Whole genomes from bacteria collected at diagnostic units around the world 2020

The Two Weeks in the World research project has resulted in a dataset of 3087 clinically relevant bacterial genomes with pertaining metadata, collected from 59 diagnostic units in 35 countries around the world during 2020. A relational database is available with metadata and summary data from selected bioinformatic analysis, such as species prediction and identification of acquired resistance genes.

Insight into pathogenomics and phylogeography of hypervirulent and highly-lethal Mycobacterium tuberculosis strain cluster

BACKGROUND

. The Mycobacterium tuberculosis Beijing genotype is globally spread lineage with important medical properties that however vary among its subtypes. M. tuberculosis Beijing 14717-15-cluster was recently discovered as both multidrug-resistant, hypervirulent, and highly-lethal strain circulating in the Far Eastern region of Russia. Here, we aimed to analyze its pathogenomic features and phylogeographic pattern.

RESULTS

. The study collection included M. tuberculosis DNA collected between 1996 and 2020 in different world regions. The bacterial DNA was subjected to genotyping and whole genome sequencing followed by bioinformatics and phylogenetic analysis. The PCR-based assay to detect specific SNPs of the Beijing 14717-15-cluster was developed and used for its screening in the global collections. Phylogenomic and phylogeographic analysis confirmed endemic prevalence of the Beijing 14717-15-cluster in the Asian part of Russia, and distant common ancestor with isolates from Korea (> 115 SNPs). The Beijing 14717-15-cluster isolates had two common resistance mutations RpsL Lys88Arg and KatG Ser315Thr and belonged to spoligotype SIT269. The Russian isolates of this cluster were from the Asian Russia while 4 isolates were from the Netherlands and Spain. The cluster-specific SNPs that significantly affect the protein function were identified in silico in genes within different categories (lipid metabolism, regulatory proteins, intermediary metabolism and respiration, PE/PPE, cell wall and cell processes).

CONCLUSIONS

. We developed a simple method based on real-time PCR to detect clinically significant MDR and hypervirulent Beijing 14717-15-cluster. Most of the identified cluster-specific mutations were previously unreported and could potentially be associated with increased pathogenic properties of this hypervirulent M. tuberculosis strain. Further experimental study to assess the pathobiological role of these mutations is warranted.

The global case fatality rate of coronavirus disease 2019 by continents and national income: A meta-analysis

The aim of this study is to provide a more accurate representation of COVID‐19's case fatality rate (CFR) by performing meta‐analyses by continents and income, and by comparing the result with pooled estimates. We used multiple worldwide data sources on COVID‐19 for every country reporting COVID‐19 cases. On the basis of data, we performed random and fixed meta‐analyses for CFR of COVID‐19 by continents and income according to each individual calendar date. CFR was estimated based on the different geographical regions and levels of income using three models: pooled estimates, fixed‐ and random‐model. In Asia, all three types of CFR initially remained approximately between 2.0% and 3.0%. In the case of pooled estimates and the fixed model results, CFR increased to 4.0%, by then gradually decreasing, while in the case of random‐model, CFR remained under 2.0%. Similarly, in Europe, initially, the two types of CFR peaked at 9.0% and 10.0%, respectively. The random‐model results showed an increase near 5.0%. In high‐income countries, pooled estimates and fixed‐model showed gradually increasing trends with a final pooled estimates and random‐model reached about 8.0% and 4.0%, respectively. In middle‐income, the pooled estimates and fixed‐model have gradually increased reaching up to 4.5%. in low‐income countries, CFRs remained similar between 1.5% and 3.0%. Our study emphasizes that COVID‐19 CFR is not a fixed or static value. Rather, it is a dynamic estimate that changes with time, population, socioeconomic factors, and the mitigatory efforts of individual countries.

Europe showed the highest COVID‐19 case fatality rate (CFR) until mid‐October 2020, and North America and South America follows.

Asia showed the highest CFR since the first confirmed case of COVID‐19 emerged, however, it had shown a declining tendency since March 2020.

