Vaginal colonization with virulent and methicillin resistant Staphylococcus aureus among Ugandan women in Labour.

BACKGROUND: Staphylococcus aureus (S. aureus) often colonizes the human skin, upper respiratory and genital tracts. In the female genital tract, it can be passed on to the newborn during vaginal delivery leading to either ordinary colonization, or neonatal infections notably umbilical stump sepsis, scalded skin syndrome, arthritis, or bacteraemia/sepsis. These infections are mediated by staphylococcal virulence factors such as (i) Staphylococcal Enterotoxins A, B, C, D, and E encoded by the sea, seb, sec, sed, see genes, (ii) Exfoliative Toxins A and B encoded by the eta and etb genes, (iii) Toxic Shock Syndrome Toxin 1 (TSST-1) encoded by the tst gene, (iv) Panton-Valentine Leukocidin (PVL) encoded by the pvl gene, and (v) Hemolysins alpha and delta encoded by the hla and hld genes, respectively. We determined the prevalence of S. aureus possessing one or more virulence factor genes and of methicillin resistant Staphylococcus aureus (MRSA) in this population. METHODS: This was a cross-sectional study, which used 85 S. aureus isolates from the Chlorohexidine (CHX) clinical trial study in Uganda. The isolates had been obtained by culturing vaginal swabs (VS) from 1472 women in labour, frozen at minus 80oC, then thawed, sub-cultured, and tested for the selected virulence genes sea, seb, sec, sed, see eta, etb, tst, pvl, hla and hld, and for the methicillin resistance determining gene (mecA). Data were analyzed using SPSS version 20. RESULTS: Of the 85 S. aureus isolates 13 (15.3%) were positive for one or more virulence factor genes, as follows: pvl 9/85 (10.6%), hld 5/85 (5.9%), sea 1/85 (1.2%) and seb genes 1/85 (1.2%). The other virulence genes (sec, sed, see, eta, etb, hla and tst) were not detected in any of the isolates. MRSA was detected in 55.3% (47/85) of the isolates, but only two of these carried the pvl virulence gene. CONCLUSION: This study demonstrated that 15% of the S. aureus colonizing the female lower genital tract of mothers in labour in central Uganda carried one or more virulence genes, mostly pvl, indicating potential for newborn infection with S. aureus acquired in the maternal birth canal. More than half of the isolates were MRSA.

Reduced CCR5 expression among Uganda HIV controllers.

BACKGROUND: Several mechanisms including reduced CCR5 expression, protective HLA, viral restriction factors, broadly neutralizing antibodies, and more efficient T-cell responses, have been reported to account for HIV control among HIV controllers. However, no one mechanism universally accounts for HIV control among all controllers. In this study we determined whether reduced CCR5 expression accounts for HIV control among Ugandan HIV controllers. We determined CCR5 expression among Ugandan HIV controllers compared with treated HIV non-controllers through ex-vivo characterization of CD4 + T cells isolated from archived PBMCs collected from the two distinct groups. RESULTS: The percentage of CCR5 + CD4 + T cells was similar between HIV controllers and treated HIV non-controllers (ECs vs. NCs, P = 0.6010; VCs vs. NCs, P = 0.0702) but T cells from controllers had significantly reduced CCR5 expression on their cell surface (ECs vs. NCs, P = 0.0210; VCs vs. NCs, P = 0.0312). Furthermore, we identified rs1799987 SNP among a subset of HIV controllers, a mutation previously reported to reduce CCR5 expression. In stark contrast, we identified the rs41469351 SNP to be common among HIV non-controllers. This SNP has previously been shown to be associated with increased perinatal HIV transmission, vaginal shedding of HIV-infected cells and increased risk of death. CONCLUSION: CCR5 has a non-redundant role in HIV control among Ugandan HIV controllers. HIV controllers maintain high CD4 + T cells despite being ART naïve partly because their CD4 + T cells have significantly reduced CCR5 densities.

Antibiotic resistance profiles and population structure of disease-associated Staphylococcus aureus infecting patients in Fort Portal Regional Referral Hospital, Western Uganda.

