Next Article in Journal
Towards the Identification of Antibiotic-Resistant Bacteria Causing Urinary Tract Infections Using Volatile Organic Compounds Analysis—A Pilot Study
Previous Article in Journal
The Safety and Efficacy of Phage Therapy for Bone and Joint Infections: A Systematic Review
 
 
Search for Articles:
Title / Keyword
Author / Affiliation / Email
Journal
Article Type
 
 
Advanced Search
 
Section
Special Issue
Volume
Issue
Number
Page
 
Journals
Antibiotics
Volume 9
Issue 11
10.3390/antibiotics9110796
antibiotics-logo
Submit to this Journal Review for this Journal Propose a Special Issue
► Article Menu

Article Menu

share Share announcement Help format_quote Cite question_answer Discuss in SciProfiles thumb_up
...
Endorse textsms
...
Comment
first_page
settings
Order Article Reprints
Font Type:
Arial Georgia Verdana
Font Size:
Aa Aa Aa
Line Spacing:
Column Width:
Background:
Article

High Prevalence of blaCTX-M-15 Gene among Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolates Causing Extraintestinal Infections in Bangladesh

by
Razib Mazumder
,
Ahmed Abdullah
,
Dilruba Ahmed
and
Arif Hussain
*
Laboratory Sciences and Services Division, International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b), Dhaka-1212, Bangladesh
*
Author to whom correspondence should be addressed.
Antibiotics 2020, 9(11), 796; https://doi.org/10.3390/antibiotics9110796
Submission received: 4 September 2020 / Revised: 6 October 2020 / Accepted: 10 October 2020 / Published: 11 November 2020
Versions Notes

Abstract

:
The emergence of multidrug-resistant (MDR) Escherichia coli (E. coli) clonal lineages with high virulence potential is alarming. Lack of sufficient data on molecular epidemiology of such pathogens from countries with high infection burden, such as Bangladesh, hinders management and infection control measures. In this study, we assessed the population structure, virulence potential and antimicrobial susceptibility of clinical E. coli isolates from Dhaka, Bangladesh. A high prevalence of MDR (69%) and extended-spectrum β-lactamase production (ESBL) (51%) was found. Most E. coli isolates were susceptible to amikacin (95%), meropenem (94%) and nitrofurantoin (89%) antibiotics. A high prevalence of ST131 (22%) and ST95 (9%) followed by ST69 (4%) and ST73 (3%) was observed. Phylogroups B2 (46%), B1 (16%), D (10%) and F (9%) were prominent. blaCTX-M-15 (52%) and blaNDM-1 (5%) were the most prevalent ESBL and carbapenem resistance genes, respectively. Moreover, the predominant pathotype identified was extraintestinal pathogenic E. coli (ExPEC) (41%) followed by enteric pathogens (11%). In conclusion, our results suggest the transmission of clonal E. coli groups amidst diverse E. coli population that are associated with high virulence potential and MDR phenotype. This is of high concern and mandates more efforts towards molecular surveillance of antimicrobial resistance (AMR) in clinically significant pathogens.