CFRs in high‐income countries showed an explosive increase compared with those in low‐income countries, which can be interpreted as due to the under‐reporting of mortality cases from COVID‐19.

Candida auris: A Quick Review on Identification, Current Treatments, and Challenges

Candida auris is a novel and major fungal pathogen that has triggered several outbreaks in the last decade. The few drugs available to treat fungal diseases, the fact that this yeast has a high rate of multidrug resistance and the occurrence of misleading identifications, and the ability of forming biofilms (naturally more resistant to drugs) has made treatments of C. auris infections highly difficult. This review intends to quickly illustrate the main issues in C. auris identification, available treatments and the associated mechanisms of resistance, and the novel and alternative treatment and drugs (natural and synthetic) that have been recently reported.

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.

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 β-lactams (bla_NDM-1, bla_CMY-6, bla_CTX-M-15and bla_SHV-28), aminoglycosides (rmtC, aac(6')-Ib3), fluoroquinolones (oqxA, oqxB, aac(6')-Ib-cr), fosfomycin (fosA) and sulfonamides (sul1). The bla_NDM-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 bla_NDM-1-carrying isolates.

Evaluation of Mycobacterium tuberculosis viability in OMNIgene-SPUTUM reagent upon multi-day transport at ambient temperature

Background

Maintaining the quality of clinical specimens for tuberculosis (TB) testing is a major challenge in many high TB burden-limited resources countries. Sample referral systems in low and middle income countries are often weak and the maintenance of the cold-chain challenging and very costly for TB programs. The development of transport media allowing the preservation of samples without refrigeration is critical for increasing access to TB diagnostic services and for reducing the costs related to testing.

Methods

We evaluated the performance of OMNIgene-SPUTUM (OM-S) reagent for the maintenance of Mycobacterium tuberculosis (MTB) viability in sputum samples in the absence of refrigeration and its capacity to stabilize nucleic acid for molecular testing. A total of 329 sputum specimens from presumptive TB cases collected at the National Reference Laboratory in Tirana, Albania, were either decontaminated by a conventional method or processed with OM-S reagent and stored at room temperature. Samples in OM-S were shipped to the Supranational Reference Laboratory in Milan, Italy, at various times and processed for liquid culture.

Results

Our data show that OM-S maintains MTB viability for at least three weeks in the absence of refrigeration and improves the quality of culture resulting in a contamination rate lower than 0.5%. However, a significant delay in the time to culture positivity was observed for samples stored for more than two weeks in OM-S.

Conclusions

Overall, OM-S offers multiple benefits both at laboratory and TB national program level by increasing the availability to quality diagnostics, promoting access to health care services and strengthening TB patient care especially in hard to reach populations.

Mycobacterium tuberculosis complex CRISPR genotyping: improving efficiency, throughput and discriminative power of 'spoligotyping' with new spacers and a microbead-based hybridization assay

The aims of the present study were to implement a microbead-based 'spoligotyping' technique and to evaluate improvements by the addition of a panel of 25 extra spacers that we expected to provide an increased resolution on principal genetic group 1 (PGG 1) strains. We confirmed the high sensitivity and reproducibility of the classical technique using the 43 spacer panel and we obtained perfect agreement between the membrane-based and the microbead-based techniques. We further demonstrated an increase in the discriminative power of an extended 68 spacer format for differentiation of PGG 1 clinical isolates, in particular for the East African-Indian clade. Finally, we define a limited yet highly informative reduced 10 spacer panel set which could offer a more cost-effective option for implementation in resource-limited countries and that could decrease the need for additional VNTR (variable number of tandem repeats) genotyping work in molecular epidemiological studies. We also present an economic analysis comparing membrane-based and microbead-based techniques.

TB situation in Albania, 2001-2008

SETTING

Albania, population 3.4 million.

OBJECTIVE

To describe DOTS (directly observed treatment-short course chemotherapy) implementation, treatment outcomes and epidemiological situation in Albania from 2001 to 2008.