Tackling antimicrobial resistance (AMR) is particularly challenging in low-resource settings such as Fort Portal Regional Referral Hospital (FPRRH) in Western Uganda. Specific knowledge of local AMR epidemiology is required to inform evidence-based improvement of antibiotic stewardship measures in the hospital. To address this, we combined existing antimicrobial susceptibility testing (AST) from FPRRH, with whole genome sequencing (WGS) of 41 Staphylococcus aureus isolates (2017-2019). AST revealed 73 % (30 of 41) of isolates were resistant to one or more antibiotics and 29 % (12 of 41) were multi-drug resistant (MDR). Resistance phenotypes were largely explained by the presence of antibiotic resistance genes in WGS data. Five isolates were methicillin-resistant S. aureus (MRSA) and MDR. Although all isolates were susceptible to clindamycin, a 24 % carriage of erm genes suggests potential for rapid development of resistance. We inferred a population structure for the S. aureus isolates by comparing their core genomes. Twenty isolates formed a tight cluster corresponding to multilocus sequence typing clonal complex (CC) 152, a CC found to be particularly prevalent in northern Africa. The frequency of genes associated with methicillin, chloramphenicol and ciprofloxacin resistance were significantly lower among CC152 strains than non-CC152 strains; thus, in keeping with previous work, we find that CC152 is almost exclusively methicillin-sensitive S. aureus (MSSA). Also, in agreement with other studies, we observed that the occurrence of Panton-Valentine leukocidin toxin-encoding genes was significantly higher among CC152 strains than non-CC152 strains. However, we also observed that the coagulase gene was over-represented in this CC, further defining the virulence strategy of this important pathogen. By generating detailed information about the epidemiology of circulating S. aureus and their antibiotic susceptibility, our study has provided, for the first time, data on which evidence-based infection and AMR interventions at FPRRH can be based.

Pancreatic acinar cell carcinoma: A multi-center series on clinical characteristics and treatment outcomes.

BACKGROUND: Acinar cell carcinoma (ACC) is a very rare tumor of the exocrine pancreas, representing less than 1% of all pancreatic malignancies. The majority of data regarding ACC are limited to small case series. METHODS: This is a retrospective study conducted at a large healthcare system from 1996 to 2019. Patients with pathologically confirmed ACC were included, and demographic data, tumor characteristics, and treatment outcomes were abstracted by chart review. Survival curves were obtained by using the Kaplan-Meier method and compared using the log-rank test. RESULTS: Sixty-six patients with ACC were identified. The median patient age at diagnosis was 64, and 42% presented with metastatic disease. The majority presented with abdominal pain or pancreatitis (69%), and laboratory parameters did not correlate with tumor size, metastatic disease, or survival. Several somatic abnormalities were noted in tumors (BRCA2, TP53, and mismatch-repair genes). In patients with localized disease that underwent resection, the median time to develop metastatic lesions was 13 months. The median overall survival (OS) was 24.7 months from diagnosis, with a survival difference based on metastatic disease at diagnosis (median 15 vs 38 mos). Surgery was associated with improved survival in non-metastatic cases (p = 0.006) but not metastatic cases (p = 0.22), and chemotherapy showed OS benefit in metastatic disease (p < 0.01). Patients with metastatic ACC treated after 2010 utilized more platinum-based agents, and there was a OS benefit to FOLFOX or FOLFIRINOX chemotherapy compared to gemcitabine or capecitabine-based regimens (p = 0.006). CONCLUSION: Pancreatic ACC patients often present with advanced disease. Surgery was associated with survival benefit among patients presenting with localized disease. The use of FOLFOX or FOLFIRINOX chemotherapy regimens was associated with improved OS in metastatic patients. These data add to our knowledge in this rare malignancy, and improves understanding about the genomic underpinnings, prognosis and treatment for acinar cancers.

Rates of HIV-1 virological suppression and patterns of acquired drug resistance among fisherfolk on first-line antiretroviral therapy in Uganda.

