Rapid emergence of antibiotic-resistant bacteria has made it harder for us to combat infectious diseases and to develop new antibiotics. The clustered regularly interspaced short palindromic repeats-CRISPR-associated (CRISPR-Cas) system, as a bacterial adaptive immune system, is recognized as one of the new strategies for controlling antibioticresistant strains. The programmable Cas nuclease of this system used against bacterial genomic sequences could be lethal or could help reduce resistance of bacteria to antibiotics. Therefore, this study aims to review using the CRISPR-Cas system to promote sensitizing bacteria to antibiotics. We envision that CRISPR-Cas approaches may open novel ways for the development of smart antibiotics, which could eliminate multidrug-resistant (MDR) pathogens and differentiate between beneficial and pathogenic microorganisms. These systems can be exploited to quantitatively and selectively eliminate individual bacterial strains based on a sequence-specific manner, creating opportunities in the treatment of MDR infections, the study of microbial consortia, and the control of industrial fermentation.

Objective To determine if immediate compared to deferred initiation of antiretroviral therapy (ART) in healthy persons living with HIV (PLWH) had a more favorable impact on health-related quality of life (QOL), or self-assessed physical, mental and overall health status. Design QOL was measured in START (Strategic Timing of Antiretroviral Therapy), which randomized healthy ART naive PLWH with >500 CD4+ cells/μl from 35 countries to immediate versus deferred ART. Methods At baseline, months 4 and 12, then annually, participants completed a visual analogue scale (VAS) for “perceived current health” and the Short-Form 12-Item Health Survey version 2 from which were computed: (1) General health (GH) perception; (2) Physical Component Summary (PCS), and (3) Mental Component Summary (MCS); the VAS and GH were rated from 0=lowest to 100=highest. Results QOL at study entry was high (mean scores: VAS=80.9, GH=72.5, PCS=53.7, MCS=48.2). Over a mean follow-up of 3 years, changes in all QOL measures favored the immediate group (p<0.001); estimated differences were: VAS=1.9, GH=3.6, PCS=0.8, MCS=0.9. When QOL changes were assessed across various demographic and clinical subgroups, treatment differences continued to favor the immediate group. QOL was poorer in those experiencing primary outcomes; however, when excluding those with primary events, results remained favorable for immediate ART recipients. Conclusions In an international randomized trial in ART-naive participants with >500 CD4+ cells/μl, there were modest but significant improvements in self-assessed QOL among those initiating ART immediately compared to deferring treatment, supporting patient-perceived health benefits of initiating ART as soon as possible after an HIV diagnosis.

Bacterial leaf streak (BLS) caused by Xanthomonas oryzae pv. oryzicola was first reported in Africa in the 1980s. Recently, a substantial reemergence of this disease was observed in West Africa. Samples were collected at various sites in five and three different rice-growing regions of Burkina Faso and Mali, respectively. Sixty-seven X. oryzae pv. oryzicola strains were isolated from cultivated and wild rice varieties and from weeds showing BLS symptoms. X. oryzae pv. oryzicola strains were evaluated for virulence on rice and showed high variation in lesion length on a susceptible cultivar. X. oryzae pv. oryzicola strains were further characterized by multilocus sequence analysis (MLSA) using six housekeeping genes. Inferred dendrograms clearly indicated different groups among X. oryzae pv. oryzicola strains. Restriction fragment length polymorphism analysis using the transcriptional activator like effector avrXa7 as probe resulted in the identification of 18 haplotypes. Polymerase chain reaction-based analyses of two conserved type III effector (T3E) genes (xopAJ and xopW) differentiated the strains into distinct groups, with xopAJ not detected in most African X. oryzae pv. oryzicola strains. XopAJ functionality was confirmed by leaf infiltration on 'Kitaake' rice Rxo1 lines. Sequence analysis of xopW revealed four groups among X. oryzae pv. oryzicola strains. Distribution of 43 T3E genes shows variation in a subset of X. oryzae pv. oryzicola strains. Together, our results show that African X. oryzae pv. oryzicola strains are diverse and rapidly evolving, with a group endemic to Africa and another one that may have evolved from an Asian strain.

dMultilocus variable-number tandem-repeat analysis (MLVA) is efficient for routine typing and for investigating the genetic structures of natural microbial populations. Two distinct pathovars of Xanthomonas oryzae can cause significant crop losses in tropical and temperate rice-growing countries. Bacterial leaf streak is caused by X. oryzae pv. oryzicola, and bacterial leaf blight is caused by X. oryzae pv. oryzae. For the latter, two genetic lineages have been described in the literature. We developed a universal MLVA typing tool both for the identification of the three X. oryzae genetic lineages and for epidemiological analyses. Sixteen candidate variable-number tandem-repeat (VNTR) loci were selected according to their presence and polymorphism in 10 draft or complete genome sequences of the three X. oryzae lineages and by VNTR sequencing of a subset of loci of interest in 20 strains per lineage. The MLVA-16 scheme was then applied to 338 strains of X. oryzae representing different pathovars and geographical locations. Linkage disequilibrium between MLVA loci was calculated by index association on different scales, and the 16 loci showed linear Mantel correlation with MLSA data on 56 X. oryzae strains, suggesting that they provide a good phylogenetic signal. Furthermore, analyses of sets of strains for different lineages indicated the possibility of using the scheme for deeper epidemiological investigation on small spatial scales. M olecular typing of pathogen populations is essential to gain insight into their genetic diversity and population dynamics in order to elaborate efficient strategies for disease control (1, 2). In agricultural systems, pests are ideally controlled by integrated approaches, including eradication or treatment of diseased organisms and planting of resistant varieties. However, the durability of resistance can be challenged if pathogen diversity is significant. Importantly, gene flow between pathogen populations can facilitate the breakdown of resistance in crop plants (3). Hence, efficient and precise molecular-typing tools for identifying strains and differentiating among related bacterial isolates are essential for microevolutionary reconstruction as a population genetics approach for integrated plant protection.Rice, one of the major crops worldwide, is affected by two bacterial diseases that are caused by strains of Xanthomonas oryzae, bacterial leaf blight (BLB), caused by X. oryzae pv. oryzae, and bacterial leaf streak (BLS), caused by X. oryzae pv. oryzicola. Collectively, these two diseases cause significant yield losses in tropical and temperate rice-growing areas. X. oryzae pv. oryzae colonizes xylem vessels upon entry into the vascular system. X. oryzae pv. oryzicola infects the plant via natural openings and colonizes the mesophyll (4). Genomes of members of both pathovars have been sequenced; however, the determinants of tissue specificity are still largely unknown (5, 6). While X. oryzae pv. oryzicola has been shown to be seedborne and seed transmitted (7,8), the evidenc...

