Journal Article > ResearchFull Text
J. Infect.. 2020 January 17; Volume 80 (Issue 3); DOI:10.1016/j.jinf.2019.11.023
Linton NM, Keita M, de Almeida MM, Cuesta JG, Guha-Sapir D, et al.
J. Infect.. 2020 January 17; Volume 80 (Issue 3); DOI:10.1016/j.jinf.2019.11.023
OBJECTIVE:
To estimate the time-dependent measles effective reproduction number (Rt) as an indicator of the impact of three outbreak response vaccination (ORV) campaigns on measles transmission during a nationwide outbreak in Guinea.
METHODS:
Rt represents the average number of secondary cases generated by a single primary case in a partially immune population during a given time period. Measles Rt was estimated using daily incidence data for 3,952 outbreak-associated measles cases in Guinea in 2017 for the time periods prior to, between, and following each of three ORV campaigns using a simple and extensible mathematical model.
RESULTS:
Rt was estimated to be above the threshold value of 1 during the initial growth period of the outbreak until the first ORV campaign began on March 13 (Rt =1.60, 95% CI: 1.55-1.67). It subsequently dropped below 1 and remained < 1 through the end of the year (range: 0.71-0.91), although low levels of transmission persisted.
CONCLUSIONS:
Reduction in Rt coincided with implementation of the ORV campaigns, indicating success of the campaigns at maintaining measles transmission intensity below epidemic growth levels. However, persistent measles transmission remains an issue in Guinea due to insufficient levels of herd immunity. Estimation of Rt should be further leveraged to help decision makers and field staff understand outbreak progress and the timing and type of vaccination efforts needed to halt transmission.
To estimate the time-dependent measles effective reproduction number (Rt) as an indicator of the impact of three outbreak response vaccination (ORV) campaigns on measles transmission during a nationwide outbreak in Guinea.
METHODS:
Rt represents the average number of secondary cases generated by a single primary case in a partially immune population during a given time period. Measles Rt was estimated using daily incidence data for 3,952 outbreak-associated measles cases in Guinea in 2017 for the time periods prior to, between, and following each of three ORV campaigns using a simple and extensible mathematical model.
RESULTS:
Rt was estimated to be above the threshold value of 1 during the initial growth period of the outbreak until the first ORV campaign began on March 13 (Rt =1.60, 95% CI: 1.55-1.67). It subsequently dropped below 1 and remained < 1 through the end of the year (range: 0.71-0.91), although low levels of transmission persisted.
CONCLUSIONS:
Reduction in Rt coincided with implementation of the ORV campaigns, indicating success of the campaigns at maintaining measles transmission intensity below epidemic growth levels. However, persistent measles transmission remains an issue in Guinea due to insufficient levels of herd immunity. Estimation of Rt should be further leveraged to help decision makers and field staff understand outbreak progress and the timing and type of vaccination efforts needed to halt transmission.
Journal Article > ResearchFull Text
J. Infect.. 2021 July 1; Volume 83 (Issue 1); 84-91.; DOI:10.1016/j.jinf.2021.04.013
Farooq HZ, Davies E, Brown B, Whitfield T, Tilston P, et al.
J. Infect.. 2021 July 1; Volume 83 (Issue 1); 84-91.; DOI:10.1016/j.jinf.2021.04.013
OBJECTIVES
SARS-CoV-2 emerged in South Asia in 2019 and has resulted in a global pandemic. Public Health England (PHE) Manchester rapidly escalated testing for SARS-CoV-2 in the highest COVID-19 incidence location in England. The results of the PHE Manchester SARS-CoV-2 surveillance during the first wave are presented.
METHODS
Retrospective data were collected for patients fitting the PHE SARS-CoV-2 case definition from 11th February to 31st August 2020. Respiratory tract, tissue, faecal, fluid and cerebrospinal (CSF) samples were tested for SARS-CoV-2 by a semi-quantitative real-time reverse-transcription PCR.
RESULTS
Of the 204,083 tests for SARS-CoV-2, 18,011 were positive demonstrating a positivity of 8.90%. Highest positivity was in nasal swabs (20.99%) followed by broncheo-alveolar lavage samples (12.50%). None of the faecal, fluid or CSF samples received were positive for SARS-CoV-2.