OBJECTIVES: We examined virological outcomes, patterns of acquired HIV drug resistance (ADR), correlates of virological failure (VF) and acquired drug resistance among fisherfolk on first-line ART. METHODS: We enrolled 1169 adults on ART for a median duration of 6, 12, 24, 36 and ≥48 months and used a pooled VL testing approach to identify VF (VL ≥1000 copies/mL). We performed genotyping among VF cases and determined correlates of VF and ADR by logistic regression. RESULTS: The overall virological suppression rate was 91.7% and ADR was detected in 71/97 (73.2%) VF cases. The most prevalent mutations were M184V/I (53.6%) for NRTIs and K103N (39.2%) for NNRTIs. Thymidine analogue mutations were detected in 21.6% of VF cases while PI mutations were absent. A zidovudine-based ART regimen, duration on ART (≥24 months) and secondary/higher education level were significantly associated with VF. A nevirapine-based regimen [adjusted OR (aOR): 1.87; 95% CI: 0.03-0.54)] and VL ≥10000 copies/mL (aOR: 3.48; 95% CI: 1.37-8.85) were ADR correlates. The pooling strategies for VL testing with a negative predictive value (NPV) of ≥95.2% saved US $20320 (43.5%) in VL testing costs. CONCLUSIONS: We observed high virological suppression rates among these highly mobile fisherfolk; however, there was widespread ADR among those with VF at the first VL testing prior to intensive adherence counselling. Timely treatment switching and adherence support is recommended for better treatment outcomes. Adoption of pooled VL testing could be cost effective, particularly in resource-limited settings.

Nasopharyngeal carriage, spa types and antibiotic susceptibility profiles of Staphylococcus aureus from healthy children less than 5 years in Eastern Uganda.

BACKGROUND: Staphylococcus aureus carriage is a known risk factor for staphylococcal disease. However, the carriage rates vary by country, demographic group and profession. This study aimed to determine the S. aureus carriage rate in children in Eastern Uganda, and identify S. aureus lineages that cause infection in Uganda. METHODS: Nasopharyngeal samples from 742 healthy children less than 5 years residing in the Iganga/Mayuge Health and Demographic Surveillance Site in Eastern Uganda were processed for isolation of S. aureus. Antibiotic susceptibility testing based on minimum inhibitory concentrations (MICs) was determined by the BD Phoenix™ system. Genotyping was performed by spa and SCCmec typing. RESULTS: The processed samples yielded 144 S. aureus isolates (one per child) therefore, the S. aureus carriage rate in children was 19.4% (144/742). Thirty one percent (45/144) of the isolates were methicillin resistant (MRSA) yielding a carriage rate of 6.1% (45/742). All isolates were susceptible to rifampicin, vancomycin and linezolid. Moreover, all MRSA were susceptible to vancomycin, linezolid and clindamycin. Compared to methicillin susceptible S. aureus (MSSA) isolates (68.8%, 99/144), MRSA isolates were more resistant to non-beta-lactam antimicrobials -trimethoprim/sulfamethoxazole 73.3% (33/45) vs. 27.3% (27/99) [p < 0.0001]; erythromycin 75.6% (34/45) vs. 24.2% (24/99) [p < 0.0001]; chloramphenicol 60% (27/45) vs. 19.2% (19/99) [p < 0.0001]; gentamicin 55.6% (25/45) vs. 25.3% (25/99) [p = 0.0004]; and ciprofloxacin 35.6% (16/45) vs. 2% (2/99) [p < 0.0001]. Furthermore, 42 MRSA (93.3%) were multidrug resistant (MDR) and one exhibited high-level resistance to mupirocin. Overall, 61 MSSA (61.6%) were MDR, including three mupirocin and clindamycin resistant isolates. Seven spa types were detected among MRSA, of which t037 and t064 were predominant and associated with SCCmec types I and IV, respectively. Fourteen spa types were detected in MSSA which consisted mainly of t645 and t4353. CONCLUSIONS: S. aureus carriage rate in healthy children in Eastern Uganda is high and comparable to rates for hospitalized patients in Kampala. The detection of mupirocin resistance is worrying as it could rapidly increase if mupirocin is administered in a low-income setting. S. aureus strains of spa types t064, t037 (MRSA) and t645, t4353 (MSSA) are prevalent and could be responsible for majority of staphylococcal infections in Uganda.

Frequency and patterns of second-line resistance conferring mutations among MDR-TB isolates resistant to a second-line drug from eSwatini, Somalia and Uganda (2014-2016).

