MRAGDATASET/citation_with_pmcid · Datasets at Hugging Face

source_paper string	source_section string	premise string	target_doi string	target_paper string
PMC10010521	Introduction	Globally, Shigella species are a leading cause of diarrhoeal mortality, causing an estimated 200,000 deaths in 2016 [11].	10.1016/S1473-3099(18)30475-4	PMC6202441
PMC10010521	Introduction	In contrast, the highest rates of shigellosis in high-income countries typically occur through person-to-person contact in crowded communities and childcare centres, in travellers returning from overseas or in MSM [9,13].	10.1093/jpids/piab045	PMC8744073
PMC10010521	Introduction	Increasing transmission of Shigella among MSM, particularly antimicrobial resistant strains, have been reported in several high-income countries, including the United States, Canada, Germany and the United Kingdom [14–17].	10.3201/eid2302.161203	PMC5324786
PMC10010521	Introduction	The most commonly reported species in high-income countries is S. sonnei, with this species accounting for over 80% of shigellosis infections in the United States and Israel, and over 50% of infections in the United Kingdom [18–20].	10.3201/eid2806.220131	PMC9155871
PMC10010521	Introduction	The most commonly reported species in high-income countries is S. sonnei, with this species accounting for over 80% of shigellosis infections in the United States and Israel, and over 50% of infections in the United Kingdom [18–20].	10.1128/JCM.01692-19	PMC7098776
PMC10010521	Introduction	Currently, PCR assays for detecting Shigella target the invasion plasmid antigen H (ipaH) gene, which is also common to entero-invasive Escherichia coli (EIEC) [25].	10.1128/JCM.42.5.2031-2035.2004	PMC404673
PMC10010521	Discussion	While S. flexneri is traditionally linked to low and middle income countries and S. sonnei to high income countries, in recent years the expansion of S. sonnei has been documented in many economically transitional regions in Asia, Latin America and the Middle East [28].	10.1371/journal.pntd.0003708	PMC4466244
PMC10010521	Discussion	Globally, data on the epidemiology of S. boydii is limited, with this species being predominantly endemic in the Indian Subcontinent [29].	10.1093/nar/gki954	PMC1278947
PMC10010521	Discussion	S. dysenteriae serotype 1, which is the only Shigella species and serotype that expresses the Shiga toxin gene, has high epidemic potential and has been identified as a cause of several large scale outbreaks of dysentery, particularly in settings associated with civil unrest [30–34].	10.1128/AEM.69.12.7028-7031.2003	PMC310026
PMC10010521	Discussion	S. dysenteriae serotype 1, which is the only Shigella species and serotype that expresses the Shiga toxin gene, has high epidemic potential and has been identified as a cause of several large scale outbreaks of dysentery, particularly in settings associated with civil unrest [30–34].	10.3389/fcimb.2016.00045	PMC4835486
PMC10010521	Discussion	This strain is also notorious for developing drug resistance, with epidemic strains typically resistant to multiple antibiotics [35,36].	10.1128/IAI.05814-11	PMC3232646
PMC10010521	Discussion	The epidemiology of S. dysenteriae is distinct from the other species of Shigella, with epidemics tending to disappear and then reappear years later, with few sporadic cases reported in between outbreaks [37,38].	10.1186/1471-2164-15-355	PMC4038718
PMC10010521	Discussion	The epidemiology of S. dysenteriae is distinct from the other species of Shigella, with epidemics tending to disappear and then reappear years later, with few sporadic cases reported in between outbreaks [37,38].	10.3389/fcimb.2017.00064	PMC5364150
PMC10010521	Discussion	While large scale outbreaks of S. dysenteriae serotype 1 were prevalent in the second half of the twentieth century in Asia, Africa and Central America, there has been a drastic decline in the incidence of S. dysenteriae in the last few decades, which remains largely unexplained [7,34,39].	10.1007/s40475-014-0019-6	PMC4126259
PMC10010521	Discussion	While large scale outbreaks of S. dysenteriae serotype 1 were prevalent in the second half of the twentieth century in Asia, Africa and Central America, there has been a drastic decline in the incidence of S. dysenteriae in the last few decades, which remains largely unexplained [7,34,39].	10.3389/fcimb.2016.00045	PMC4835486
PMC10010521	Discussion	It is widely documented that people living in remote areas have poorer health outcomes, including higher rates of hospitalisation and death, and also have more limited access to, and use of, health care services [41,42].	10.1017/S1463423620000481	PMC7737170
PMC10010521	Discussion	Antimicrobial resistance has also been reported in endemic strains of Shigella affecting First Nations Australians [45].	10.1007/s10096-020-04029-w	PMC7473701
PMC10010521	Discussion	Overcrowding and lack of safe removal and treatment of sewage has shown to be positively associated with gastrointestinal infections in First Nations Australian households [47].	10.3390/ijerph15122827	PMC6313733
PMC10010521	Discussion	Consistent with global trends, the burden of shigellosis in Australia was highest in children aged less than five years [31,48].	10.1371/journal.pmed.0030353	PMC1564174
PMC10010521	Discussion	Additionally, the low infectious dose of Shigella results in person-to-person transmission, which often occurs between children in childcare settings through close contact [7,51].	10.1007/s40475-014-0019-6	PMC4126259
PMC10010521	Discussion	This is likely to reflect ongoing transmission among MSM in these states, with outbreaks occurring over several years in three of the most populous states (Victoria (VIC), New South Wales (NSW) and Queensland) [23,52–54].	10.1128/JCM.40.4.1538-1540.2002	PMC140385
PMC10010521	Discussion	Several studies have demonstrated the increased capability of CIDT in identifying the aetiology of diarrhoeal patients when compared to culture dependent methods, with estimates ranging from two to four times when using CIDT [58–60].	10.1016/S0140-6736(16)31529-X	PMC5471845
