Skip to main content

Fluoroquinolone resistance among fecal extended spectrum βeta lactamases positive Enterobacterales isolates from children in Dar es Salaam, Tanzania



Fluoroquinolones have been, and continue to be, routinely used for treatment of many bacterial infections. In recent years, most parts of the world have reported an increasing trend of fluoroquinolone resistant (FQR) Gram-negative bacteria.


A cross-sectional study was conducted between March 2017 and July 2018 among children admitted due to fever to referral hospitals in Dar es Salaam, Tanzania. Rectal swabs were used to screen for carriage of extended-spectrum β-lactamase-producing Enterobacterales (ESBL-PE). ESBL-PE isolates were tested for quinolone resistance by disk diffusion method. Randomly selected fluroquinolone resistant isolates were characterized by using whole genome sequencing.


A total of 142 ESBL-PE archived isolates were tested for fluoroquinolone resistance. Overall phenotypic resistance to ciprofloxacin, levofloxacin and moxifloxacin was found in 68% (97/142). The highest resistance rate was seen among Citrobacter spp. (100%, 5/5), followed by Klebsiella. pneumoniae (76.1%; 35/46), Escherichia coli (65.6%; 42/64) and Enterobacter spp. (31.9%; 15/47). Whole genome sequencing (WGS) was performed on 42 fluoroquinolone resistant-ESBL producing isolates and revealed that 38/42; or 90.5%, of the isolates carried one or more plasmid mediated quinolone resistance (PMQR) genes. The most frequent PMQR genes were aac(6’)-lb-cr (74%; 31/42), followed by qnrB1 (40%; 17/42), oqx, qnrB6 and qnS1. Chromosomal mutations in gyrA, parC and parE were detected among 19/42 isolates, and all were in E. coli. Most of the E. coli isolates (17/20) had high MIC values of > 32 µg/ml for fluoroquinolones. In these strains, multiple chromosomal mutations were detected, and all except three strains had additional PMQR genes. Sequence types, ST131 and ST617 predominated among E. coli isolates, while ST607 was more common out of 12 sequence types detected among the K. pneumoniae. Fluoroquinolone resistance genes were mostly associated with the IncF plasmids.


The ESBL-PE isolates showed high rates of phenotypic resistance towards fluoroquinolones likely mediated by both chromosomal mutations and PMQR genes. Chromosomal mutations with or without the presence of PMQR were associated with high MIC values in these bacteria strains. We also found a diversity of PMQR genes, sequence types, virulence genes, and plasmid located antimicrobial resistance (AMR) genes towards other antimicrobial agents.

Peer Review reports


Since the introduction of fluoroquinolones in the 1980s, these agents have been routinely used for treatment of several bacterial infections. In the recent years, ciprofloxacin has been the most consumed antibacterial agent world-wide [1]. In 2014, the World Health Organization (WHO) highlighted fluoroquinolone resistance in Escherichia coli and related organisms as a principal public health threat [2]. Reports from North America and Europe indicated that the rate of fluoroquinolone-resistant (FQR) Gram-negative bloodstream isolates exceeded 20% while in China a higher rate up to 75% has been reported [3,4,5]. A study from Togo, West Africa, reported that 69% of clinical isolates carried genes responsible for FQR [6]. Like other antimicrobial resistant pathogenic bacteria, FQR bacteria have negative clinical implications including treatment failure, increasing treatment costs and protracted therapy [7][7]. It has also been reported that previous colonization with FQR E. coli can lead to the spread of extended-spectrum β-lactamase-producing Enterobacterales (ESBL-PE) after the use of quinolone prophylaxis [9, 10].

Among Gram-negative bacteria, the primary target of quinolones is topoisomerase ii (DNA gyrase). In Enterobacterales, resistance to fluoroquinolones may be due plasmid mediated resistance genes or chromosomal mutations which can be found together in the same bacteria. Plasmid-mediated quinolone resistance (PMQR) genes have been reported since 1990’s [11] and in recent years a global increase in the prevalence of PMQR genes have been observed [11]. These PMQR genes include the qnr family genes; qnrA, qnrB, qnrC, qnrD etc., gene encoding aminoglycoside-modifying enzyme; aac-(6′)-Ib-cr, and antibiotic efflux pump encoding genes; oqxAB and qepA [12]. Because quinolones act by binding to enzyme–DNA complexes, which form between cleaved bacterial DNA and DNA gyrase (gyrA, gyrB) or topoisomerase IV, mutations in the chromosomal genes coding for type II topoisomerases also confer resistance to quinolones [13]. Mutations associated with quinolone resistance are located in a specific region called “quinolone resistance-determining region” (QRDR). Studies have reported multiple mechanisms of quinolone resistance [14,15,16].

In Dar es Salaam, Tanzania, a steady increase of FQR has been observed over time; in 2001–2002 it was reported to be 5.3% among ESBL-PE isolates obtained from children with septicemia and few years later i.e., in 2010 it was six times more (34.4%) among urinary pathogens obtained from children and adults. In 2011 the incidence of FQR was observed to be 40.5% among children in the same study settings [17,18,19]. Furthermore, multiple mechanisms of quinolone resistance have been reported from other continents, but there is a paucity of data from sub-Saharan Africa, particularly in Tanzania, on the molecular mechanisms responsible for quinolone resistance. Using whole genome sequencing, this study was conducted to determine quinolone resistance mechanisms among ESBL positive isolates from fecal samples from hospitalized children in Dar es Salaam, Tanzania.

