Detection of OXA-181 Carbapenemase in Shigella flexneri.

We report the detection of OXA-181 carbapenemase in an azithromycin-resistant Shigella spp. bacteria in an immunocompromised patient. The emergence of OXA-181 in Shigella spp. bacteria raises concerns about the global dissemination of carbapenem resistance in Enterobacterales and its implications for the treatment of infections caused by Shigella bacteria.

Genomic epidemiology reveals multidrug resistant plasmid spread between Vibrio cholerae lineages in Yemen.

Since 2016, Yemen has been experiencing the largest cholera outbreak in modern history. Multidrug resistance (MDR) emerged among Vibrio cholerae isolates from cholera patients in 2018. Here, to characterize circulating genotypes, we analysed 260 isolates sampled in Yemen between 2018 and 2019. Eighty-four percent of V. cholerae isolates were serogroup O1 belonging to the seventh pandemic El Tor (7PET) lineage, sub-lineage T13, whereas 16% were non-toxigenic, from divergent non-7PET lineages. Treatment of severe cholera with macrolides between 2016 and 2019 coincided with the emergence and dominance of T13 subclones carrying an incompatibility type C (IncC) plasmid harbouring an MDR pseudo-compound transposon. MDR plasmid detection also in endemic non-7PET V. cholerae lineages suggested genetic exchange with 7PET epidemic strains. Stable co-occurrence of the IncC plasmid with the SXT family of integrative and conjugative element in the 7PET background has major implications for cholera control, highlighting the importance of genomic epidemiological surveillance to limit MDR spread.

Molecular identification of Aspergillus fumigatus complex from lung transplant recipients using multilocus sequencing analysis (MLSA).

BACKGROUND: Aspergillus infection causes significant morbidity and mortality among lung transplant recipients (LTRs). It is primarily caused by Aspergillus fumigatus. Other closely related species belonging to the section Fumigati have also been found. These cryptic species are often misidentified as A. fumigatus. Thus, we used multilocus sequencing analysis (MLSA) of the calmodulin, ß-tubulin, and hydrophobin gene sequences to identify these species and to determine the frequency with which they occur among LTRs. METHODS: A total of 81 A. fumigatus isolates were initially isolated from bronchoalveolar lavage fluid or sputum specimens collected from lung transplant patients. These isolates were then sub-cultured and genotyped using MLSA. Of these isolates, 53, 17, and 11 were isolated from double LTRs, single LTRs, and pre-LTRs, respectively. RESULTS: All isolates (100%) carried DNA sequences identical to those of A. fumigatus reference strains and thus clustered in the same clade with A. fumigatus. Analysis of the MLSA data revealed that A. fumigatus species were the only species recovered in this population of LTRs. The MLSA results were consistent with those routinely obtained by conventional mycological procedures in the microbiology laboratory. CONCLUSIONS: A. fumigatus appears to be the primary causative agent of colonization or invasive aspergillosis among LTRs. No cryptic species were identified.

HISTORIQUE: L'infection à Aspergillus est responsable d'une morbidité et d'une mortalité importantes chez les transplantés du poumon (TP). Elle est surtout causée par l'Aspergillus fumigatus. D'autres espèces proches, de la famille des fumigati, ont également été observées. Ces espèces cryptiques sont souvent identifiées à tort comme un A. fumigatus. Les chercheurs ont fait appel à l'analyse de séquençage multilocus (ASML) des séquences géniques de la calmoduline, de la ß-tubuline et de l'hydrophobine pour repérer ces espèces et en déterminer la fréquence chez les TP. MÉTHODOLOGIE: Au total, les chercheurs ont d'abord mis en culture 81 isolats d'A. fumigatus dans le liquide de lavage bronchoalvéolaire ou les échantillons d'expectoration de TP. Ils en ont ensuite fait une sous-culture et ont procédé au génotypage par ASML. Au total, 53, 17 et 11 d'entre eux provenaient de doubles TP, de TP simples et de futurs TP, respectivement. RÉSULTATS: Tous les isolats (100 %) contenaient des séquences d'ADN pareilles à celles des souches de référence d'A. fumigatus et ont donc été groupés dans le même clade que l'A fumigatus. L'ASML a révélé que les espèces d'A. fumigatus étaient les seules à être récupérées dans cette population de TP. Les résultats de l'ASML étaient conformes à ceux obtenus systématiquement lors d'interventions classiques au laboratoire de microbiologie. CONCLUSIONS: L'A. fumigatus semble être l'agent causal primaire de colonisation ou d'aspergillose invasive chez les TP. Aucune espèce cryptique n'a été observée.

Medications and Supplements Prescription Patterns during COVID 19 Pandemic in Yemen: A Questionnaire-Based Study.

