doi:10.1093/infdis/jir876
PMCID: PMC3415951  PMID: 22315279
16.  Molecular Epidemiology of HIV-Associated Tuberculosis in Dar es Salaam, Tanzania: Strain Predominance, Clustering, and Polyclonal Disease 
Journal of Clinical Microbiology  2012;50(8):2645-2650.
Molecular typing of Mycobacterium tuberculosis can be used to elucidate the epidemiology of tuberculosis, including the rates of clustering, the frequency of polyclonal disease, and the distribution of genotypic families. We performed IS6110 typing and spoligotyping on M. tuberculosis strains isolated from HIV-infected subjects at baseline or during follow-up in the DarDar Trial in Tanzania and on selected community isolates. Clustering occurred in 203 (74%) of 275 subjects: 124 (80%) of 155 HIV-infected subjects with baseline isolates, 56 (69%) of 81 HIV-infected subjects with endpoint isolates, and 23 (59%) of 39 community controls. Overall, 113 (41%) subjects had an isolate representing the East Indian “GD” family. The rate of clustering was similar among vaccine and placebo recipients and among subjects with or without cellular immune responses to mycobacterial antigens. Polyclonal disease was detected in 6 (43%) of 14 patients with multiple specimens typed. Most cases of HIV-associated tuberculosis among subjects from this study in Dar es Salaam resulted from recently acquired infection. Polyclonal infection was detected and isolates representing the East Indian GD strain family were the most common.
doi:10.1128/JCM.00624-12
PMCID: PMC3421504  PMID: 22649022
17.  Prevalence, persistence, and microbiology of Staphylococcus aureus nasal carriage among hemodialysis outpatients at a major New York Hospital☆,☆☆ 
The study aimed to determine the natural history of Staphylococcus aureus nasal colonization in hemodialysis outpatients. Surveillance cultures were taken from patients presenting for hemodialysis or routine care to identify S. aureus nasal carriers. A prospective cohort study was performed to identify risks for persistent colonization. Detailed microbiologic and molecular studies of colonizing isolates were performed. Only 23/145 (15.9%) dialysis patients were persistently colonized, and only HIV-positive status was associated with persistence (P = 0.05). Prior hospitalization was the only risk factor for methicillin-resistant S. aureus carriage (OR 2.5, P = 0.03). In isolates from patients with ≤42 days of vancomycin exposure, vancomycin minimum bactericidal concentrations (MBCs) increased with duration of exposure. Among dialysis patients, S. aureus colonization was limited and transient; only HIV status was associated with persistence. Nevertheless, duration of vancomycin exposure was associated with increasing vancomycin MBCs. Vancomycin exposure in S. aureus carriers may be involved in increasing resistance.
doi:10.1016/j.diagmicrobio.2010.12.005
PMCID: PMC3534839  PMID: 21334154
Staphylococcus aureus; Hemodialysis; Colonization; Vancomycin
18.  Induction of Mycobacterial Resistance to Quinolone Class Antimicrobials 
An agar plate assay was developed for detecting the induction of drug-resistant mycobacterial mutants during exposure to inhibitors of DNA gyrase. When Mycobacterium smegmatis on drug-containing agar, resistant colonies arose over a period of 2 weeks. A recA deficiency reduced mutant recovery, consistent with involvement of the SOS response in mutant induction. The C-8-methoxy compounds gatifloxacin and moxifloxacin allowed the recovery of fewer resistant mutants than either ciprofloxacin or levofloxacin when present at the same multiple of the MIC; a quinolone-like 8-methoxy-quinazoline-2,4-dione was more effective at restricting the emergence of resistant mutants than its cognate fluoroquinolone. Thus, the structure of fluoroquinolone-like compounds affects mutant recovery. A spontaneous mutator mutant of M. smegmatis, obtained by growth in medium containing both isoniazid and rifampin, increased mutant induction during exposure to ciprofloxacin. Moreover, the mutator increased the size of spontaneous resistant mutant subpopulations, as detected by population analysis. Induction of ciprofloxacin resistance was also observed with Mycobacterium tuberculosis H37Rv. When measured with clinical isolates, no difference in mutant recovery was observed between multidrug-resistant (MDR) and pansusceptible isolates. This finding is consistent with at least some MDR isolates of M. tuberculosis lacking mutators detectable by the agar plate assay. Collectively, the data indicate that the use of fluoroquinolones against tuberculosis may induce resistance and that the choice of quinolone may be important for restricting the recovery of induced mutants.
