Ciprofloxacin

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.

Minimum inhibitory concentrations (MICs) to ampicillin, gentamicin, vancomycin, teicoplanin, ciprofloxacin, tigecycline, linezolid, daptomycin and quinupristin/dalfopristin were examined by E-test (Liofilchem, Italy). MICs results were interpreted according to the recommendations of The European Committee on Antimicrobial Susceptibility Testing (EUCAST Breakpoint tables for interpretation of MICs and zone diameters, version 11.0, 2021, http://www.eucast.org/clinical_breakpoints/). The Clinical and Laboratory Standards Institute (CLSI) guidelines, 2021, https://clsi.org/standards/ were used to interpret the MICs for daptomycin. The presence of vanABCDMN genes was investigated by colony multiplex PCR assay using the primer sequences and PCR protocol described by Nomura et al. [22 (link)]. Briefly, a modified PCR mix for detection of the investigated genes was applied containing 0.4 µM (each) primer, 200 µM (each) dNTP, 1 U of Taq (Canvax, Spain), 1X reaction buffer, 2.5 mM MgCl₂, ultrapure PCR H₂O and 10 ng DNA template to a final volume of 20 µL. The PCR thermal conditions consisted of initial denaturation (94 °C for 4 min), followed by 30 cycles of denaturation (94 °C for 30 s), annealing (62 °C for 35 s) and extension (68 °C for 1 min), with a single final extension of 7 min at 68 °C. The amplified PCR products were analyzed by capillary electrophoresis.

Positive blood cultures were identified in the database and the sample date, age, sex and microbiological findings were retrieved. For species with clinically used names that were changed during the study period (such as Cutibacterium acnes previously called Propionibacterium acnes) we have consistently aimed to use the valid names as of 2022 according to the International Code of Nomenclature of Prokaryotes [12 (link)]. Antimicrobial susceptibility was described for Enterobacterales only, for fluoroquinolones (ciprofloxacin), third generation cephalosporins (cefotaxime) and aminoglycosides (gentamicin). Due to a database update in 2010, susceptibility data were available from 2011 to 2019 only. In addition, zone diameters were incomplete in > 50% of records. Therefore, clinical classification into susceptible (S), increased exposure (I) and resistant (R) was used to describe susceptibility, using breakpoints as per the original microbiology reports [13 (link)]. For cases with zone data, susceptibility testing according to the 2022 EUCAST breakpoints was compared with the original SIR classification in a sensitivity analysis [11 ]. Negative blood cultures were retrieved on an aggregate level (only the total number of blood culture sets per year was available). Population data were retrieved from Statistics Sweden [14 ].