PMC10010521	Discussion	Several studies have demonstrated the increased capability of CIDT in identifying the aetiology of diarrhoeal patients when compared to culture dependent methods, with estimates ranging from two to four times when using CIDT [58–60].	10.3389/fmicb.2016.00386	PMC4811922
PMC10010521	Discussion	The process to obtain this information is faster as WGS does not require the application of multiple subtyping methodologies [62].	10.1128/AEM.00165-19	PMC6585509
PMC10010521	Discussion	Additionally, WGS can differentiate between Shigella and EIEC, which have many biochemical properties and virulence genes in common [62,63].	10.1128/AEM.00165-19	PMC6585509
PMC10010531	Introduction	syphilis, gonorrhoea, chlamydia, and trichomoniasis [5].	10.1371/journal.pone.0143304	PMC4672879
PMC10010531	Introduction	hepatitis B, herpes simplex virus (HSV or herpes), HIV, and human papillomavirus (HPV) [5].	10.1371/journal.pone.0143304	PMC4672879
PMC10010531	Introduction	Mother-to-child transmission of STIs has effects like stillbirth, neonatal death, low-birth weight and prematurity, sepsis, pneumonia, neonatal conjunctivitis, and congenital deformities [6].	10.2471/BLT.18.228486	PMC6653813
PMC10010531	Introduction	STIs remain a major public health challenge for people belonging to high-risk groups (for HIV) around the world [6].	10.2471/BLT.18.228486	PMC6653813
PMC10010531	Materials and methods	Inclusion of studies from Grey literature will be carried out after being checked through a quality assessment tool (Axis Tool) [14].	10.1136/bmjopen-2016-011458	PMC5168618
PMC10010531	Materials and methods	6.0) generated modified data extraction form [16].	10.1186/s12859-018-2334-8	PMC6196404
PMC10010531	Materials and methods	To evaluate publication bias Egger’s [18] and Begg and Mazumdar’s [19] assessments will be used along with the Funnel diagram.	10.1136/bmj.315.7109.629	PMC2127453
PMC10010533	Introduction	SARS-CoV-2 primarily spreads via aerosols and droplets, and the degree of aerosolization is related to multiple factors, including ventilation [1–4].	10.1016/S0140-6736(21)00869-2	PMC8049599
PMC10010533	Introduction	SARS-CoV-2 primarily spreads via aerosols and droplets, and the degree of aerosolization is related to multiple factors, including ventilation [1–4].	10.1002/ppul.25330	PMC8014227
PMC10010533	Introduction	Within the built environment, the floor is the most common location where the virus can be detected [5–9].	10.1186/s40168-021-01083-0	PMC8186369
PMC10010533	Introduction	The floor was the most common surface where the virus was detected, and this observation has been replicated in other studies [5, 6, 8].	10.1136/thoraxjnl-2021-218035	PMC8646974
PMC10010533	Introduction	conducted a study at four hospitals in Korea assessing both air and surface contamination, as well as the impact of surface cleaning on the ability to detect SARS-CoV-2 [10].	10.3346/jkms.2020.35.e332	PMC7505729
PMC10010533	Introduction	They collected 330 swabs, of which 27% were positive for SARS-CoV-2 [10].	10.3346/jkms.2020.35.e332	PMC7505729
PMC10010533	Introduction	did not conduct serial swabs surrounding the patient, it is unknown how the viral burden surrounding a patient changes over space and time [8, 10].	10.3346/jkms.2020.35.e332	PMC7505729
PMC10010533	Introduction	One single-centre study in the United States swabbed within the rooms of patients with COVID-19 to determine how severity of illness and distance from the patient’s bed affected the recovery of SARS-CoV-2 from floors and high touch surfaces [11].	10.1017/ice.2021.530	PMC8755533
PMC10010533	Introduction	The probability of detecting SARS-CoV-2 from the floor was approximately 80% and did not vary over distance, but was higher for patients with more severe disease (e.g., requiring positive pressure ventilation) [11].	10.1017/ice.2021.530	PMC8755533
PMC10010533	Methods	For this study, we considered a positive result to be a Cq less than 45, which is an accepted cut-off used for environmental surveillance of SARS-CoV-2 [12].	10.1016/j.scitotenv.2021.146749	PMC8007530
PMC10010533	Discussion	We did not evaluate whether swabbing immediately after cleaning resulted in an inability to detect SARS-COV-2; however, prior studies have done so [10, 14, 15].	10.3346/jkms.2020.35.e332	PMC7505729
PMC10010533	Discussion	We did not evaluate whether swabbing immediately after cleaning resulted in an inability to detect SARS-COV-2; however, prior studies have done so [10, 14, 15].	10.1017/ice.2020.1278	PMC7653228
PMC10010533	Discussion	We did not evaluate whether swabbing immediately after cleaning resulted in an inability to detect SARS-COV-2; however, prior studies have done so [10, 14, 15].	10.1371/journal.pone.0261365	PMC8782535
PMC10010533	Discussion	In the study by Kim et al., RNA was not detected in a room routinely cleaned by disinfectant wipes, demonstrating how cleaning removes SARS-CoV-2 from the surface; however, RNA was detected in a room sprayed with disinfectant, suggesting disinfectant sprays may not be effective in reducing exposure [10].	10.3346/jkms.2020.35.e332	PMC7505729
PMC10010533	Discussion	Thus, our ability to consistently detect the virus at increasing distances from the patient’s bed goes against the historically referenced “Six-Foot Rule” [16].	10.1073/pnas.2018995118	PMC8092463
PMC10010533	Discussion	However, a prior study observed higher rates of surface contamination with SARS-CoV-2 for patients who required high-flow oxygen or positive pressure ventilation compared to hospitalized patients with less severe illness (OR = 1.6, 95% credible interval [CrI] 1.03–1.25) [11].	10.1017/ice.2021.530	PMC8755533
PMC10010538	Introduction	Injuries continue to have significant weight on the global disease burden, and are among the main causes of morbidity and mortality in adolescents, young people and adults [2].	10.1016/S0140-6736(20)30925-9	PMC7567026
PMC10010538	Introduction	Economic analysis of the implementation of interventions to assess the results and costs of these interventions aimed at improving the health of the population are recommended [4, 8] and are used to demonstrate the disease burden in monetary terms [9–11].	10.1371/journal.pone.0234300	PMC7282655