doi:10.1128/AAC.00474-12
PMCID: PMC3393424  PMID: 22564842
19.  Multiplex Real-Time PCR for Detection of an Epidemic KPC-Producing Klebsiella pneumoniae ST258 Clone 
We describe a multiplex real-time PCR assay capable of identifying both the epidemic Klebsiella pneumoniae ST258 clone and blaKPC carbapenemase genes in a single reaction. The assay displayed excellent sensitivity (100%) and specificity (100%) for identification of ST258 clone and blaKPC in a collection of 75 K. pneumoniae isolates comprising 41 sequence types. Our results suggest that this assay is an effective tool for surveillance of this clone among carbapenem-resistant K. pneumoniae clinical isolates.
doi:10.1128/AAC.00316-12
PMCID: PMC3370784  PMID: 22450983
20.  Community-associated methicillin-resistant Staphylococcus aureus 
Lancet  2010;375(9725):1557-1568.
Summary
Methicillin-resistant Staphylococcus aureus (MRSA) is endemic in hospitals worldwide and a significant cause of morbidity and mortality. Healthcare-associated MRSA infections occur in individuals with predisposing risk factors for disease, such as surgery or presence of an indwelling medical device. By contrast, community-associated MRSA (CA-MRSA) infections often occur in otherwise healthy individuals who lack such risk factors. In addition, CA-MRSA infections are epidemic in some countries. These observations suggest that CA-MRSA strains are more virulent and transmissible than traditional hospital-associated MRSA strains. Relatively limited treatment options for CA-MRSA infections compound the problem of enhanced virulence and transmission. Although progress has been made toward understanding emergence of CA-MRSA, virulence, and treatment of infections, our knowledge in these areas remains incomplete. Here were review the most current knowledge in these areas and provide perspective on future outlook for prophylaxis and/or new therapies for CA-MRSA infections.
doi:10.1016/S0140-6736(09)61999-1
PMCID: PMC3511788  PMID: 20206987
21.  Methicillin-Resistant Staphylococcus aureus Sequence Type 239-III, Ohio, USA, 2007–20091 
Emerging Infectious Diseases  2012;18(10):1557-1565.
Identification of virulent strains emphasizes the need for molecular surveillance.
doi:10.3201/eid1810.120468
PMCID: PMC3471631  PMID: 23018025
Staphylococcus aureus; methicillin-resistant Staphylococcus aureus; MRSA; MRSA ST239-III; bacteria; sequence type; virulent clones; Brazilian clone; Portuguese clone; Ohio; United States
22.  Partial Excision of blaKPC from Tn4401 in Carbapenem-Resistant Klebsiella pneumoniae 
We describe a novel Tn4401 variant (Tn4401d) in epidemic Klebsiella pneumoniae clone ST258, from which a partial blaKPC fragment has been excised along with ISKpn7 and a partial tnpA fragment. Nested-PCR experiments confirmed that this region can be removed from distinct Tn4401 isoforms in both K. pneumoniae and Escherichia coli. This study highlights that the region surrounding blaKPC is undergoing recombination and that Tn4401 itself is heterogeneous and highly plastic.