Materials and methods

Study site and population

This was part of a prospective cross-sectional study, which was conducted from March 2017 to July 2018 in Dar es Salaam, Tanzania [20]. The study enrolled children below five years of age who were hospitalized because of fever (> 37.5 °C) at three regional hospitals: (a) Amana, (b) Temeke, (c) Mwananyamala and one tertiary hospital, (d) Muhimbili National Hospital (MNH). The study settings have been previously described in detail [20]. For this study, we randomly selected archived rectal swabs from 200 children for analysis.

Data and specimen collection

As previously described [20], the study used Research Electronic Data Capture (REDCap), to gather demographic and clinical information including date of birth, sex, duration of fever, history of antibiotic use one month prior to admission, and history of hospitalization in the last six months. From each child, Carry Blair transport media was used to collect rectal swab which was stored at − 80 °C until the time of analysis.

Phenotypic detection of fluoroquinolone resistant-ESBL producing Enterobacterales and antimicrobial susceptibility testing

First, the frozen rectal swabs were suspended in brain heart infusion (BHI) media for overnight incubation at 37 °C. Two microliter (2 µl) of BHI were then inoculated onto CHROMID® ESBL agar (BioMérieux, Marcy l’Etoile, France) and incubated for 24 h to screen for ESBL production. ESBL positive isolates were then identified by Matrix-assisted laser desorption/ionization-time of flight (MALDI-TOF) mass spectrometry (MS) using the Microflex 99 LT instrument and MALDI Biotyper 3.1 software (Bruker Daltonics, Bremen, Germany). The identified bacterial isolates were subjected to antimicrobial susceptibility testing (AST) by disk diffusion method to test for fluoroquinolone resistance using ciprofloxacin disks (5 µg). Minimum inhibitory concentration (MIC) values for all ciprofloxacin resistant isolates were then determined by E-test, using ciprofloxacin, levofloxacin and moxifloxacin strips. Interpretation of results was done based on the Clinical and Laboratory Standards Institute (CLSI) guidelines [21]. Intermediate susceptible isolates were regarded as resistant. Klebsiella pneumoniae ATCC 700603 and Escherichia coli ATCC 25922 were used as control organisms.

Whole genome sequencing and in silico analyses

Among the FQR isolates from the phenotypic testing, 42 isolates with ciprofloxacin levels ≥ 0.5 µg/ml were randomly selected for whole genome sequencing (WGS). WGS was performed by MicrobesNG (MicrobesNG, Birmingham, UK.) using Illumina HiSeq technology [22]. DNA for sequencing was extracted using the MagNA Pure 96 DNA and Viral NA Large Volume kit (Roche Diagnostics GmbH, Mannheim, Germany) according to manufacturer’s instructions and genomic libraries were prepared using the Nextera XT DNA library preparation kit (Illumina, San Diego, CA, USA). A 150-bp paired-end sequencing was performed using the HiSeq × 10 system (Illumina). Long and short read sequences were assembled using Unicycler (v., and genome annotation was done with Prokka (v.1.14.6). Sequences were analyzed for multisequence typing (MLST), and plasmid replicon types using MLST 1.8, ResFinder [23] and Plasmidfinder software [24].

Phylogenetic analysis

Phylogeny reconstruction was done using CSI Phylogeny ( Genomes of the isolates obtained from the present study have been submitted to Biosample Database, National Centre for Biotechnology Information (NCBI) with project accession numbers PRJNA911701 and PRJNA911976 for E. coli and K. pneumoniae respectively.


Characteristics of study population

We performed antimicrobial susceptibility test for 142 phenotypically isolated ESBL-PE from children below five years of age. The characteristics of the children are described elsewhere [20]. Among the isolates, 64 were E. coli, 46 were K. pneumoniae, 47 were Enterobacter spp. and 5 were Citrobacter spp.

Fluoroquinolone resistance in different species

A total of 142 ESBL-PE isolates were tested for fluoroquinolone resistance. Phenotypic resistance to fluoroquinolones, as determined by disk diffusion and E-test, was found in 97/142 (68%) of the bacterial isolates. Table 1 shows the MIC values of the three tested fluoroquinolones among different bacteria isolates. More than half of the E. coli isolates had high MIC levels (> 32 µg/ml) for the three tested quinolones: 69% (29/42) for ciprofloxacin and 68% (28/42) for both levofloxacin and moxifloxacin. Conversely, the majority of K. pneumoniae isolates had low MIC levels ranging from 0.5 µg/ml to 1 µg/ml and only 3 K. pneumoniae isolates had MIC levels of > 32 µg/ml (9%; 3/35). All Enterobacter spp. And Citrobacter spp. had low MIC values ranging from 05 to 3 µg/ml.