PMC10010538	Materials and methods	To estimate the disease burden of premature mortality, measures of years of potential life lost (YPLL), years of potential productive life lost (YPPLL) and cost of productivity lost CPL were used [9, 10, 19, 20].	10.1371/journal.pone.0234300	PMC7282655
PMC10010538	Materials and methods	To estimate the disease burden of premature mortality, measures of years of potential life lost (YPLL), years of potential productive life lost (YPPLL) and cost of productivity lost CPL were used [9, 10, 19, 20].	10.1136/bmjopen-2014-005386	PMC4127933
PMC10010538	Materials and methods	These concepts estimate the average time a person would live if they did not die prematurely, taking into account the age limit (death/retirement) and the cause [9].	10.1371/journal.pone.0234300	PMC7282655
PMC10010538	Materials and methods	For this study it was assumed that the individual’s productivity did not change until retirement [9].	10.1371/journal.pone.0234300	PMC7282655
PMC10010538	Discussion	The findings of this study were similar to those reported in similar studies where the active population accounted for the largest proportion of fatal victims due to injury [26, 28].	10.2471/BLT.14.145771	PMC4431514
PMC10010538	Discussion	[33, 34] reported traffic accidents and suicides as the principal external causes of death and finally, Corassa et al.	10.1155/2020/7303897	PMC7193292
PMC10010538	Discussion	The prevalence of suicide has been associated with mental disorders and sociodemographic characteristics and aggression with socioeconomic inequalities, alcohol and drug-related harm, respectively [26, 33].	10.2471/BLT.14.145771	PMC4431514
PMC10010538	Discussion	In addition, traffic accidents were among the leading causes of death in Sub-Saharan Africa and while globally, traffic accidents, falls and interpersonal violence were identified as the leading causes of death due to injury [25, 36].	10.1136/injuryprev-2015-041616	PMC4752630
PMC10010538	Discussion	Comprehensive road safety laws and their proper enforcement could contribute to the reduction of mortality from road accidents [25, 36].	10.1136/injuryprev-2015-041616	PMC4752630
PMC10010538	Discussion	In Seychelles, drowning was the leading cause of death due to external causes [41].	10.1038/s41598-020-79228-8	PMC7746745
PMC10010538	Discussion	[41] suggested the promotion of swimming programs as a measure to reduce the risk of drowning in the population.	10.1038/s41598-020-79228-8	PMC7746745
PMC10010538	Discussion	The estimated YPLL corresponded to a total of 7,222 and, a mean of 34.2 YPLL per death, which was higher than the mean obtained in Tanzania [9] and in line with the findings from Brazil which showed that males were responsible for the highest proportion of calculated YPLL, while the age ranges from 20 to 39 were responsible for approximately 60% of YPLL [35].	10.1371/journal.pone.0234300	PMC7282655
PMC10010538	Discussion	Similar to the current study, males contributed to a higher proportion of YPLL due to injuries, and overall injuries affected the potentially productive population [10, 35, 43].	10.1136/bmjopen-2014-005386	PMC4127933
PMC10010538	Discussion	In other studies, CPL due to injury was significantly higher among men than among women [10, 48].	10.1136/bmjopen-2014-005386	PMC4127933
PMC10010538	Discussion	In other studies, CPL due to injury was significantly higher among men than among women [10, 48].	10.5334/aogh.1355	PMC6997525
PMC10010538	Discussion	[10] reported that the highest average loss per death was due to trauma, amounting to 72,571 USD/death while Davey et al.	10.1136/bmjopen-2014-005386	PMC4127933
PMC10010538	Discussion	[48] presented a mean value of approximately 2500 USD per death.	10.5334/aogh.1355	PMC6997525
PMC10010538	Discussion	Results of this study demonstrate the need to standardize the classification of injuries and this could improve current estimates of mortality from external causes and complement national and global disease burden estimates [7, 26].	10.2471/BLT.14.145771	PMC4431514
PMC10010538	Discussion	Standardization can be achieved through regular training of health professionals on current guidelines [41] and the digitization of health information systems.	10.1038/s41598-020-79228-8	PMC7746745
PMC10010538	Discussion	Available data on economic costs of diseases, shows that two main methods are used to evaluate the economic impact, namely the friction method and the human capital method, with the human capital method being the most used methodology in cost-of-disease analyses [49].	10.1007/s40258-018-0416-4	PMC6467569
PMC10011442	Methods	Data preprocessing after the defacing included linear resampling to 2 mm isotropic resolution with the intensity scaled into a range of [-1,1].	10.5195/jmla.2017.88	PMC5370619
PMC10013005	Materials and Methods	The hyperparameter tuning is in the form of a 100-iteration randomized search of a set of predefined hyperparameter distributions:{‘max_iter’: [2000],‘loss’: [‘least_squares’],‘random_state’: [42],‘early_stopping’: [True],‘learning_rate’: loguniform(0.005, 0.1),‘max_leaf_nodes’: randint(2, 10),‘min_samples_leaf’: randint(100,200)}	10.6061/clinics/2019/e477	PMC6445156
PMC10013005	Materials and Methods	‘random_state’: [42],	10.6061/clinics/2019/e477	PMC6445156
PMC10013882	Introduction	Studies in sub-Saharan Africa (SSA) suggest that only 67% of patients remain in ART programs after five years, with loss to follow-up (patients with unknown outcomes) accounting for 33% of all attrition [1].	10.1002/jia2.25084	PMC5897849
PMC10013882	Introduction	DSD models aim to improve long-term ART retention by removing barriers to care, making service delivery more patient-centered [2], generate greater patient satisfaction, reduce costs to patients (and to providers in some cases), and create efficient and convenient service delivery [3].	10.1097/QAI.0000000000002070	PMC6625870
PMC10013882	Introduction	DSD models differ from conventional HIV care in the location of service delivery, frequency of interactions with the healthcare system, cadre of provider involved, and/or types of services provided [4].	10.1111/tmi.12460	PMC4670701
