Accuracy of the QIAxcel Automated System for MIRU-VNTR Genotyping of Mycobacterium tuberculosis in Two Limited Resource Settings.

Mycobacterial interspersed repetitive units variable number tandem repeat (MIRU-VNTR) typing of Mycobacterium tuberculosis complex (MTBC) isolates, based on 24 loci, is still widely used as the standard for routine molecular surveillance of tuberculosis (TB). QIAxcel system is proposed as an affordable tool that could replace conventional gel electrophoresis and provide high concordance with the reference methods regarding MIRU-VNTR typing of MTBC. We aimed to evaluate the QIAxcel accuracy for allele calling of MIRU-VNTR loci in two regional reference laboratories. A total of 173 DNA were used for the study. Results obtained with QIAxcel were compared to the reference results obtained with an ABI 3730 DNA analyzer. In Albania, the overall agreement with the reference method was 97.92%. A complete agreement result was obtained for 17 loci. In Tunisia, the overall agreement with the reference method was 98.95%. A complete agreement result was obtained for 17 loci. Overall agreement in both centers was 98.43%. In our opinion, use of QIAxcel technology has the potential to be reliable, given an optimized algorithm. Inaccuracies in sizing of long fragments should be solved, especially regarding locus 4052.

Whole-Genome Sequences of Two NDM-1-Producing Pseudomonas aeruginosa Strains Isolated in a Clinical Setting in Albania in 2018.

Isolation of metallo-ß-lactamase-producing, carbapenem-resistant, Pseudomonas aeruginosa strains is increasingly being documented worldwide; their presence constitutes a public health threat. Here, we report draft genome sequences of two New Delhi metallo-ß-lactamase-1-producing, multidrug-resistant, P. aeruginosa strains of sequence type 235 that were isolated from the surgical wound of two patients hospitalized in the same ward.

Peculiar features of the Mycobacterium tuberculosis population structure in Albania.

Albania is a Balkan country with moderate to low incidence of tuberculosis (TB) and very low prevalence of drug resistant TB. Here, we analyzed a country-wide multi-year Mycobacterium tuberculosis collection in order to detect possible dynamic trends of TB in Albania, with a focus on drug resistance and endemic/epidemic clones. In total, 743 isolates collected in 2007 to 2011 were divided into 107 spoligotypes and 351 MIRU-types. Based on the MIRU-VNTR phylogenetic analysis, the isolates were assigned to the following lineages/families: animal ecotypes (5 M. bovis and 2 M. caprae isolates), Lineage 2 (5 Beijing isolates), Lineage 3 (1 CAS-Delhi isolate) and, mostly and overwhelmingly, Lineage 4 (Cameroon, Uganda, Ghana and related; NEW-1-related; Ural, Haarlem, LAM, S, TUR; and unclassified isolates). Most of the isolates (452/743) were intermediately located on the global VNTR tree and did not cluster with any reference profile; they were distantly related to different families within Lineage 4 and we designated them as "unclassified L4" isolates. The significantly higher proportion of drug resistance was observed in (i) Beijing genotype compared to all other isolates (60%, P = .008), (ii) "unclassified L4" compared to all other isolates (13.9%, P = .04) and (iii) SIT2936 compared to other "unclassified L4" (34.3%, P = .0006). Analysis of the yearly collections revealed (i) some decrease of the large heterogeneous "unclassified L4" from 65% to 57%; (ii) steadily increasing gradient of LAM from 3.4 to 13.3%; (iii) stable prevalence of Haarlem (15-20%); and (iv) decrease of TUR with only 1.1% in 2011. Most of the LAM (33/49) and Beijing (3/5) isolates belonged to the VNTR types specific for Russia and former Soviet Union countries. To conclude, our results highlight a peculiar nature of M. tuberculosis population in Albania that is dominated by local and unclassified genotypes within Lineage 4, and also features European genotypes and epidemically relevant clones originating from the former Soviet Union countries. At the same time, these imported clones remain drug susceptible and prevalence of drug resistance on a whole is low.

