Molecular Analysis of Human Immunodeficiency Virus Type 1 (HIV-1)-Infected Individuals in a Network-Based Intervention (Transmission Reduction Intervention Project): Phylogenetics Identify HIV-1-Infected Individuals With Social Links.

Background: The Transmission Reduction Intervention Project (TRIP) is a network-based intervention that aims at decreasing human immunodeficiency virus type 1 (HIV-1) spread. We herein explore associations between transmission links as estimated by phylogenetic analyses, and social network-based ties among persons who inject drugs (PWID) recruited in TRIP. Methods: Phylogenetic trees were inferred from HIV-1 sequences of TRIP participants. Highly supported phylogenetic clusters (transmission clusters) were those fulfilling 3 different phylogenetic confidence criteria. Social network-based ties (injecting or sexual partners, same venue engagement) were determined based on personal interviews, recruitment links, and field observation. Results: TRIP recruited 356 individuals (90.2% PWID) including HIV-negative controls; recently HIV-infected seeds; long-term HIV-infected seeds; and their social network members. Of the 150 HIV-infected participants, 118 (78.7%) were phylogenetically analyzed. Phylogenetic analyses suggested the existence of 13 transmission clusters with 32 sequences. Seven of these clusters included 14 individuals (14/32 [43.8%]) who also had social ties with at least 1 member of their cluster. This proportion was significantly higher than what was expected by chance. Conclusions: Molecular methods can identify HIV-infected people socially linked with another person in about half of the phylogenetic clusters. This could help public health efforts to locate individuals in networks with high transmission rates.

Molecular Tracing of the Geographical Origin of Human Immunodeficiency Virus Type 1 Infection and Patterns of Epidemic Spread Among Migrants Who Inject Drugs in Athens.

BACKGROUND: High numbers of human immunodeficiency virus type 1 (HIV-1) infections among people who inject drugs (PWID) have been diagnosed in Athens, Greece, since 2011. We aimed to trace the geographic origin of HIV-1 infection for migrants who inject drugs and to investigate whether transmissions occur more frequently among migrants than among Greek nationals. METHODS: Multiple cross-sectional studies were pooled to assemble all persons diagnosed with HIV-1 in Greece between 1 January 2011 and 31 October 2014. Phylogenetic analyses used maximum likelihood estimation. The hypothesis of ethnic compartmentalization was tested by reconstructing ancestral states of characters at the tips using the criterion of parsimony over a set of bootstrap trees. RESULTS: Of 2274 persons, 38.4% were PWID. Phylogenetic analyses showed the existence of 4 major PWID-specific local transmission networks (LTNs): CRF14_BG (437 [58.6%]), CRF35_AD (139 [18.6%]), subtype B (116 [15.6%]), and subtype A (54 [7.2%]). Of 184 non-Greek PWID, 78.3% had been infected within the PWID-LTNs. For 173 (94.3%), the origin of their infection was assumed to be in Greece (postmigration). For PWID infected within LTNs, transmissions for subtype A and CRF14_BG occurred more frequently among migrants than would be expected by chance (phyloethnic study). CONCLUSIONS: Our analysis showed that the majority of infections among migrants occurred postmigration. The existence of significant transmission networking among migrants highlights that this population is a priority for HIV prevention. As molecular analysis can estimate the probable country of HIV infection, it can help to inform the design of public health strategies.

Association Between Candiduria and Candidemia: A Clinical and Molecular Analysis of Cases.

The risk of developing candidemia after candiduria is reportedly very low, but it has not been adequately investigated. The aim of this study was to examine the molecular relatedness between Candida strains isolated from adult patients with candidemia and concomitant candiduria in association with the clinical characteristics of the cases. All episodes of candidemia occurring in a tertiary care academic hospital during a 5-year period were recorded prospectively. Patients with episodes of candiduria occurring two weeks preceding to or one week following a positive for Candida blood culture were included in the study. The genotypic relatedness of Candida strains isolated from blood and urine was investigated by pulsed-field gel electrophoresis after digestion with the BssHII restriction endonuclease. We recorded 141 candidemia episodes, occurring in 134 patients. Twelve episodes of candidemia with concomitant candiduria occurred in 11 patients (8% of all candidemias). In six of these episodes, the strains in the blood-urine pairs belonged to different species. In two episodes, the isolates belonged to the same species but were not genetically related, and only in four (2.8% of all candidemias), the strains were related. All four patients were severely ill and had multiple risk factors for candidemia. These findings indicate that in hospitalized patients with candidemia, concomitant candiduria is rare and usually an independent event, confirming previous reports. In the critically ill, however, the existence of genetically related strains in blood and urine appears to be more frequent, with more probable the hematogenous dissemination.