1. Introduction

Urinary tract infection (UTI) is one of the most common bacterial infections, which has become a major public health burden worldwide [1]. The most frequent causative agent of community-acquired UTIs is uropathogenic E. coli (UPEC) accounting for 75–85% of infections [1]. As an extraintestinal pathogen, E. coli is also frequently implicated in bloodstream infections and neonatal meningitis [2,3]. The emergence of multidrug-resistant (MDR) E. coli producing extended-spectrum β-lactamase (ESBL) enzymes and carbapenemases has made empirical therapy void, leading to high morbidity and mortality [4]. Strikingly, an increasing number of ExPEC strains producing β-lactamase such as CTX-M-15 is being associated with clonal lineages such as ST131 [5]. Isolates belonging to this lineage have spread extensively, and they are responsible for the rapid worldwide increase in the prevalence of bloodstream and urinary tract infections. Moreover, the development of resistance to carbapenems among such pathogens is the greatest threat to public health because there are still no effective and safe therapeutic options available for treating carbapenem-resistant pathogens causing life-threatening infections [6].
Currently, the CTX-M-group enzymes that belong to class A ESBLs are the most predominant ESBLs worldwide, including the developing world. The genes for these ESBLs were detected on several plasmid incompatibility groups but are sometimes also present on chromosomes [7]. There are more than 50 allelic variants, which are clustered into six groups: CTX-M-1, CTX-M-2, CTX-M-8, CTX-M-9, CTX-M-25 and KLUC. CTX-M groups 1, 2, 8 and 9 are the four most common CTX-M groups harbored by Gram-negative pathogens [7]. Extraintestinal infections are usually opportunistic in nature and often occur due to conditions such as dysfunctional urinary tract or systemic immunocompromise [8]. E. coli isolates in general consist of a clonal population comprising of seven major phylogenetic groups (A, B1, B2, C, D, E and F). These phylogenetic groups have varying propensities to virulence factors, association with host and the environment [9]. Moreover, the presence of specific set of virulence factors is attributable to the ability of E. coli strains to cause disease by various pathotypes that are broadly classified into intestinal and extraintestinal pathogenic E. coli [9]. Characterization of clinical E. coli strains with respect to their pathotypes, AMR profiles and virulence gene will promote understanding of the epidemiology of such infections.
AMR is a global problem that has real implications for human health [10]. Moreover, developing countries such as Bangladesh are highly vulnerable to the growing threat of AMR due to its high population density, inadequate sanitation and excessive use of antimicrobials in clinical, animal and agriculture sectors [11]. This together with the high burden of infectious diseases makes it pertinent to elucidate the molecular characteristics of circulating pathogens for which the data available are sparse. Therefore, this study aimed to assess the population structure, virulence potential and antimicrobial susceptibility profiles of clinical E. coli isolates from Dhaka, Bangladesh.

2. Results

2.1. Multidrug Resistance

Disc diffusion test entailing 16 antibiotics showed a high level of resistance among the E. coli isolates analyzed. The frequencies of resistance/susceptibilities are mentioned in Table 1. Overall, 69% (88/128) of isolates were resistant to at least three antibiotic classes, indicating they were multidrug-resistant. In fact, around 50% of isolates were resistant to at least seven antibiotics, with resistance ranging up to 15 antibiotics. Interestingly, the E. coli isolates assessed were highly susceptible to following antibiotics, carbapenems (meropenem (94%) and imipenem (91%)), amikacin (95%) and nitrofurantoin (89%). The intI1 gene corresponding to class 1 integron was present in 27 (21%) of the 128 isolates analyzed. The IncF replicon types including FIA and FIB each were detected in over half (55%) of the E. coli isolates (Table 2).

2.2. Group B2 Was the Most Prevalent Phylogenetic Group

With respect to phylogenetic groups, most E. coli isolates belonged to the pathogenic phylogroup B2 (46%), followed by groups B1 (16%), D (10%), C (7%), F (9%), A (5%) and E (2%) (Table 2). Strains belonging to three phylogroups C, D and E strongly correlated with the MDR (78%, 85% and 100%, respectively) and ESBL production (89%, 69% and 100%, respectively). However, a majority of B2 phylogroup (68%) isolates were found to be MDR. All the three major ESBL genes detected [blaCTX-M (with extended hydrolyzing activity against extended-spectrum cephalosporins), blaTEM (that has limited activity against newer cephalosporins) and blaOXA-1 (that has limited activity against newer cephalosporins)] were identified in multiple phylogenetic backgrounds.

2.3. Over Half of the Isolates Were ESBL Producers with blaCTX-M-15 Gene Being Dominant

Genotypically (taking into account the presence of, CTX-M-1, -2 and -9 groups, blaCTX-M-15, blaTEM and blaOXA-1) the overall prevalence of ESBL E. coli isolates was 66% (84/128 isolates carried at least one ESBL gene screened), whereas phenotypically (using CHROMagarESBL) only 51% isolates (65/128) were found to be ESBL producers. The difference observed between results of genotypic and phenotypic ESBL detection might be due to lower sensitivity of phenotypic methods. The blaCTX-M-15 gene was significantly associated with the ESBL phenotype (p = 0.004), with 55 isolates carrying the blaCTX-M-15 gene out of 65 ESBL-producing E. coli. In addition, the most prevalent ESBL genotype was the CTX-M-1 group (52%), particularly the blaCTX-M-15 gene (Table 2). The other ESBL genotypes detected were blaOXA-1 (17%), blaTEM (20%), CTX-M-9 group (3%) and CTX-M-2 group (1%). Multiple β-lactamase genes in combinations of blaCTX-M-15 or blaOXA-1 and blaTEM were detected in 23% of the isolates.

