Article
Biology
Fabrizio Menardo, Caroline Colijn
Summary: Detecting factors associated with transmission is crucial for understanding disease epidemics and designing effective public health measures. In this study, the author used a simulation-based approach to investigate the influence of various epidemiological processes on clustering and TBL analyses of Mycobacterium tuberculosis genomic data sets. The results show that different factors, except the length of the infectious period, affect the outcomes of clustering and TBL distributions. The study also highlights the limitations of current interpretations of these analyses and suggests that optimal clustering thresholds and TBL distributions may vary depending on epidemiological conditions.
Article
Immunology
Jitendra Singh, Niti Singh, Gayatri Suresh, Rahul Srivastava, Upasna Aggarwal, Digamber Behera, Murali Munisamy, Anvita Gupta Malhotra, Sarman Singh
Summary: This study aimed to identify the distribution of different genotypes of M. tuberculosis among HIV-positive and HIV-negative patients seen at a tertiary care dedicated TB hospital in New Delhi, India. The results showed that the Beijing lineage was predominant in HIV-TB coinfected cases, while the Central Asian Strain (CAS) was overall more predominant in the region.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Editorial Material
Biology
Erin Brintnell, Art Poon
Summary: Combining clinical and genetic data can improve the effectiveness of virus tracking.
Article
Multidisciplinary Sciences
Ana Cristina Jimenez-Ruano, Carlos Francisco Madrazo-Moya, Irving Cancino-Munoz, Paulina M. Mejia-Ponce, Cuauhtemoc Licona-Cassani, Inaki Comas, Raquel Muniz-Salazar, Roberto Zenteno-Cuevas
Summary: Whole genome sequencing has been shown to be superior to traditional genotyping methods for tuberculosis, but its application in drug-resistant TB isolates in Mexico has been relatively unknown. This study aimed to identify and characterize the lineages and genomic transmission clusters present in 67 drug-resistant TB isolates in southeastern Mexico. The results revealed the presence of three major lineages, with sublineage 4.1.1.3 (X3) being predominant and exclusive to multidrug-resistant isolates in Mexico for at least 17 years.
SCIENTIFIC REPORTS
(2021)
Article
Multidisciplinary Sciences
Arif M. Tanmoy, Yogesh Hooda, Mohammad S. I. Sajib, Kesia E. da Silva, Junaid Iqbal, Farah N. Qamar, Stephen P. Luby, Gordon Dougan, Zoe A. Dyson, Stephen Baker, Denise O. Garrett, Jason R. Andrews, Samir K. Saha, Senjuti Saha
Summary: This study sequenced Salmonella Paratyphi A isolates from different countries and developed a new genotyping scheme called Paratype. By using Paratype, spatiotemporal genomic variation and antimicrobial resistance markers can be identified, aiding in tracking the transmission of Salmonella Paratyphi A globally.
NATURE COMMUNICATIONS
(2022)
Article
Genetics & Heredity
Belen Saavedra Cervera, Mariana G. Lopez, Alvaro Chiner-Oms, Ana Maria Garcia, Irving Cancino-Munoz, Manuela Torres-Puente, Luis Villamayor, Carlos Madrazo-Moya, Edson Mambuque, Guillermo Victor Sequera, Durval Respeito, Silvia Blanco, Orvalho Augusto, Elisa Lopez-Varela, Alberto L. Garcia-Basteiro, Inaki Comas
Summary: In this study, a 1-year prospective surveillance-based study was conducted in Mozambique to investigate the population structure and transmission dynamics of Mycobacterium tuberculosis complex (MTBC). Whole-genome sequencing was applied to 295 positive cultures, and the MTBC isolates were fully characterized and analyzed for molecular epidemiology. The majority of the strains belonged to lineage 4, with a high proportion in genomic transmission clusters. Two "likely endemic" clades belonging to L1.2 were identified, dating back to the late 19th century and associated with recent spread among people living with HIV. The study reveals weaknesses in TB control activities and questions the role of HIV in TB transmission.
