This study assessed factors associated with HIV positivity among infants in Malawi and turnaround... more This study assessed factors associated with HIV positivity among infants in Malawi and turnaround times for infant HIV testing. Methods: HIV testing data for infants aged 0-18 months from 2012 to 2015 were extracted from the Malawi HIV laboratory information management system and analysed using logistic regression. Turnaround time was defined as time between collection of samples to results dispatch from the laboratory. Results: A total of 106 997 tests were included in the analyses. A subset of 76 006 observations with complete dates were included in the turnaround time analysis. Overall positivity was 4.2%. Factors associated with positivity were increasing age (infants aged 3-6 months: adjusted odds ratio [aOR] = 2.24; infants aged 6-9 months: aOR = 3.42; infants aged > 9 months: aOR = 4.24), female sex (aOR = 1.08) and whether the mother was alive and not on antiretroviral therapy at time of the infant's test (aOR = 1.57). Provision of HIV prophylaxis to the infant after birth (aOR = 0.38) was found to be protective against HIV positivity. The median turnaround time was 24 days (increased from 19 to 34 days between 2012 and 2015). Conclusion: Infant HIV positivity has decreased in Malawi, whereas turnaround time has increased. Factors associated with positivity include increasing age, female sex, and whether the mother was alive and not on antiretroviral therapy at the time of the infant's test.
Introduction The US President’s Emergency Plan for AIDS Relief (PEPFAR) was launched to increase ... more Introduction The US President’s Emergency Plan for AIDS Relief (PEPFAR) was launched to increase access to antiretroviral treatment (ART) among people living with HIV (PLHIV) and to prevent new HIV infections globally. As new infections have decreased in many PEPFAR-supported countries, PEPFAR is increasingly focusing on understanding and decreasing mortality among PLHIV, specifically by addressing advanced HIV disease (AHD) and its attendant opportunistic infections (OIs). Several developments in identifying AHD, in preventing, diagnosing, and treating selected OIs, and in PEPFAR’s support for mortality surveillance make this an opportune moment for PEPFAR to address HIV-related mortality. Discussion AHD upon diagnosis or re-engagement in HIV care is not uncommon, and it substantially increases risk of death from OIs. The World Health Organization provides evidence-based guidelines for a package of interventions for preventing, diagnosing, and treating common OIs, including tubercu...
Community-acquired pneumonia (CAP) is usually caused by a single microorganism. Streptococcus pne... more Community-acquired pneumonia (CAP) is usually caused by a single microorganism. Streptococcus pneumoniae is the most common organism associated with CAP. However, in immunocompromised patients, especially those infected with human immunodeficiency virus (HIV), pneumonia may be caused by multiple organisms simultaneously. This report describes a previously healthy 29-year-old man who presented with acute CAP. Blood tests showed that he was positive for HIV antigen/antibody, and urinalysis showed that he was initially positive for pneumococcal antigen. Although blood cultures showed growth of Streptococcus pneumoniae, he did not respond to invasive anti-pneumococcal treatment with ceftriaxone and vancomycin. Rather, his pneumonia worsened, and he was intubated for hypoxic respiratory failure. His bronchoalveolar lavage fluid was positive for Pneumocystis pneumonia and methicillin-resistant Staphylococcus aureus. These findings indicate that pneumonia in immunocompromised patients may be caused by multiple organisms. Patients who fail to respond to treatment for a single identified organism should be suspected of being infected with other pathogenic organisms.
Morbidity and mortality weekly report. Surveillance summaries (Washington, D.C. : 2002), Jan 21, 2018
Use of human immunodeficiency virus (HIV)-mortality surveillance data can help public health offi... more Use of human immunodeficiency virus (HIV)-mortality surveillance data can help public health officials monitor, evaluate, and improve HIV treatment programs. Many high-income countries have high-coverage civil registration and vital statistics (CRVS) systems linked to case-based HIV surveillance on which to base HIV mortality estimates. However, in the absence of comprehensive CRVS systems in low- and medium-income countries, such as Kenya, mortuary surveillance can be used to understand the occurrence of HIV infection among cadavers. In 2015, a pilot HIV-related mortuary surveillance system was implemented in the two largest mortuaries in Nairobi, Kenya. CDC conducted an evaluation to assess performance attributes and identify strengths and weaknesses of the surveillance system pilot. Data collection: January 29-March 3, 2015; evaluation: November 2015. The surveillance system objectives were to determine HIV positivity among cadavers at two mortuary sites in Nairobi, Kenya, and to...
