Genotypes and population genetics of cryptococcus neoformans and cryptococcus gattii species complexes in Europe and the mediterranean area.

A total of 476 European isolates (310 Cryptococcus neoformans var. grubii, 150 C. neoformans var. neoformans, and 16 C. gattii species complex) from both clinical and environmental sources were analyzed by multi-locus sequence typing. Phylogenetic and population genetic analyses were performed. Sequence analysis identified 74 sequence types among C. neoformans var. neoformans (VNIV), 65 among C. neoformans var. grubii (56 VNI, 8 VNII, 1 VNB), and 5 among the C. gattii species complex (4 VGI and 1 VGIV) isolates. ST23 was the most frequent genotype (22%) among VNI isolates which were mostly grouped in a large clonal cluster including 50% of isolates. Among VNIV isolates, a predominant genotype was not identified. A high percentage of autochthonous STs were identified in both VNI (71%) and VNIV (96%) group of isolates. The 16 European C. gattii species complex isolates analyzed in the present study originated all from the environment and all belonged to a large cluster endemic in the Mediterranean area. Population genetic analysis confirmed that VNI group of isolates were characterized by low variability and clonal expansion while VNIV by a higher variability and a number of recombination events. However, when VNI and VNIV environmental isolates were compared, they showed a similar population structure with a high percentage of shared mutations and the absence of fixed mutations. Also linkage disequilibrium analysis reveals differences between clinical and environmental isolates showing a key role of PLB1 allele combinations in host infection as well as the key role of LAC1 allele combinations for survival of the fungus in the environment. The present study shows that genetic comparison of clinical and environmental isolates represents a first step to understand the genetic characteristics that cause the shift of some genotypes from a saprophytic to a parasitic life style.

Fundamental niche prediction of the pathogenic yeasts Cryptococcus neoformans and Cryptococcus gattii in Europe.

Fundamental niche prediction of Cryptococcus neoformans and Cryptococcus gattii in Europe is an important tool to understand where these pathogenic yeasts have a high probability to survive in the environment and therefore to identify the areas with high risk of infection. In this study, occurrence data for C. neoformans and C. gattii were compared by MaxEnt software with several bioclimatic conditions as well as with soil characteristics and land use. The results showed that C. gattii distribution can be predicted with high probability along the Mediterranean coast. The analysis of variables showed that its distribution is limited by low temperatures during the coldest season, and by heavy precipitations in the driest season. C. neoformans var. grubii is able to colonize the same areas of C. gattii but is more tolerant to cold winter temperatures and summer precipitations. In contrast, the C. neoformans var. neoformans map was completely different. The best conditions for its survival were displayed in sub-continental areas and not along the Mediterranean coasts. In conclusion, we produced for the first time detailed prediction maps of the species and varieties of the C. neoformans and C. gattii species complex in Europe and Mediterranean area.

Antimicrobial resistance activity and molecular characterization of methicillin-resistant staphylococci isolates in Tripoli Central Hospital, Libya

Background: Nosocomial infections caused by methicillin-resistant Staphylococci could lead to increased morbidity and mortality, but little is known about the prevalence of infections with these organisms in healthcare facilities and in the community in Tripoli. This study investigated the in vitro susceptibility of methicillin-resistant Staphylococcus aureus (MRSA) and methicillin-resistant coagulase negative staphylococci (MRCNS) to antimicrobial agents, and determined the molecular characteristics of MRSA.Methods: This is a retrospective observational study aiming at determining the prevalence and antibiotic resistance pattern of (MRSA) and (MRCNS) isolated from non-duplicated clinical specimens in Tripoli Central Hospital (TCH) between June 2013 and June 2014. Isolates were identified using standard laboratory procedures. Antimicrobial susceptibility tests were carried out by disk diffusion method and automated systems. DNA of the MRSA isolates was used for PCR to determine the molecular analysis.Results: 218 isolates of Staphylococci were obtained, 71.6% were coagulase positive staphylococci (CPS) and 28.4% were coagulase negative staphylococci (CNS). 39.7% of CPS were MRSA, while 75.8% of CNS were MRCNS. The rates of hospital-acquired MRSA (HA-MRSA) and community-acquired MRSA (CA-MRSA) among MRSA isolates were 61.3% and 38.7% respectively. A similar trend was detected among MRCNS isolates, where 74.5% were HA-MRCNS and 25.5% were CA-MRCNS. All the MRSA and MRCNS isolates were susceptible (100%) to vancomycin, tigecycline, linezolid, quinupristin/dalfopristin, daptomycin and moxifloxacin. Generally, hospital-acquired strains showed higher resistance rates than community-acquired ones to the most commonly tested non-beta-lactam antibiotics. 35.5% of all staphylococcal isolates exhibited mecA+ gene and 12.9% expressed mecC+. Meanwhile, 38.7% of MRSA isolates harbored both mecA and mecC. However, 12.9% of MSSA isolates were negative for both mecA and mecC. The mecA gene was detectable in 59.1% and 40.9 % of HA-MRSA and CA-MRSA isolates respectively.Conclusion: Hospital-acquired MRSA and MRCNS isolates had higher resistance rates to non-beta lactam antimicrobial drugs than the respective community-acquired isolates. This was shown by early detection of mecC gene among MRSA isolates

Environmental distribution of Cryptococcus neoformans and C. gattii around the Mediterranean basin.