doi:10.1128/AAC.06182-11
PMCID: PMC3294926  PMID: 22203593
23.  Characterization of Nasal and Blood Culture Isolates of Methicillin-Resistant Staphylococcus aureus from Patients in United States Hospitals 
A total of 299 nares and 194 blood isolates of methicillin-resistant Staphylococcus aureus (MRSA), each recovered from a unique patient, were collected from 23 U.S. hospitals from May 2009 to March 2010. All isolates underwent spa and staphylococcal cassette chromosome mec element (SCCmec) typing and antimicrobial susceptibility testing; a subset of 84 isolates was typed by pulsed-field gel electrophoresis (PFGE) using SmaI. Seventy-six spa types were observed among the isolates. Overall, for nasal isolates, spa type t002-SCCmec type II (USA100) was the most common strain type (37% of isolates), while among blood isolates, spa type t008-SCCmec type IV (USA300) was the most common (39%). However, the proportion of all USA100 and USA300 isolates varied by United States census region. Nasal isolates were more resistant to tobramycin and clindamycin than blood isolates (55.9% and 48.8% of isolates versus 36.6% and 39.7%, respectively; for both, P < 0.05). The USA300 isolates were largely resistant to fluoroquinolones. High-level mupirocin resistance was low among all spa types (<5%). SCCmec types III and VIII, which are rare in the United States, were observed along with several unusual PFGE types, including CMRSA9, EMRSA15, and the PFGE profile associated with sequence type 239 (ST239) isolates. Typing data from this convenience sample suggest that in U.S. hospitalized patients, USA100 isolates of multiple spa types, while still common in the nares, have been replaced by USA300 isolates as the predominant MRSA strain type in positive blood cultures.
doi:10.1128/AAC.05804-11
PMCID: PMC3294931  PMID: 22155818
24.  Real-Time Nucleic Acid Sequence-Based Amplification Assay for Rapid Detection and Quantification of agr Functionality in Clinical Staphylococcus aureus Isolates 
Journal of Clinical Microbiology  2012;50(3):657-661.
Staphylococcus aureus infections are a significant cause of morbidity and mortality in health care settings. S. aureus clinical isolates vary in the function of the accessory gene regulator (agr), which governs the expression of virulence determinants, including surface and exoproteins, while agr activity has been correlated with patient outcome and treatment efficiency. Here we describe a duplex real-time nucleic acid sequence-based amplification (NASBA) detection and quantification platform for rapid determination of agr functionality in clinical isolates. Using the effector of agr response, RNAIII, as the assay target, and expression of the gyrase gene (gyrB) as a normalizer, we were able to accurately discriminate agr functionality in a single reaction. Time to positivity (TTP) ratios between gyrB and RNAIII showed very good correlation with the ratios of RNAIII versus gyrB RNA standard inputs and were therefore used as a simple readout to evaluate agr functionality. We validated the assay by characterizing 106 clinical S. aureus isolates, including strains with genetically characterized agr mutations. All isolates with dysfunctional agr activity exhibited a TTP ratio (TTPgyrB/TTPRNAIII) lower than 1.10, whereas agr-positive isolates had a TTP ratio higher than this value. The results showed that the assay was capable of determining target RNA ratios over 8 logs (10−3 to 104) with high sensitivity and specificity, suggesting the duplex NASBA assay may be useful for rapid determination of agr phenotypes and virulence potential in S. aureus clinical isolates.
doi:10.1128/JCM.06253-11
PMCID: PMC3295125  PMID: 22219302
25.  Molecular Characterization of an Early Invasive Staphylococcus epidermidis Prosthetic Joint Infection 
Microbial Drug Resistance  2011;17(3):345-350.
Historically regarded as a skin commensal, Staphylococcus epidermidis has been increasingly implicated in invasive foreign body infections such as catheter-related bloodstream infections, indwelling device infections, and prosthetic joint infections. We report a case of an aggressive, difficult-to-eradicate, invasive prosthetic hip infection occurring early after hardware implant and associated with a high-grade bacteremia and assess its salient molecular characteristics. The clinical and molecular characteristics of this isolate mirror the pathogenesis and persistence commonly seen with invasive methicillin-resistant S. aureus and may be attributed to the combination of resistance genes (SCCmec type IV), putative virulence factors (arcA and opp3a), cytolytic peptide production (α-type phenol-soluble modulins), and biofilm adhesion, interaction, and maturation (bhp, aap, and β-type phenol-soluble modulins).
doi:10.1089/mdr.2010.0157
PMCID: PMC3161624  PMID: 21510745

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