PMC10013882	Introduction	The attractiveness of DSD models is generally considered to be conditional on maintaining at least equivalent clinical outcomes to conventional care, but there remains relatively little evidence on ART retention among patients enrolled in DSD models as part of large-scale routine care in SSA [5, 6].	10.1186/s12889-021-11053-8	PMC8194040
PMC10013882	Introduction	The attractiveness of DSD models is generally considered to be conditional on maintaining at least equivalent clinical outcomes to conventional care, but there remains relatively little evidence on ART retention among patients enrolled in DSD models as part of large-scale routine care in SSA [5, 6].	10.1002/jia2.25640	PMC7696000
PMC10013882	Introduction	Zambia, a high-HIV burden country with more than 1.5 million people living with HIV and more than 81% of those individuals on ART, has rapidly scaled up a variety of DSD models [7].	10.1002/jia2.25808	PMC8554218
PMC10013882	Methods	The SmartCare database covers approximately three-quarters of all ART patients in Zambia, with the remainder accessing care at clinics that do not utilize the system [11].	10.1136/bmjopen-2019-030428	PMC6731929
PMC10013882	Methods	Source: Table modified from [6]	10.1002/jia2.25640	PMC7696000
PMC10013882	Discussion	Our findings are generally consistent with those of other studies of DSD model outcomes in SSA [5].	10.1186/s12889-021-11053-8	PMC8194040
PMC10013882	Discussion	Previous studies found high retention of patients in adherence clubs and home-based care models in South Africa and Kenya, among other countries [13, 14].	10.1371/journal.pmed.1002874	PMC6650049
PMC10013882	Discussion	Previous studies found high retention of patients in adherence clubs and home-based care models in South Africa and Kenya, among other countries [13, 14].	10.1097/QAI.0000000000002634	PMC8126486
PMC10013882	Discussion	Studies in Zambia have showed that DSD models achieve comparable or better outcomes than conventional care [15, 16].	10.1097/QAD.0000000000002737	PMC7810408
PMC10013882	Discussion	Studies in Zambia have showed that DSD models achieve comparable or better outcomes than conventional care [15, 16].	10.1371/journal.pmed.1003116	PMC7329062
PMC10013882	Discussion	In ART programs in SSA, males have traditionally been at higher risk of attrition than females [17], but we found that rural males in most DSD models in Zambia were retained in care as well as or relatively better than females in the same models and settings.	10.1371/journal.pone.0246471	PMC7861356
PMC10013882	Discussion	Other studies have also suggested that while DSD models may not improve retention among currently eligible patients, who are already “stable” at the time of DSD model enrollment and thus likely to continue to demonstrate high retention, it can still offer other benefits to patients and providers by reducing costs and improving quality [18, 19].	10.12688/gatesopenres.13458.2	PMC8907143
PMC10013882	Discussion	Similarly, the same model may be assigned to different dispensing intervals for a slightly different population of patients [14].	10.1097/QAI.0000000000002634	PMC8126486
PMC10013922	Introduction	Streptococcus agalactiae, commonly known as Group B Streptococcus (GBS), is an important bacterial pathogen causing morbidity and mortality in pregnant women and their babies and is also increasingly recognised as a cause of disease in nonpregnant adults [1–3].	10.1016/S2214-109X(22)00093-6	PMC9090904
PMC10013922	Introduction	Streptococcus agalactiae, commonly known as Group B Streptococcus (GBS), is an important bacterial pathogen causing morbidity and mortality in pregnant women and their babies and is also increasingly recognised as a cause of disease in nonpregnant adults [1–3].	10.1093/cid/cix664	PMC5849940
PMC10013922	Introduction	In 2020, an estimated 20 million pregnant women globally were colonised with GBS resulting in 231,000 (114,000 to 455,000) cases of EOGBS and a further 162,000 (70,000 to 394,000) LOGBS cases [1].	10.1016/S2214-109X(22)00093-6	PMC9090904
PMC10013922	Introduction	Furthermore, survivors of iGBS are at risk of long-term neurological sequelae with an estimated 37,000 (14,000 to 96,000) surviving infants developing moderate or severe neurodevelopmental impairment (NDI) [1,4].	10.1016/S2214-109X(22)00093-6	PMC9090904
PMC10013922	Introduction	Furthermore, survivors of iGBS are at risk of long-term neurological sequelae with an estimated 37,000 (14,000 to 96,000) surviving infants developing moderate or severe neurodevelopmental impairment (NDI) [1,4].	10.1016/j.eclinm.2022.101358	PMC9142788
PMC10013922	Introduction	Many higher-income countries have reduced EOGBS incidence through IAP with eligible pregnant women identified either through risk factor–based screening or routine testing based on microbiological culture [5].	10.1093/cid/cix654	PMC5850619
PMC10013922	Introduction	In addition, the need for access to laboratory testing for microbiological screening–based strategies and the requirement to deliver antibiotics intravenously substantially limits the prospect of attaining high IAP coverage in many low-resource settings where the burden of iGBS is highest [5].	10.1093/cid/cix654	PMC5850619
PMC10013922	Introduction	There are also concerns that routine administration of antibiotics could contribute to antimicrobial resistance and might also have unintended impacts on the gut microbiota of newborns [6].	10.3389/fped.2018.00027	PMC5827363
PMC10013922	Introduction	In 2015, development of a maternal vaccine against GBS was identified as a priority by the WHO Product Development for Vaccines Advisory Committee (PDVAC) [9], and 3 GBS maternal vaccine candidates have progressed to Phase II clinical trials [10].	10.1016/j.vaccine.2017.09.087	PMC6892248
PMC10013922	Introduction	In 2015, development of a maternal vaccine against GBS was identified as a priority by the WHO Product Development for Vaccines Advisory Committee (PDVAC) [9], and 3 GBS maternal vaccine candidates have progressed to Phase II clinical trials [10].	10.2147/IDR.S203454	PMC7196769
PMC10013922	Introduction	There have been previous economic evaluations of maternal GBS vaccination in the United States [12–14], Europe [15–17], and sub-Saharan Africa [18–20].	10.1136/bmj.39325.681806.AD	PMC1995477