Table 1 Fluroquinolone MIC values among different bacterial species

Plasmid mediated fluoroquinolone resistance genes and chromosomal mutations

Forty-two FQR ESBL-PE were analyzed by WGS, 20 were E. coli, 16 K. pneumoniae, 4 were E. Cloacae and 2 were Citrobacter sedlakii. Out of 42 FQR-ESBL-PE analyzed, 38 (90.5%) had PMQR genes and four (9.5%) bacteria isolates did not have any identifiable PMQR genes. As shown in Table 2. Twenty bacteria isolates (52.4%) had two or more resistance genes with the most common combination of genes being aac(6’)-lb-cr, qnrB1 and oqx. The aminoglycoside acetyltransferase-coding gene aac(6’)-lb-cr was detected in most of the isolates (76.2%;32/42), followed by qnrB1 (40%;17/42) and oqx (35.7%; 15/42). Other qnr genes qnrB6 and qnS1 were detected in 3 and 4 isolates each. Distribution of PMQR genes varied among different species. Among 20 E. coli isolates 15 had aac(6’)-lb-cr, (of these one had both aac(6’)-lb-cr and qnrB1), one had qnS1 only and four had no detectable PMQR genes. In the 16 K. pneumoniae isolates, the frequency of PMQR genes detected were; 15-oqx, 11-aac(6’)-lb-cr, 11-qnrB1, 3-qnrB6 and 2-qnS1. Of note, plasmid-mediated efflux pump genes (oqx) and qnrB6 genes were detected only in K. pneumoniae isolates. All the four E. cloacae isolates had both aac(6’)-lb-cr and qnrB1 genes detected while one C. sedlakii had both aac(6’)-lb-cr and qnrB1 genes and the second had only aac(6’)-lb-cr gene detected.

Table 2 Phenotypic and genotypic characterization of fluoroquinolone resistant isolates

Regarding chromosomal mechanisms of quinolone resistance, QRDR mutations were observed in 19/42; 45.2% bacteria isolates, all of which were on E. coli while one E. coli strain did have any detectable QRDR mutations. Of the 19 E. coli strains with QRDR mutations, 17 had triple mutations i.e., gyrA, parC and parE. One E. coli strain had single gyrA mutation and one had single parE mutation.

When analyzing the correlation between MIC values and the presence of plasmid/ chromosomal resistance mechanisms we observed that out of the 20 E. coli strains 17 had MIC values of > 32 µg/ml. These isolates had the triple QRDR mutations detected i.e., gyrA, parC and parE and most of them had dual gyrA mutations (S83L and D87N) as shown in Table 2. In addition, all except three of these 17 E. coli strains had PMQR genes. Three of the 20 E. coli strains had low MIC values, one had single gyrA mutation with no additional detectable PMQR genes, the second had a single parE mutation also with no additional PMQR genes and the third had 2 PMQR genes without any detectable chromosomal mutations.

In all the 16 K. pneumoniae strains we did not detect any chromosomal mutations and three strains had high MIC values of > 32 µg/ml. In these three strains, two had only one plasmid-mediated efflux pump gene (oqx) while the third strain had combination of PMQR genes (aac(6’)-lb-cr and qnrB1).

Multi-locus sequence types

Through analyses of MLST profiles of E. coli, we identified eight different sequence types (STs); ST131 (n = 5), ST617 (n = 5), ST1193 (n = 3), ST167 (n = 2) and five singletons; ST10, ST34, ST155, ST410 and ST4981 (Table 3). As shown in Table 4, a total of 12 different STs were found among the K. pneumoniae isolates; ST14, ST16, ST38, ST39, ST231, ST336, ST348, ST429, ST479, ST607, ST985 and ST3559. ST607 was more prevalent than others (3/12; 25%).

Table 3 Sequence types, virulence genes and plasmids of 20 fluoroquinolone resistant E. coli isolates
Table 4 K. pneumoniae isolates (n = 16) characterization including sequence type, wzi, plasmid and virulence profiles by WGS

All the three K. pneumoniae strains with qnrB6 PMQR gene belonged to ST607 and had low MIC values ranging from 0.5 to 1 µg/ml. There was no other pattern or correlation established between ST types and the presence of PMQR genes, chromosomal mutations or MIC value of the other bacteria.

Genes conferring resistance towards other antimicrobial agents

Phenotypic resistance towards gentamicin was observed in 71% (30/42) of the isolates. Of these, 90% (27/30) carried the aac(6’)-lb-cr gene which confers resistance to both aminoglycosides and fluoroquinolones. As shown in Table 5, we detected other antimicrobial resistance genes in 57% (24/42) of the whole genome sequenced isolates. All 24 isolates carried genes conferring resistance to aminoglycosides (100%, 24/24) and folate pathway antagonists (100%, 24/24). In most cases, the aminoglycoside-related genes appeared in combinations (96%, 23/24) except for one isolate, which carried a single gene, aadA2. The most detected aminoglycoside resistance gene was aminoglycoside phosphotransferase aph (6)-ld. The tetracycline resistance gene, tetA was detected in 83% (20/24), while the sul2 gene, which is responsible for causing folate pathway antagonist resistance, was detected in 86% (21/24) of the isolates. Furthermore, resistance genes towards macrolides (mphA) and macrolides, lincosamides plus streptogramin b (erm(B)) were only detected in E. coli isolates, while fosfomycin resistance genes (fosA, fosA5) were only observed in K. pneumoniae isolates.