MICROBIAL GENOMICS
(2022)
Article
Immunology
Hai Viet Nguyen, Edine Tiemersma, Nhung Viet Nguyen, Hoa Binh Nguyen, Frank Cobelens
Summary: Among children aged 6-10 years, living with patients with clinical or subclinical tuberculosis increases the risk of tuberculin skin test positivity. The transmission of subclinical tuberculosis is still inconclusive. The findings support the hypothesis that smear-positive subclinical tuberculosis contributes to Mycobacterium tuberculosis transmission.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Immunology
Jessy J. Duran Ramirez, Tala Ballouz, Huyen Nguyen, Katharina Kusejko, Sandra E. Chaudron, Michael Huber, Hans H. Hirsch, Matthieu Perreau, Alban Ramette, Sabine Yerly, Matthias Cavassini, Marcel Stockle, Hansjakob Furrer, Pietro Vernazza, Enos Bernasconi, Huldrych F. Gunthard, Roger D. Kouyos
Summary: The study reveals a significant increase in non-B subtypes of HIV-1 among men who have sex with men (MSM) in Switzerland, with CRF01_AE being the most prevalent subtype. The majority of molecular transmission clusters (MTCs) among MSM were found to be comprised of Europeans.
JOURNAL OF INFECTIOUS DISEASES
(2022)
Article
Immunology
Jessica Comin, Jan Madacki, Isabel Rabanaque, Maria Zuniga-Anton, Daniel Ibarz, Alberto Cebollada, Jesus Vinuelas, Luis Torres, Juan Sahagun, Christophe Klopp, Jesus Gonzalo-Asensio, Roland Brosch, Maria-Jose Iglesias, Sofia Samper
Summary: Through analysis of a tuberculosis outbreak and molecular characteristics of the MtZ strain, several SNPs in genes related to virulence, pathogenesis, and survival, as well as other genomic polymorphisms, were identified, which may contribute to its success in transmission among the population.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Microbiology
Robeena Farzand, Richard D. Haigh, Philip Monk, Pranabashis Haldar, Hemu Patel, Manish Pareek, Raman Verma, Michael R. Barer, Gerrit Woltmann, Lauren Ahyow, Heena Jagatia, Jonathan Decker, Galina V. Mukamolova, Andrea M. Cooper, Natalie J. Garton, Helen M. O'Hare
Summary: The genetic diversity of Mycobacterium tuberculosis plays a role in disease severity and transmissibility. In this study, the phenotyping of M. tuberculosis from a persistent outbreak in the UK revealed higher lipid contents and more hydrophobic cell surfaces compared to nonoutbreak isolates. Deletions in specific genes were also found in the outbreak isolates, potentially altering the interactions between the bacteria and immune cells. Reintroduction of one of these genes led to a phenotype resembling nonoutbreak strains. Understanding the microbiological characteristics and genetic polymorphisms associated with outbreaks can inform tuberculosis control strategies.
Article
Immunology
Kang Li, Meiliang Liu, Huanhuan Chen, Jianjun Li, Yanling Liang, Yi Feng, Hui Xing, Yiming Shao
Summary: The study indicates that HIV-1 CRF08_BC remains a significant epidemic in southern China, with over one third of infected individuals clustered in transmission networks. It helps identify active CRF08_BC spreaders in local communities and greatly facilitates targeted interventions for AIDS prevention.
EMERGING MICROBES & INFECTIONS
(2021)
Article
Immunology
Qin Fan, Jiafeng Zhang, Mingyu Luo, Yi Feng, Rui Ge, Yong Yan, Ping Zhong, Xiaobei Ding, Yan Xia, Zhihong Guo, Xiaohong Pan, Chengliang Chai
Summary: This study conducted a detailed molecular epidemiological analysis of HIV-1 epidemic strains in different sexual risk behavior groups, highlighting the rapid transmission and importance of CRF07_BC among men who have sex with men (MSM).