Endotoxin Translocation and Gut Barrier Dysfunction Are Related to Variceal Bleeding in Patients With Liver Cirrhosis.

Background: Bacterial infections are associated with the risk of variceal bleeding through complex pathophysiologic pathways. Objectives: The primary objective of the present case-control study was to investigate the role of bacterial translocation and intestinal barrier dysfunction in the pathogenesis of variceal bleeding. A secondary objective was to determine independent predictors of key outcomes in variceal bleeding, including bleeding-related mortality. Methods: Eighty-four (n = 84) consecutive patients participated in the study, 41 patients with acute variceal bleeding and 43 patients with stable cirrhosis, and were followed up for 6 weeks. Peripheral blood samples were collected at patient admission and before any therapeutic intervention. Results: Child-Pugh (CP) score (OR: 1.868; p = 0.044), IgM anti-endotoxin antibody levels (OR: 0.954; p = 0.016) and TGF-ß levels (OR: 0.377; p = 0.026) were found to be significant predictors of variceal bleeding. Regression analysis revealed that albumin (OR: 0.0311; p = 0.023), CRP (OR: 3.234; p = 0.034) and FABP2 levels (OR:1.000, p = 0.040), CP score (OR: 2.504; p = 0.016), CP creatinine score (OR: 2.366; p = 0.008), end-stage liver disease model (MELD), Na (OR: 1.283; p = 0.033), portal vein thrombosis (OR: 0.075; p = 0.008), hepatocellular carcinoma (OR: 0.060; p = 0.003) and encephalopathy (OR: 0.179; p = 0.045) were significantly associated with 6-week mortality. Conclusions: Bacterial translocation and gut barrier impairment are directly related to the risk of variceal bleeding. Microbiota-modulating interventions and anti-endotoxin agents may be promising strategies to prevent variceal bleeding.

Survival predictors after intubation in medical wards: A prospective study in 151 patients.

INTRODUCTION: In health care systems in need of additional intensive care unit (ICU) beds, the decision to mechanically ventilate critically ill patients in Internal Medicine (IM) Department wards needs to balance patients' health outcomes, possible futility, and logistics. We aimed to examine the survival rates and predictors in these patients. METHODS: We prospectively enrolled consecutive patients receiving mechanical ventilation during their care in the IM wards of a tertiary University hospital between April 2016 and December 2018. Primary outcome was 90-day mortality and secondary outcomes were in-hospital mortality and ICU transfer. RESULTS: Our cohort consisted of 151 unique patient intubations, of whom 74 (49%) patients were transferred to ICU within a median of 0 days (range 0-7). Compared to patients who remained in the wards, patients transferred to ICU had lower in-hospital and 90-day mortality (65% vs. 97%, and 70% vs. 99%, respectively, p<0.001 for both). Amongst several possible predictors of survival in the ICU, sequential organ failure assessment (SOFA) score at the time of intubation had the best prognostic accuracy with an AUROC of 0.818 and 0.855 for in-hospital and 90-day mortality, respectively. A baseline SOFA score ≤8 had a 100% sensitivity for survival prediction in ICU. However, out of 26 patients with SOFA score ≤8 who remained in the wards, only one survived, whereas 19 patients with SOFA score >8 who were transferred to ICUs received futile care. CONCLUSION: Mortality for patients receiving mechanical ventilation in IM wards is almost inevitable when ICU availability is lacking. Therefore, applying additional transfer criteria beyond the SOFA score is imperative.

Risk factors for nasopharyngeal carriage of drug-resistant Streptococcus pneumoniae: data from a nation-wide surveillance study in Greece.

BACKGROUND: A nation-wide surveillance study was conducted in Greece in order to provide a representative depiction of pneumococcal carriage in the pre-vaccination era and to evaluate potential risk factors for carriage of resistant strains in healthy preschool children attending daycare centers. METHODS: A study group was organized with the responsibility to collect nasopharyngeal samples from children. Questionnaires provided demographic data, data on antibiotic consumption, family and household data, and medical history data. Pneumococcal isolates were tested for their susceptibility to various antimicrobial agents and resistant strains were serotyped. RESULTS: Between February and May 2004, from a total population of 2536 healthy children, a yield of 746 pneumococci was isolated (carriage rate 29.41%). Resistance rates differed among geographic regions. Recent antibiotic use in the last month was strongly associated with the isolation of resistant pneumococci to a single or multiple antibiotics. Serotypes 19F, 14, 9V, 23F and 6B formed 70.6% of the total number of resistant strains serotyped. CONCLUSION: Recent antibiotic use is a significant risk factor for the colonization of otherwise healthy children's nasopharynx by resistant strains of S pneumoniae. The heptavalent pneumococcal conjugate vaccine could provide coverage for a significant proportion of resistant strains in the Greek community. A combined strategy of vaccination and prudent antibiotic use could provide a means for combating pneumococcal resistance.