PMC10010521

Introduction

Globally, Shigella species are a leading cause of diarrhoeal mortality, causing an estimated 200,000 deaths in 2016 [11].

10.1016/S1473-3099(18)30475-4

PMC6202441

PMC10010521

Introduction

In contrast, the highest rates of shigellosis in high-income countries typically occur through person-to-person contact in crowded communities and childcare centres, in travellers returning from overseas or in MSM [9,13].

10.1093/jpids/piab045

PMC8744073

PMC10010521

Introduction

Increasing transmission of Shigella among MSM, particularly antimicrobial resistant strains, have been reported in several high-income countries, including the United States, Canada, Germany and the United Kingdom [14–17].

10.3201/eid2302.161203

PMC5324786

PMC10010521

Introduction

The most commonly reported species in high-income countries is S. sonnei, with this species accounting for over 80% of shigellosis infections in the United States and Israel, and over 50% of infections in the United Kingdom [18–20].

10.3201/eid2806.220131

PMC9155871

PMC10010521

Introduction

The most commonly reported species in high-income countries is S. sonnei, with this species accounting for over 80% of shigellosis infections in the United States and Israel, and over 50% of infections in the United Kingdom [18–20].

10.1128/JCM.01692-19

PMC7098776

PMC10010521

Introduction

Currently, PCR assays for detecting Shigella target the invasion plasmid antigen H (ipaH) gene, which is also common to entero-invasive Escherichia coli (EIEC) [25].

10.1128/JCM.42.5.2031-2035.2004

PMC404673

PMC10010521

Discussion

While S. flexneri is traditionally linked to low and middle income countries and S. sonnei to high income countries, in recent years the expansion of S. sonnei has been documented in many economically transitional regions in Asia, Latin America and the Middle East [28].

10.1371/journal.pntd.0003708

PMC4466244

PMC10010521

Discussion

Globally, data on the epidemiology of S. boydii is limited, with this species being predominantly endemic in the Indian Subcontinent [29].

10.1093/nar/gki954

PMC1278947

PMC10010521

Discussion

S. dysenteriae serotype 1, which is the only Shigella species and serotype that expresses the Shiga toxin gene, has high epidemic potential and has been identified as a cause of several large scale outbreaks of dysentery, particularly in settings associated with civil unrest [30–34].

10.1128/AEM.69.12.7028-7031.2003

PMC310026

PMC10010521

Discussion

S. dysenteriae serotype 1, which is the only Shigella species and serotype that expresses the Shiga toxin gene, has high epidemic potential and has been identified as a cause of several large scale outbreaks of dysentery, particularly in settings associated with civil unrest [30–34].

10.3389/fcimb.2016.00045

PMC4835486

PMC10010521

Discussion

This strain is also notorious for developing drug resistance, with epidemic strains typically resistant to multiple antibiotics [35,36].

10.1128/IAI.05814-11

PMC3232646

PMC10010521

Discussion

The epidemiology of S. dysenteriae is distinct from the other species of Shigella, with epidemics tending to disappear and then reappear years later, with few sporadic cases reported in between outbreaks [37,38].

10.1186/1471-2164-15-355

PMC4038718

PMC10010521

Discussion

The epidemiology of S. dysenteriae is distinct from the other species of Shigella, with epidemics tending to disappear and then reappear years later, with few sporadic cases reported in between outbreaks [37,38].

10.3389/fcimb.2017.00064

PMC5364150

PMC10010521

Discussion

While large scale outbreaks of S. dysenteriae serotype 1 were prevalent in the second half of the twentieth century in Asia, Africa and Central America, there has been a drastic decline in the incidence of S. dysenteriae in the last few decades, which remains largely unexplained [7,34,39].

10.1007/s40475-014-0019-6

PMC4126259

PMC10010521

Discussion

While large scale outbreaks of S. dysenteriae serotype 1 were prevalent in the second half of the twentieth century in Asia, Africa and Central America, there has been a drastic decline in the incidence of S. dysenteriae in the last few decades, which remains largely unexplained [7,34,39].

10.3389/fcimb.2016.00045

PMC4835486

PMC10010521

Discussion

It is widely documented that people living in remote areas have poorer health outcomes, including higher rates of hospitalisation and death, and also have more limited access to, and use of, health care services [41,42].

10.1017/S1463423620000481

PMC7737170

PMC10010521

Discussion

Antimicrobial resistance has also been reported in endemic strains of Shigella affecting First Nations Australians [45].

10.1007/s10096-020-04029-w

PMC7473701

PMC10010521

Discussion

Overcrowding and lack of safe removal and treatment of sewage has shown to be positively associated with gastrointestinal infections in First Nations Australian households [47].

10.3390/ijerph15122827

PMC6313733

PMC10010521

Discussion

Consistent with global trends, the burden of shigellosis in Australia was highest in children aged less than five years [31,48].

10.1371/journal.pmed.0030353

PMC1564174

PMC10010521

Discussion

Additionally, the low infectious dose of Shigella results in person-to-person transmission, which often occurs between children in childcare settings through close contact [7,51].

10.1007/s40475-014-0019-6

PMC4126259

PMC10010521

Discussion

This is likely to reflect ongoing transmission among MSM in these states, with outbreaks occurring over several years in three of the most populous states (Victoria (VIC), New South Wales (NSW) and Queensland) [23,52–54].

10.1128/JCM.40.4.1538-1540.2002

PMC140385

PMC10010521

Discussion

Several studies have demonstrated the increased capability of CIDT in identifying the aetiology of diarrhoeal patients when compared to culture dependent methods, with estimates ranging from two to four times when using CIDT [58–60].

10.1016/S0140-6736(16)31529-X

PMC5471845

PMC10010521

Discussion

Several studies have demonstrated the increased capability of CIDT in identifying the aetiology of diarrhoeal patients when compared to culture dependent methods, with estimates ranging from two to four times when using CIDT [58–60].