EMERGING MICROBES & INFECTIONS
(2022)
Article
Multidisciplinary Sciences
Tesfaneh Debele Batu, Legesse Lemecha Obsu, Chernet Tuge Deressa
Summary: The study investigates the impact of intervention strategies on the death risk of people living with HIV when infected with COVID-19. It develops a mathematical model to analyze the transmission dynamics of COVID-19 and HIV co-infection. The findings indicate that increasing COVID-19 vaccination and treating co-infected individuals can reduce the death risk of HIV-infected individuals due to the co-infection burden.
SCIENTIFIC REPORTS
(2023)
Article
Infectious Diseases
Zhiying Han, Jing Li, Guomei Sun, Kaikan Gu, Yangyi Zhang, Hui Yao, Yuan Jiang
Summary: The study used whole-genome sequencing and field epidemiological investigation to analyze the transmission pattern of an MDR-TB outbreak in the Jing'an District of Shanghai. The results showed that the ten MDR-TB patients were infected through recent transmission of M. tuberculosis, with genetic analysis confirming definite links between the cases. The integration of genomic analysis into routine tuberculosis surveillance can help detect MDR-TB transmission events and improve efforts to interrupt transmission.
BMC INFECTIOUS DISEASES
(2021)
Article
Immunology
Zhangwen Ge, Yi Feng, Hua Zhang, Abdur Rashid, Silvere D. Zaongo, Kang Li, Yueyang Yu, Bowen Lv, Jia Sun, Yanling Liang, Hui Xing, Anders Sonnerborg, Ping Ma, Yiming Shao
Summary: The study found that CRF07_BC in China has evolved into two clusters, 07BC_O and 07BC_N, spreading in different risk groups and geographical regions. Of the two clusters, 07BC_N shows a higher transmission risk and has gradually replaced the original 07BC_O. Strengthening interventions for men having sex with men could help reduce the rapid transmission of 07BC_N across all risk groups.
EMERGING MICROBES & INFECTIONS
(2021)
Article
Public, Environmental & Occupational Health
Fatima Laher, Kennedy Otwombe, Ofentse Mokwena, Linda-Gail Bekker, Mary Allen
Summary: This study retrospectively evaluated HIV vaccine clinical trials in South Africa and found that cohorts with low HIV incidence can be identified primarily through sexual behavior and clinical characteristics.
Article
Health Policy & Services
Kirsty Brittain, Yolanda Gomba, Sandisiwe Noholoza, Jennifer Pellowski, Claude A. Mellins, Linda-Gail Bekker, Ashraf Kagee, Robert H. Remien, Elaine J. Abrams, Landon Myer
Summary: Young pregnant and postpartum women living with HIV face stigma and judgement from their community, leading to limited disclosure of their HIV status. However, disclosure in certain situations can result in emotional support and support for ART adherence.
AIDS CARE-PSYCHOLOGICAL AND SOCIO-MEDICAL ASPECTS OF AIDS/HIV
(2023)
Article
Immunology
Nora E. Rosenberg, Bonnie E. Shook-Sa, Mincen Liu, Lynda Stranix-Chibanda, Marcel Yotebieng, Nadia A. Sam-Agudu, Michael G. Hudgens, Sam J. Phiri, Wilbroad Mutale, Linda-Gail Bekker, Sizulu Moyo, Khangelani Zuma, Manhattan E. Charurat, Jessica Justman, Benjamin H. Chi
Summary: This study estimated the HIV-1 incidence rates and number of new infections in sub-Saharan Africa, based on population-based surveys. The results showed variations in HIV-1 incidence by age, sex, and subregion, indicating the need for risk stratification to guide comprehensive HIV-1 prevention.
Article
Public, Environmental & Occupational Health
Danielle Giovenco, Audrey Pettifor, Linda-Gail Bekker, Lindsey M. Filiatreau, Tao Liu, Morayo Akande, Katherine Gill, Millicent Atujuna, Dan J. Stein, Caroline Kuo
Summary: This study examined the interest of adolescents in oral PrEP and its association with perceived parental support and PrEP stigma. The results showed that a significant percentage of adolescents were interested in using PrEP and believed that their parents would support them. However, low parental support and high PrEP stigma were associated with reduced interest in PrEP among adolescents. Therefore, interventions should focus on improving communication between adolescents and parents regarding sexual health and effective HIV prevention tools.