Introduction: the study aims to better understand the COVID-19 prescription treatments and over the counter regimens in Yemen in view of limited published data and limited availability of COVID-19 testing. Methods: A 34 question web-based survey was distributed on social media outlets targeting people in Yemen. Data aggregation, analysis, and visualization were performed using Tableau and Microsoft Excel. Results: 2341 individuals reported symptoms concerning for COVID-19 infection, with 25.4% reporting a chronic medical condition. Female patients were less likely to receive medications for treatment in all age groups examined. Azithromycin was the most prescription medication prescribed (32.8%) and vitamin C being the most supplement used (62%). Around 5.5% were on Hydroxychloroquine prophylaxis prior to their diagnosis and only 12.9% of them continued using after diagnosis. Conclusions: This study provides some important information about the commonly observed treatments and prescription patterns during the COVID-19 pandemic in Yemen during May- July of 2020. The study reflects the influence of global trends in medication prescription even in resource-limited countries.

Ongoing diphtheria outbreak in Yemen: a cross-sectional and genomic epidemiology study.

BACKGROUND: An outbreak of diphtheria, declared in Yemen in October, 2017, is ongoing. We did a cross-sectional study to investigate the epidemiological, clinical, and microbiological features of the outbreak. METHODS: Probable cases of diphtheria that were defined clinically and recorded through a weekly electronic diseases early warning system (from 2017, week 22, to 2020, week 17) were used to identify trends of the outbreak (we divided the epidemic into three time periods: May 29, 2017, to June 10, 2018; June 11, 2018, to June 3, 2019; and June 4, 2019, to April 26, 2020). We used the line list of diphtheria reports for governorate-level descriptions. Vaccination coverage was estimated using the 2017 and 2018 annual reports by the national Expanded Programme on Immunization. To confirm cases biologically, Corynebacterium diphtheriae was isolated and identified from throat swabs using standard microbiological culture and identification procedures. We assessed differences in the temporal and geographical distributions of cases, including between different age groups. For in-depth microbiological analysis, tox gene and species-specific rpoB real-time PCR, Illumina genomic sequencing, antimicrobial susceptibility analysis (disk diffusion, E-test), and the Elek diphtheria toxin production test were done on confirmed cases. We used genomic data for phylogenetic analyses and to estimate the nucleotide substitution rate. FINDINGS: The Yemen diphtheria outbreak affected almost all governorates (provinces), with 5701 probable cases and 330 deaths recorded up to April 26, 2020. We collected clinical data for 888 probable cases with throat swab samples referred for biological confirmation, and genomic data for 42 positive cases, corresponding to 43 isolates (two isolates from one culture were included due to distinct colony morphologies). The median age of patients was 12 years (range 0·2-80). The proportion of cases in children aged 0-4 years was reduced during the second time period, after a vaccination campaign, compared with the first period (19% [95% CI 18-21] in the first period vs 14% [12-15] in the second period, p<0·0001). Among 43 tested isolates, 39 (91%) produced the diphtheria toxin and two had low level (0·25 mg/L) antimicrobial resistance to penicillin. We identified six C diphtheriae phylogenetic sublineages, four of which are genetically related to isolates from Saudi Arabia, Eritrea, and Somalia. Inter-sublineage genomic variations in genes associated with antimicrobial resistance, iron acquisition, and adhesion were observed. The predominant sublineage (30 [70%] of 43 isolates) was resistant to trimethoprim and was associated with unique genomic features, more frequent neck swelling (p=0·0029) and a younger age of patients (p=0·060) compared with the other sublineages. Its evolutionary rate was estimated at 1·67 × 10-6 substitutions per site per year, placing its most recent common ancestor in 2015, and indicating silent circulation of C diphtheriae in Yemen before the outbreak was declared. INTERPRETATION: In the Yemen outbreak, C diphtheriae shows high phylogenetic, genomic, and phenotypic variation. Laboratory capacity and real-time microbiological monitoring of diphtheria outbreaks need to be scaled up to inform case management and transmission control of diphtheria. Catch-up vaccination might have provided some protection to the targeted population (children aged 0-4 years). FUNDING: National Centre of the Public Health Laboratories (Yemen), Institut Pasteur, and the French Government Investissement d'Avenir Programme. TRANSLATION: For the Arabic translation of the abstract see Supplementary Materials section.

COVID-19 pandemic in Yemen: A questionnaire based survey, what do we know?

