Background. Sustainable suppression of HIV replication forms the basis of anti-retroviral therapy (ART) medication. Thus, reliable quantification of HIV viral load has become an essential factor to monitor the effectiveness of the ART. Longer turnaround-time (TAT), batch testing and technical skills are major drawbacks of standard real-time PCR assays.
Methods. The performance of the point-of-care Xpert HIV-1 viral load assay was evaluated against the Abbott RealTime PCR m2000rt system. A total of 96 plasma specimens ranging from 2.5 log10 copies ml−1 to 4.99 log10 copies ml−1 and proficiency testing panel specimens were used. Precision and accuracy were checked using the Pearson correlation co-efficient test and Bland–Altman analysis.
Results. Compared to the Abbott RealTime PCR, the Xpert HIV-1 viral load assay showed a good correlation (Pearson r=0.81; P<0.0001) with a mean difference of 0.27 log10 copies ml−1 (95 % CI, −0.41 to 0.96 log10 copies ml−1; sd, 0.35 log10 copies ml−1).
Conclusion. Reliable and ease of testing individual specimens could make the Xpert HIV-1 viral load assay an efficient alternative method for ART monitoring in clinical management of HIV disease in resource-limited settings. The rapid test results (less than 2 h) could help in making an immediate clinical decision, which further strengthens patient care.
Purpose. The rise in the incidence of fungal infections and the expanding spectrum of fungal pathogens make early and broad detection of fungal pathogens essential. In the present study, a panfungal real-time PCR assay for the broad-range detection of fungal DNA (Fungi assay) in a wide variety of clinical specimens was developed.
Methodology. Our in-house, HybProbe real-time PCR assay targets the ITS2 region of fungal DNA. The applicability was evaluated by testing 105 clinical samples from 98 patients with suspected fungal infection. Samples included tissue biopsies, paraffin embedded tissues, aspirates, EDTA-anticoagulated blood, cerebrospinal fluids and bronchoalveolar lavages.
Results. Fungal pathogens were identified by the Fungi assay in 47 samples. In all of these cases, conventional methods and clinical data were also indicative for a fungal infection. Five samples were interpreted false negative. blast analyses of the amplicons derived from 11 samples revealed the presence of environmental fungal species while other tests and clinical data did not suggest a fungal infection. This fact might indicate contaminated samples. The remaining 42 samples were negative by the Fungi assay as well as the conventional methods and were therefore regarded as true negatives. Thus, sensitivity was 90.4 % and specificity 79.2 %.
Conclusion. The Fungi assay improved the targeted diagnosis of fungal infections allowing pathogen identification in samples that were histologically positive but culture negative. For reliable diagnosis, results have to be interpreted in context with conventional methods and clinical data.
Purpose. Fidaxomicin, a macrocyclic antibiotic, has been approved for the treatment of Clostridium difficile infection (CDI). Previous work by our group has demonstrated that some antibiotics at sub-inhibitory concentrations stimulate early toxin production and sporulation by C. difficile. Prior studies revealed that fidaxomicin, when added to late stationary-phase organisms, reduced exotoxin production and spore formation by C. difficile. However, the ability of fidaxomicin to trigger early virulence factor production and spore formation has never been investigated.
Methodology. Sub-inhibitory concentrations of the RNA synthesis inhibitor fidaxomicin (1/4×, 1/8×, 1/16× MIC) were added immediately to lag-phase cultures of historical (strain 9689) and epidemic BI/NAP1/027 (strain 5325) strains of C. difficile, and their effects on sporulation and toxin A (TcdA) and toxin B (TcdB) production were compared.
Results/Key findings. Even at sub-inhibitory concentrations, all doses of fidaxomicin reduced both TcdA and TcdB gene expression and protein production in the historical and epidemic C. difficile strains. Fidaxomicin also dose-dependently reduced viable spore production by the 9689 and 5325 strains. Reductions in spore formation were also observed in both strains treated with tigecycline and vancomycin. However, all concentrations of metronidazole stimulated a ~2 log increase in spore production by the 5325 isolate.
Conclusion. The ability of fidaxomicin to suppress early exotoxin production and endospore formation by historical and epidemic strains of C. difficile may explain its clinical success in treating severe and recurrent cases of CDI disease.