BACKGROUND: Pulmonary tuberculosis is a leading cause of morbidity and mortality in developing countries. Drug resistance, a huge problem in this contagious disease, is driven by point mutations in the Mycobacterium tuberculosis genome however, their frequencies vary geographically and this affects applicability of molecular diagnostics for rapid detection of resistance. Here, we report the frequency and patterns of mutations associated with resistance to second-line anti-TB drugs in multidrug-resistant (MDR) M. tuberculosis isolates from eSwatini, Somalia and Uganda that were resistant to a second-line anti-TB drug. METHODS: The quinolone resistance determining region (QRDR) of gyrA/gyrB genes and the drug resistance associated fragment of rrs gene from 80 isolates were sequenced and investigated for presence of drug resistance mutations. Of the 80 isolates, 40 were MDR, of which 28 (70%) were resistant to a second-line anti-TB injectable drug, 18 (45%) were levofloxacin resistant while 12 (30%) were extensively drug resistant (XDR). The remaining 40 isolates were susceptible to anti-TB drugs. MIRU-VNTR analysis was performed for M/XDR isolates. RESULTS: We successfully sub-cultured 38 of the 40 M/XDR isolates. The gyrA resistance mutations (Gly88Ala/Cys/Ala, Ala90Val, Ser91Pro, Asp94Gly/Asn) and gyrB resistance mutations (Asp500His, Asn538Asp) were detected in 72.2% (13/18) and 22.2% (4/18) of the MDR and levofloxacin resistant isolates, respectively. Overall, drug resistance mutations in gyrA/gyrB QRDRs occurred in 77.8% (14/18) of the MDR and levofloxacin resistant isolates. Furthermore, drug resistance mutations a1401g and g1484 t in rrs occurred in 64.3% (18/28) of the MDR isolates resistant to a second-line anti-TB injectable drug. Drug resistance mutations were not detected in drug susceptible isolates. CONCLUSIONS: The frequency of resistance mutations to second-line anti-TB drugs in MDR-TB isolates resistant to second line anti-TB drugs from eSwatini, Somalia and Uganda is high, implying that rapid molecular tests are useful in detecting second-line anti-TB drug resistance in those countries. Relatedly, the frequency of fluoroquinolone resistance mutations in gyrB/QRDR is high relative to global estimates, and they occurred independently of gyrA/QRDR mutations implying that their absence in panels of molecular tests for detecting fluoroquinolone resistance may yield false negative results in our setting.

Application of antibodies to recombinant heat shock protein 70 in immunohistochemical diagnosis of mycobacterium avium subspecies paratuberculosis in tissues of naturally infected cattle.

BACKGROUND: Detection of Mycobacterium avium subspecies paratuberculosis (MAP) infection is key to the control of Johne's disease. Immunohistochemistry is one of the methods of detection of MAP infection in tissues. However, unavailability of commercial antibodies that can detect the organism is a limiting factor for the use of immunohistochemistry. This study was aimed at developing an immunohistochemistry method to diagnose MAP in infected tissues using antibodies against MAP recombinant heat shock protein 70kd. RESULTS: MAP Heat shock protein 70 gene was amplified and cloned into an expression vector, Champion pET-SUMO, then expressed in E coli, purified and used to produce polyclonal rabbit antibodies against the Heat shock protein. Immunohistochemistry was performed in 35 MAP infected tissues with anti-HSP70 polyclonal antibodies. All 35 MAP infected tissues were positive for MAP within macrophages, epithelioid cells and giant cells either in clumps or singly as individual bacilli. No positive staining was seen in the three uninfected normal tissues and in MAP infected tissues where primary antibodies were substituted with PBS or pre-immune serum from the same rabbit. CONCLUSION: Anti-HSP70 produced in this study offers an opportunity for improved diagnosis, screening of MAP in animal tissues and in studies on the pathogenesis of MAP.

On the systematics of Trimeresurus labialis Fitzinger in Steindachner, 1867, a pitviper from the Nicobar Islands (India), with revalidation of Trimeresurus mutabilis Stoliczka, 1870 (Squamata, Viperidae, Crotalinae).