10.3389/fmicb.2016.00386

PMC4811922

PMC10010521

Discussion

The process to obtain this information is faster as WGS does not require the application of multiple subtyping methodologies [62].

10.1128/AEM.00165-19

PMC6585509

PMC10010521

Discussion

Additionally, WGS can differentiate between Shigella and EIEC, which have many biochemical properties and virulence genes in common [62,63].

10.1128/AEM.00165-19

PMC6585509

PMC10010531

Introduction

syphilis, gonorrhoea, chlamydia, and trichomoniasis [5].

10.1371/journal.pone.0143304

PMC4672879

PMC10010531

Introduction

hepatitis B, herpes simplex virus (HSV or herpes), HIV, and human papillomavirus (HPV) [5].

10.1371/journal.pone.0143304

PMC4672879

PMC10010531

Introduction

Mother-to-child transmission of STIs has effects like stillbirth, neonatal death, low-birth weight and prematurity, sepsis, pneumonia, neonatal conjunctivitis, and congenital deformities [6].

10.2471/BLT.18.228486

PMC6653813

PMC10010531

Introduction

STIs remain a major public health challenge for people belonging to high-risk groups (for HIV) around the world [6].

10.2471/BLT.18.228486

PMC6653813

PMC10010531

Materials and methods

Inclusion of studies from Grey literature will be carried out after being checked through a quality assessment tool (Axis Tool) [14].

10.1136/bmjopen-2016-011458

PMC5168618

PMC10010531

Materials and methods

6.0) generated modified data extraction form [16].

10.1186/s12859-018-2334-8

PMC6196404

PMC10010531

Materials and methods

To evaluate publication bias Egger’s [18] and Begg and Mazumdar’s [19] assessments will be used along with the Funnel diagram.

10.1136/bmj.315.7109.629

PMC2127453

PMC10010533

Introduction

SARS-CoV-2 primarily spreads via aerosols and droplets, and the degree of aerosolization is related to multiple factors, including ventilation [1–4].

10.1016/S0140-6736(21)00869-2

PMC8049599

PMC10010533

Introduction

SARS-CoV-2 primarily spreads via aerosols and droplets, and the degree of aerosolization is related to multiple factors, including ventilation [1–4].

10.1002/ppul.25330

PMC8014227

PMC10010533

Introduction

Within the built environment, the floor is the most common location where the virus can be detected [5–9].

10.1186/s40168-021-01083-0

PMC8186369

PMC10010533

Introduction

The floor was the most common surface where the virus was detected, and this observation has been replicated in other studies [5, 6, 8].

10.1136/thoraxjnl-2021-218035

PMC8646974

PMC10010533

Introduction

conducted a study at four hospitals in Korea assessing both air and surface contamination, as well as the impact of surface cleaning on the ability to detect SARS-CoV-2 [10].

10.3346/jkms.2020.35.e332

PMC7505729

PMC10010533

Introduction

They collected 330 swabs, of which 27% were positive for SARS-CoV-2 [10].

10.3346/jkms.2020.35.e332

PMC7505729

PMC10010533

Introduction

did not conduct serial swabs surrounding the patient, it is unknown how the viral burden surrounding a patient changes over space and time [8, 10].

10.3346/jkms.2020.35.e332

PMC7505729

PMC10010533

Introduction

One single-centre study in the United States swabbed within the rooms of patients with COVID-19 to determine how severity of illness and distance from the patient’s bed affected the recovery of SARS-CoV-2 from floors and high touch surfaces [11].

10.1017/ice.2021.530

PMC8755533

PMC10010533

Introduction

The probability of detecting SARS-CoV-2 from the floor was approximately 80% and did not vary over distance, but was higher for patients with more severe disease (e.g., requiring positive pressure ventilation) [11].

10.1017/ice.2021.530

PMC8755533

PMC10010533

Methods

For this study, we considered a positive result to be a Cq less than 45, which is an accepted cut-off used for environmental surveillance of SARS-CoV-2 [12].

10.1016/j.scitotenv.2021.146749

PMC8007530

PMC10010533

Discussion

We did not evaluate whether swabbing immediately after cleaning resulted in an inability to detect SARS-COV-2; however, prior studies have done so [10, 14, 15].

10.3346/jkms.2020.35.e332

PMC7505729

PMC10010533

Discussion

We did not evaluate whether swabbing immediately after cleaning resulted in an inability to detect SARS-COV-2; however, prior studies have done so [10, 14, 15].

10.1017/ice.2020.1278

PMC7653228

PMC10010533

Discussion

We did not evaluate whether swabbing immediately after cleaning resulted in an inability to detect SARS-COV-2; however, prior studies have done so [10, 14, 15].

10.1371/journal.pone.0261365

PMC8782535

PMC10010533

Discussion

In the study by Kim et al., RNA was not detected in a room routinely cleaned by disinfectant wipes, demonstrating how cleaning removes SARS-CoV-2 from the surface; however, RNA was detected in a room sprayed with disinfectant, suggesting disinfectant sprays may not be effective in reducing exposure [10].

10.3346/jkms.2020.35.e332

PMC7505729

PMC10010533

Discussion

Thus, our ability to consistently detect the virus at increasing distances from the patient’s bed goes against the historically referenced “Six-Foot Rule” [16].

10.1073/pnas.2018995118

PMC8092463

PMC10010533

Discussion

However, a prior study observed higher rates of surface contamination with SARS-CoV-2 for patients who required high-flow oxygen or positive pressure ventilation compared to hospitalized patients with less severe illness (OR = 1.6, 95% credible interval [CrI] 1.03–1.25) [11].

10.1017/ice.2021.530

PMC8755533

PMC10010538

Introduction

Injuries continue to have significant weight on the global disease burden, and are among the main causes of morbidity and mortality in adolescents, young people and adults [2].

10.1016/S0140-6736(20)30925-9

PMC7567026

PMC10010538

Introduction

Economic analysis of the implementation of interventions to assess the results and costs of these interventions aimed at improving the health of the population are recommended [4, 8] and are used to demonstrate the disease burden in monetary terms [9–11].