MMWR. Morbidity and mortality weekly report, Jan 23, 2018
On March 16, 2018, this report was posted as an MMWR Early Release on the MMWR website (https://w... more On March 16, 2018, this report was posted as an MMWR Early Release on the MMWR website (https://www.cdc.gov/mmwr). Yellow fever virus is a mosquito-borne flavivirus that causes yellow fever, an acute infectious disease that occurs in South America and sub-Saharan Africa. Most patients with yellow fever are asymptomatic, but among the 15% who develop severe illness, the case fatality rate is 20%-60%. Effective live-attenuated virus vaccines are available that protect against yellow fever (1). An outbreak of yellow fever began in Brazil in December 2016; since July 2017, cases in both humans and nonhuman primates have been reported from the states of São Paulo, Minas Gerais, and Rio de Janeiro, including cases occurring near large urban centers in these states (2). On January 16, 2018, the World Health Organization updated yellow fever vaccination recommendations for Brazil to include all persons traveling to or living in Espírito Santo, São Paulo, and Rio de Janeiro states, and certain cities in Bahia state, in addition to areas where vaccination had been recommended before the recent outbreak (3). Since January 2018, 10 travel-related cases of yellow fever, including four deaths, have been reported in international travelers returning from Brazil. None of the 10 travelers had received yellow fever vaccination. Five of the 10 cases were reported by ProMED since January 15, including two from Argentina and three from Chile; two of the travelers from Chile died. In addition, during January 1-March 15, 2018, five confirmed cases of yellow fever in unvaccinated travelers returning from Brazil were reported by GeoSentinel (http://www.istm.org/geosentinel), the global clinician-based sentinel surveillance system for travel-related illness among international travelers and migrants (4). These five yellow fever cases represent the first such cases identified by GeoSentinel (Table), which was initiated in 1995 by the International Society of Travel Medicine with support from CDC and now consists of 70 specialized travel and tropical medicine clinical sites around the world. The first of the GeoSentinel-reported cases occurred in a Dutch man aged 46 years who traveled to São Paulo state for 3 weeks during December 2017-January 2018. The second case occurred in a French woman, aged 42 years, who traveled to Minas Gerais state in Brazil for 4 weeks during December 2017-January 2018. She received a diagnosis of yellow fever in Brazil and was examined at a GeoSentinel site after returning to France to convalesce. The third and Died Died Abbreviations: IgG = Immunoglobulin G; IgM = Immunoglobulin M; PCR = polymerase chain reaction; RT-PCR = reverse transcription-PCR; YF = yellow fever; YFV = YF virus. * In addition to the five patients reported by GeoSentinel sites, five additional cases of yellow fever have been reported by ProMED among persons who traveled to Brazil from Argentina (two) and Chile (three) since January 2018. Two of the patients from Chile died.
Objective To determine current seroepidemiology of CT infection in children in a US inner city po... more Objective To determine current seroepidemiology of CT infection in children in a US inner city population. Design/methods Anonymized serum samples were obtained from children in 2 hospitals in Brooklyn, NY from 2012-2015. CT IgG was determined using EIA (Ani Labsystems). The following age strata were used: 11-12, 13-14, 15-16, 17-18, 19-20 y. Results 512 sera were included in the final analysis. Mean age 17 y. There were 192 (37.5%) males and 320 (62.5%) females. CT antibody was first detected at 16 y and 18 y for females and males, respectively. The prevalence per age-cohort were:
We used transmission-dynamic modeling to estimate the added effectiveness of vaccinating multiple... more We used transmission-dynamic modeling to estimate the added effectiveness of vaccinating multiple cohorts of females (12-26 years) in Australia compared with the theoretical introduction of routine-only (12-13 years) vaccination. Our results suggest that vaccinating multiple cohorts produced markedly faster direct/herd effects, and it added benefits that last for 20-70 years. Furthermore, the number needed to vaccinate to prevent 1 anogential warts (AGW) case or cervical cancer (CC) was similar for routine + catch-up (AGW = 9.9, CC = 678) and routine-only vaccination (AGW = 9.9, CC = 677), thus providing similar levels of efficiency per person vaccinated.