Molecular investigation of HIV-1 cross-group transmissions during an outbreak among people who inject drugs (2011-2014) in Athens, Greece.

New diagnoses of HIV-1 infection among people who inject drugs (PWID) rocketed in Athens, Greece between 2011 and 2014 (HIV-1 outbreak). Our aim was to identify, during that period, potential cross-group transmissions between the within-Greece PWID and other risk or national groups using molecular methods. Sequences from 33 PWID were outside the PWID-outbreak networks in Greece (PWID-imported transmissions). Phylogenetic analyses on 28 of these sequences (subtypes A and B) showed that 11 subtype B infections originated from Greece, whereas 8 and 7 subtype A strains were from former Soviet Union countries (AFSU) and Greece, respectively. The putative source in half of the PWID-imported transmissions with Greek origin was an individual who acquired HIV via sexual contact. During four years of an HIV-1 outbreak among PWID in Athens, Greece, 33 individuals in this group (4.6% of all diagnoses with phylogenetic analyses) are likely to represent infections, sexually or injection-acquired, outside the within-Greece-PWID-outbreak networks. Combined molecular and traditional HIV surveillance to monitor introductions of new strains, and interventions that aim at reducing the rate of both injection and sexual risky practices are needed during drug injection-related HIV outbreaks.

Integrase Strand Transfer Inhibitors and the Emergence of Immune Reconstitution Inflammatory Syndrome (IRIS).

BACKGROUND: Immune reconstitution inflammatory syndrome (IRIS) is a major concern when starting highly active anti-retroviral therapy (HAART) in new patients and especially late presenters. This study attempts to identify risk factors for IRIS and investigate whether certain treatment regimens increase the probability of IRIS for patients at risk. METHODS: Retrospective single-centre study of HIV patients treated with HAART. RESULTS: A total of 417 patients were included. We identified 45 cases of IRIS in 37 patients; an incidence of 13.3 cases over 1000 person-years. In univariate analysis, IRIS development was significantly associated with CDC stage, the presence of an opportunistic infection (OI) at diagnosis, CD4 cell count and viral load at diagnosis and HAART initiation and the use of integrase strand inhibitors (INSTIs). In multivariate analysis, INSTIs use (OR 2.89; 95%CI 1.26-6.64; p=0.012), CD4≤200/mm3 (OR 5.56; 95%CI 2.2-13.98; p<0.001), and the presence of an OI (OR 4.74; 95%CI 2.13-10.23; p=0.012) were independent risk factors. Among INSTI regimens, dolutegravir (OR 4.99 vs. NNRTI; 95%CI 1.11-22.55; p=0.037) and elvitegravir (OR 4.82 vs. NNRTI; 95%CI 1.43-16.19; p=0.011) seem to carry increased risk. Mortality was 18.9% (7/37) for IRIS patients compared to 9.7% (37/380) in the non-IRIS group. Mortality at any given time during follow-up was significantly higher in the IRIS group (HR 3.2; 95%CI 1.39-7.36; p=0.006). CONCLUSION: The use of INSTIs and especially DTG and EVG is associated with a higher probability for the development of IRIS in the background of late presentation and the presence of OIs. These data highlight the need for further research.

Detailed Molecular Surveillance of the HIV-1 Outbreak Among People who Inject Drugs (PWID) in Athens During a Period of Four Years.