DESIGN

DOTS strategy was introduced in 2001 and gradually expanded. A retrospective analysis of treatment outcomes and epidemiological data on TB patients was analyzed for this period.

RESULTS

DOTS was expanded to 76% of the country in 2008. Treatment success among new smear-positive patients ranged from 82% in 2001 to 86% in 2007. The incidence of TB in Albania decreased from 17 per 100,000 inhabitants in 2001 to 12/100,000 in 2008 and estimated case detection for smear positive cases improved from 42% in 2001 to 75% in 2007.

CONCLUSIONS

The TB incidence has fallen progressively since DOTS was initiated. Treatment outcome was better in DOTS areas compared to Non-DOTS areas and overall treatment outcome was improved during DOTS implementation. Despite gradually, DOTS was successfully implemented and full expansion is necessary.

Net fluid accumulation and outcome. A randomized clinical trial

Outcome measures are the first step in determining the consequences of health care. These include mortality, morbidity, and quality of life. As major burns are life-threatening conditions, the main priority in discussing outcome measures is mortality as a problem-specific measure. A number of studies have shown that mortality is predominantly determined by many variables obtained as "admission" predictors" as also by numerous variables obtained during the hospital course. Net fluid accumulation (NFA) is one of the many important factors that correlate with clinical outcome. The purpose of this paper is thus to evaluate NFA during resuscitation with Ringer's lactate (RL) and its relationship with mortality. We hypothesized that rigorous monitoring of fluid replacement therapy might result in lower fluid retention, which could be effective in the prognosis of severely burned patients. In this prospective randomized study, the patients were divided into two groups of 55 cases each. In RL group 1, the patients were resuscitated using the Parkland formula in adults and the Galveston Shriner formula in children, without modifications, while in RL group 2 the formula was utilized as a starting-point only and the amount of fluid was modified in each case on the basis of the clinical situation and urine output. It was found that there was a statistically significant difference in NFA between the two groups (p = 0.001), as also a statistically significant difference between the amount of fluids given and the complications (p = 0.08). The majority of patients who died (70%) presented higher NFA values in the period of resuscitation. There was a statistically significant difference between mortality and total body surface area burned (p = 0.036), comorbidities (p = 0.015), cause of burn (p = 0.004), inhalation injury (p = 0.027). The degree of NFA correlated, with a linear positive relationship, with morbidity (Kendall's tau_br = 0.143, p = 0.019) and, with a negative relationship, with mortality (Kendall's tau_br = 0.234, p = 0.001). Mortality as the primary endpoint was 16% in group 1 and 9% in group 2. Giving the smallest amount of fluids necessary for adequate resuscitation can be effective in creating a successful and specific therapy for all burn patients. With regard to morbidity and mortality, predictor factors, as also the method of resuscitation, have an influence in maintaining constant NFA values.

External quality control of Mycobacterium tuberculosis drug susceptibility testing: results of two rounds in endemic countries

SETTING

Quality assurance for the World Health Organization (WHO)/International Union Against Tuberculosis and Lung Disease (The Union) global tuberculosis (TB) drug resistance surveillance programme.

OBJECTIVE

To monitor the quality of drug susceptibility testing (DST) in different countries.

METHODS

In 2002-2003 and 2005-2006, 20 Mycobacterium tuberculosis strains were sent by the WHO/Union Supranational Reference Laboratory of Rome to TB reference laboratories in Albania, Bahrain, Kosovo, Mozambique, Oman, Qatar and Turkey for external quality control (EQC).

RESULTS

In 2002-2003, the specificity, sensitivity, efficiency, reproducibility and predictive values for resistance/susceptibility were >or=90% for streptomycin (SM), isoniazid (INH) and ethambutol (EMB). In 2005-2006, all statistical values were >or=96% for SM, INH, rifampicin and EMB.

CONCLUSION

EQC improved the quality of M. tuberculosis DST in the participating countries.