CONCLUSIONS
There was a high incidence of SARS-CoV-2 patients in the North-West of England during the first UK wave of the Covid-19 pandemic. Highest positivity rate was in nasal specimens suggesting this is the optimum sample type within this dataset for detecting SARS-CoV-2. Further studies are warranted to assess the utility of testing faecal, fluid and CSF samples. Rapid escalation of testing via multiple platforms was required to ensure prompt diagnosis and isolate infected cases to reduce transmission of the virus.
SARS-CoV-2 emerged in South Asia in 2019 and has resulted in a global pandemic. Public Health England (PHE) Manchester rapidly escalated testing for SARS-CoV-2 in the highest COVID-19 incidence location in England. The results of the PHE Manchester SARS-CoV-2 surveillance during the first wave are presented.
METHODS
Retrospective data were collected for patients fitting the PHE SARS-CoV-2 case definition from 11th February to 31st August 2020. Respiratory tract, tissue, faecal, fluid and cerebrospinal (CSF) samples were tested for SARS-CoV-2 by a semi-quantitative real-time reverse-transcription PCR.
RESULTS
Of the 204,083 tests for SARS-CoV-2, 18,011 were positive demonstrating a positivity of 8.90%. Highest positivity was in nasal swabs (20.99%) followed by broncheo-alveolar lavage samples (12.50%). None of the faecal, fluid or CSF samples received were positive for SARS-CoV-2.
CONCLUSIONS
There was a high incidence of SARS-CoV-2 patients in the North-West of England during the first UK wave of the Covid-19 pandemic. Highest positivity rate was in nasal specimens suggesting this is the optimum sample type within this dataset for detecting SARS-CoV-2. Further studies are warranted to assess the utility of testing faecal, fluid and CSF samples. Rapid escalation of testing via multiple platforms was required to ensure prompt diagnosis and isolate infected cases to reduce transmission of the virus.
Journal Article > ResearchFull Text
J. Infect.. 2004 May 1; Volume 48 (Issue 4); DOI:10.1016/S0163-4453(03)00122-1
Colebunders R
J. Infect.. 2004 May 1; Volume 48 (Issue 4); DOI:10.1016/S0163-4453(03)00122-1
Organising health care was one of the tasks of the International Scientific and Technical Committee during the 1998-1999 outbreak in Durba/Watsa, in the north-eastern province (Province Orientale), Democratic Republic of Congo. With the logistical support of Médecins sans Frontières (MSF), two isolation units were created: one at the Durba Reference Health Centre and the other at the Okimo Hospital in Watsa. Between May 6th, the day the isolation unit was installed and May 19th, 15 patients were admitted to the Durba Health Centre. In only four of them were the diagnosis of Marburg haemorrhagic fever (MHF) confirmed by laboratory examination. Protective equipment was distributed to health care workers and family members caring for patients. Information about MHF, modes of transmission and the use of barrier nursing techniques was provided to health care workers and sterilisation procedures were reviewed. In contrast to Ebola outbreaks, there was little panic among health care workers and the general public in Durba and all health services remained operational.
Journal Article > ResearchAbstract Only
J. Infect.. 2022 May 16; Volume S0163-4453 (Issue 22); 00292-4.; DOI:10.1016/j.jinf.2022.05.010
Dhana A, Hamada Y, Kengne AP, Kerkhoff AD, Broger T, et al.
J. Infect.. 2022 May 16; Volume S0163-4453 (Issue 22); 00292-4.; DOI:10.1016/j.jinf.2022.05.010
BACKGROUND
WHO recommends urine lateral-flow lipoarabinomannan (LF-LAM) testing with AlereLAM in HIV-positive inpatients only if screening criteria are met. We assessed the performance of WHO screening criteria and alternative screening tests/strategies to guide LF-LAM testing and compared diagnostic accuracy of the WHO AlereLAM algorithm (WHO screening criteria → AlereLAM) with AlereLAM and FujiLAM (a novel LF-LAM test).