2.4. Molecular Characteristics of Carbapenem Resistant Strains

Carbapenemases are the β lactamase enzymes that can hydrolyze carbapenems including all other β lactam antibiotics. The most common carbapenem resistance genes are blaNDM-1, blaOXA-48, blaKPC-2, blaVIM-1 and blaIMP. Overall, 7% of E. coli isolates assessed in this study were carbapenem-resistant (nine out of 128 E. coli isolates carried at least one carbapenem resistance gene). The most prevalent carbapenem resistance gene was blaNDM-1 (5%, 6/128), followed by blaOXA-48 (2%, 2/128) and blaIMP (1%, 1/128) (Table 2). Interestingly, in this study, the genes blaVIM-1 and blaKPC-2 were not identified. All NDM-1 positive E. coli were MDR; in fact, a majority of them (5/6) were pandrug resistant and co-harbored the blaCTX-M-15 gene. All nine carbapenem-resistant isolates were phenotypically resistant to an average of 11.6 antimicrobial agents and 4.2 different antibiotic classes (Table 3). Only 44% (4/9) isolates carrying carbapenemase genes showed resistance to meropenem and imipenem by disc diffusion methods. These strains mainly belonged to non-pathogenic phylogroups and none of them was affiliated to any of the four major STs screened.

2.5. All Four Major Sequence Types (STs) Were Detected

Analysis of major E. coli sequence types revealed that ST131 was the most prevalent ST, accounting for 22% (28/128) of the studied isolates; 100% of the ST131 E. coli isolates were associated with the phylogroup B2 and fluoroquinolone (ciprofloxacin) resistance; and 82% (23/28) of ST131 E. coli harbored blaCTX-M-15 gene. The other prevalent STs were ST95 (9%), followed by ST69 (4%) and ST73 (3%) (Table 2). All (100%) of ST131 and ST95 isolates were identified as phylogroup B2 strains. All these four major STs were predominantly from ExPEC pathotype.

2.6. Pathotype Assignment

Overall, 52% (66/128) of all E. coli isolates were potentially pathogenic, as defined by the presence of characteristic virulence markers (Table 2). ExPECs (isolates positive for three or more ExPEC virulence markers) constituted 41% (52/128) of all E. coli isolates. The prevalence of ExPEC in urine isolates was 44% (45/103), whereas the prevalence in isolates cultured from other body fluids was 28% (7/25). The diarrheagenic variants constituted 11% (14/128) of all E. coli isolates. Pathogenic E. coli isolates were significantly associated with the ESBL-genotype blaCTX-M-15 and phylogenetic group B2 (p < 0.05 for both). The proportion of MDR was higher in pathogenic E. coli variants compared to non-pathogenic E. coli isolates (p < 0.05). In addition, the pks pathogenicity island that encodes a genotoxin called colibactin was detected in 9% (11/128) of the E. coli isolates. The presence of pks pathogenicity island strongly correlated with ExPEC pathotype as all nine isolates were classified as ExPEC. These 11 strains majorly belonged to ST95 (5/11) and ST73 (3/11), and none were from ST131.