The known The Australian HPV vaccination program has led to significant declines in a number of H... more The known The Australian HPV vaccination program has led to significant declines in a number of HPV-related conditions, including diagnoses of genital warts in young women and heterosexual men at sexual health clinics. Methods Routinely collected de-identified data were collated from
Background: Mycoplasma genitalium is a common cause of non-gonococcal non-chlamydial urethritis a... more Background: Mycoplasma genitalium is a common cause of non-gonococcal non-chlamydial urethritis and cervicitis. Testing of asymptomatic populations has been proposed, but prevalence rates in asymptomatic populations are not well established. We aimed to estimate the prevalence of M. genitalium in adults in the general population, in clinic-based samples, pregnant women, men who have sex with men (MSM) and female sex workers (FSW). Methods: We searched Embase, Medline, IndMED, AIM and LILACS from 1 January 1991 to 12 July 2016 without language restrictions. We included studies with 500 participants or more. We screened and selected studies and extracted data in duplicate. We examined eligible studies in forest plots and conducted random effects meta-analysis to estimate prevalence, if appropriate. Between study heterogeneity was examined using the I 2 statistic and meta-regression. Results: Of 3,316 screened records, 63 were included. In randomly selected samples from the general pop...
Background Efforts to reach UNAIDS' treatment and viral suppression targets have increased demand... more Background Efforts to reach UNAIDS' treatment and viral suppression targets have increased demand for viral load (VL) testing and strained existing laboratory networks, affecting turnaround time. Longer VL turnaround times delay both initiation of formal adherence counseling and switches to second-line therapy for persons failing treatment and contribute to poorer health outcomes. Methods We utilized descriptive statistics and logistic regression to analyze VL testing data collected in Malawi between January 2013 and March 2016. The primary outcomes assessed were greater-than-median pretest phase turnaround time (days elapsed from specimen collection to receipt at the laboratory) and greater-than-median test phase turnaround time (days from receipt to testing). Results The median number of days between specimen collection and testing increased 3-fold between 2013 (8 days, interquartile range (IQR) = 6-16) and 2015 (24, IQR = 13-39) (p<0.001). Multivariable analysis indicated that the odds of longer pretest phase turnaround time were significantly higher for specimen collection districts without laboratories capable of conducting viral load tests (adjusted odds ratio (aOR) = 5.16; 95% confidence interval (CI) = 5.04-5.27) as well as for Malawi's Northern and Southern regions. Longer test phase turnaround time was significantly associated with use of dried blood spots instead of plasma (aOR = 2.30; 95% CI = 2.23-2.37) and for certain testing months and testing laboratories.