Isolation of the first New Delhi metallo-ß-lactamase-1 (NDM-1)-producing and colistin-resistant Klebsiella pneumoniae sequence type ST15 from a digestive carrier in Albania, May 2018.

OBJECTIVES: Carbapenemases represent a public health threat, as they can spread through horizontal gene transfer and cause outbreaks. New Delhi metallo-ß-lactamase-1 (NDM-1) is a metallo-ß-lactamase that has spread rapidly in the last decade, causing worldwide alarm. This study aimed to describe the first isolate of NDM-1-producing and extensively drug resistant Klebsiella pneumoniae in Albania, its clinical context and genetic characterization. METHODS: Strain was isolated from both oral and rectal intensive care unit admission screening swabs of a 70-year-old male patient with no history of international travel in the previous 6 months. Sequencing was performed by Illumina NextSeq500 platform, with a paired-end run of 2 by 150bp, after Nextera XT paired-end library preparation. Sequencing reads were assembled using SPAdes Genome (version 3.6.1) with accurate de novo settings. The assembled contigs were uploaded into the online tools: BIGSdb-Kp, ResFinder and PlasmidFinder. RESULTS: Isolate was resistant to all tested antibiotics but tigecycline and trimethoprim-sulfamethoxazole. Sequencing revealed the presence of acquired resistance genes conferring resistance to ß-lactams (blaNDM-1, blaCMY-6, blaCTX-M-15and blaSHV-28), aminoglycosides (rmtC, aac(6')-Ib3), fluoroquinolones (oqxA, oqxB, aac(6')-Ib-cr), fosfomycin (fosA) and sulfonamides (sul1). The blaNDM-1 gene was located on an IncA/C2 plasmid. Plasmid mediated mcr-1 to mcr-8 genes were absent in both isolates. Resistance to colistin was due to an amino acid substitution (Thr157Pro) in PmrB protein. CONCLUSIONS: NDM-1-producing Enterobacteriaceae are spreading in the Balkans. Identification of NDM-1-producing and extensively drug resistant K. pneumoniae ST15 in Albania is a cause for serious concern. There should be a continuous national and Balkan multinational surveillance of blaNDM-1-carrying isolates.

Pancoast tumor approach through oesophagus.

Patient with Pancoast Tumor usually present in advanced stage of the disease which requires chemotherapy and radiotherapy as options of treatment. Histologic confirmation is a key for further treatment of these patients. Normally in bronchoscopy the lesion can't be visualised and in result making biopsy difficult to perform. Transthoracic biopsy through computed tomography poses anatomic difficulties and not always the pulmonary lesion can be reached. We report a case of pancoast tumor in a 68 year old male who presented with left arm pain and upper lobe increased density mass in chest x ray. Computed tomography confirmed an upper lobe mass of the left lung with invasion of the chest wall. It was successfully diagnosed with biopsy taken through the oesophagus of intrapulmonary mass with the EBUS bronchoscope (EUS- B FNA). No complication were observed during and after the procedure. To our knowledge this is the first case of making the diagnosis of lung carcinoma Pancoast tumor using EBUS bronchoscope with approach through oesophagus (EUS-B FNA). There may be a role in using EBUS specifically to diagnose a pancoast tumor in the right patient population.

Implementation of a Consensus Set of Hypervariable Mycobacterial Interspersed Repetitive-Unit-Variable-Number Tandem-Repeat Loci in Mycobacterium tuberculosis Molecular Epidemiology.

This study shows that the addition of a consensus 4-locus set of hypervariable mycobacterial interspersed repetitive-unit-variable-number tandem repeat (MIRU-VNTR) loci to the spoligotyping-24-locus MIRU-VNTR typing strategy is a well-standardized approach that can contribute to an improvement of the true cluster definition while retaining high typeability in non-Beijing strains.