BACKGROUND: New diagnoses of HIV-1 infection among people who inject drugs (PWID) increased significantly during 2011 in Athens. OBJECTIVE: Our aim was to investigate the patterns of HIV epidemic spread among PWID and to estimate the transmission dynamics for the major local transmission networks (LTNs). METHODS: We analyzed sequences from 2,274 HIV-infected subjects sampled in Greece during 01/01/2011-31/10/2014. Of specimens in our sample, 874 sequences were isolated from HIV-infected PWID. Phylodynamic analysis was performed using birth-death serial skyline models. RESULTS: Phylogenetic analysis revealed that the majority of sequences from PWID (N=746, 85.4%) fell within four LTNs: CRF14_BG (N=456, 58.3%), CRF35_AD (N=149, 19.1%), subtype B (N=118, 15.1%) and A1 (N=59, 7.5%). In addition to PWID, we also found that sequences from 36 non-PWID belonged to the LTNs corresponding to cross-group transmissions. Based on the estimated plots of the effective reproductive number (Re) over time, subtype A1 and CRF35_AD LTNs showed a sharp increase before and during 2011 (maximum value of Re=3.0 and Re=4.6, respectively). For subtype B and CRF14_BG LTNs, the Re was increasing until the end of 2012 (maximum value of Re=3.2 and Re=3.0, respectively). CONCLUSION: HIV transmissions within subtype A1 and CRF35_AD LTNs increased sharply during the early stage of the outbreak, in contrast to subtype B and CRF14_BG. A significant reduction in the number of infections was estimated on all transmission networks from the beginning of 2013 onwards. Prevention measures that took place in the Athens metropolitan area at the end of 2012 including also the ARISTOTLE program may explain this decrease.

Transmission Dynamics of HIV-1 Drug Resistance among Treatment-Naïve Individuals in Greece: The Added Value of Molecular Epidemiology to Public Health.

The presence of human immunodeficiency virus type 1 (HIV-1) drug resistance among drug-naïve patients remains stable, although the proportion of patients with virological failure to therapy is decreasing. The dynamics of transmitted resistance among drug-naïve patients remains largely unknown. The prevalence of non-nucleoside reverse transcriptase inhibitors (NNRTI) resistance was 16.9% among treatment-naïve individuals in Greece. We aimed to investigate the transmission dynamics and the effective reproductive number (Re) of the locally transmitted NNRTI resistance. We analyzed sequences with dominant NNRTI resistance mutations (E138A and K103N) found within monophyletic clusters (local transmission networks (LTNs)) from patients in Greece. For the K103N LTN, the Re was >1 between 2008 and the first half of 2013. For all E138A LTNs, the Re was >1 between 1998 and 2015, except the most recent one (E138A_4), where the Re was >1 between 2006 and 2011 and approximately equal to 1 thereafter. K103N and E138A_4 showed similar characteristics with a more recent origin, higher Re during the first years of the sub-epidemics, and a declining trend in the number of transmissions during the last two years. In the remaining LTNs the epidemic was still expanding. Our study highlights the added value of molecular epidemiology to public health.

Dissemination of Methicillin-Susceptible CC398 Staphylococcus aureus strains in a rural Greek area.

A large collection of Staphylococcus aureus including a. 745 clinically significant isolates that were consecutively recovered from human infections during 2012-2013, b. 19 methicillin-susceptible (MSSA), randomly selected between 2006-2011 from our Staphylococcal Collection, c. 16 human colonizing isolates, and d. 10 strains from colonized animals was investigated for the presence and the molecular characteristics of CC398. The study was conducted in Thessaly, a rural region in Greece. The differentiation of livestock-associated clade from the human clade was based on canSNPs combined with the presence of the φ3 bacteriophage and the tetM, scn, sak, and chp genes. Among the 745 isolates, two MRSA (0.8% of total MRSA) and thirteen MSSA (2.65% of total MSSA) were found to belong to CC398, while, between MSSA of our Staphylococcal Collection, one CC398, isolated in 2010, was detected. One human individual, without prior contact with animals, was found to be colonized by a MSSA CC398. No CC398 was identified among the 10 S. aureus isolated from animals. Based on the molecular markers, the 17 CC398 strains were equally placed in the livestock-associated and in the human clades. This is the first report for the dissemination of S. aureus CC398 among humans in Greece.

Determination of colistin A and colistin B in human plasma by UPLC-ESI high resolution tandem MS: application to a pharmacokinetic study.