INTRODUCTION: Coronavirus infectious disease 2019 (COVID-19) is currently one of the most important public health crises affecting the global human population. It continues to spread widely, as the world still lacks specific treatments and a vaccine for the virus. The scenario of COVID-19 in Yemen seems obscure due to the lack of adequate data, therefore, we developed an electronic questionnaire and distributed it online among Yemeni people. The aim of this study was to understand the COVID-19 epidemiological situation in Yemen better since there is currently limited published data and limited availability of COVID-19 testing. METHODOLOGY: A 34-question web-based survey was distributed on social media outlets targeting people in Yemen. Data aggregation, analysis, and visualization were performed using Tableau and Microsoft Excel. RESULTS: 2,341 individuals reported symptoms concerning for COVID-19 infection, with 25.4% reporting a chronic medical condition. Diabetes, hypertension, asthma, and immune deficiency were associated with increased severity of the disease, while obesity, cardiovascular disease, kidney disease, and liver disease were not. Only 37 individuals (1.6%) had a confirmatory COVID-19 PCR test. The presence of high fever, dyspnea, chest pain, and dysphagia were symptoms that tended to be correlated to worse clinical outcomes. CONCLUSIONS: This study provides some important information about the early overspread of COVID-19 within the Yemeni community in May, June, and July of 2020. It shows that online questionnaires may help in collecting data about pandemics in resource-limited countries where testing availability is limited.

Imipenem Treatment Induces Expression of Important Genes and Phenotypes in a Resistant Acinetobacter baumannii Isolate.

Acinetobacter baumannii has emerged as a notorious multidrug-resistant pathogen, and development of novel control measures is of the utmost importance. Understanding the factors that play a role in drug resistance may contribute to the identification of novel therapeutic targets. Pili are essential for A. baumannii adherence to and biofilm formation on abiotic surfaces as well as virulence. In the present study, we found that biofilm formation was significantly induced in an imipenem-resistant (Imp(r)) strain treated with a subinhibitory concentration of antibiotic compared to that in an untreated control and an imipenem-susceptible (Imp(s)) isolate. Using microarray and quantitative PCR analyses, we observed that several genes responsible for the synthesis of type IV pili were significantly upregulated in the Imp(r) but not in the Imp(s) isolate. Notably, this finding is corroborated by an increase in the motility of the Imp(r) strain. Our results suggest that the ability to overproduce colonization factors in response to imipenem treatment confers biological advantage to A. baumannii and may contribute to clinical success.

Evidence of Bacterial Biofilms among Infected and Hypertrophied Tonsils in Correlation with the Microbiology, Histopathology, and Clinical Symptoms of Tonsillar Diseases.

Diseases of the tonsils are becoming more resistant to antibiotics due to the persistence of bacteria through the formation of biofilms. Therefore, understanding the microbiology and pathophysiology of such diseases represent an important step in the management of biofilm-related infections. We have isolated the microorganisms, evaluated their antimicrobial susceptibility, and detected the presence of bacterial biofilms in tonsillar specimens in correlation with the clinical manifestations of tonsillar diseases. Therefore, a total of 140 palatine tonsils were collected from 70 patients undergoing tonsillectomy at University Malaya Medical Centre. The most recovered isolate was Staphylococcus aureus (39.65%) followed by Haemophilus influenzae (18.53%). There was high susceptibility against all selected antibiotics except for cotrimoxazole. Bacterial biofilms were detected in 60% of patients and a significant percentage of patients demonstrated infection manifestation rather than obstruction. In addition, an association between clinical symptoms like snore, apnea, nasal obstruction, and tonsillar hypertrophy was found to be related to the microbiology of tonsils particularly to the presence of biofilms. In conclusion, evidence of biofilms in tonsils in correlation with the demonstrated clinical symptoms explains the recalcitrant nature of tonsillar diseases and highlights the importance of biofilm's early detection and prevention towards better therapeutic management of biofilm-related infections.

In vitro activity of tigecycline against Acinetobacter baumannii isolates from a teaching hospital in Malaysia.

The In vitro susceptibility of clinical and environmental isolates of Acinetobacter baumannii to tigecycline and other antibiotics was determined by disk diffusion method. The E-test was used to determine the minimum inhibitory concentration (MIC). The growth curves of tigecycline treated environmental and clinical strains were established. Fifty-seven percent and 75% of the clinical and environmental isolates were MDR strains, respectively. Ninety-five percent of the clinical isolates were susceptible to tigecycline and 5% showed intermediate resistance with MIC ranging between 0.032 and 3 mg/l. Tigecycline susceptible and intermediate resistance among the environmental isolates were 40% and 60%, respectively, with a significantly lower MIC range of 0.5-4 mg/l. The bacterial growth curves demonstrated the higher ability of the environmental strains to tolerate the antibiotic effects than the clinical strains. The relatively high resistance profile among the environmental isolate suggests an insidious emergence of tigecycline resistance amongst A. baumannii. Strict infection control procedures are imperative to prevent the dissemination of tigecycline-resistant A. baumannii strains in the hospital environment.