Table 5 Distribution of antimicrobial resistance genes other than PMQR among ESBL producing Gram negative bacteria

Virulence genes, plasmids and beta-lactam resistance genes of E. coli isolates

The commonest beta-lactam resistance gene across all strains was blaCTX-M-15 (11/20), Table 3. Three out of the five ST131 E. coli isolates carried a combination of blaCTX-M-15, blaTEM-1B and blaOXA-1. The rest of the ST131 strains carried blaCTX-M-27 or blaTEM-1B. We identified several virulence genes among the E. coli isolates and each isolate had three or more virulence genes. Among the different ST types, E. coli strains with sequence type 131 had more virulence genes compared to other STs, including those encoding for; increased serum survival (iss), heat-resistant agglutinin (hrA), fimbrial protein (yfcV) and plasmid-encoded enterotoxin (senB). The uropathogenic specific protein (usp)-encoding gene was only detected in ST131 isolates. Additionally, terC and traT were the most common virulence genes which were found across almost all different ST types. All strains harbored at least one of the three plasmids of the incompatibility group F (IncF), namely the IncFII, IncFIB and IncFIA, the most common one being IncFII. Furthermore, some of the strains harbored IncH, Col and IncX plasmids.

Virulence genes, plasmids and beta-lactam resistance genes of K. pneumoniae isolates

Nine different wzi types were identified. The most frequently detected was wzi-133, which was assigned to all (3/3) ST607 isolates. Three isolates carried the wzi-2 allele, which encodes the type K2 capsular antigen. Regarding virulence genes, all isolates had a sidephore iutA, which is a ferric aerobactin receptor. Additionally, all but two (14/16) isolates carried the invasion gene tratT, and three isolates (ST16, ST38 and ST39) carried a receptor for the yersiniabactin system (fyuA). Other virulence genes detected were irp2 and terC. Plasmid analysis revealed diversity of incompatibility (Inc) group plasmids (n = 8) among the isolates. The most frequent was IncFII(K) detected in 12/16 isolates followed by IncFIB(K) detected among 11/12 isolates. In addition, several variants of Col plasmids (Col440I, Col440II, ColMG828) were detected in four isolates.

Phylogenetic analysis

Whole-genome phylogenetic analysis revealed that our isolates are highly diversified, with a SNP count between genomes being 3-38590 for E. coli and 11-2128 for K. pneumoniae isolates. (Fig. 1A, B). Two E. coli isolates belonging to ST167 were closely related with SNP difference 3. Also, E. coli ST131 isolates were related with a SNP count 9–12, however these isolates were not related to the refence strain E. coli isolate ST131 isolated from United Kingdom (SNP difference 47–55). For K. pneumoniae isolates, the isolates with sequence type ST348 were somewhat closely related with a SNP difference of 11 while the SNP difference between the two ST14 isolates was 22 showing some degree of relatedness. Although having the same sequence type, K. pneumoniae ST607 isolates had no genetic relationship (SNP difference 72–15,650).

Fig. 1
figure 1

Phylogenetic tree for E. coli isolates from this study. A Phylogenetic analysis of 20 Fluroquinolone resistant ESBL-producing Escherichia coli rooted with E. coli NZHG941718.1 genome. Indicated in boxes are sequence types of the analyzed isolates. B Phylogenetic tree for K. pneumoniae isolates from this study. B Phylogenetic analysis of 16 Fluroquinolone resistant ESBL-producing Klebsiella pneumoniae compared with K. pneumoniae RDK39_16/NTUH-K2044 genome. Indicated in boxes are sequence types of the analyzed isolates


The present study identified a high proportion (68%) of fluoroquinolone resistance among ESBL-producing Enterobacterales isolates obtained from fecal samples from children below five years of age hospitalized in Dar es Salaam healthcare facilities. This proportion is high compared to what has been reported in similar settings over the past two decades [17,18,19]. This high proportion of resistance is concerning, considering that the use of fluoroquinolones in children is discouraged due to potential adverse effects [25]. Presumably, the high prevalence reported here might not be directly associated with the selective pressure caused by the quinolone use in this age group, but rather due to microbial transmission from adults and / or another reservoir such as the environment [26]. A report from Tanzania points out that fluoroquinolones are the most prescribed antibiotic in the country [27, 28], and it is known that exposure to quinolone even in low concentrations increases the risk for selection of resistance [26]. Therefore, the fact that expanded-spectrum cephalosporins and aminoglycosides are widely used among Tanzanian children may also contribute to the high prevalence reported here. Furthermore, previous reports have shown genetic linkage between resistance to beta-lactams and quinolones in ESBL-producing isolates, whereby quinolone resistance rate is found to be high [29]. This is because PMQR genes are frequently found on the same resistance plasmids as genes conferring ESBL and aminoglycosides [30]. Some studies have reported high rate of quinolone resistance among ESBL-positive isolates [29]. In this study, all bacteria isolates are ESBL-positive, and this could partly explain the high rate of quinolone resistance found.

Nonetheless, we cannot rule out the difference in timeline between our study and previous studies and differences in settings rural/urban, hospital/community as potential contributors to the observed difference. Comparable proportions of fluoroquinolone-resistant Enterobacteriaceae have also been documented in other parts of the world [31], while lower resistance rates have been reported in Kenya [32] and in Ethiopia [31]. The difference may be attributed by numerous factors such as varying third generation cephalosporins use in the different settings. The observed difference highlights the importance of relevant local data. We observed variation in the rate of fluoroquinolone resistance among different bacteria species with high rate in K. pneumoniae compared to E. coli. Fluoroquinolone resistance is reported to be mainly due to chromosomal mutations in the genes encoding type ii topoisomerases. This process is usually sequential, the appearance of the first mutation in gyrA favors the appearance of new mutations in parC, and additional number of mutations causes an increase in the ciprofloxacin MIC above 2 mg/l [33]. Furthermore, studies have shown an interplay between plasmid and chromosomal mediated quinolone resistance where combination of PMQR and QRDR increases MIC values [34]. Of note, majority of E. coli strains in this study had high MIC values of above > 32 µg/ml. The high MIC values in E. coli strains could partly be due to high number of mutations as well as presence of both PMQR genes and chromosomal mutations in the same strains. On the other hand, most K. pneumoniae strains had low MIC values and none of the strains had any detectable chromosomal mutations, which could be the reason behind low MIC values in these strains.