Purpose. The pathogenesis of chronic pulmonary aspergillosis (CPA) has seldom been studied due partly to a lack of animal models. Since hypha is the main morphology colonizing the airway in CPA, it’s critical to study the immune reaction to chronic pulmonary infection of hyphae of Aspergillus fumigatus, which also has seldom been studied in vivo before.
Methodology. We established a novel murine model of chronic pulmonary infection of hyphae by challenging immunocompetent mice with tightly-structured hyphae balls intratracheally, and described the ensuing immunoreaction to hyphae and conidia, and the pathogenesis of CPA.
Results. Our experiment proved that the hyphae balls could induce a chronic pulmonary infection for 28 days with a considerable recrudescence at day 28 post-infection. Lungs infected with hyphae balls were remarkable for the many neutrophils and macrophages that flooded into airway lumens, with peribronchiolar infiltration of leukocytes. There was a transient increase of Th2 cells and Th17 cells at day 7 post-infection in the lung tissue. In contrast, lungs infected with conidia showed no peribronchiolar infiltration of leukocytes, but an influx of a great number of macrophages, and a much less number of neutrophils in the lumen. Besides, conidia activated the co-response of Th1, Th2 and Th17 cells with an increase of Treg cells in the lung tissue (quite different from most previous studies).
Conclusion. We established a new murine model of chronic infection of hyphae to mimic the formation of CPA, and provide a new marker for different immune responses to hyphae and conidia.
Purpose. Pili contribute significantly to the pathogenesis of infection of group B Streptococcus (GBS) by facilitating adhesion and invasion of host cells. GBS pilin subunits (the backbone pilin protein, BP, and the ancillary pilin proteins, AP) as well as the specific enzymes required for pilus assembly are encoded by genes located in two separate genomic regions, known as pilus island 1 (PI-1) and PI-2. Our aim was to characterize the pilus profile of a collection of GBS isolates from metropolitan Toronto, Canada.
Methodology. The pilus profile of 1332 invasive and colonizing GBS isolates was determined by PCR and, in selected cases, by whole genome sequencing.
Results. While investigating the pilus profile of a collection of GBS organisms, we discovered that 51 isolates possessed a novel variant of the PI-1 BP, which we named BP-1b. The predicted translated sequences of archetypical GBS BP-1 and novel BP-1b variants shared only 63 % amino acid sequence homology. The novel BP-1b variant was most common among strains of serotype Ib and VI, but was also found among strains of serotypes Ia, II, III and VIII.
Conclusion. We describe a relatively frequent occurrence of a novel PI-1 BP that cannot be detected by a commonly used multiplex PCR scheme, which could lead to strains being mistyped as PI-1 negative. We present PCR primers that can easily be incorporated into the multiplex PCR assay to identify strains with novel BP-1b variant.
Purpose. Lactic acid bacteria (LAB) have been associated with many beneficial effects in human digestive physiology. The aim of this study was to evaluate such effect, including attachment, antiproliferation and anti-pathogenic/antibacterial/antimicrobial properties of LAB isolated from healthy humans.
Methodology. Thirteen isolates, obtained from fecal samples of healthy individuals, were identified by phenotypic and molecular methods. Human colon adenocarcinoma cell line HT‐29 and the cell proliferation kit II (XTT) assay were used for examination of the Lactobacillus adherence and antiproliferative activity, respectively. In addition, the inhibitory effect of Lactobacillus isolates against pathogenic bacteria was examined.
Results. Out of 13 Lactobacillus isolates, 5 (38 %) isolates were non-adhesive, 4 (31 %) were adhesive and 4 (31 %) were strongly adhesive. Amongst the isolated lactobacilli, L. reuteri showed the highest degree of inhibitory effect against the attachment of the enteropathogens. The XTT assay showed that 3 different isolates had the strongest antiproliferative activity with the maximum effect observed by L. plantarum isolates.
Conclusion. Our results described that different Lactobacillus species isolated from normal fecal samples had different degrees of antiproliferative and anti-pathogenic/antibacterial/antimicrobial activities. However, no isolates showed all of the examined properties concurrently, suggestive that a combination of Lactobacillus species is needed for an active biological defense system.