Poster presentations Background In low-risk women, in vitro inhibition of E. coli by genital trac... more Poster presentations Background In low-risk women, in vitro inhibition of E. coli by genital tract secretions is associated with Lactobacillus crispatus and jensenii proteins. However in at-risk populations, HIV seroconversion was associated with greater E. coli bactericidal activity and inflammatory immune mediators. We therefore analysed the relationship between inflammation, E. coli bactericidal activity, and microbiota in vaginal swabs from participants in a safety study of VivaGel ®. Methods Swabs were collected before and after product use from subjects randomised to vaginal VivaGel ® (n = 66), VivaGel ® placebo (n = 65), or hydroxyethylcellulose (HEC) placebo (n = 54). Cytokines were quantified by multiplex proteome array and lactoferrin and SLPI by ELISA to generate a cumulative inflammatory score using principal components analysis. E. coli bactericidal activity in swab supernatants was quantified by a colony reduction assay. Vaginal bacteria were characterised by quantitative cultures. Generalized estimating equations controlling for product use were used for analyses. Results Higher inflammatory score was associated with detection of Gardnerella vaginalis (OR 1.5; p = 0.02) and anaerobic grammenegative rods (OR 1.4, p = 0.03), a trend towards diminished hydrogen peroxide-producing lactobacilli (OR 0.7, p = 0.1), and increased E. coli bactericidal activity (p < 0.001). The combined presence of group B streptococcus, E. coli, S. aureus, and enterococcus (potential pathogens) was associated with decreased E. coli bactericidal activity (p = 0.06). However these results were modified by gel type. Higher inflammatory score was associated with greater E. coli bactericidal activity only in the placebo arms (VivaGel ® p < 0.001; HEC p = 0.002), while pathogenic bacteria were associated with decreased E. coli bactericidal activity in the VivaGel ® arm (p = 0.001). Conclusion Mucosal inflammation was associated with E. coli bactericidal activity in women using placebo gels, which could contribute to the previously observed link between bactericidal activity and HIV seroconversion. However bactericidal activity in women using VivaGel ® was influenced by pathogenic bacterial populations, which may reflect an altered genital mucosal milieu.
Human papillomavirus (HPV) vaccination programmes were first implemented in several countries wor... more Human papillomavirus (HPV) vaccination programmes were first implemented in several countries worldwide in 2007. We did a systematic review and meta-analysis to assess the population-level consequences and herd effects after female HPV vaccination programmes, to verify whether or not the high efficacy reported in randomised controlled clinical trials are materialising in real-world situations. We searched the Medline and Embase databases (between Jan 1, 2007 and Feb 28, 2014) and conference abstracts for time-trend studies that analysed changes, between the pre-vaccination and post-vaccination periods, in the incidence or prevalence of at least one HPV-related endpoint: HPV infection, anogenital warts, and high-grade cervical lesions. We used random-effects models to derive pooled relative risk (RR) estimates. We stratified all analyses by age and sex. We did subgroup analyses by comparing studies according to vaccine type, vaccination coverage, and years since implementation of the...
Background Gonorrhoea notifications have been increasing in Australia’s cities, in both men and w... more Background Gonorrhoea notifications have been increasing in Australia’s cities, in both men and women. We investigated if this could be, at least in part, a result of a testing artefact. Methods: We surveyed 28 laboratories that were known to test for both Neisseria gonorrhoeae (NG) and Chlamydia trachomatis (CT) to determine their testing and reporting practices, and when these practices were instituted. Results: By 2012, 23 (82%) of the laboratories were routinely performing duplex nucleic acid amplification tests for both CT and NG even if a test for only one organism was requested, up from 9 (32%) laboratories before 2007. Although written reports of negative NG tests were not provided if the test was not requested, positive NG tests were always communicated to the attending clinician. Conclusions: The move towards routine duplex testing for CT and NG has probably resulted in more Australians being tested for NG than ever before. While this change has advantages for case-finding...