In this study we report detection of different PMQR genes, the most predominant one being aac (6̍)-Ib-cr gene which is also prevalent in other parts of Tanzania [35, 36]. The predominance of the qnrB gene has previously been reported in bacterial strains from Africa [37]. Contrary to our findings, Mshana et al. [36] reported the predominance of another plasmid mediated resistance gene qnS1 in Mwanza, among children and adults in the northern part of Tanzania. This difference may be attributed to different geographical locations or different study populations between the two studies. Previous studies have shown that PMQR genes are usually found in plasmids which also carry resistance genes towards cephalosporins (ESBL), aminoglycosides, chloramphenicol, rifampicin, sulphonamides, tetracycline and trimethoprim [38].

Co-localization of antibiotic resistance genes on the same mobile genetic element such as plasmids is of great concern because it makes the transfer and spread of resistance genes between and within bacteria species easy. Some studies have demonstrated PMQR genes are easily transferable by conjugation [38,39,40].

Noteworthy is the phenotypic expression observed in isolates with combination of qnrB1 and aac(6’)-lb-cr genes. We observed that isolates which had both qnrB1 and aac(6’)-lb-cr genes had lower MIC levels. The two genes have been known to cause low level resistance which might not reach the breakpoints for phenotypic resistance; however, this finding poses a risk since these genes, especially when in combination, can facilitate selection of higher-level quinolone resistance.

The presence of genes encoding resistance to aminoglycosides, folate pathways inhibitors, fosfomycin, macrolides, lincosamide plus streptogramin b were also identified in the present study. Of concern is the detection of fosfomycin resistance genes among K. pneumoniae isolates. Faced with the growing AMR problem and shortage of new antimicrobial agents, there is renewed interest in older antibiotics such as fosfomycin that is currently used as a last-resort, rescue treatment against multidrug‐resistant bacteria especially ESBL-PE and carbapenemase‐producing Enterobacteriaceae [41]. Hence detection of these genes in the isolates is worrisome and warrants further studies.

The predominance of E. Coli ST617 and ST131 observed in the current study has also been reported by others [42, 43]. Similar to previous reports these strains harbor blaCTX-M-15 genes in multiple IncF, which is considered pandemic, as they have been detected in several parts of the world and in bacteria of different origins and sources [44]. A rare IncY plasmid was observed in two isolates: ST34 and ST617 carrying blaCTX-M-15, blaOXA-1and blaTEM-1B. This plasmid was also detected by Mshana et al. among clinical isolates in Mwanza, Tanzania [45]. Moreover, we report a high-risk clone ST155 which has not been reported in Tanzania. Furthermore, we report correlation of ST607 K. pneumoniae isolates which was the most prevalent sequence type with PMQR gene qnrB6. The predominance of plasmid mediated qnr genes has also been reported in Egypt [14]. Our isolates were highly diversified, with only few showing some degree of relatedness. Those that were clonally related were isolated from children attending the same hospital.

Fluoroquinolones have broad spectrum of activity and are effective in treating a wide spectrum of infections caused by aerobic Gram-negative organisms, particularly Enterobacteriaceae, and provide additional activity against Gram-positive organisms [1]. Although, fluoroquinolones have restricted use in pediatric population [25], the current trend of increase resistance towards other antimicrobial agents such as cephalosporins, cotrimoxazole and aminoglycosides has led to an increased use of fluoroquinolone in children as alternative therapeutic agent. It is therefore important to monitor the trend and resistance mechanisms of fluoroquinolone in settings where this antimicrobial is the remaining relatively affordable treatment alternative.


This study indicates that there is a high prevalence of fluoroquinolone resistance caused by both chromosomal mutations and plasmid mediated genes (PMQR) among ESBL producing Enterobacterales. We report differences in MIC values towards fluoroquinolones among different bacteria species. High number of chromosomal mutations with or without the presence of PMQR genes was associated with increased MIC values in these bacteria strains. A variety of PMQRs were detected, but the most predominant ones were aac(6′)-Ib-cr, qnrB1 and oqx. The variety of different fluoroquinolone resistance genes detected in this single study should be taken into account when designing molecular epidemiological surveys to determine the mechanisms responsible for observed fluoroquinolone resistant phenotypes.

Availability of data and materials

All data generated or analyzed during this study are included in this manuscript and its Additional file.