In order to elucidate the distribution of Cryptococcus neoformans and C. gattii in the Mediterranean basin, an extensive environmental survey was carried out during 2012-2015. A total of 302 sites located in 12 countries were sampled, 6436 samples from 3765 trees were collected and 5% of trees were found to be colonized by cryptococcal yeasts. Cryptococcus neoformans was isolated from 177 trees and C. gattii from 13. Cryptococcus neoformans colonized 27% of Ceratonia, 10% of Olea, Platanus and Prunus trees and a lower percentage of other tree genera. The 13 C. gattii isolates were collected from five Eucalyptus, four Ceratonia, two Pinus and two Olea trees. Cryptococcus neoformans was distributed all around the Mediterranean basin, whereas C. gattii was isolated in Greece, Southern Italy and Spain, in agreement with previous findings from both clinical and environmental sources. Among C. neoformans isolates, VNI was the prevalent molecular type but VNII, VNIV and VNIII hybrid strains were also isolated. With the exception of a single VGIV isolate, all C. gattii isolates were VGI. The results confirmed the presence of both Cryptococcus species in the Mediterranean environment, and showed that both carob and olive trees represent an important niche for these yeasts.

Isolation, Identification and Molecular Typing of Cryptococcus neoformans from Pigeon Droppings and Other Environmental Sources in Tripoli, Libya.

Cryptococcus neoformans and C. gattii are the major cause of fungal meningitis, a potentially lethal mycosis. Since pigeon excreta and other environmental sources can be considered a significant environmental reservoir of this species in urban areas, 100 samples of pigeon excreta and 420 samples from Eucalyptus camaldulensis and Olea europaea (olive tree) around the city of Tripoli, Libya, were collected. C. neoformans was isolated and identified using standard biochemical assays from 46 samples: 34 from pigeon droppings, 3 from Eucalyptus trees and 9 from olive trees. Molecular typing revealed that all isolates from pigeon droppings belonged to molecular type VNI (C. neoformans var. grubii) and mating type αA, whereas those from trees included also the molecular type VNII and VNIII (AD hybrids). The present study reports, for the first time, information about the distribution of species, mating types and molecular types of C. neoformans/C. gattii species complex in Libya.

Changing pattern of neonatal bacteremia. Microbiology and antibiotic resistance.

OBJECTIVE: To determine the most important causative agents of bacteremia in a neonatal intensive care unit (NICU); their changing distribution and their antibiotic susceptibility patterns over a 5-year period. METHODS: This study was performed between January 1997 and January 2001 at the Microbiology Section, Tripoli Medical Center, Tripoli, Libya. During this period 1431 Oxoid Signal Blood Cultures sets were obtained from 1092 NICU with suspected bacteremia. Conventional methods, API 20 E and API 20 NE were used to identify the isolated bacteria. The Kirby-Bauer disk diffusion method was performed to assess their antibiotic susceptibilities in accordance with National Committee for Clinical Laboratory Standards. RESULTS: During the study period, 801 sets out of the total 1431 blood cultures were positive for microbial growth, which represented 648 cases of neonatal bacteremia from a total of 1092 cases. From the total number of isolates, the members of Enterobacteriaceae Serratia, Klebsiella and Enterobacter spp were the most common cause of bacteremia. The coagulase negative and positive Staphylococci were also frequently isolated. A changing pattern of causative pathogen was observed during this study between members of the 3 leading genera of Enterobacteriaceae. Antibiotic susceptibility testing showed a high level of resistance among the most common pathogens. Resistance to aztreonam, imipenem, ciprofloxacin and piperacillin/tazobactam was less frequently encountered. Staphylococcus resistance to anti-staphylococcal antibiotic and due to hyperproduction of penicillinase enzyme was also high and all isolates were remained sensitive to vancomycin. CONCLUSION: Gram-negative bacteria especially members of the Enterobacteriaceae are important causes of bacteremia in NICUs. Although most isolates remain sensitive to the new antibiotics, emergence of resistant strains cannot be excluded in the future. For that reason, new strategies and continuous surveillance are required to monitor the changing epidemiology of pathogens, antibiotic susceptibilities and antibiotic use needed to overcome the increasing incidence of resistance to conventional drugs.

Trichophyton violaceum is the dominant cause of tinea capitis in children in Tripoli, Libya: results of a two year survey.

The causative agents of tinea capitis in Libyan nationals attending the out patient Dermatology Clinic of the Tripoli Medical Centre over the period December 1997 to December 1999 were investigated. Samples (hair and scalp scrapings) were taken from 940 patients who presented with suspected tinea capitis. The etiological agents were identified in 584 cases. Trichophyton violaceum was found to be the most prevalent organism isolated being responsible for 64.4% (376/584) of culture positive cases, followed by Microsporum canis at 24.7% (144/584) and T. mentagrophytes at 5.5% (32/584). The majority of infections (380/584) occurred in females and in children with ages less than 12 years (554/584).