10.1371/journal.pone.0234300

PMC7282655

PMC10010538

Materials and methods

To estimate the disease burden of premature mortality, measures of years of potential life lost (YPLL), years of potential productive life lost (YPPLL) and cost of productivity lost CPL were used [9, 10, 19, 20].

10.1371/journal.pone.0234300

PMC7282655

PMC10010538

Materials and methods

To estimate the disease burden of premature mortality, measures of years of potential life lost (YPLL), years of potential productive life lost (YPPLL) and cost of productivity lost CPL were used [9, 10, 19, 20].

10.1136/bmjopen-2014-005386

PMC4127933

PMC10010538

Materials and methods

These concepts estimate the average time a person would live if they did not die prematurely, taking into account the age limit (death/retirement) and the cause [9].

10.1371/journal.pone.0234300

PMC7282655

PMC10010538

Materials and methods

For this study it was assumed that the individual’s productivity did not change until retirement [9].

10.1371/journal.pone.0234300

PMC7282655

PMC10010538

Discussion

The findings of this study were similar to those reported in similar studies where the active population accounted for the largest proportion of fatal victims due to injury [26, 28].

10.2471/BLT.14.145771

PMC4431514

PMC10010538

Discussion

[33, 34] reported traffic accidents and suicides as the principal external causes of death and finally, Corassa et al.

10.1155/2020/7303897

PMC7193292

PMC10010538

Discussion

The prevalence of suicide has been associated with mental disorders and sociodemographic characteristics and aggression with socioeconomic inequalities, alcohol and drug-related harm, respectively [26, 33].

10.2471/BLT.14.145771

PMC4431514

PMC10010538

Discussion

In addition, traffic accidents were among the leading causes of death in Sub-Saharan Africa and while globally, traffic accidents, falls and interpersonal violence were identified as the leading causes of death due to injury [25, 36].

10.1136/injuryprev-2015-041616

PMC4752630

PMC10010538

Discussion

Comprehensive road safety laws and their proper enforcement could contribute to the reduction of mortality from road accidents [25, 36].

10.1136/injuryprev-2015-041616

PMC4752630

PMC10010538

Discussion

In Seychelles, drowning was the leading cause of death due to external causes [41].

10.1038/s41598-020-79228-8

PMC7746745

PMC10010538

Discussion

[41] suggested the promotion of swimming programs as a measure to reduce the risk of drowning in the population.

10.1038/s41598-020-79228-8

PMC7746745

PMC10010538

Discussion

The estimated YPLL corresponded to a total of 7,222 and, a mean of 34.2 YPLL per death, which was higher than the mean obtained in Tanzania [9] and in line with the findings from Brazil which showed that males were responsible for the highest proportion of calculated YPLL, while the age ranges from 20 to 39 were responsible for approximately 60% of YPLL [35].

10.1371/journal.pone.0234300

PMC7282655

PMC10010538

Discussion

Similar to the current study, males contributed to a higher proportion of YPLL due to injuries, and overall injuries affected the potentially productive population [10, 35, 43].

10.1136/bmjopen-2014-005386

PMC4127933

PMC10010538

Discussion

In other studies, CPL due to injury was significantly higher among men than among women [10, 48].

10.1136/bmjopen-2014-005386

PMC4127933

PMC10010538

Discussion

In other studies, CPL due to injury was significantly higher among men than among women [10, 48].

10.5334/aogh.1355

PMC6997525

PMC10010538

Discussion

[10] reported that the highest average loss per death was due to trauma, amounting to 72,571 USD/death while Davey et al.

10.1136/bmjopen-2014-005386

PMC4127933

PMC10010538

Discussion

[48] presented a mean value of approximately 2500 USD per death.

10.5334/aogh.1355

PMC6997525

PMC10010538

Discussion

Results of this study demonstrate the need to standardize the classification of injuries and this could improve current estimates of mortality from external causes and complement national and global disease burden estimates [7, 26].

10.2471/BLT.14.145771

PMC4431514

PMC10010538

Discussion

Standardization can be achieved through regular training of health professionals on current guidelines [41] and the digitization of health information systems.

10.1038/s41598-020-79228-8

PMC7746745

PMC10010538

Discussion

Available data on economic costs of diseases, shows that two main methods are used to evaluate the economic impact, namely the friction method and the human capital method, with the human capital method being the most used methodology in cost-of-disease analyses [49].

10.1007/s40258-018-0416-4

PMC6467569

PMC10011442

Methods

Data preprocessing after the defacing included linear resampling to 2 mm isotropic resolution with the intensity scaled into a range of [-1,1].

10.5195/jmla.2017.88

PMC5370619

PMC10013005

Materials and Methods

The hyperparameter tuning is in the form of a 100-iteration randomized search of a set of predefined hyperparameter distributions:{‘max_iter’: [2000],‘loss’: [‘least_squares’],‘random_state’: [42],‘early_stopping’: [True],‘learning_rate’: loguniform(0.005, 0.1),‘max_leaf_nodes’: randint(2, 10),‘min_samples_leaf’: randint(100,200)}

10.6061/clinics/2019/e477

PMC6445156

PMC10013005

Materials and Methods

‘random_state’: [42],

10.6061/clinics/2019/e477

PMC6445156

PMC10013882

Introduction

Studies in sub-Saharan Africa (SSA) suggest that only 67% of patients remain in ART programs after five years, with loss to follow-up (patients with unknown outcomes) accounting for 33% of all attrition [1].

10.1002/jia2.25084

PMC5897849

PMC10013882

Introduction

DSD models aim to improve long-term ART retention by removing barriers to care, making service delivery more patient-centered [2], generate greater patient satisfaction, reduce costs to patients (and to providers in some cases), and create efficient and convenient service delivery [3].

10.1097/QAI.0000000000002070

PMC6625870

PMC10013882

Introduction

DSD models differ from conventional HIV care in the location of service delivery, frequency of interactions with the healthcare system, cadre of provider involved, and/or types of services provided [4].