American Type Culture Collection


Clinical Laboratory Standard Institute


Deoxyribonucleic acid


Extended spectrum beta-lactamase- producing Enterobacterales


Fluroquinolone resistant


Minimum inhibitory concentration


Multi locus sequence typing


Muhimbili National Hospital


Plasmid mediated quinolone resistance genes


Quinolone resistance determining regions




Sequence type


Whole genome sequencing


World Health Organization


  1. Sisay M, Weldegebreal F, Tesfa T, Ataro Z, Marami D, Mitiku H, et al. Resistance profile of clinically relevant bacterial isolates against fluoroquinolone in Ethiopia: a systematic review and meta-analysis. BMC Pharmacol Toxicol. 2018;19:86.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  2. WHO. Antimicrobial resistance. Global report on surveillance. World Heal Organ 2014.

  3. Yang P, Chen Y, Jiang S, Shen P, Lu X, Xiao Y. Association between the rate of fluoroquinolones-resistant gram-negative bacteria and antibiotic consumption from China based on 145 tertiary hospitals data in 2014. BMC Infect Dis 2020; 20.

  4. Koliscak LP, Johnson JW, Beardsley JR, Miller DP, Williamson JC, Luther VP, et al. Optimizing empiric antibiotic therapy in patients with severe β-lactam allergy. Antimicrob Agents Chemother. 2013;57:5918–23.

    Article  PubMed  PubMed Central  Google Scholar 

  5. Peirano G, Pitout JDD. Fluoroquinolone-resistant escherichia coli sequence type 131 isolates causing bloodstream infections in a canadian region with a centralized laboratory system: rapid emergence of the H30-RX sublineage. Antimicrob Agents Chemother. 2014;58:2699–703.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  6. Salah FD, Soubeiga ST, Ouattara AK, Sadji AY, Metuor-Dabire A, Obiri-Yeboah D, et al. Distribution of quinolone resistance gene (qnr) in ESBL-producing Escherichia coli and Klebsiella spp. in Lomé. Togo Antimicrob Resist Infect Control. 2019;8:104.

    Article  PubMed  Google Scholar 

  7. Vien LTM, Minh NNQ, Thuong TC, Khuong HD, Nga TVT, Thompson C, et al. The co-selection of fluoroquinolone resistance genes in the gut flora of Vietnamese children. PLoS ONE. 2012;7:42919.

    Article  CAS  Google Scholar 

  8. Nelson JM, Smith KE, Vugia DJ, Rabatsky-Ehr T, Segler SD, Kassenborg HD, et al. Prolonged diarrhea due to ciprofloxacin-resistant campylobacter infection. J Infect Dis. 2004;190:1150–7.

    Article  PubMed  Google Scholar 

  9. Sawa T, Shimizu M, Moriyama K, Wiener-Kronish JP. Association between Pseudomonas aeruginosa type III secretion, antibiotic resistance, and clinical outcome: a review. Crit Care. 2014;18:1–11.

    Article  Google Scholar 

  10. Chong Y, Shimoda S, Yakushiji H, Ito Y, Aoki T, Miyamoto T, et al. Clinical impact of fluoroquinolone-resistant Escherichia coli in the fecal flora of hematological patients with neutropenia and levofloxacin prophylaxis. PLoS ONE. 2014;9:e85210.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  11. Strahilevitz J, Jacoby GA, Hooper DC, Robicsek A. Plasmid-mediated quinolone resistance: a multifaceted threat. Clin Microbiol Rev. 2009;22:664.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  12. Juraschek K, Deneke C, Schmoger S, Grobbel M, Malorny B, Käsbohrer A, et al. Phenotypic and genotypic properties of fluoroquinolone-resistant, qnr-carrying Escherichia coli isolated from the German food chain in 2017. Microorganisms 2021;9.

  13. Wiener ES, Heil EL, Hynicka LM, Kristie JJ. Are fluoroquinolones appropriate for the treatment of extended-spectrum β-lactamase-producing gram-negative bacilli? J Pharm Technol. 2016;32:16.

    Article  CAS  PubMed  Google Scholar 

  14. Kotb DN, Mahdy WK, Mahmoud MS, Khairy RMM. Impact of co-existence of PMQR genes and QRDR mutations on fluoroquinolones resistance in Enterobacteriaceae strains isolated from community and hospital acquired UTIs. BMC Infect Dis. 2019;19.

  15. Osei Sekyere J, Amoako DG. Genomic and phenotypic characterisation of fluoroquinolone resistance mechanisms in Enterobacteriaceae in Durban, South Africa. PLoS ONE. 2017;12:e0178888.

    Article  PubMed  PubMed Central  Google Scholar 

  16. Mitra S, Mukherjee S, Naha S, Chattopadhyay P, Dutta S, Basu S. Evaluation of co-transfer of plasmid-mediated fluoroquinolone resistance genes and blaNDM gene in Enterobacteriaceae causing neonatal septicaemia. Antimicrob Resist Infect Control. 2019;8.

  17. Blomberg B, Jureen R, Manji KP, Tamim BS, Mwakagile DSM, Urassa WK, et al. High rate of fatal cases of pediatric septicemia caused by gram-negative bacteria with extended-spectrum beta-lactamases in Dar es Salaam, Tanzania. J Clin Microbiol. 2005;43:745.

    Article  PubMed  PubMed Central  Google Scholar 

  18. Moyo SJ, Aboud S, Kasubi M, Lyamuya EF, Maselle SY. Antimicrobial resistance among producers and non-producers of extended spectrum beta-lactamases in urinary isolates at a tertiary Hospital in Tanzania. BMC Res Notes. 2010;3:348.