The Asian pitviper currently identified as Trimeresurus labialis Fitzinger in Steindachner, 1867 is revised on the basis of morphological data obtained from 37 preserved specimens originating from seven islands of the Nicobar Islands. Multivariate analyses shows that these specimens can be divided into two clusters of populations which differ by a series of constant taxonomically informative morphological characters. The first cluster, which includes the name-bearing types of Trimeresurus labialis Fitzinger in Steindachner, 1867, is present only on Car Nicobar Island. The second cluster, which includes the name-bearing types of Trimeresurus mutabilis Stoliczka, 1870, is distributed on the Central Nicobar Islands. We regard these clusters as distinct species, which are morphologically diagnosable and isolated from each other. As a consequence, Trimeresurus mutabilis, long considered a synonym of T. labialis, is here resurrected to specific level. A lectotype is designated for Trimeresurus mutabilis.

A new species of the genus Opisthotropis Günther, 1872 from northern Laos (Squamata: Natricidae).

Two specimens, a male and a female, of the genus Opisthotropis Günther, 1872 were collected in a karst formation of northern Louangphabang (or Luang Prabang) Province, North Laos. These specimens are assigned to the genus Opisthotropis on the basis of their morphology, dentition and cephalic scalation. However, they differ from all other known species of Opisthotropis by a combination of the following characters: (1) 21-19 scale rows on the fore part of the body, (2) 17 scale rows at midbody, (3) 22/23 maxillary teeth, (4) 177-181 ventrals, (5) 1 loreal on each side, in contact with internasal, (6) 7 supralabials, 4th entering orbit, (7) dorsum dark bronze-brown, with upper part of dorsum darker than lateral sides, without bands or crossbars, and (8) chin and throat blackish-brown with a sharp, transversal limit with the ventral colour crossing the posterior part of the throat. As a consequence, these specimens are here referred to a new species, Opisthotropis durandi spec. nov. The new species is compared with other species of the genus, especially the most similar species O. spenceri Smith, 1918 and O. atra Günther, 1872, the type species of the genus. An updated key to the genera Opisthotropis is provided. Opisthotropis durandi spec. nov. represents the first confirmed record of a species of Opisthotropis sensu stricto from Laos and it is the 108th snake species currently recorded from the Lao People's Democratic Republic.

On the status of Helicops wettsteini Amaral, 1929, a senior synonym of Hypsiscopus murphyi (SERPENTES: Homalopsidae).

We redescribe the name-bearing types of Helicops wettsteini Amaral, 1929, a species described from central Costa Rica. However, while Helicops wettsteini has been considered in the literature a synonym of Hypsiscopus plumbeus (previously Enhydris plumbea), we present here morphological evidence for considering Helicops wettsteini a synonym of the recently described species Hypsiscopus murphyi Bernstein, Voris, Stuart, Phimmachak, Seateun, Sivongxay, Neang, Karns, Andrews, Osterhage, Phipps & Ruane, 2022, which hence becomes a junior subjective synonym of Hypsiscopus wettsteini (Amaral, 1929).

Polymorphisms in Immune Genes and Their Association with Tuberculosis Susceptibility: An Analysis of the African Population.

Tuberculosis remains a global health concern, with substantial mortality rates worldwide. Genetic factors play a significant role in influencing susceptibility to tuberculosis. This review examines the current progress in studying polymorphisms within immune genes associated with tuberculosis susceptibility, focusing on African populations. The roles of various proteins, including Toll-like receptors, Dendritic Cell-Specific Intercellular Adhesion Molecule-3 Grabbing Non-Integrin, vitamin D nuclear receptor, soluble C-type lectins such as surfactant proteins A and D, C-type Lectin Domain Family 4 Member E, and mannose-binding lectin, phagocyte cytokines such as Interleukin-1, Interleukin-6, Interleukin-10, Interleukin-12, and Interleukin-18, and chemokines such as Interleukin-8, monocyte chemoattractant protein 1, Regulated upon activation, normal T-cell expressed and secreted are explored in the context of tuberculosis susceptibility. We also address the potential impact of genetic variants on protein functions, as well as how these findings align with the genetic polymorphisms not associated with tuberculosis. Functional studies in model systems provide insights into the intricate host-pathogen interactions and susceptibility mechanisms. Despite progress, gaps in knowledge remain, highlighting the need for further investigations. This review emphasizes the association of Single Nucleotide Polymorphisms with diverse aspects of tuberculosis pathogenesis, including disease detection and Mycobacterium tuberculosis infection.

