Correction: High seroprevalence of antibodies against SARS-CoV-2 among healthcare workers 8 months after the first wave in Aden, Yemen.

[This corrects the article DOI: 10.1371/journal.pgph.0000767.].

Application of diagnostic network optimization in Kenya and Nepal to design integrated, sustainable and efficient bacteriology and antimicrobial resistance surveillance networks.

Antimicrobial resistance (AMR) is a major global public health concern, particularly in low- and middle-income countries, which experience the highest burden of AMR. Critical to combatting AMR is ensuring there are effective, accessible diagnostic networks in place to diagnose, monitor and prevent AMR, but many low- and middle-income countries lack such networks. Consequently, there is substantial need for approaches that can inform the design of efficient AMR laboratory networks and sample referral systems in lower-resource countries. Diagnostic network optimization (DNO) is a geospatial network analytics approach to plan diagnostic networks and ensure greatest access to and coverage of services, while maximizing the overall efficiency of the system. In this intervention, DNO was applied to strengthen bacteriology and AMR surveillance network design in Kenya and Nepal for human and animal health, by informing linkages between health facilities and bacteriology testing services and sample referral routes between farms, health facilities and laboratories. Data collected from the target settings in each country were entered into the open-access DNO tool OptiDx, to generate baseline scenarios, which depicted the current state of AMR laboratory networks and sample referral systems in the countries. Subsequently, baselines were adjusted to evaluate changing factors such as samples flows, transport frequency, transport costs, and service distances. Country stakeholders then compared resulting future scenarios to identify the most feasible solution for their context. The DNO analyses enabled a wealth of insights that will facilitate strengthening of AMR laboratory and surveillance networks in both countries. Overall, the project highlights the benefits of using a data-driven approach for designing efficient diagnostic networks, to ensure better health resource allocation while maximizing the impact and equity of health interventions. Given the critical need to strengthen AMR laboratory and surveillance capacity, DNO should be considered an integral part of diagnostic strategic planning in the future.

Seroprevalence of anti-SARS-CoV-2 antibodies among blood donors from December 2020 to June 2021 in Koutiala district, Mali.

Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is the virus associated with coronavirus disease (COVID-19). At the time of the study, little data on the level of exposure of the population in Koutiala district in Mali to SARS-CoV-2 was available. Although blood donors are not representative of the general population, a COVID-19 seroprevalence estimate in this population was intended to assess the extent of community transmission, serve as a health alert system, and help guide the public health response. We measured seroprevalence of anti-SARS-CoV-2 antibodies using NG-Biotech SARS-Cov-2 RDT and ECLIA test between January and June 2020. This is a cross-sectional study of volunteer blood donors aged 18 to 60 years, independent of any previous COVID-19 disease. A stratified analysis of seroprevalence by month of sample collection and a comparison of the results of the NG-Biotech SARS-Cov-2 RDT with those of the ECLIA test was performed. The overall prevalence of antibodies to SARS-Cov-2 virus assessed by the NG-Biotech SARS-Cov-2 RDT was 24.6% (95% CI 21.8-27.4) and by the ECLIA test was 70.2 (95% CI 64.9-75.5). Both estimates remained relatively stable over the study period. We observed SARS-CoV-2 exposure much higher than indicated by case-based surveillance. The national surveillance system, as it was, was not able to detect variations in incidence, and as such, we do not recommend it as an alert system. However, the discrepancy between the results of the rapid test and the ECLIA test shows that further research is required to assess the validity of these test before a more solid conclusion can be drawn it their use in surveillance.

Performance Comparison of Infection Prediction Scores in a South African Neonatal Unit: A Retrospective Case-Control Study.

Background and objectives: Infection prediction scores are useful ancillary tests in determining the likelihood of neonatal hospital-acquired infection (HAI), particularly in very low birth weight (VLBW; <1,500 g) infants who are most vulnerable to HAI and have high antibiotic utilization rates. None of the existing infection prediction scores were developed for or evaluated in South African VLBW neonates. Methods: We identified existing infection prediction scores through literature searches and assessed each score for suitability and feasibility of use in resource-limited settings. Performance of suitable scores were compared using a retrospective dataset of VLBW infants (2016-2017) from a tertiary hospital neonatal unit in Cape Town, South Africa. Sensitivity, specificity, predictive values, and likelihood ratios were calculated for each score. Results: Eleven infection prediction scores were identified, but only five were suitable for use in resource-limited settings (NOSEP1, Singh, Rosenberg, and Bekhof scores). The five selected scores were evaluated using data from 841 episodes of HAI in 659 VLBW infants. The sensitivity for the scores ranged between 3% (NOSEP1 ≥14; proven and presumed infection), to a maximum of 74% (Singh score ≥1; proven infection). The specificity of these scores ranged from 31% (Singh score ≥1; proven and presumed infection) to 100% (NOSEP1 ≥11 and ≥14, NOSEP-NEW-1 ≥11; proven and presumed infection). Conclusion: Existing infection prediction scores did not achieve comparable predictive performance in South African VLBW infants and should therefore only be used as an adjunct to clinical judgment in antimicrobial decision making. Future studies should develop infection prediction scores that have high diagnostic accuracy and are feasible to implement in resource-limited neonatal units.