The resistance of gram-negative bacteria to most available antibiotics and the lack of new antimicrobial agents have prompted the re-emergence of colistin (CS) as potent treatment against most gram-negative microorganisms. Optimal dosing with CS suffers from poor pharmacokinetic characterization mainly due to the analytical challenge of assaying CS in biological fluids and the limited information on quantitative analysis of CS in plasma using high resolution mass spectrometry (MS). Hence, a rapid, simple and accurate analytical method based on ultra performance liquid chromatography (UPLC) combined with electrospray ionization (ESI) tandem mass spectrometry (MS/MS) on a hybrid quadrupole time of flight (QTOF) instrument has been developed and fully validated for the quantification of CS in human plasma. After the pretreatment of plasma samples by solid phase extraction (SPE) and the addition of the internal standard (reserpine, RSP) the analytes were chromatographed on an Acquity BEH C8 column (100 mm × 2.1 mm, 1.7 µm) using gradient elution with 0.5% aqueous acetic acid (AcOH) and acetonitrile with 0.5% AcOH (with CSA and CSB eluting at 1.39 and 1.31 min, respectively). Accurate mass measurement correction was performed on line using the leukine-enkephaline standard. The method presented good fit (regression coefficient≥0.998) over the quantitation range of 0.2-300 and 0.03-4.5 µg mL(-1) with the lower limit of quantitation (LLOQ) being 0.02 and 0.03 µg mL(-1) for CSA and CSB in human plasma, respectively. The intra- and inter-day precision, measured as %relative standard deviation, was better than 10%, whereas the accuracy expressed as %relative error was also better than 10%. The short term, freeze-thaw (three cycles) and in process stability showed non-significant degradation of CS under these conditions. The validation results showed that the developed method demonstrated adequate selectivity and sensitivity. The method has been successfully applied to plasma samples from patients suffering from cystic fibrosis and treated with CS, and the pharmacokinetic profile has been calculated.

Transmission dynamics of carbapenemase-producing Klebsiella pneumoniae and anticipated impact of infection control strategies in a surgical unit.

BACKGROUND: Carbapenemase-producing Klebsiella pneumoniae (CPKP) has been established as important nosocomial pathogen in many geographic regions. Transmission from patient to patient via the hands of healthcare workers is the main route of spread in the acute-care setting. METHODOLOGY/PRINCIPAL FINDINGS: Epidemiological and infection control data were recorded during a prospective observational study conducted in a surgical unit of a tertiary-care hospital in Greece. Surveillance culture for CPKP were obtained from all patients upon admission and weekly thereafter. The Ross-Macdonald model for vector-borne diseases was applied to obtain estimates for the basic reproduction number R(0) (average number of secondary cases per primary case in the absence of infection control) and assess the impact of infection control measures on CPKP containment in endemic and hyperendemic settings. Eighteen of 850 patients were colonized with CPKP on admission and 51 acquired CPKP during hospilazation. R(0) reached 2 and exceeded unity for long periods of time under the observed hand hygiene compliance (21%). The minimum hand hygiene compliance level necessary to control transmission was 50%. Reduction of 60% to 90% in colonized patients on admission, through active surveillance culture, contact precautions and isolation/cohorting, in combination with 60% compliance in hand hygiene would result in rapid decline in CPKP prevalence within 8-12 weeks. Antibiotics restrictions did not have a substantial benefit when an aggressive control strategy was implemented. CONCLUSIONS/SIGNIFICANCE: Surveillance culture on admission and isolation/cohorting of colonized patients coupled with moderate hand hygiene compliance and contact precautions may lead to rapid control of CPKP in endemic and hyperendemic healthcare settings.

Increasing prevalence of HIV-1 subtype A in Greece: estimating epidemic history and origin.

BACKGROUND: In North America and Europe, human immunodeficiency virus (HIV)-1 infection has typically been dominated by subtype B transmission. More recently, however, non-B subtypes have been increasingly reported in Europe. METHODS: We analyzed 1158 HIV-1-infected individuals in Greece by DNA sequencing and phylogenetic analyses of protease and partial reverse-transcriptase regions. RESULTS: We found that the prevalence of non-B subtypes has increased over time and that this significant trend can be mainly attributed to subtype A, which eventually surpassed subtype B in prevalence in 2004 (42% and 33%, respectively). Multivariate analysis revealed that the year of HIV diagnosis was independently associated with subtype A infection (odds ratio for being infected with subtype A for a 10-year increase in the time period of diagnosis, 2.09 [95% confidence interval, 1.36-3.24]; P<.001). Phylogenetic analysis revealed that the subtype A epidemic in Greece is the result of a single founder event. The date of the most recent common ancestor of the subtype A in Greece was estimated to be 1977.9 (95% highest posterior density interval, 1973.7-1981.9). CONCLUSIONS: Subtype A circulates among the long-term residents of Greece. This is in contrast to the situation in most European countries, in which infection with non-B genetic forms is associated either with being an immigrant or heterosexual or with intravenous drug use.