Distribution and antifungal susceptibility profile of oropharyngeal Candida species isolated from people living with HIV in the era of universal test and treat policy in Uganda.

Background: Despite the increased frequency of oropharyngeal candidiasis among people living with human immunodeficiency virus (HIV), its management is no longer effective due to empirical treatment and emergence of antifungal resistance (AFR). This study sought to investigate the prevalence of oropharyngeal candidiasis and assess the antifungal susceptibility profile of oropharyngeal Candida species isolated from people living with human immunodeficiency virus. Additionally, we evaluated the correlation between oropharyngeal candidiasis and CD4 T cell as well as viral load counts. Methods: A descriptive cross-sectional study was carried out from April to October 2023 in which 384 people living with HIV underwent clinical examination for oral lesions. Oropharyngeal swabs were collected and cultured on Sabouraud Dextrose agar to isolate Candida species which were identified using the matrix assisted laser desorption ionization time of flight mass spectrometry. Additionally, the antifungal susceptibility profile of Candida isolates to six antifungal drugs was determined using VITEK® (Marcy-l'Étoile, France) compact system. Data on viral load were retrieved from records, and CD4 T cell count test was performed using Becton Dickinson Biosciences fluorescent antibody cell sorter presto. Results: The prevalence of oropharyngeal candidiasis was 7.6%. Oropharyngeal candidiasis was significantly associated with low CD4 T cell count and high viral load. A total of 35 isolates were obtained out of which Candida albicans comprised of 20 (57.1%) while C. tropicalis and C. glabrata comprised 4 (11.4%) each. C. parapsilosis, C. dubliniensis and C. krusei accounted for 2 (5.7%) each. Additionally, 7 (20%) isolates were resistant to fluconazole, 1 (2.9%) to flucytocine and 0.2 (5.7%) isolates were intermediate to caspofungin. However, specific specie isolates like C. albicans showed 20% (4/20), C. glabrata 50% (2/4) and C. krusei 50% (1/2) resistance to fluconazole. Additionally, C. krusei showed 50% resistance to flucytosine. Conclusion: The prevalence of oropharyngeal candidiasis (OPC) among people living with HIV was low, and there was a significant association between OPC and CD4 T cell count as well as viral load. C. albicans was the most frequently isolated oropharyngeal Candida species. C. glabrata and C. krusei exhibited the highest AFR among the non-albicans Candida species. The highest resistance was demonstrated to fluconazole.

Metagenomic sequencing of the skin microbiota of the scalp predicting the risk of surgical site infections following surgery of traumatic brain injury in sub-Saharan Africa.

BACKGROUND: Surgical site infections (SSI) are a significant concern following traumatic brain injury (TBI) surgery and often stem from the skin's microbiota near the surgical site, allowing bacteria to penetrate deeper layers and potentially causing severe infections in the cranial cavity. This study investigated the relationship between scalp skin microbiota composition and the risk of SSI after TBI surgery in sub-Saharan Africa (SSA). METHODS: This was a prospective cohort study, enrolling patients scheduled for TBI surgery. Sterile skin swabs were taken from the surrounding normal skin of the head and stored for analysis at -80°Celcius. Patients were monitored postoperatively for up to three months to detect any occurrences of SSI. 16S rRNA sequencing was used to analyze the skin microbiota composition, identifying different taxonomic microorganisms at the genus level. The analysis compared two groups: those who developed SSI and those who did not. RESULTS: A total of 57 patients were included, mostly male (89.5%) with a mean age of 26.5 years, predominantly from urban areas in Uganda and victims of assault. Graphical visualization and metagenomic metrics analysis revealed differences in composition, richness, and evenness of skin microbiota within samples (α) or within the community (ß), and showed specific taxa (phylum and genera) associated with either the group of SSI or the No SSI. CONCLUSIONS: Metagenomic sequencing analysis uncovered several baseline findings and trends regarding the skin microbiome's relationship with SSI risk. There is an association between scalp microbiota composition (abundancy and diversity) and SSI occurrence following TBI surgery in SSA. We hypothesize under reserve that the scalp microbiota dysbiosis could potentially be an independent predictor of the occurrence of SSI; we advocate for further studies with larger cohorts.