Article
Microbiology
Adijat O. Jimoh, Christina Balle, Bryan Brown, Colin Feng, Enock Havyarimana, Iyaloo N. Konstantinus, Katherine Gill, Linda-Gail Bekker, Jo-Ann S. Passmore, Heather B. Jaspan, Arvind Varsani, Anna-Ursula Happel
Summary: Apart from papillomaviruses, there is a lack of whole-genome sequences for bacteriophages and eukaryote-infecting viruses isolated from the female genital tract. In this study, we identified the genome sequences of 16 microviruses, 3 anelloviruses, 2 polyomaviruses, 1 genomovirus, and 1 caudovirus in vaginal secretion samples from adolescents in South Africa.
MICROBIOLOGY RESOURCE ANNOUNCEMENTS
(2023)
Article
Infectious Diseases
Ilhaam Abrahams, Angela Dramowski, Kedisaletse Moloto, Lizel Lloyd, Andrew Whitelaw, Adrie Bekker
Summary: This study retrospectively analyzed the clinical characteristics, treatment methods and outcomes of neonates with carbapenem-resistant Enterobacterales (CRE) infections in a neonatal unit in South Africa, as well as the adverse reactions related to colistin. The results showed that colistin was used for premature infants with lower gestational age and lower birth weight, but the mortality rate was high. In addition, the outbreak isolates were found to be blaNDM-1 prevalent strains.
SOUTHERN AFRICAN JOURNAL OF INFECTIOUS DISEASES
(2023)
Article
Multidisciplinary Sciences
Geetha Beauchamp, Sybil Hosek, Deborah J. Donnell, Kwun C. G. Chan, Brian P. Flaherty, Peter L. Anderson, Bonnie J. Dye, Nyaradzo Mgodi, Linda-Gail Bekker, Sinead Delany-Moretlwe, Connie Celum
Summary: This study developed an HIV prevention readiness measure to identify African adolescent girls and young women who are motivated to take pre-exposure prophylaxis (PrEP) and in need of adherence support. The measure showed good reliability and validity in assessing medication adherence and prevention readiness. These findings are important for the development and implementation of PrEP adherence support programs.
Article
Infectious Diseases
Sinead Delany-Moretlwe, Nyaradzo Mgodi, Linda-Gail Bekker, Jared M. Baeten, Chuwen Li, Deborah Donnell, Yaw Agyei, Denni Lennon, Scott M. Rose, Marcia Mokgatle, Sheetal Kassim, Shorai Mukaka, Adeola Adeyeye, Connie Celum
Summary: This study investigated the prevalence, incidence, and factors associated with sexually transmitted infections (STIs) among young African women seeking HIV pre-exposure prophylaxis (PrEP). The findings showed that despite PrEP usage, 55% of the participants had at least one STI detected. Therefore, alternative approaches for diagnosis and treatment are needed to reduce the burden of STIs in this population.
SEXUALLY TRANSMITTED INFECTIONS
(2023)
Article
Virology
Anna-Ursula Happel, Christina Balle, Enock Havyarimana, Bryan Brown, Brandon S. Maust, Colin Feng, Byung H. Yi, Katherine Gill, Linda-Gail Bekker, Jo-Ann S. Passmore, Heather B. Jaspan, Arvind Varsani
Summary: The study assessed the interaction between cervicovaginal virome, bacteriome and genital inflammation. It found various DNA viruses in the vaginal virome, including human papillomavirus (HPV), with HPV-35 being the most prevalent high-risk genotype. The presence of certain bacterial taxa correlated with HPV infection, while bacterial vaginosis was associated with increased genital inflammation. This study provides a foundation for future research on the vaginal virome and its impact on women's health.
