What could explain the late emergence of COVID-19 in Africa?

At the end of November 2019, a novel coronavirus responsible for respiratory tract infections emerged in China. Despite drastic containment measures, this virus, known as severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), spread in Asia and Europe. The pandemic is ongoing with a particular hotspot in southern Europe and America in spring 2020. Many studies predicted an epidemic in Africa similar to that currently seen in Europe and the USA. However, reported data do not confirm these predictions. Several hypotheses that could explain the later emergence and spread of the coronavirus disease 2019 (COVID-19) pandemic in African countries are being discussed, including the lack of health-care infrastructure capable of clinically detecting and confirming COVID-19 cases, the implementation of social distancing and hygiene, international air traffic flows, the climate, the relatively young and rural population, the genetic polymorphism of the angiotensin-converting enzyme 2 receptor, cross-immunity and the use of antimalarial drugs.

Peptoniphilus lacydonensis sp. nov., a new human-associated species isolated from a patient with chronic refractory sinusitis.

Strain EL1T was isolated from a sinus sample of an 85-year-old man with chronic refractory sinusitis complicating ethmoidal adenocarcinoma. We studied its phenotypic and genomic characteristics. This is a Gram stain-positive, anaerobic and microaerophilic coccus. Cells are catalase negative, nonmotile and non-spore forming. The major fatty acids are saturated hexadecanoic acid (34%), unsaturated 9-octadecenoic acid (32%) and 9.12-octadecadienoic acid (21%). The 1.86 Mb long genome exhibits a 29.9% G+C content and contains 1750 protein-coding and 43 RNA genes. On the basis of these data, we propose the creation of the new human-associated bacterial species Peptoniphilus lacydonensis sp. nov.

"Lascolabacillus massiliensis": a new species isolated from the human gut.

We report here the main characteristics of "Lascolabacillus massiliensis" strain SIT8 (CSUR P1560) that was isolated from the stool of a healthy 28-month-old boy.

Characterization of NDM-1- and OXA-23-producing Acinetobacter baumannii isolates from inanimate surfaces in a hospital environment in Algeria.

BACKGROUND: Investigation of several outbreaks of multidrug-resistant Acinetobacter baumannii infection has demonstrated that contamination of the inanimate hospital environment could be implicated in the spread of these multidrug-resistant strains. AIM: To investigate the occurrence of carbapenem-resistant A. baumannii on inanimate surfaces and possible dissemination in the hospital environment in Algeria as a potential source of infection in humans. METHODS: A. baumannii strains were isolated from the hospital environment and identified by matrix-assisted laser desorption ionization time-of-flight mass spectrometry (MALDI-TOF MS). Antimicrobial susceptibility was determined using disc diffusion and E-test methods. Carbapenemase activity was detected using microbiological tests, including modified Hodge test, modified Carba NP test, and EDTA test. Carbapenem resistance determinants were studied by polymerase chain reaction (PCR) and sequencing. Clonal relatedness was determined using multi-locus sequence typing (MLST). RESULTS: A total of 67 A. baumannii isolates were obtained from 868 environmental samples and identified by MALDI-TOF MS. Among them, 61 isolates were resistant to imipenem with minimum inhibitory concentration >32 µg/mL and positive by the modified Hodge test and modified Carba NP test. In addition, the activity of carbapenemase was inhibited by EDTA in 32 strains. PCR and sequencing showed the presence of blaOXA-23 gene in 29 strains, and the blaNDM-1 gene in 32 isolates. MLST demonstrated the presence of five types of ST (ST19, ST2, ST85, ST98, and ST115). CONCLUSION: Our study demonstrated the dissemination of carbapenemase-producing A. baumannii strains recovered from inanimate surfaces in a hospital environment, surrounding patients, healthcare workers and visitors, in Algeria as a potential source for nosocomial infection.

Non-contiguous finished genome sequence and description of Streptococcus varani sp. nov.

Strain FF10(T) (= CSUR P1489 = DSM 100884) was isolated from the oral cavity of a lizard (Varanus niloticus) in Dakar, Senegal. Here we used a polyphasic study including phenotypic and genomic analyses to describe the strain FF10(T). Results support strain FF10(T) being a Gram-positive coccus, facultative anaerobic bacterium, catalase-negative, non-motile and non-spore forming. The sequenced genome counts 2.46 Mb with one chromosome but no plasmid. It exhibits a G+C content of 40.4% and contains 2471 protein-coding and 45 RNA genes. On the basis of these data, we propose the creation of Streptococcus varani sp. nov.

Emergence of KPC-producing Klebsiella pneumoniae ST512 isolated from cerebrospinal fluid of a child in Algeria.

We report class A carbapenemase (KPC)-3-producing Klebsiella pneumoniae meningitis in a 6-month-old child in Algeria. Multilocus sequence typing showed that the sequence type obtained corresponded to ST512, an allelic single-locus variant of the pandemic ST258 widely distributed in KPC producers from Europe. To our knowledge, this is the first report of KPC-3-producing K. pneumoniae ST512 in a North African country.

Rapid identification of carbapenemase-producing Enterobacteriaceae, Pseudomonas aeruginosa and Acinetobacter baumannii using a modified Carba NP test.

Biochemical tests have been previously developed to identify carbapenemase-producing Enterobacteriaceae, Pseudomonas spp. (Carba NP test) and Acinetobacter spp. (CarbAcineto NP test). We evaluated a modified Carba NP test to detect carbapenemase production in Enterobacteriaceae, Pseudomonas and Acinetobacter species using a single protocol with rapid results and found good reliability and speed.

Risk factors associated with endometrial polyps in abnormal uterine bleeding.