Airway microbiome signature accurately discriminates Mycobacterium tuberculosis infection status.

Mycobacterium tuberculosis remains one of the deadliest infectious agents globally. Amidst efforts to control TB, long treatment duration, drug toxicity, and resistance underscore the need for novel therapeutic strategies. Despite advances in understanding the interplay between microbiome and disease in humans, the specific role of the microbiome in predicting disease susceptibility and discriminating infection status in tuberculosis still needs to be fully investigated. We investigated the impact of M.tb infection and M.tb-specific IFNγ immune responses on airway microbiome diversity by performing TB GeneXpert and QuantiFERON-GOLD assays during the follow-up phase of a longitudinal HIV-Lung Microbiome cohort of individuals recruited from two large independent cohorts in rural Uganda. M.tb rather than IFNγ immune response mainly drove a significant reduction in airway microbiome diversity. A microbiome signature comprising Streptococcus, Neisseria, Fusobacterium, Prevotella, Schaalia, Actinomyces, Cutibacterium, Brevibacillus, Microbacterium, and Beijerinckiacea accurately discriminated active TB from Latent TB and M.tb-uninfected individuals.

Practical depolarization-ratio-based inversion procedure: lidar measurements of the Eyjafjallajökull ash cloud over the Netherlands.

In this paper we present a technique for estimating optical backscatter and extinction profiles using lidar, which exploits the difference between the observed linear volume depolarization ratio at 355 nm and the corresponding expected aerosol-only depolarization ratio. The technique is specific to situations where a single strongly depolarizing species is present and the associated linear particulate depolarization ratio may be presumed to be known to within a reasonable degree of accuracy (on the order of 10%). The basic principle of the technique is extended to deal with situations where a depolarizing fraction is mixed with nondepolarizing aerosol. In general, since the relative depolarization interchannel calibration is much more stable than the absolute system calibration, the depolarization-based technique is easier to implement than conventional techniques that require a profile-by-profile calibration or, equivalently, an identification of aerosol-free altitude intervals. This in particular allows for unattended data analysis and makes the technique well-suited to be part of a broader (volcanic ash) surveillance system. The technique is demonstrated by applying it to the analysis of aerosol layers resulting from the 2010 eruptions of the Eyjafjallajökull volcano in Iceland. The measurements were made at the Cabauw remote-sensing site in the central Netherlands. By comparing the results of the depolarization-based inversion with a more conventional manual inversion procedure as well as Raman lidar results, it is demonstrated that the technique can be successfully applied to the particular case of 355 nm depolarization lidar volcanic ash soundings, including cases in which the ash is mixed with nondepolarizing aerosol.

On some taxonomically confused species of the genus Amphiesma Duméril, Bibron & Duméril, 1854 related to Amphiesma khasiense (Boulenger, 1890) (Squamata, Natricidae).

Three species of the genus Amphiesma Duméril, Bibron & Duméril, 1854 have long been confused in the literature, with each other and with other species of the genus. Amphiesma khasiense (Boulenger, 1890) has been considered to inhabit a large geographical region, extending from north-eastern India, east to Vietnam and southern Thailand. Amphiesma boulengeri (Gressitt, 1937) has been regarded as a species endemic to south-eastern China. Amphiesma inas (Laidlaw, 1901) has been recorded from West Malaysia, Thailand and Indonesia (Sumatra). A multivariate analysis of morphometric and meristic characters shows that these three species can be separated by combinations of characters in the scalation and pattern, the most obvious being the structure of the postocular streak. On the basis of our analysis and after comparison with name-bearing type specimens, Amphiesma khasiense is restricted to north-eastern India, Myanmar, western Yunnan Province of China, northern Laos and northern and western Thailand. Other populations from south-eastern China, Vietnam, other parts of Laos, Cambodia and central Thailand, which have been recorded in the literature as A. khasiense, A.johannis or Amphiesma modestum (Günther, 1875), should be referred to Amphiesma boulengeri. Amphiesma inas (Laidlaw, 1901) is a valid species endemic to mountain ranges of southern Peninsular Thailand and West Malaysia. The mention of Amphiesma inas in Sumatra is erroneous, being based on the second known specimen of Amphiesma kerinciense David & Das, 2003, which is here redescribed. A key to species of the Amphiesma khasiense group and other species sharing a greyish-brown background without conspicuous dark and pale stripes, is provided.