METHODS
We searched MEDLINE, Embase, and Cochrane Library from Jan 1, 2011 to March 1, 2020 for studies among adult/adolescent HIV-positive inpatients regardless of tuberculosis signs and symptoms. The reference standards were 1) AlereLAM or FujiLAM for screening tests/strategies and 2) culture or Xpert for AlereLAM/FujiLAM. We determined proportion of inpatients eligible for AlereLAM using WHO screening criteria; assessed accuracy of WHO criteria and alternative screening tests/strategies to guide LF-LAM testing; compared accuracy of WHO AlereLAM algorithm with AlereLAM/FujiLAM in all; and determined diagnostic yield of AlereLAM, FujiLAM, and Xpert MTB/RIF (Xpert). We estimated pooled proportions with a random-effects model, assessed diagnostic accuracy using random-effects bivariate models, and assessed diagnostic yield descriptively.
FINDINGS
We obtained data from all 5 identified studies (n=3,504). The pooled proportion of inpatients eligible for AlereLAM using WHO criteria was 93% (95%CI 91, 95). Among screening tests/strategies to guide LF-LAM testing, WHO criteria, C-reactive protein (≥5 mg/L), and CD4 count (<200 cells/μL) had high sensitivities but low specificities; cough (≥2 weeks), haemoglobin (<8 g/dL), body mass index (<18.5 kg/m2), lymphadenopathy, and WHO-defined danger signs had higher specificities but suboptimal sensitivities. AlereLAM in all had the same sensitivity (62%) and specificity (88%) as WHO AlereLAM algorithm. Sensitivity of FujiLAM and AlereLAM was 69% and 48%, while specificity was 48% and 96%, respectively. Diagnostic yield of sputum Xpert was 29-41%, AlereLAM was 39-76%, and urine Xpert was 35-62%. In one study, FujiLAM diagnosed 80% of tuberculosis cases (vs 39% for AlereLAM), and sputum Xpert combined with AlereLAM, urine Xpert, or FujiLAM diagnosed 69%, 81%, and 92% of all cases, respectively.
INTERPRETATION
WHO criteria and alternative screening tests/strategies have limited utility in guiding LF-LAM testing, suggesting that AlereLAM testing in all HIV-positive medical inpatients be implemented. Routine FujiLAM may improve tuberculosis diagnosis.
WHO recommends urine lateral-flow lipoarabinomannan (LF-LAM) testing with AlereLAM in HIV-positive inpatients only if screening criteria are met. We assessed the performance of WHO screening criteria and alternative screening tests/strategies to guide LF-LAM testing and compared diagnostic accuracy of the WHO AlereLAM algorithm (WHO screening criteria → AlereLAM) with AlereLAM and FujiLAM (a novel LF-LAM test).
METHODS
We searched MEDLINE, Embase, and Cochrane Library from Jan 1, 2011 to March 1, 2020 for studies among adult/adolescent HIV-positive inpatients regardless of tuberculosis signs and symptoms. The reference standards were 1) AlereLAM or FujiLAM for screening tests/strategies and 2) culture or Xpert for AlereLAM/FujiLAM. We determined proportion of inpatients eligible for AlereLAM using WHO screening criteria; assessed accuracy of WHO criteria and alternative screening tests/strategies to guide LF-LAM testing; compared accuracy of WHO AlereLAM algorithm with AlereLAM/FujiLAM in all; and determined diagnostic yield of AlereLAM, FujiLAM, and Xpert MTB/RIF (Xpert). We estimated pooled proportions with a random-effects model, assessed diagnostic accuracy using random-effects bivariate models, and assessed diagnostic yield descriptively.
FINDINGS
We obtained data from all 5 identified studies (n=3,504). The pooled proportion of inpatients eligible for AlereLAM using WHO criteria was 93% (95%CI 91, 95). Among screening tests/strategies to guide LF-LAM testing, WHO criteria, C-reactive protein (≥5 mg/L), and CD4 count (<200 cells/μL) had high sensitivities but low specificities; cough (≥2 weeks), haemoglobin (<8 g/dL), body mass index (<18.5 kg/m2), lymphadenopathy, and WHO-defined danger signs had higher specificities but suboptimal sensitivities. AlereLAM in all had the same sensitivity (62%) and specificity (88%) as WHO AlereLAM algorithm. Sensitivity of FujiLAM and AlereLAM was 69% and 48%, while specificity was 48% and 96%, respectively. Diagnostic yield of sputum Xpert was 29-41%, AlereLAM was 39-76%, and urine Xpert was 35-62%. In one study, FujiLAM diagnosed 80% of tuberculosis cases (vs 39% for AlereLAM), and sputum Xpert combined with AlereLAM, urine Xpert, or FujiLAM diagnosed 69%, 81%, and 92% of all cases, respectively.