OBJECTIVES: To evaluate the significance of various risk factors associated with endometrial polyps in women with abnormal uterine bleeding. METHODS: A prospective cohort study of 248 consecutive patients evaluated for abnormal uterine bleeding in a Rapid Access Ambulatory Diagnostic (RAAD) clinic was carried out from 1996 to 1997. Endometrial polyps were diagnosed using outpatient hysteroscopy and their histological nature was confirmed in all patients by performing inpatient polypectomy. Multivariate logistic regression modeling was used to evaluate the effects of age, parity, menopausal status, hormone replacement therapy and tamoxifen treatment on the occurrence of polyps. RESULTS: In an analysis adjusted for the effects of age, parity and menopausal status, tamoxifen treatment was associated with endometrial polyps (adjusted odds ratio 11.21, 95% confidence interval 2.70-46.46, P=0.0009) but hormone replacement therapy was not (adjusted odds ratio 1.48, 95% confidence interval 0.68-3.20, P=0.32). CONCLUSION: Our study confirmed that tamoxifen is associated with endometrial polyps. However, it rejects the hypothesis that hormone replacement therapy is a risk factor for endometrial polyps.

Outcome of ruptured uterus at University Teaching Hospital Aleppo, Syria.

A 10-year review of ruptured gravid uterus at the University Teaching Hospital, Aleppo, Syria showed an incidence of one ruptured uterus in 565 deliveries. This is an average figure compared with published studies but is still high compared with developed countries. Sixty-four per cent of the cases of ruptured uterus had no antenatal care. It is no surprise therefore that maternal and fetal mortality was highest amongst the unbooked labouring women. In survivors the morbidity was also higher. Ruptured uterus is therefore a major cause of maternal and perinatal mortality and morbidity in Syria. The overall hospital maternal and perinatal mortalities for the period under review were 4.3% and 2.6% respectively. The main risk factor identified is scarring from previous caesarean sections. Other risk factors are discussed.

The risk of premalignant and malignant pathology in endometrial polyps.

OBJECTIVE: To evaluate the risk of premalignant and malignant pathology among endometrial polyps. DESIGN: Prospective cohort study. SETTING: Minimal Access Surgical Training (MAST) center in a large teaching hospital. METHODS: Among 248 patients seen in outpatient hysteroscopy clinic (1996-97), 62 had endometrial polyps. All patients had endometrial sampling for histological assessment. To determine the magnitude of malignant potential among polyps, we compared the pathological findings in polyps (cases) with non-polypoidal specimens (controls). RESULTS: Out of 62 polyps, histologically 53 (85.5%) were benign, seven (11.3%) had hyperplasia, and two (3.2%) were associated with malignancy. Hyperplasia was more frequent in endometrial specimens with polyps than in those without (11.3% vs 4.3%, p=0.04), but the incidence of carcinoma in the two groups was the same (3.2% vs 3.2%, p= 1.0). CONCLUSION: In abnormal uterine bleeding, hyperplasia was, but cancer was not, more common in women with endometrial polyps compared to those without polyps.

Controlled analysis of factors associated with insufficient sample on outpatient endometrial biopsy.

We examined the relative significance of hysteroscopic and ultrasonographic evidence of endometrial atrophy in relation to insufficient sample on outpatient endometrial biopsy in women with abnormal uterine bleeding. Multivariate logistic regression modelling was used to evaluate the independent effects of age, menopausal status, hysteroscopic findings and sonographic endometrial thickness on outpatient endometrial sampling (sufficient or insufficient) used as the binary dependent variable. Insufficient sample on endometrial biopsy was associated with hysteroscopic finding of endometrial atrophy (OR 4.79, 95% CI 1.05-21.91, P = 0.04) and sonographic endometrial thickness below 5 mm (OR 0- 19. 95% CI 0.07-0.53, P = 0.001). There was no association with patient's age and menopausal status. In conclusion, when reassuring women with insufficient sample on outpatient endometrial biopsy, one can be confident about absence of pathology provided the hysteroscopic and sonographic endometrial assessment is consistent with endometrial atrophy.

The diagnostic accuracy of ultrasound scan in predicting endometrial hyperplasia and cancer in postmenopausal bleeding.

OBJECTIVE: To determine the accuracy of ultrasound scan in the diagnosis of endometrial hyperplasia and cancer in postmenopausal bleeding. DESIGN: A prospective diagnostic accuracy study (1996-97). SETTING: Minimal access surgical training centers in two large teaching hospitals. METHODS: Ultrasound scan and outpatient endometrial sampling were performed on 96 patients with postmenopausal bleeding. Patients unable to have these outpatient procedures had a formal inpatient hysteroscopy and curettage. Test performance characteristics were computed for ultrasound scan comparing its estimate of endometrial thickness with histologic diagnosis that served as a 'gold' standard. OUTCOME MEASURES: Accuracy of the ultrasonic endometrial thickness was estimated using sensitivity, specificity and predictive values for binary data. For multilevel data, the diagnostic accuracy was computed using likelihood ratios (LRs). An LR < decreased the probability that endometrial hyperplasia/cancer was present, whereas an LR > 1 increased the probability that such lesion was present. RESULTS: Using endometrial thickness > or =4 mm, the sensitivity of ultrasound to detect the endometrial malignancy was 92.9%, the specificity was 500%, and the positive and negative predictive values were 24.1% and 97.6% respectively. Analysis using likelihood ratio (LR) revealed that LR was 0.14 for endometrial thickness > or =4.0 mm, 0.94 for endometrial thickness 4.1-9.0 mm, and 3.3 for endometrial thickness >9.0 mm. CONCLUSION: In women with postmenopausal bleeding, malignancy can probably be safely excluded if sonographic endometrial thickness is < or = 4.0 mm. However, the probability of endometrial hyperplasia/cancer is not particularly altered by the knowledge that endometrial thickness on scan is >4.0 mm.