A new green pitviper of the Trimeresurus albolabris complex (Reptilia, Serpentes, Viperidae) from central and southern Myanmar.

In the frame of our investigations on the systematics of the complex of species of Trimeresurus albolabris, we came across specimens from Myanmar variously referred to as Trimeresurus albolabris Gray, 1842 or T. septentrionalis Kramer, 1977 in the literature. We describe a new species of green pitviper of the genus Trimeresurus Lacpde, 1804 from central and southern Myanmar based on molecular analyses drawn from previously published phylogenies and new morphological data. This new species, Trimeresurus uetzi sp. nov., is broadly similar to both Trimeresurus albolabris and T. septentrionalis, but it differs from these latter species by a series of morphological characters such as presence of white pre- and postocular streaks in male, iris copper in male or green gold in female, more ventral plates, and a much shorter hemipenis. We compare this new species with Trimeresurus albolabris as currently defined and other species of this complex. We also emphasize the need for additional integrated studies on Trimeresurus albolabris sensu lato populations distributed in southern Indochina and Sundaland.

Coluber korros Lesson, 1831 and Coluber korros Schlegel, 1837 (Reptilia: Squamata: Colubridae): there is a korros too many in the family.

The purpose of this paper is to solve an overlooked nomenclatural problem involving two taxa of Colubridae, both described as Coluber korros. The first one is Coluber korros Schlegel, 1837, now Ptyas korros, a well-known and widespread species in south-east Asia. Its senior homonym is Coluber korros Lesson, 1831, a long forgotten taxon. Furthermore, these taxa are undoubtedly non-conspecific. We tentatively identify the holotype of this latter taxon as a large specimen of Coelognathus radiatus (F. Boie, 1827) and we specify its type locality as "Region of Kolkata, West Bengal State, eastern India" (the same specification of type-locality can hence be applied to the elapid Naja kaouthia Lesson, 1831). Nevertheless, following the strict principle of priority, Coluber korros Lesson, 1831 has priority over Coluber korros Schlegel, 1837. Based on the Code, we use Article 23.9 on reversal of precedence in order to preserve the use of the well-known taxon Coluber korros Schlegel, 1837 (now Ptyas korros) against its senior primary homonym Coluber korros Lesson, 1831. Finally, we consider Coluber boncorage Lesson, 1831 to be a nomen dubium.

Air pollution and mobility patterns in two Ugandan cities during COVID-19 mobility restrictions suggest the validity of air quality data as a measure for human mobility.

We explored the viability of using air quality as an alternative to aggregated location data from mobile phones in the two most populated cities in Uganda. We accessed air quality and Google mobility data collected from 15th February 2020 to 10th June 2021 and augmented them with mobility restrictions implemented during the COVID-19 lockdown. We determined whether air quality data depicted similar patterns to mobility data before, during, and after the lockdown and determined associations between air quality and mobility by computing Pearson correlation coefficients ([Formula: see text]), conducting multivariable regression with associated confidence intervals (CIs), and visualized the relationships using scatter plots. Residential mobility increased with the stringency of restrictions while both non-residential mobility and air pollution decreased with the stringency of restrictions. In Kampala, PM2.5 was positively correlated with non-residential mobility and negatively correlated with residential mobility. Only correlations between PM2.5 and movement in work and residential places were statistically significant in Wakiso. After controlling for stringency in restrictions, air quality in Kampala was independently correlated with movement in retail and recreation (- 0.55; 95% CI = - 1.01- - 0.10), parks (0.29; 95% CI = 0.03-0.54), transit stations (0.29; 95% CI = 0.16-0.42), work (- 0.25; 95% CI = - 0.43- - 0.08), and residential places (- 1.02; 95% CI = - 1.4- - 0.64). For Wakiso, only the correlation between air quality and residential mobility was statistically significant (- 0.99; 95% CI = - 1.34- - 0.65). These findings suggest that air quality is linked to mobility and thus could be used by public health programs in monitoring movement patterns and the spread of infectious diseases without compromising on individuals' privacy.