Background MDR-TB is a major threat to global TB control. In 2015, 580,000 were treated for MDR-TB worldwide. The worldwide roll-out of GeneXpert MTB/RIF ® has improved diagnosis of MDR-TB; however, in many countries laboratories are unable to assess drug resistance and clinical predictors of MDR-TB could help target suspected patients. In this study, we aimed to determine the clinical factors associated with MDR-TB in Bamako, Mali. Methods We performed a cross-sectional study of 214 patients with presumed MDR-TB admitted to University of Bamako Teaching Hospital, Point-G between 2007 and 2016. We calculated crude and adjusted odds ratios for MDR-TB disease diagnosis using SPSS. Results We found that age ≤40years (OR = 2.56. 95% CI: 1.44–4.55), two courses of prior TB treatment (OR = 3.25,95% CI: 1.44–7.30), TB treatment failure (OR = 3.82,95% CI 1.82–7.79), sputum microscopy with 3+ bacilli load (OR = 1.98, 95% CI: 1.13–3.48) and a history of contact with a TB patient (OR = 2.48, 95% CI: 1.11–5.50) were significantly associated with confirmation of MDR-TB disease. HIV was not a risk factor for MDR-TB (aOR = 0.88, 95% CI: 0.34–1.94). Conclusion We identified several risk factors that could be used to identify MDR-TB suspects and prioritize them for laboratory confirmation. Prospective studies are needed to understand factors associated with TB incidence and clinical outcomes of TB treatment and disease.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) disease, which started in Wuhan, Chin, has now become a public health challenge in most countries around the world. Proper preventive measures are necessary to prevent the spread of the virus to help control the pandemic. Because, SARS-CoV-2 is new, its transmission route has not been fully understood. In this study, we aimed to investigate the presence of SARS‐CoV‐2 in the sweat secretion of COVID‐19 patients. Sweat specimens of 25 COVID- 19 patients were collected and tested for SARS‐CoV‐2 RNA by Real‐time Polymerase Chain Reaction (RT-PCR) method. After RNA extraction and cDNA amplification, all samples were examined for the presence of ORF-1ab and N genes related to COVID-19. Results annotated by Realtime PCR machines software based on Dynamic algorithm. The results of this study showed the absence of SARS-CoV-2 in the sweat samples taken from the foreheads of infected people. Therefore, it can be concluded that the sweat of patients with COVID- 19 cannot transmit SARS-CoV-2. However they can be easily contaminated with other body liquids.

Investment in SARS-CoV-2 sequencing in Africa over the past year has led to a major increase in the number of sequences generated, now exceeding 100,000 genomes, used to track the pandemic on the continent. Our results show an increase in the number of African countries able to sequence domestically, and highlight that local sequencing enables faster turnaround time and more regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and shed light on the distinct dispersal dynamics of Variants of Concern, particularly Alpha, Beta, Delta, and Omicron, on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve, while the continent faces many emerging and re-emerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century.

BackgroundAlthough Drug resistance tuberculosis is not a new phenomenon, Mali remains one of the “blank” countries without systematic data.MethodsBetween 2006 and 2014, we enrolled pulmonary TB patients from local TB diagnostics centers and a university referral hospital in several observational cohort studies. These consecutive patients had first line drug susceptibility testing (DST) performed on their isolates. A subset of MDR was subsequently tested for second line drug resistance.ResultsA total of 1186 mycobacterial cultures were performed on samples from 522 patients, including 1105 sputa and 81 blood samples, yielding one or more Mycobacterium tuberculosis complex (Mtbc) positive cultures for 343 patients. Phenotypic DST was performed on 337 (98.3%) unique Mtbc isolates, of which 127 (37.7%) were resistant to at least one drug, including 75 (22.3%) with multidrug resistance (MDR). The overall prevalence of MDR-TB was 3.4% among new patients and 66.3% among retreatment patients. Second line DST was available for 38 (50.7%) of MDR patients and seven (18.4%) had resistance to either fluoroquinolones or second-line injectable drugs.ConclusionThe drug resistance levels, including MDR, found in this study are relatively high, likely related to the selected referral population. While worrisome, the numbers remained stable over the study period. These findings prompt a nationwide drug resistance survey, as well as continuous surveillance of all retreatment patients, which will provide more accurate results on countrywide drug resistance rates and ensure that MDR patients access appropriate second line treatment.Electronic supplementary materialThe online version of this article (doi:10.1186/s12879-016-2060-7) contains supplementary material, which is available to authorized users.