Purpose. This study assessed clinical manifestations and prognostic factors of critically ill patients with severe influenza admitted to the intensive care unit (ICU) in Taiwan’s recent outbreak.
Methodology. Patients admitted to ICU for severe influenza between January 1, 2015, and March 31, 2016, were identified and their medical records were retrospectively reviewed. The primary endpoints were outcomes and predictors of in-hospital mortality.
Results. There were 125 patients with an average Acute Physiology and Chronic Health Evaluation II (APACHE II) score of 20.8. Hypertension (62.4 %) and diabetes mellitus (40.8 %) were the two most common underlying diseases. Ninety-eight (78.4 %) patients had at least one organ failure: the lungs were the most common (71.2 %), followed by the heart (53.6 %). Two of the most common symptoms of patients at ICU admission were fever (68.0 %) and cough (78.4 %). Thirty-three patients (26.4 %) died; most (40.9 %) were middle-aged (50–65 years old). A Cox regression analysis showed that multiple organ failure (MOF) [hazard ratio (HR)=3.618; 95 % CI=1.058–13.662] was significantly associated with higher risk of death. In contrast, a fluid-negative balance within 7 days of admission (HR=0.362; 95 % CI=0.140–0.934) was significantly associated with a lower risk of death.
Conclusion. The mortality rate of severe influenza patients admitted to the ICU was high, especially in middle-aged adults. The risk of mortality was associated with ≥2 organ failures. A negative fluid balance predicts survival.
Purpose. This study investigates the virulence and antimicrobial resistance in association with common clonal complexes (CCs) of enteroaggregative Escherichia coli (EAEC) isolated from Bangladesh. The aim was to determine whether specific CCs were more likely to be associated with putative virulence genes and/or antimicrobial resistance.
Methodology. The presence of 15 virulence genes (by PCR) and susceptibility to 18 antibiotics were determined for 151 EAEC isolated from cases and controls during an intestinal infectious disease study carried out between 2007–2011 in the rural setting of Mirzapur, Bangladesh (Kotloff KL, Blackwelder WC, Nasrin D, Nataro JP, Farag TH et al. Clin Infect Dis 2012;55:S232–S245). These data were then analysed in the context of previously determined serotypes and clonal complexes defined by multi-locus sequence typing.
Results. Overall there was no association between the presence of virulence or antimicrobial resistance genes in isolates of EAEC from cases versus controls. However, when stratified by clonal complex (CC) one CC associated with cases harboured more virulence factors (CC40) and one CC harboured more resistance genes (CC38) than the average. There was no direct link between the virulence gene content and antibiotic resistance. Strains within a single CC had variable virulence and resistance gene content indicating independent and multiple gene acquisitions over time.
Conclusion. In Bangladesh, there are multiple clonal complexes of EAEC harbouring a variety of virulence and resistance genes. The emergence of two of the most successful clones appeared to be linked to either increased virulence (CC40) or antimicrobial resistance (CC38), but increased resistance and virulence were not found in the same clonal complexes.
Purpose. Purulent or exudative genitourinary infections are a frequent cause of consultation in primary and specialized healthcare. The objectives of this study were: to determine the prevalence of Trichomonas vaginalis and co-infections with Candida spp. and Gardnerella vaginalis in vaginal secretion; and to use multilocus sequence typing (MLST) to analyse the genetic diversity of T. vaginalis strains.
Methodology. The samples were submitted for analysis (n=5230) to a third-level hospital in Granada (Southern Spain) between 2011 and 2014; eight T. vaginalis strains isolated during 2015 were randomly selected for MLST analysis. Culture and nucleic acid hybridization techniques were used to detect microorganisms in the samples.
Results. The prevalence of T. vaginalis was 2.4 % between 2011 and 2014, being higher during the first few months of both 2011 and 2012. Among samples positive for T. vaginalis, co-infection with G. vaginalis was detected in 29 samples and co-infection with Candida spp. in 6, while co-infection with all three pathogens was observed in 3 samples. The only statistically significant between-year difference in co-infection rates was observed for T. vaginalis with G. vaginalis due to an elevated rate in 2011. MLST analysis results demonstrated a high genetic variability among strains circulating in our setting.