Utility of InTray COLOREX Screen agar and InTray COLOREX ESBL agar for urine culture in the Lao PDR.

BACKGROUND: There is a need for simple microbiology diagnostics to enable antimicrobial resistance surveillance in low- and middle-income countries. OBJECTIVES: To investigate the field utility of InTray COLOREX plates for urine culture and ESBL detection. METHODS: Clinical urine samples from Mahosot Hospital, Vientiane, Lao PDR were inoculated onto chromogenic media and InTray COLOREX Screen plates between June and August 2020. Urine and isolates from other clinical specimens were inoculated onto COLOREX ESBL plates. A simulated field study investigating the field utility of the InTray COLOREX plates was also completed. RESULTS: In total, 355 urine samples were inoculated onto standard chromogenic agar and InTray COLOREX Screen plates, and 154 urine samples and 54 isolates from other clinical specimens on the COLOREX ESBL plates. Growth was similar for the two methods (COLOREX Screen 41%, standard method 38%) with 20% discordant results, mainly due to differences in colony counts or colonial appearance. Contamination occurred in 13% of samples, with the COLOREX Screen plates showing increased contamination rates, potentially due to condensation. ESBL producers were confirmed from 80% of isolates from the COLOREX ESBL plates, and direct plating provided rapid detection of presumptive ESBL producers. Burkholderia pseudomallei also grew well on the ESBL plates, a relevant finding in this melioidosis-endemic area. CONCLUSIONS: The InTray COLOREX Screen and ESBL plates were simple to use and interpret, permitting rapid detection of uropathogens and ESBLs, and have the potential for easy transport and storage from field sites and use in laboratories with low capacity.

High seroprevalence of antibodies against SARS-CoV-2 among healthcare workers 8 months after the first wave in Aden, Yemen.

The true burden of COVID-19 in Yemen is underestimated. The healthcare system is dysfunctional and there is a high shortage of health care workers in the country. Testing for SARS-CoV-2 remains limited and official surveillance data is restricted to those who are severe or highly suspected. In this study, Médecins Sans Frontières (MSF) aimed to conduct serological screening using rapid tests for asymptomatic staff at the MSF Aden Trauma Center to determine the SARS-CoV-2 antibody seropositivity. Four months after the peak of the first wave, we offered all the staff at the MSF Aden Trauma Center PCR if symptomatic, and a baseline SARS-CoV-2 serology screening followed by follow-up screenings. A final round was scheduled four months after the baseline. A rapid serology lateral flow test, NG-Test IgM-IgG was used in all rounds and in the final round, an electrochemiluminescence immunoassay (ECLIA) (Elecsys Anti-SARS-CoV-2 assay). Univariate and multivariate analyses were used to identify risk factors for seropositivity. The level of agreement between the different serology assays used was investigated. Overall 69 out of 356 participants (19.4%, 95% CI 17.9-20.8) tested positive by NG-Test between September and November 2020. A sub-sample of 161 staff members were retested in January 2021. Of these, the NG-Test detected only 13 positive cases, whereas the ECLIA detected 109 positive cases. The adjusted seroprevalence by ECLIA was 59% (95%CI 52.2-65.9). The non-medical staff had significantly lower odds of seropositivity compared to the medical staff (AOR 0.43, 95% CI 0.15-0.7, p<0.001). The positive percent agreement between the two tests was very low (11%). Our results suggest a very high SARS-CoV-2 seroprevalence in healthcare workers in Yemen, highlighting the need for regular testing and rapid vaccination of all healthcare workers in the country.

Performance of six rapid diagnostic tests for SARS-CoV-2 antigen detection and implications for practical use.

