Prevalence of SARS-CoV-2 infection among health care workers in a reference hospital in Brazil

ABSTRACT Health care workers (HCW) are the frontline workforce for COVID-19 patient care and, consequently, are exposed to SARS-CoV-2 infection due to close contact to infected patients. Here, we evaluate the prevalence of SARS-CoV-2 infection among HCW from an infectious disease hospital, reference center for COVID-19 care in the metropolitan area of Sao Paulo city, Brazil. Among 2,204 HCW, 1,417 (64.29%) were subjected to detection of anti-SARS-CoV-2 antibodies by chemiluminescent immunoassay. Out of the total, 271 (19.12%) presented anti-SARS-CoV-2 antibodies. Prevalence varied according to HCW categories. The highest prevalence was observed in workers from outsourced companies, cooks and kitchen assistants, hospital cleaning workers, and maintenance workers. On the other hand, resident physicians and HCW from the institution itself presented lower prevalence (nurses, nursing assistants, physicians, laboratory technicians). Social and environmental factors are important determinants, associated with exposure in the hospital environment, which can determine the greater or lesser risk of infection by pathogens that spread rapidly by air.

New insights on tuberculosis transmission dynamics and drug susceptibility profiles among the prison population in Southern Brazil based on whole-genome sequencing

ABSTRACT Background: The rate of tuberculosis (TB) infection among the prison population (PP) in Brazil is 28 times higher than that in the general population, and prison environment favors the spread of TB. Objective: To describe TB transmission dynamics and drug resistance profiles in PP using whole-genome sequencing (WGS). Methods: This was a retrospective study of Mycobacterium tuberculosis cultivated from people incarcerated in 55 prisons between 2016 and 2019; only one isolate per prisoner was included. Information about movement from one prison to another was tracked. Clinical information was collected, and WGS was performed on isolates obtained at the time of TB diagnosis. Results: Among 134 prisoners included in the study, we detected 16 clusters with a total of 58 (43%) cases of M. tuberculosis. Clusters ranged from two to seven isolates with five or fewer single nucleotide polymorphism (SNP) differences, suggesting a recent transmission. Six (4.4%) isolates were resistant to at least one anti-TB drug. Two of these clustered together and showed resistance to rifampicin, isoniazid, and fluoroquinolones, with 100% concordance between WGS and phenotypic drug-susceptibility testing. Prisoners with clustered isolates had a high amount of movement between prisons (two to eight moves) during the study period. Conclusions: WGS demonstrated the recent transmission of TB within prisons in Brazil. The high movement among prisoners seems to be related to the transmission of the same M. tuberculosis strain within the prison system. Screening for TB before and after the movement of prisoners using rapid molecular tests could play a role in reducing transmission.

GenoType MTBDRsl for detection of second-line drugs and ethambutol resistance in multidrug-resistant Mycobacterium tuberculosis isolates at a high-throughput laboratory

We assessed the performance of MTBDRsl for detection of resistance to fluoroquinolones, aminoglycosides/cyclic peptides, and ethambutol compared to BACTEC MGIT 960 by subjecting simultaneously to both tests 385 phenotypically multidrug-resistant-Mycobacterium tuberculosis isolates from Sao Paulo, Brazil. Discordances were resolved by Sanger sequencing. MTBDRsl correctly detected 99.7% of the multidrug-resistant isolates, 87.8% of the pre-XDR, and 73.9% of the XDR. The assay showed sensitivity of 86.4%, 100%, 85.2% and 76.4% for fluoroquinolones, amikacin/kanamycin, capreomycin and ethambutol, respectively. Specificity was 100% for fluoroquinolones and aminoglycosides/cyclic peptides, and 93.6% for ethambutol. Most fluoroquinolone-discordances were due to mutations in genome regions not targeted by the MTBDRsl v. 1.0: gyrA_H70R and gyrB_R446C, D461N, D449V, and N488D. Capreomycin-resistant isolates with wild-type rrs results on MTBDRsl presented tlyA mutations. MTBDRsl presented good performance for detecting resistance to second-line drugs and ethambutol in clinical isolates. In our setting, multidrug-resistant. isolates presented mutations not targeted by the molecular assay.

Padronização e implantação do teste de susceptibilidade aos fármacos de 2° linha para Mycobacterium tuberculosis: panorama da tuberculose extensivamente resistente no estado de São Paulo / Standardization and implantation of the susceptibility test for the drugs of 2nd line for Mycobacterium tuberculosis: panorama of the tuberculosis extensively resistant in the state of São Paulo

A resistência do Mycobacterium tuberculosis aos fármacos de 1º e 2ªlinha utilizados no tratamento da tuberculose (TB) é um problema de saúde pública. Em 2015, a Organização Mundial da Saúde estimou que 9,5% de todos os casos mundiais de TB multirresistente eram de TB extensivamente resistente (TBXDR). Este estudo teve como objetivo, padronizar o teste de susceptibilidade aos fármacos de 2ª linha pelo método BD BACTEC™MGIT™ 960 e descrever o panorama da TBXDR no estado de São Paulo nos anos de 2006 e 2011-2013. Dados clínicos, epidemiológicos e demográficos foram obtidos do sistema de notificação e acompanhamento de TB e os dados laboratoriais do Sistema de Informação e Gestão Hospitalar do Instituto Adolfo Lutz. Análises estatísticas foram realizadas com o auxílio do programa SPSS. O método BD BACTEC™ MGIT™ 960 demonstrou 100% de reprodutibilidade e foi validado por ensaio de proficiência. A prevalência de TBXDR em 2006, 2011, 2012 e 2013 foi de4,4%, 9,3%, 12% e 13,7% respectivamente. A ofloxacina foi o fármaco de 2ªlinha com maior porcentagem de resistência. Quanto aos fatores associados à TBXDR, a variável sexo, história anterior de TB, tipo de notificação e desfecho apresentaram diferenças estatisticamente significantes. A caracterização molecular demonstrou que 24 (63,1%) isolados de pacientes com TBXDR foram agrupados em nove grupos genéticos por RFLP-IS6110,e relações epidemiológicas foram observadas para onze pacientes (28,9%).Por meio da técnica de Spoligotyping foram observadas as famílias: Haarlem, T, LAM e X. O estudo possibilitou uma melhor compreensão do cenário da TBXDR no estado de São Paulo.

Performance of an in-house real-time polymerase chain reaction for identification of Mycobacterium tuberculosis isolates in laboratory routine diagnosis from a high burden setting

Abstract Brazil is one of the high burden countries for tuberculosis, and a rapid diagnosis is essential for effective control of the disease. In the present study, an in-house real-time polymerase chain reaction (PCR) assay targeting the mpt64 gene for identification of Mycobacterium tuberculosis complex isolates was evaluated under routine diagnosis conditions in a reference laboratory. From May 2011 to July 2012, 1,520 isolates of mycobacteria were prospectively submitted for phenotypic and/or PRA-hsp65 identification and to real-time PCR. The mpt64 real-time PCR showed 99.7% sensitivity and 96% specificity and detected 79.4% of the cases missed by phenotypic and PRA-hsp65 identification. The in-house real-time PCR assay showed high sensitivity and specificity and was successfully implemented in the routine diagnosis of tuberculosis in a reference laboratory from a high burden setting.