10.1111/tmi.12460

PMC4670701

PMC10013882

Introduction

The attractiveness of DSD models is generally considered to be conditional on maintaining at least equivalent clinical outcomes to conventional care, but there remains relatively little evidence on ART retention among patients enrolled in DSD models as part of large-scale routine care in SSA [5, 6].

10.1186/s12889-021-11053-8

PMC8194040

PMC10013882

Introduction

The attractiveness of DSD models is generally considered to be conditional on maintaining at least equivalent clinical outcomes to conventional care, but there remains relatively little evidence on ART retention among patients enrolled in DSD models as part of large-scale routine care in SSA [5, 6].

10.1002/jia2.25640

PMC7696000

PMC10013882

Introduction

Zambia, a high-HIV burden country with more than 1.5 million people living with HIV and more than 81% of those individuals on ART, has rapidly scaled up a variety of DSD models [7].

10.1002/jia2.25808

PMC8554218

PMC10013882

Methods

The SmartCare database covers approximately three-quarters of all ART patients in Zambia, with the remainder accessing care at clinics that do not utilize the system [11].

10.1136/bmjopen-2019-030428

PMC6731929

PMC10013882

Methods

Source: Table modified from [6]

10.1002/jia2.25640

PMC7696000

PMC10013882

Discussion

Our findings are generally consistent with those of other studies of DSD model outcomes in SSA [5].

10.1186/s12889-021-11053-8

PMC8194040

PMC10013882

Discussion

Previous studies found high retention of patients in adherence clubs and home-based care models in South Africa and Kenya, among other countries [13, 14].

10.1371/journal.pmed.1002874

PMC6650049

PMC10013882

Discussion

Previous studies found high retention of patients in adherence clubs and home-based care models in South Africa and Kenya, among other countries [13, 14].

10.1097/QAI.0000000000002634

PMC8126486

PMC10013882

Discussion

Studies in Zambia have showed that DSD models achieve comparable or better outcomes than conventional care [15, 16].

10.1097/QAD.0000000000002737

PMC7810408

PMC10013882

Discussion

Studies in Zambia have showed that DSD models achieve comparable or better outcomes than conventional care [15, 16].

10.1371/journal.pmed.1003116

PMC7329062

PMC10013882

Discussion

In ART programs in SSA, males have traditionally been at higher risk of attrition than females [17], but we found that rural males in most DSD models in Zambia were retained in care as well as or relatively better than females in the same models and settings.

10.1371/journal.pone.0246471

PMC7861356

PMC10013882

Discussion

Other studies have also suggested that while DSD models may not improve retention among currently eligible patients, who are already “stable” at the time of DSD model enrollment and thus likely to continue to demonstrate high retention, it can still offer other benefits to patients and providers by reducing costs and improving quality [18, 19].

10.12688/gatesopenres.13458.2

PMC8907143

PMC10013882

Discussion

Similarly, the same model may be assigned to different dispensing intervals for a slightly different population of patients [14].

10.1097/QAI.0000000000002634

PMC8126486

PMC10013922

Introduction

Streptococcus agalactiae, commonly known as Group B Streptococcus (GBS), is an important bacterial pathogen causing morbidity and mortality in pregnant women and their babies and is also increasingly recognised as a cause of disease in nonpregnant adults [1–3].

10.1016/S2214-109X(22)00093-6

PMC9090904

PMC10013922

Introduction

Streptococcus agalactiae, commonly known as Group B Streptococcus (GBS), is an important bacterial pathogen causing morbidity and mortality in pregnant women and their babies and is also increasingly recognised as a cause of disease in nonpregnant adults [1–3].

10.1093/cid/cix664

PMC5849940

PMC10013922

Introduction

In 2020, an estimated 20 million pregnant women globally were colonised with GBS resulting in 231,000 (114,000 to 455,000) cases of EOGBS and a further 162,000 (70,000 to 394,000) LOGBS cases [1].

10.1016/S2214-109X(22)00093-6

PMC9090904

PMC10013922

Introduction

Furthermore, survivors of iGBS are at risk of long-term neurological sequelae with an estimated 37,000 (14,000 to 96,000) surviving infants developing moderate or severe neurodevelopmental impairment (NDI) [1,4].

10.1016/S2214-109X(22)00093-6

PMC9090904

PMC10013922

Introduction

Furthermore, survivors of iGBS are at risk of long-term neurological sequelae with an estimated 37,000 (14,000 to 96,000) surviving infants developing moderate or severe neurodevelopmental impairment (NDI) [1,4].

10.1016/j.eclinm.2022.101358

PMC9142788

PMC10013922

Introduction

Many higher-income countries have reduced EOGBS incidence through IAP with eligible pregnant women identified either through risk factor–based screening or routine testing based on microbiological culture [5].

10.1093/cid/cix654

PMC5850619

PMC10013922

Introduction

In addition, the need for access to laboratory testing for microbiological screening–based strategies and the requirement to deliver antibiotics intravenously substantially limits the prospect of attaining high IAP coverage in many low-resource settings where the burden of iGBS is highest [5].

10.1093/cid/cix654

PMC5850619

PMC10013922

Introduction

There are also concerns that routine administration of antibiotics could contribute to antimicrobial resistance and might also have unintended impacts on the gut microbiota of newborns [6].

10.3389/fped.2018.00027

PMC5827363

PMC10013922

Introduction

In 2015, development of a maternal vaccine against GBS was identified as a priority by the WHO Product Development for Vaccines Advisory Committee (PDVAC) [9], and 3 GBS maternal vaccine candidates have progressed to Phase II clinical trials [10].

10.1016/j.vaccine.2017.09.087

PMC6892248

PMC10013922

Introduction

In 2015, development of a maternal vaccine against GBS was identified as a priority by the WHO Product Development for Vaccines Advisory Committee (PDVAC) [9], and 3 GBS maternal vaccine candidates have progressed to Phase II clinical trials [10].

10.2147/IDR.S203454

PMC7196769

PMC10013922

Introduction

There have been previous economic evaluations of maternal GBS vaccination in the United States [12–14], Europe [15–17], and sub-Saharan Africa [18–20].

10.1136/bmj.39325.681806.AD

PMC1995477