BACKGROUND: Direct detection of SARS-CoV-2 viral proteins in nasopharyngeal swabs using lateral flow immunoassays is a simple, fast and cheap approach to diagnose the infection. AIMS AND METHODS: The performance of 6 SARS-CoV-2 antigen rapid diagnostic tests has been assessed in 634 hospitalized patients or outpatients including 297 patients found to be positive for SARS-CoV-2 RNA by means of RT-PCR and 337 patients presumed to be SARS-CoV-2 RNA-negative. RESULTS: The specificity of SARS-CoV-2 RDTs was generally high (398.5%). One assay had a lower specificity of 93.2%. The overall sensitivity of the 6 RDTs was variable, from 32.3% to 61.7%. Sensitivity correlated with the delay of sampling after the onset of symptoms and the viral load estimated by the Ct value in RT-PCR. Four out of 6 RDTs tested achieved sensitivities 380% when clinical specimens were collected during the first 3 days following symptom onset or with a Ct value ≤25. CONCLUSIONS: The present study shows that SARS-CoV-2 antigen can be easily and reliably detected by RDTs. These tests are easy and rapid to perform. However, the specificity and sensitivity of COVID-19 antigen RDTs may widely vary across different tests and must therefore be carefully evaluated before releasing these assays for realworld applications.

Evaluation of the InTray and Compact Dry culture systems for the diagnosis of urinary tract infections in patients presenting to primary health clinics in Harare, Zimbabwe.

Antimicrobial resistance surveillance data is lacking from many resource-limited settings mainly due to limited laboratory testing. Novel culture systems may address some of the limitations of conventional culture media and expand the availability of microbiology services. The aims of this study were to evaluate the performance of InTray COLOREX Screen/ESBL and Compact Dry for the detection of uropathogens and of extended-spectrum beta-lactamase (ESBL)-producing organisms from urine samples. Urines samples were collected from patients presenting with symptoms of urinary tract infection to primary care clinics in Harare. Performance of the InTray COLOREX Screen, ESBL and Compact Dry chromogenic media were compared to the reference of culture using Brilliance UTI agar and conventional antimicrobial susceptibility testing. A total of 414 samples were included in the analysis. Of the included samples, 98 were positive on Brilliance UTI agar and 83 grew Enterobacterales. The sensitivities and specificities for Enterobacterales were 89.2% (95% CI 80.4-94.9) and 98.2% (95% CI 96.1-99.3) for InTray Screen and 95.2% (95% CI 88.1-98.7) and 99.7% (95% CI 98.3-100) for Compact Dry. Extended-spectrum beta-lactamases were present in 22 isolates from the Brilliance UTI agar. The sensitivity of the InTray COLOREX ESBL culture plates for the detection of ESBL-producing organisms was 95.5% (95% CI 77.2-99.9) and specificity was 99.5% (95% CI 98.2-99.9%). Our findings show good performance of the novel culture systems for the detection of uropathogens and ESBL-producing organisms. Both systems have several advantages over conventional media and have the potential to expand and decentralize laboratory testing.

Evaluation of a Novel Culture System for Rapid Pathogen Identification and Detection of Cephalosporin Resistance in Neonatal Gram-negative Sepsis at a Tertiary Referral Unit in Harare, Zimbabwe.

BACKGROUND: Neonatal sepsis accounts for a large proportion of neonatal deaths in sub-Saharan Africa. The lack of access to diagnostic testing and excessively long turnaround times to result contributes to delays in sepsis identification and initiation of appropriate treatment. This study aims to evaluate the novel InTrays COLOREX Screen and extended-spectrum beta-lactamase for rapid identification of bacterial pathogens causing sepsis and detection of resistance. METHODS: Neonates with suspected sepsis admitted to the Harare Central Hospital were prospectively enrolled. One blood culture was collected and incubated using the BacT/ALERT automated system. Positive blood cultures with potential pathogens identified by Gram stain were inoculated on the InTray COLOREX Screen and extended-spectrum beta-lactamase culture plates. RESULTS: A total of 216 neonates with suspected sepsis were recruited. Pathogens were isolated from blood cultures in 56 (25.9%) neonates of which 54 were Klebsiella pneumoniae. All K. pneumoniae were resistant to ceftriaxone and 53 (98%) were resistant to gentamicin. Sensitivity and specificity for ceftriaxone-resistant K. pneumoniae detection using InTrays were 100%. InTrays results were interpretable as early as 5-10 hours (median 7 hours, interquartile range 7-7) post blood culture positivity enabling rapid identification and notification of result and leading to a 60% reduction in time to result from blood culture collection. CONCLUSIONS: This study shows that the implementation of a novel culture method was feasible and reduced turnaround times for results by 60% compared with standard microbiologic techniques. An impact on patient outcomes and cost-effectiveness of this method needs to be demonstrated.

AI-based mobile application to fight antibiotic resistance.