Background: Chlamydia infections are notified at much higher rates in Aboriginal and/or Torres St... more Background: Chlamydia infections are notified at much higher rates in Aboriginal and/or Torres Strait Islander people compared to non-Indigenous people. The Australian Collaboration Chlamydia Enhanced Sentinel Surveillance System (ACCESS) was established to complement population-based surveillance. Methods: We describe patient demographics, completeness of recording of Aboriginal and/or Torres Strait Islander ('Aboriginal') status, chlamydia testing rates and positivity rates from the Aboriginal Community Controlled Health Service (ACCHSs), General Practice (GP) clinics and Sexual Health Services (SHSs) networks in ACCESS during 2009. Data were extracted from electronic medical records of each participating health service for consultations with patients aged 16-29 years and for chlamydia testing and positivity. Results: Data were included from 16-29 year olds attending six ACCHSs (n = 4,950); 22 SHSs (n = 20,691) and 25 GP clinics (n = 34,462). Aboriginal status was unknown for 79.3% of patients attending GP clinics, 4.5% attending SHSs and 3.8% of patients attending ACCHSs. Chlamydia testing rates among Aboriginal patients were 19.8% (95% CI:18.6%-21.0%) at ACCHSs, 75.5% (95% CI:72.5%-78.4%) at SHSs and 4.3% (95% CI: 2.6%-6.6%) at GP clinics. Positivity rates were highest in Aboriginal patients tested at SHSs at 22.7% (95% CI:19.5%-26.2%), followed by 15.8% (95% CI:3.8%-43.4%) at GP clinics and 8.6% at ACCHSs (95% CI:7.9%-12.4%). This compared with non-Indigenous patients positivity rates at SHSs of 12.7% (95% CI:12.2-13.2%); 8.6% (7.2%-11.3%) at GP clinics and 11.3% at ACCHSs (95% CI:15.4%-24.9%). Conclusions: Higher chlamydia positivity in Aboriginal people across a range of clinical services is reflected in national notification data. Targeted efforts are required to improve testing rates in primary care services; to improve identification of Aboriginal patients in mainstream services such as GP clinics; and to better engage with young Aboriginal Australians.
Chlamydia trachomatis (CT) screening programs have been established in educational settings in ma... more Chlamydia trachomatis (CT) screening programs have been established in educational settings in many countries during the past 2 decades. However, recent evidence suggests that high uptake of screening and management (treatment, partner notification, and retesting for reinfection) improves program effectiveness. We conducted a systematic review to understand the screening strategies, the extent of screening conducted, and uptake of management strategies in educational settings. Screening studies in educational settings were identified through a systematic search of published literature from 2005 to 2011. We identified 27 studies describing 30 screening programs in the United States/Canada (n = 10), Europe (n = 8), Australia/New Zealand (n = 5), and Asia (n = 4). Most studies targeted both male and female students (74%). Classroom-based strategies resulted in 21,117 testes overall (4 programs), followed by opportunistic screening during routine health examination (n = 13,470; 5 progra...
Directly measuring disease incidence in a population is difficult and not feasible to do routinel... more Directly measuring disease incidence in a population is difficult and not feasible to do routinely. We describe the development and application of a new method for estimating at a population level the number of incident genital chlamydia infections, and the corresponding incidence rates, by age and sex using routine surveillance data. A Bayesian statistical approach was developed to calibrate the parameters of a decision-pathway tree against national data on numbers of notifications and tests conducted (2001-2013). Independent beta probability density functions were adopted for priors on the time-independent parameters; the shapes of these beta parameters were chosen to match prior estimates sourced from peer-reviewed literature or expert opinion. To best facilitate the calibration, multivariate Gaussian priors on (the logistic transforms of) the time-dependent parameters were adopted, using the Matérn covariance function to favour small changes over consecutive years and across adj...
Journal of Ayub Medical College, Abbottabad : JAMC
Pakistan is home to approximately 10 million HCV infected people. HCV prevalence is expected to b... more Pakistan is home to approximately 10 million HCV infected people. HCV prevalence is expected to be higher in the earthquake affected area of Tehsil Oghi. The aim of this study was to estimate HCV prevalence in three Union Councils of Tehsil Oghi, i.e., Oghi, Shamdhara and Kathai, and to assess HCV knowledge and awareness in the population. This is an observational study carried out during June 2010. Blood samples of 648 participants were analysed for the presence of anti HCV antibodies using Immuno-chromatographic method and a knowledge and awareness questionnaire was administered to the participants. 394 (61%) participants were females, while 254 (39%) were males. The overall prevalence of HCV in the study area was recorded as 67 (10.3%). Prevalence among male participants was 30 (11.8%), whereas, that among female participants was 37 (9.4%). Prevalence estimates in Oghi, Shamdhara and Kathai were 10.3%, 11% and 9% respectively. Knowledge and awareness regarding HCV was inadequate ...
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Papers by Hammad Ali