    Article  PubMed  PubMed Central  Google Scholar 

  19. Tellevik MG, Blomberg B, Kommedal Ø, Maselle SY, Langeland N, Moyo SJ. High prevalence of faecal carriage of ESBL-producing enterobacteriaceae among children in Dar es Salaam, Tanzania. PLoS ONE. 2016;11:e0168024.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  20. Moyo SJ, Manyahi J, Blomberg B, Tellevik MG, Masoud NS, Aboud S, et al. Bacteraemia, malaria, and case fatality among children hospitalized with fever in Dar es Salaam, Tanzania. Front Microbiol. 2020;11:2118.

    Article  PubMed  PubMed Central  Google Scholar 

  21. Wayne P. Clinical and Laboratory Standards Intitute Performance Standards for Antimicrobial Susceptibility Testing. 29th ed. CLSI supllement M100. 950 West Valley Road, Suite 2500 Wayne, PA 19087 USA: CLSI; 2019.

  22. MicrobesNG n.d.

  23. Carattoli A, Zankari E, Garciá-Fernández A, Larsen MV, Lund O, Villa L, et al. In Silico detection and typing of plasmids using plasmidfinder and plasmid multilocus sequence typing. Antimicrob Agents Chemother. 2014;58:3895–903.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  24. Zankari E, Hasman H, Cosentino S, Vestergaard M, Rasmussen S, Lund O, et al. Identification of acquired antimicrobial resistance genes. J Antimicrob Chemother. 2012;67:2640–4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  25. Possomato-Vieira, José S, Khalil RAK. Safety Concerns Surrounding Quinolone Use in Children 乳鼠心肌提取 HHS Public Access. Physiol Behav 2016;176:139–48.

  26. Wang A, Yang Y, Lu Q, Wang Y, Chen Y, Deng L, et al. Presence of qnr gene in Escherichia coli and Klebsiella pneumoniae resistant to ciprofloxacin isolated from pediatric patients in China. BMC Infect Dis. 2008;8:68.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  27. Sangeda RZ, Saburi HA, Masatu FC, Aiko BG, Mboya EA, Mkumbwa S, et al. National antibiotics utilization trends for human use in Tanzania from 2010 to 2016 inferred from Tanzania medicines and medical devices authority importation data. Antibiotics. 2021;10:1–16.

    Article  Google Scholar 

  28. van den Boogaard J, Semvua HH, Boeree MJ, Aarnoutse RE, Kibiki GS. Sale of fluoroquinolones in northern Tanzania: a potential threat for fluoroquinolone use in tuberculosis treatment. J Antimicrob Chemother. 2009;65:145–7.

    Article  CAS  Google Scholar 

  29. Lautenbach E, Strom BL, Bilker WB, Patel JB, Edelstein PH, Fishman NO. Epidemiological investigation of fluoroquinolone resistance in infections due to extended-spectrum 2-lactamase-producing Escherichia coli and Klebsiella pneumoniae. Clin Infect Dis. 2001;33:1288–94.

    Article  CAS  PubMed  Google Scholar 

  30. Salah FD, Soubeiga ST, Ouattara AK, Sadji AY, Metuor-Dabire A, Obiri-Yeboah D, et al. Distribution of quinolone resistance gene (qnr) in ESBL-producing Escherichia coli and Klebsiella spp. in Lomé, Togo. Antimicrob Resist Infect Control. 2019;8.

  31. Teklu DS, Negeri AA, Legese MH, Bedada TL, Woldemariam HK, Tullu KD. Extended-spectrum beta-lactamase production and multi-drug resistance among Enterobacteriaceae isolated in Addis Ababa, Ethiopia. Antimicrob Resist Infect Control. 2019;8.

  32. Lord J, Gikonyo A, Miwa A, Odoi A. Antimicrobial resistance among Enterobacteriaceae, Staphylococcus aureus, and Pseudomonas spp. isolates from clinical specimens from a hospital in Nairobi, Kenya. PeerJ. 2021;9:e11958.

    Article  PubMed  PubMed Central  Google Scholar 

  33. Bansal S, Tandon V. Contribution of mutations in DNA gyrase and topoisomerase IV genes to ciprofloxacin resistance in Escherichia coli clinical isolates. Int J Antimicrob Agents. 2011;37:253–5.

    Article  CAS  PubMed  Google Scholar 

  34. Machuca J, Briales A, Labrador G, Díaz-de-Alba P, López-Rojas R, Docobo-Pérez F, et al. Interplay between plasmid-mediated and chromosomal-mediated fluoroquinolone resistance and bacterial fitness in Escherichia coli. J Antimicrob Chemother. 2014;69:3203–15.

    Article  CAS  PubMed  Google Scholar 

  35. Sonda T, Kumburu H, van Zwetselaar M, Alifrangis M, Mmbaga BT, Aarestrup FM, et al. Whole genome sequencing reveals high clonal diversity of Escherichia coli isolated from patients in a tertiary care hospital in Moshi, Tanzania. Antimicrob Resist Infect Control. 2018;7:1–12.

    Article  Google Scholar 

  36. Mshana SE, Falgenhauer L, Mirambo MM, Mushi MF, Moremi N, Julius R, et al. Predictors of blaCTX-M-15 in varieties of Escherichia coli genotypes from humans in community settings in Mwanza, Tanzania. BMC Infect Dis. 2016;16:187.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  37. Breurec S, Guessennd N, Timinouni M, Le TTH, Cao V, Ngandjio A, et al. Klebsiella pneumoniae resistant to third-generation cephalosporins in five African and two Vietnamese major towns: multiclonal population structure with two major international clonal groups, CG15 and CG258. Clin Microbiol Infect. 2013;19:349–55.