Antimicrobial resistance is a major global health threat and its development is promoted by antibiotic misuse. While disk diffusion antibiotic susceptibility testing (AST, also called antibiogram) is broadly used to test for antibiotic resistance in bacterial infections, it faces strong criticism because of inter-operator variability and the complexity of interpretative reading. Automatic reading systems address these issues, but are not always adapted or available to resource-limited settings. We present an artificial intelligence (AI)-based, offline smartphone application for antibiogram analysis. The application captures images with the phone's camera, and the user is guided throughout the analysis on the same device by a user-friendly graphical interface. An embedded expert system validates the coherence of the antibiogram data and provides interpreted results. The fully automatic measurement procedure of our application's reading system achieves an overall agreement of 90% on susceptibility categorization against a hospital-standard automatic system and 98% against manual measurement (gold standard), with reduced inter-operator variability. The application's performance showed that the automatic reading of antibiotic resistance testing is entirely feasible on a smartphone. Moreover our application is suited for resource-limited settings, and therefore has the potential to significantly increase patients' access to AST worldwide.

Inclusion of Real-Time Hand Hygiene Observation and Feedback in a Multimodal Hand Hygiene Improvement Strategy in Low-Resource Settings.

Importance: Hand hygiene adherence monitoring and feedback can reduce health care-acquired infections in hospitals. Few low-cost hand hygiene adherence monitoring tools exist in low-resource settings. Objective: To pilot an open-source application for mobile devices and an interactive analytical dashboard for the collection and visualization of health care workers' hand hygiene adherence data. Design, Setting, and Participants: This prospective multicenter quality improvement study evaluated preintervention and postintervention adherence with the 5 Moments for Hand Hygiene, as suggested by the World Health Organization, among health care workers from April 23 to May 25, 2018. A novel data collection form, the Hand Hygiene Observation Tool, was developed in open-source software and used to measure adherence with hand hygiene guidelines among health care workers in the inpatient therapeutic feeding center and pediatric ward of Anka General Hospital, Anka, Nigeria, and the postoperative ward of Noma Children's Hospital, Sokoto, Nigeria. Qualitative data were analyzed throughout data collection and used for immediate feedback to staff. A more formal analysis of the data was conducted during October 2018. Exposures: Multimodal hand hygiene improvement strategy with increased availability and accessibility of alcohol-based hand sanitizer, staff training and education, and evaluation and feedback in near real-time. Main Outcomes and Measures: Hand hygiene adherence before and after the intervention in 3 hospital wards, stratified by health care worker role, ward, and moment of hand hygiene. Results: A total of 686 preintervention adherence observations and 673 postintervention adherence observations were conducted. After the intervention, overall hand hygiene adherence increased from 32.4% to 57.4%. Adherence increased in both wards in Anka General Hospital (inpatient therapeutic feeding center, 24.3% [54 of 222 moments] to 63.7% [163 of 256 moments]; P < .001; pediatric ward, 50.9% [132 of 259 moments] to 68.8% [135 of 196 moments]; P < .001). Adherence among nurses in Anka General Hospital also increased in both wards (inpatient therapeutic feeding center, 17.7% [28 of 158 moments] to 71.2% [79 of 111 moments]; P < .001; pediatric ward, 45.9% [68 of 148 moments] to 68.4% [78 of 114 moments]; P < .001). In Noma Children's Hospital, the overall adherence increased from 17.6% (36 of 205 moments) to 39.8% (88 of 221 moments) (P < .001). Adherence among nurses in Noma Children's Hospital increased from 11.5% (14 of 122 moments) to 61.4% (78 of 126 moments) (P < .001). Adherence among Noma Children's Hospital physicians decreased from 34.2% (13 of 38 moments) to 8.6% (7 of 81 moments). Lowest overall adherence after the intervention occurred before patient contact (53.1% [85 of 160 moments]), before aseptic procedure (58.3% [21 of 36 moments]), and after touching a patient's surroundings (47.1% [124 of 263 moments]). Conclusions and Relevance: This study suggests that tools for the collection and rapid visualization of hand hygiene adherence data are feasible in low-resource settings. The novel tool used in this study may contribute to comprehensive infection prevention and control strategies and strengthening of hand hygiene behavior among all health care workers in health care facilities in humanitarian and low-resource settings.

Post-traumatic osteomyelitis in Middle East war-wounded civilians: resistance to first-line antibiotics in selected bacteria over the decade 2006-2016.