Conclusion. These findings emphasize the need for the routine application of diagnostic procedures to avoid the spread of this sexually transmitted infection.
To characterize members of the Mycobacterium abscessus complex, with an emphasis on the correlation between species identification and clarithromycin associated genetic polymorphisms that contribute to inducible and constitutive macrolide resistance. PCR and sequencing analysis was used to elucidate the subspecies, erm(41) genotypes and the presence of rrl mutations. M. abscessus subsp. massiliense was the dominant subspecies (70.2 %), followed by M. abscessus subsp. abscessus (23.8 %) and M. abscessus subsp. bolletii (5.9 %). The majority of M. abscessus and M. bolletii isolates possessed T28 erm(41) sequevar and were inducibly resistant to clarithromycin. All M. massiliense carried the truncated erm(41) and were largely clarithromycin-susceptible (98.3 %). Constitutive resistance involving rrl mutations was rare and seen in only 2 isolates (2.2 %). Subspecies identification was insufficient to predict clarithromycin susceptibility and required the genetic resistance to be determined via sequencing. In our context, rrl mutations were uncommon and may not be an essential test.
Because we experienced gentamicin failure in Klebsiella pneumoniae bacteraemia that was susceptible to gentamicin despite amikacin resistance, as determined by VITEK 2, we evaluated the true susceptibility and mechanism of resistance. We screened 2818 K. pneumoniae isolates during a 1-year period at a university hospital and reviewed anti-microbial susceptibility reports using the VITEK 2 system. The minimum inhibitory concentration was substantiated by broth microdilution (BMD), and the presence of 16S rRNA methylase genes and aminoglycoside-modifying enzymes was also investigated. A total of 131 amikacin-resistant isolates from 19 patients were gentamicin non-resistant according to the VITEK 2 system. Among these, we were able to collect isolates from 12 patients (63.2 %), and a single isolate from each patient was tested. Eleven of the gentamicin non-resistant isolates (91.7 %) showed high-level resistance to both amikacin and gentamicin by BMD in association with the armA gene. Gentamicin is not an adequate treatment option for amikacin-resistant K. pneumoniae, even if VITEK 2 reports susceptibility.
The macrolide azithromycin is recommended for treatment of Mycoplasma genitalium infection; however, M. genitalium strains possessing macrolide resistance-mediating mutations (MRMMs) are increasingly being reported. Here, we used the SpeeDx ResistancePlus MG kit, which provides simultaneous detection of M. genitalium and MRMMs, to assess MRMM carriage among M. genitalium infections in Queensland, Australia. Performance characteristics of the ResistancePlus MG kit for M. genitalium detection were compared to in-house PCR. Available M. genitalium PCR-positive (n=67) and negative (n=281) samples from the years 2011 to 2017 were tested using the SpeeDx ResistancePlus MG kit. In total, 63.6 % M. genitalium-positive samples were indicated to harbour MRMMs. The ResistancePlus MG method provided sensitivity and specificity of 97 and 99.6 % respectively compared to in-house PCR for M. genitalium detection. Such high levels of macrolide-resistant M. genitalium raise further concerns over future use of azithromycin for treatment of M. genitalium infection.
Dissemination of resistance to carbapenems among Enterobacteriaceae through plasmids is an increasingly important concern in health care worldwide. Here we report the first description of an IncX3 plasmid carrying the bla KPC-3 gene in a strain of Serratia marcescens isolated from a kidney-liver transplanted patient at the transplantation centre ISMETT (Istituto Mediterraneo per i Trapianti e Terapie ad Alta Specializzazione, Palermo, Italy). To localize the transposable element containing the resistance-associated gene Next-Generation Sequencing of the bacterial DNA was performed. S. marcescens was positive for bla KPC-3 and bla SHV-11 genes. The molecular analysis demonstrated that the bla KPC-3 gene of this bacterial strain was located in one copy of the Tn-3-like element Tn4401-a carried in a plasmid that is 53 392 bp in size and showed the typical IncX3 scaffold. Our data demonstrated the presence of a new bla KPC-3 harbouring the IncX3 plasmid in S. marcescens. The possible dissemination among Enterobacteriaceae of this type of plasmid should be monitored and evaluated in terms of clinical risk.