    Article  CAS  PubMed  Google Scholar 

  38. Briales A, Rodríguez-Martínez JM, Velasco C, De Alba PD, Rodríguez-Baño J, Martínez-Martínez L, et al. Prevalence of plasmid-mediated quinolone resistance determinants qnr and aac(6′)-Ib-cr in Escherichia coli and Klebsiella pneumoniae producing extended-spectrum β-lactamases in Spain. Int J Antimicrob Agents. 2012;39:431–4.

    Article  CAS  PubMed  Google Scholar 

  39. Poirel L, Van De Loo M, Mammeri H, Nordmann P. Association of plasmid-mediated quinolone resistance with extended-spectrum β-lactamase VEB-1. Antimicrob Agents Chemother. 2005;49:3091–4.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  40. Wang M, Tran JH, Jacoby GA, Zhang Y, Wang F, Hooper DC. Plasmid-mediated quinolone resistance in clinical isolates of Escherichia coli from Shanghai, China. Antimicrob Agents Chemother. 2003;47:2242–8.

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  41. Zurfluh K, Treier A, Schmitt K, Stephan R. Mobile fosfomycin resistance genes in Enterobacteriaceae—an increasing threat. Microbiologyopen. 2020;9.

  42. Aibinu I, Odugbemi T, Koenig W, Ghebremedhin B. Sequence type ST131 and ST10 complex (ST617) predominant among CTX-M-15-producing Escherichia coli isolates from Nigeria. Clin Microbiol Infect. 2012;18:E49.

    Article  CAS  PubMed  Google Scholar 

  43. Giuseppe V, et al. Prevalence and genetic diversity of extended-spectrum β-lactamase (ESBL)-producing Escherichia coli in nursing homes in Bavaria, Germany. Vet Microbiol. 2017;200:138–41.

    Article  Google Scholar 

  44. Rafaï C, Frank T, Manirakiza A, Gaudeuille A, Mbecko J-RR, Nghario L, et al. Dissemination of IncF-type plasmids in multiresistant CTX-M-15-producing Enterobacteriaceae isolates from surgical-site infections in Bangui, Central African Republic. BMC Microbiol 2015;15.

  45. Mshana SE, Imirzalioglu C, Hain T, Domann E, Lyamuya EF, Chakraborty T. Multiple ST clonal complexes, with a predominance of ST131, of Escherichia coli harbouring blaCTX-M-15 in a tertiary hospital in Tanzania. Clin Microbiol Infect. 2011;17:1279–82.

    Article  CAS  PubMed  Google Scholar 

Download references


We would like to acknowledge members of Department of Microbiology and Immunology, Muhimbili National Hospital, Dar es Salaam, Tanzania, the Department of Microbiology, Haukeland University Hospital, Bergen, Norway and the Department of Clinical Science, University of Bergen, Bergen, Norway, for their technical and financial support during the study period.


This work was supported by (i) Helse Bergen HF, Haukelande University Hospital,  Bergen, Norway, project number 912132, (ii)Norwegian National Advisory Unit on Tropical Infectious Diseases, Haukeland University Hospital, Bergen, Norway, (iii) CAMRIA-Combating Antimicrobial Resistance with Interdisciplinary Approaches, Centre for Antimicrobial Resistance in Western Norway, funded by Trond Mohn Stiftelse, grant number TMS2020TMT11, and (iv) STRESST- Antimicrobial Sterwardship in Hospitals, Resistance Selection and Transfer in a One Health Context, Liverpool School of Tropical Medicine, Liverpool, United Kingdom, funded by JPLAMR grant number NFR333432

Author information

Authors and Affiliations



UOK, SJM, SEM conceived the study. UOK, SJM, SEM, JM, NL and BB contributed to designing the study. UOK, JM and HHS performed the microbiological investigations. UOK, SJM, SEM, JM, NL, APR and BB participated in critical review of the manuscript. All authors contributed to writing the manuscript and approved the final version. All authors read and approved the final manuscript.

Corresponding author

Correspondence to Upendo O. Kibwana.

Ethics declarations

Ethics approval and consent to participate

Ethical approval was obtained from the Senate Research and Publications Committee of Muhimbili University of Health and Allied Sciences in Dar es Salaam, Tanzania and from the Regional Committee for Medical and Health Research Ethics (REK) in Western Norway. Written informed consent to participate in this study was provided by the participants’ legal guardian/next of kin. All steps/methods were performed in accordance with the standard operating procedures and study protocol.

Consent for publication

Not applicable.

Competing interests

The authors declare that they have no competing interests.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit The Creative Commons Public Domain Dedication waiver ( applies to the data made available in this article, unless otherwise stated in a credit line to the data.

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Kibwana, U.O., Manyahi, J., Sandnes, H.H. et al. Fluoroquinolone resistance among fecal extended spectrum βeta lactamases positive Enterobacterales isolates from children in Dar es Salaam, Tanzania. BMC Infect Dis 23, 135 (2023).

Download citation

  • Received:

  • Accepted:

  • Published:

  • DOI:


  • Fluoroquinolone resistance
  • Whole genome sequencing