BACKGROUND: War-wounded civilians in Middle East countries are at risk of post-traumatic osteomyelitis (PTO). We aimed to describe and compare the bacterial etiology and proportion of first-line antibiotics resistant bacteria (FLAR) among PTO cases in civilians from Syria, Iraq and Yemen admitted to the reconstructive surgical program of Médecins Sans Frontières (MSF) in Amman, Jordan, and to identify risk factors for developing PTO with FLAR bacteria. METHODS: We retrospectively analyzed the laboratory database of the MSF program. Inclusion criteria were: patients from Iraq, Yemen or Syria, admitted to the Amman MSF program between October 2006 and December 2016, with at least one bone biopsy sample culture result. Only bone samples taken during first orthopedic surgery were included in the analysis. To assess factors associated with FLAR infection, logistic regression was used to estimate odds ratio (ORs) and 95% confidence intervals (CI). RESULTS: 558 (76.7%) among 727 patients included had ≥1 positive culture results. 318 were from Iraq, 140 from Syria and 100 from Yemen. Median time since injury was 19 months [IQR 8-40]. Among the 732 different bacterial isolates, we identified 228 Enterobacteriaceae (31.5%), 193 Staphylococcus aureus (26.3%), 99 Pseudomonas aeruginosa (13.5%), and 21 Acinetobacter baumanii (2.8%). Three hundred and sixty four isolates were FLAR: 86.2% of Enterobacteriaceae, 53.4% of Pseudomonas aeruginosa, 60.5% of S. aureus and 45% of Acinetobacter baumannii. There was no difference in bacterial etiology or proportion of FLAR according to the country of origin. In multivariate analysis, a FLAR infection was associated with an infection of the lower extremity, with a time since the injury ≤12 months compared with time > 30 months and with more than 3 previous surgeries. CONCLUSIONS: Enterobacteriaceae were frequently involved in PTO in war wounded civilians from Iraq, Yemen and Syria between 2006 and 2016. Proportion of FLAR was high, particularly among Enterobacteriaceae, regardless of country of origin.

Immuno-PCR--a new tool for paleomicrobiology: the plague paradigm.

BACKGROUND: The cause of past plague pandemics was controversial but several research teams used PCR techniques and dental pulp as the primary material to reveal that they were caused by Yersinia pestis. However, the degradation of DNA limits the ability to detect ancient infections. METHODS: We used for the first time immuno-PCR to detect Yersinia pestis antigens; it can detect protein concentrations 70 times lower than the standard ELISA. After determining the cut-off value, we tested 34 teeth that were obtained from mass graves of plague, and compared previous PCR results with ELISA and immuno-PCR results. RESULTS: The immuno-PCR technique was the most sensitive (14 out of 34) followed by the PCR technique (10 out of 34) and ELISA (3 out of 34). The combination of these three methods identified 18 out of 34 (53%) teeth as presumably being from people with the plague. CONCLUSION: Immuno-PCR is specific (no false-positive samples were found) and more sensitive than the currently used method to detect antigens of ancient infections in dental pulp. The combination of three methods, ELISA, PCR and immuno-PCR, increased the capacity to identify ancient pathogens in dental pulp.

An experimental mouse model to establish Tropheryma whipplei as a diarrheal agent.

Tropheryma whipplei has long been considered as a rare bacterium causing a rare disease, Whipple's disease. However, recent advances now suggest that T. whipplei is a ubiquitous environmental bacterium that may cause gastroenteritis, commonly associated with viral pathogens. We developed an animal model to support this hypothesis. We found that orally given T. whipplei induced diarrhea in mice, without spreading into the intestines. Aggravating factors, such as damage to the intestinal mucosa, favored bacterial spreading. Indeed, bacterial presence was prolonged in stools of dextran sulfate-treated mice, and bacteria were detected in the colon. This resulted in an immune response, with T. whipplei-specific serum IgM and IgG and fecal IgA, as measured by newly introduced immuno-polymerase chain reaction technique. Our results confirm that T. whipplei is an agent causing gastroenteritis and suggest that existing mucosal damage may favor bacterial invasion of tissues.

Immuno-PCR: a promising ultrasensitive diagnostic method to detect antigens and antibodies.

Immuno-PCR (iPCR) is a method that combines the advantages of both enzyme-linked immunosorbent assay and PCR and is a powerful method for detecting low quantities of protein antigens. Despite its potential, for a long time iPCR was an underutilized method as evidenced by the low number of publications on its routine application. The introduction of ready-to-use reagents, the large choice in linker molecule, reduction of protocol time and the development of new systems is opening the way for iPCR to become a routine method for use as a microbial diagnostic. To understand how iPCR could become an indispensible microbial diagnostic, we review the evolution of iPCR, from its first classical format with numerous drawbacks to more sophisticated systems developed to circumvent these drawbacks.