Ofloxacin

We conducted a systematic review of published literature between 1990 and 2018 following the PRISMA guidelines (Additional file 1: Table S1) [22 (link)]. The protocol was registered with the international prospective register of systematic reviews (CRD42018029432). The search strategy was devised by an academic librarian (EH). MEDLINE, Ovid Embase, Global Health, Cochrane Library, Scopus, Web of Science-Core Collection and LILACS were searched using a syntax that combined Medical Subject Headings (MeSH) and free text terms for the pathogens of interest (e.g. S. Typhi, S. Paratyphi A, enteric fever) with terms for antimicrobial resistance (e.g. resistan*, suscept*, surveil*) (Additional file 1: Table S2). The extended search was conducted in October 2017 and updated in March 2019. The search was limited to publications from 1990 onwards; no restrictions on language or filters (e.g. humans) were implemented.
Included studies were required to report quantifiable in vitro antimicrobial susceptibility data for S. Typhi and/or S. Paratyphi A isolated from blood culture, examining at least 10 representative organisms and indicating the study location. Reports from travellers being diagnosed in high-income countries were excluded. Studies with pooled S. Typhi and S. Paratyphi A susceptibility data, studies reporting on isolates from stool culture and duplicate isolates were also excluded.
Prospective and retrospective hospital-, laboratory- and community-based studies were included, if they met the specified inclusion criteria. Review articles were scanned for relevant references. Studies were screened at title, abstract and full-text stage by one author (CD) and reviewed by a second author (AB). Data were extracted into a predefined database by AB and reviewed by BKH and JL. Additionally, 20% of the extracted studies were checked by a third reviewer (CD). Disagreements were resolved by discussion. Susceptibility data for antimicrobials recommended for the treatment of enteric fever by WHO, i.e. ampicillin/amoxicillin, chloramphenicol, trimethoprim-sulphamethoxazole (co-trimoxazole), fluoroquinolones (e.g. ciprofloxacin and ofloxacin), third-generation cephalosporins (e.g. ceftriaxone and cefixime) and azithromycin, were extracted [11 ]. Furthermore, multidrug resistance (MDR; defined as resistance to ampicillin/amoxicillin, chloramphenicol and co-trimoxazole) and nalidixic acid resistance, as a proxy marker for reduced ciprofloxacin susceptibility, were recorded [18 (link)].
Variables extracted included the study start and end dates, patients’ characteristics (age range, mean age, percentage of males, inpatients or outpatients), study design, number of patients screened, number of patients with positive blood culture, antimicrobial susceptibility testing (AST) method and the number (or percentage) of resistant, intermediate and susceptible isolates out of the total number of isolates tested against each antimicrobial. We also recorded case fatalities and clinical outcomes when available. Additionally, the testing standard (e.g. Clinical and Laboratory Standards Institute (CLSI)) and interpretive criteria (including version or year) used to determine resistance, use of internal quality controls and participation in external quality assessments schemes were recorded. The study setting, precise study location, country and GBD study region were recorded for each study. Data were disaggregated by serovar and study location.
We aimed to control for bias and allow for comparison across studies by adhering to the predefined inclusion and exclusion criteria. We expected that there would be differences in the quality of the AST and interpretation of results, reflecting the reality in many LMICs. We adapted a descriptive tool for quality assessment used by Arndt, based on sample size and microbiological testing methodology [23 (link)]. We reviewed the complete description of susceptibility testing methods, which included testing standard, version and/or year (i.e. breakpoints), internal quality controls and external quality assessment. No study was excluded based on this assessment, due to the lack of standardised reporting guidelines for microbiological studies.

To examine the potential analytical advantage of whole genome sequencing comparison was made with three commercial tests: (1) the Xpert MTB/RIF (Cepheid Inc., USA) which targets the rpoB gene for RMP resistance; (2) the LPA MTBDRplus for MDR-TB (Hain Lifescience, Germany) which targets rpoB, katG and inhA for resistance to RMP and INH; and (3) the LPA MTBDRsl (Hain Lifescience, Germany) which targets gyrA, rrs and embB for resistance to the fluoroquinolones (FLQ), aminoglycosides and ethambutol, respectively. In silico versions were developed based on the polymorphisms used by these assays and their performance compared to the whole genome mutation library. In particular, in silico analysis of the six datasets was performed and analytical sensitivities and specificities of the inferred resistance relative to the reported phenotype were compared (Figure 2, Additional file 1: Figures S3 and S4). KvarQ [35 (link)], a new tool that directly scans fastq files of bacterial genome sequences for known genetic polymorphisms, was run across all 792 samples using the MTBC test suite and default parameters. Sensitivity and specificity achieved by this method using phenotypic DST results as the reference standard were calculated.Figure 2