INTERPRETATION
WHO criteria and alternative screening tests/strategies have limited utility in guiding LF-LAM testing, suggesting that AlereLAM testing in all HIV-positive medical inpatients be implemented. Routine FujiLAM may improve tuberculosis diagnosis.
Journal Article > ResearchAbstract Only
J. Infect.. 2023 June 25; Volume S0163-4453 (Issue 23); 00336-5.; DOI:10.1016/j.jinf.2023.06.015
Jacquier H, Assao B, Chau F, Guindo O, Condamine B, et al.
J. Infect.. 2023 June 25; Volume S0163-4453 (Issue 23); 00336-5.; DOI:10.1016/j.jinf.2023.06.015
OBJECTIVE
Whole genome sequencing (WGS) of extended-spectrum ß-lactamase-producing Escherichia coli (ESBL-E. coli) in developing countries is lacking. Here we describe the population structure and molecular characteristics of ESBL-E. coli faecal isolates in rural Southern Niger.
METHODS
Stools of 383 healthy participants were collected among which 92.4% were ESBL-Enterobacterales carriers. A subset of 90 ESBL-E. coli containing stools (109 ESBL-E. coli isolates) were further analysed by WGS, using short- and long-reads.
RESULTS
Most isolates belonged to the commensalism-adapted phylogroup A (83.5%), with high clonal diversity. The blaCTX-M-15 gene was the major ESBL determinant (98.1%), chromosome-integrated in approximately 50% of cases, in multiple integration sites. When plasmid-borne, blaCTX-M-15 was found in IncF (57.4%) and IncY plasmids (26.2%). Closely related plasmids were found in different genetic backgrounds. Genomic environment analysis of blaCTX-M-15 in closely related strains argued for mobilisation between plasmids or from plasmid to chromosome.
CONCLUSIONS
Massive prevalence of community faecal carriage of CTX-M-15-producing E. coli was observed in a rural region of Niger due to the spread of highly diverse A phylogroup commensalism-adapted clones, with frequent chromosomal integration of blaCTX-M-15. Plasmid spread was also observed. These data suggest a risk of sustainable implementation of ESBL in community faecal carriage.
Whole genome sequencing (WGS) of extended-spectrum ß-lactamase-producing Escherichia coli (ESBL-E. coli) in developing countries is lacking. Here we describe the population structure and molecular characteristics of ESBL-E. coli faecal isolates in rural Southern Niger.
METHODS
Stools of 383 healthy participants were collected among which 92.4% were ESBL-Enterobacterales carriers. A subset of 90 ESBL-E. coli containing stools (109 ESBL-E. coli isolates) were further analysed by WGS, using short- and long-reads.
RESULTS
Most isolates belonged to the commensalism-adapted phylogroup A (83.5%), with high clonal diversity. The blaCTX-M-15 gene was the major ESBL determinant (98.1%), chromosome-integrated in approximately 50% of cases, in multiple integration sites. When plasmid-borne, blaCTX-M-15 was found in IncF (57.4%) and IncY plasmids (26.2%). Closely related plasmids were found in different genetic backgrounds. Genomic environment analysis of blaCTX-M-15 in closely related strains argued for mobilisation between plasmids or from plasmid to chromosome.
CONCLUSIONS
Massive prevalence of community faecal carriage of CTX-M-15-producing E. coli was observed in a rural region of Niger due to the spread of highly diverse A phylogroup commensalism-adapted clones, with frequent chromosomal integration of blaCTX-M-15. Plasmid spread was also observed. These data suggest a risk of sustainable implementation of ESBL in community faecal carriage.