Article
Public, Environmental & Occupational Health
Geetha Beauchamp, Deborah Donnell, Sybil Hosek, Peter L. Anderson, Kwun C. G. Chan, Bonnie J. Dye, Nyaradzo Mgodi, Linda-Gail Bekker, Sinead Delany-Moretlwe, Connie Celum
Summary: Trust is crucial in patient-provider communication. Accurate reporting of PrEP adherence is important, especially for adolescent girls and young women disproportionately affected by HIV. Educating and training providers to build trust with these individuals may lead to more accurate reporting of PrEP adherence.
Article
Immunology
Tyler S. Brown, Linrui Tang, Shaheed Vally Omar, Lavania Joseph, Graeme Meintjes, Gary Maartens, Sean Wasserman, N. Sarita Shah, Maha R. Farhat, Neel R. Gandhi, Nazir Ismail, James C. M. Brust, Barun Mathema
Summary: Characterizing serial Mycobacterium tuberculosis (Mtb) isolates collected during bedaquiline (BDQ)-based treatment provides insights into the etiologies of BDQ resistance. The study found that BDQ-resistant TB can arise through multiple processes, including transmission of strains with pre-existing resistance. Capturing the within-host diversity of these infections could potentially improve clinical diagnosis, population-level surveillance, and molecular diagnostic test development.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Biochemistry & Molecular Biology
Mia Moore, Sarah Stansfield, Deborah J. Donnell, Marie-Claude Boily, Kate M. Mitchell, Peter L. Anderson, Sinead Delany-Moretlwe, Linda-Gail Bekker, Nyaradzo M. Mgodi, Connie L. Celum, Dobromir Dimitrov
Summary: Modeling adherence to daily PrEP in cisgender women clarifies that high adherence confers high protection against HIV acquisition, while partial adherence results in lower efficacy, highlighting the need for new PrEP products and interventions to increase adherence.
Article
Infectious Diseases
Remco P. H. Peters, James A. Mcintyre, Nigel Garrett, Adrian J. Brink, Connie L. Celum, Linda -Gail Bekker
Summary: South Africa has a high burden of bacterial sexually transmitted infections (STIs) among men who have sex with men (MSM). Recent studies have shown that doxycycline post-exposure prophylaxis (PEP) is highly effective in reducing the rates of bacterial STIs in MSM. However, its effectiveness was not demonstrated among cisgender women in Kenya. Concerns remain about the development of antimicrobial resistance (AMR) and its impact on other pathogens, commensals, and the microbiome. More research is needed to understand the potential impact of doxycycline PEP on AMR at individual and population levels. In conclusion, offering doxycycline PEP to high-risk MSM on a case-by-case basis, under the supervision of experienced sexual health clinicians in settings with access to diagnostic STI testing and ongoing AMR surveillance, seems reasonable.
SOUTHERN AFRICAN JOURNAL OF HIV MEDICINE
(2023)
Article
Infectious Diseases
Jaco Horak, Willem D. F. Venter, Camilla Wattrus, Nectarios Papavarnavas, Pauline Howell, Gillian Sorour, Carole Wallis, Katherine Gill, Francesca Conradie, Linda-Gail Bekker
SOUTHERN AFRICAN JOURNAL OF HIV MEDICINE
(2023)
Article
Primary Health Care
Nadia Ahmed, Carey Pike, Jessica Lee, Colleen Wagner, Linda-Gail Bekker
Summary: Despite high rates of HIV infection, sexually transmitted infections, and unplanned pregnancies among adolescents in South African secondary schools, school-based healthcare services are not provided. This study found that inadequate stakeholder support and different views on adolescent healthcare needs are the key challenges to delivering school-based health services. Further multi-level stakeholder engagement and longer periods of school health service delivery are needed to assess the feasibility, acceptability, and potential impact on healthcare outcomes in this context.
AFRICAN JOURNAL OF PRIMARY HEALTH CARE & FAMILY MEDICINE
(2023)