Inferred analytical accuracies of the whole genome mutation library and three commercial molecular tests for resistance. In silico analysis of published sequence data using mutation libraries derived from XpertMTB/RIF (Cepheid Inc., USA) (purple), MTBDRsl (red) and MTBDRplus (orange) (Hain Life Sciences, Germany), and the curated whole genome library (blue). For each library in silico inferred resistance phenotypes were compared to reported phenotypes obtained from conventional drug susceptibility testing. Errors bars correspond to 95% confidence intervals. Abbreviations: AMK, amikacin; CAP, capreomycin; EMB, ethambutol; ETH, ethionamide; INH, Isoniazid; KAN, kanamycin; MDR, multi-drug resistance; MOX, moxifloxacin; OFX, ofloxacin; PZA, pyrazinamide; RMP, rifampicin; STR, streptomycin; XDR, extensive drug resistance.

The MICs of S. aureus to a variety of antibiotics were determined in Mueller-Hinton Broth medium as described previously (Borrero et al., 2014 (link)). For the determination of time-dependent bactericidal curves, overnight culture was diluted into fresh TSB medium at a ratio of 1:100 and incubated at 37°C and 220 rpm until OD₆₀₀ reached 1.0. The MICs of ciprofloxacin, ofloxacin, norfloxacin, levofloxacin, moxifloxacin, and garenoxacin were 0.32, 0.25, 0.48, 0.19, 0.125, and 0.03 μg/ml, respectively. Thiourea (150 mM) was added when the strains grew to OD₆₀₀ 0.6. Samples were taken out at certain time points, diluted 10-fold, and colonies counted by dropping plate.

The mice at P26 were anesthetized with isoflurane (5% for induction and 1 to 3% for maintenance). The right eye was deprived of vision by using an eyelid suture. The sutured eyelids were treated with an antibacterial ointment (ofloxacin, TOA Pharmaceuticals). Lid closure was checked daily.

The study was conducted in the KwaZulu-Natal province in South Africa. The province has the second-highest population in the country with more than 11 million people. There are 11 districts in the province and one MDR-TB treatment facility per district.
In health facilities in the KwaZulu-Natal province, the initial diagnosis of tuberculosis and rifampicin resistance is routinely done using the Xpert (Xpert MTB/RIF, Cepheid, Sunnyvale, California, United States) in all patients suspected of tuberculosis disease. The Xpert was previously used but was later replaced by its successor, the Xpert MTB/RIF Ultra (Xpert Ultra, Cepheid, Sunnyvale, California, United States), in 2017. For patients with rifampicin-susceptible tuberculosis, no further DST is performed, and they are treated using first-line tuberculosis therapy. In patients with rifampicin-resistant tuberculosis on the Xpert (Ultra), a second sample is taken for culture and DST. Other indications for tuberculosis culture include treatment failure and paucibacillary tuberculosis that shows a negative result on the Xpert (Ultra).
During the study period between January 2014 and December 2014, the automated BACTEC Mycobacteria Growth Indicator Tube 960 system (Becton Dickinson, Sparks, Maryland, United States) was used for M. tuberculosis culture, and initial DST was done on all positive cultures using the MTBDRplus version 2 assay (Hain Lifescience, Nehren, Germany) to confirm rifampicin resistance and test for isoniazid resistance. The MTBDRplus assay uses DNA strip technology where the strip contains both wild-type probes and mutation probes for the commonly occurring mutations (S450L, H455Y, H455D, and D435V for rifampicin). The labelled polymerase chain reaction products from an amplified target are hybridised with specific probes immobilised on a strip (reverse hybridisation). Resistance is reported when there is a lack of binding to the wild-type probe with or without binding to a mutation probe.¹⁴ Isolates that were resistant to either rifampicin or isoniazid on the MTBDRplus assay were further tested for resistance to critical concentrations of isoniazid (0.2 µg/mL), rifampicin (1 µg/mL), ofloxacin (2 µg/mL), streptomycin (2 µg/mL), and kanamycin (5 µg/mL) using the 1% agar proportion method on Middlebrook 7H10 agar (Becton Dickinson, Sparks, Maryland, United States).¹⁵ The simultaneous performance of molecular and phenotypic rifampicin DST allowed the detection of discordance between these two tests.