3. Discussion

Extraintestinal pathogenic E. coli (ExPEC) is the most frequent cause of community-acquired UTIs accounting for significant morbidity, mortality and health care costs. In this study, we carried out a comprehensive molecular characterization of clinical E. coli isolates from a major referral diagnostic center (icddr,b) in Dhaka and demonstrated the presence of major ESBL-E. coli clones similar to those reported in different parts of the world [12]. Overall, high resistance rates to antibiotics including cephalosporins, fluoroquinolone and trimethoprim were found, as these are the most frequently used antibiotics to treat patients with UTIs, whereas the resistance rates to aminoglycosides were moderate and those to carbapenems and nitrofurantoin were low in the studied isolates. These observations were consistent with earlier studies from Bangladesh [13].
In our study, 41% isolates were classified as ExPEC and 11% were identified as diarrhoeagenic E. coli based on the presence of predictive virulence factors. The remaining 48% isolates could not be typed as ExPEC or diarrhoeagenic E. coli. These results are similar to those described by another study [14]. Further, a majority of these isolates belonged to phylogenetic groups B2, B1 and D. Phylogroups B2 and D are considered to be associated with more virulent strains frequently linked to infections [15]. However, the presence of B1 group as the second most predominant phylogroup in our study isolates suggest colonization of urinary tract with strains from gastrointestinal tract because B1 and A groups mostly belong to commensal E. coli [15]. Phylogroups B2, D, C and E were comprised in majority of MDR isolates rather than the commensal phylogroups A and B1, an observation in line with other studies [13,16]. The two most frequently identified E. coli lineages in our studied isolates were ST131 and ST95; other STs detected include ST73 and ST69. This is in line with previous reports that showed the predominance of sequence types, 131, 95, 73 and 69 among E. coli obtained from UTI and blood stream infections [17,18]. Similar to the previous report, our results show that ST95 isolates had low prevalence of antibiotic resistance [19]. The high prevalence of ST131 isolates in this study is not surprising, as ST131 has emerged as the most predominant high-risk clone among extraintestinal infections worldwide [20]. The presence of high MDR rates together with extensive virulence gene content in these ST131 E. coli isolates are considered a double threat. However, most E. coli isolates irrespective of phylogroups and pathotypes were susceptible to amikacin, meropenem and nitrofurantoin antibiotics.
The majority of ESBL-producing E. coli isolates in this study harbored the blaCTX-M-15 gene similar to previous studies [21]. The increasing predominance of the blaCTX-M-15 allele together with the co-occurrence of other ESBL genes might probably offer the bacteria a selective advantage in overcoming multiple antibiotic pressure. Similarly, the majority of isolates from ST131 lineage identified in this study were CTX-M-15 producing. The majority of CTX-M-15 producing E. coli isolates were found to be MDR. In contrast, a majority of these isolates were susceptible to amikacin and nitrofurantoin antibiotics, suggesting that these antibiotics can still be a reliable option for empirical treatment of urinary tract infections. This is similar to data presented by other studies [22,23]. Carbapenems are antibiotics used to treat life-threatening infections caused by MDR Enterobacteriaceae such as E. coli [24]. The emergence of carbapenem-resistant bacterial isolates is of great medical concern globally. The majority of carbapenem-resistant isolates of this study carried the blaNDM-1 gene followed by blaOXA-48, similar to previous studies from Southeast Asia [24,25]. Most of the carbapenem resistant isolates in this study were resistant to a broad-spectrum of antibiotics (pan-drug resistant). None of the antibiotics out of the 16 antibiotics in our panel was 100% effective against these isolates. This is the reason why the standard treatment of carbapenem-resistant Enterobacteriaceae (CRE) include polymixin based combination therapy; other antibiotics include fosfomycin and tigecycline [26]. However, these are also less suitable for their use in neonates and infants [26]. In view of this, it is very important to strengthen and establish the epidemiological surveillance of CRE.
The pathogenicity of extraintestinal pathogenic E. coli is based on the presence of several virulence factors that help bacteria to establish a successful infection, assimilate essential nutrients and disseminate in the urinary tract. The most frequently identified virulence factors in our isolates were associated with siderophores and protectins followed by adhesins. These results are consistent with results from previous studies which showed high frequency of siderophores, adhesins and capsular polysaccharides [4,27]. The isolates harboring ExPEC associated virulence factors were predominantly affiliated to B2 phylogroup and MDR phenotype. Another commonly found gene in our isolates was hlyD gene associated with toxins and is required for the dissemination of pathogens in the urinary tract. We also detected the presence of a genotoxin encoded by pks pathogenicity island in 9% (11/128) isolates. This is in agreement with the findings of others [28]. The presence of pks island was strongly correlated with ExPEC pathotype, besides these strains showed low rates of antibiotic resistance, this is similar to data presented in other reports [28].
In conclusion, this study provides evidence for prevalence and widespread dissemination of MDR mainly via phylogenetic group B2 strains and coexistence of multiple ESBL-genes (CTX-M-group1, blaTEM and blaOXA-1) in clinical E. coli isolates. Notably, E. coli ST131, the pandemic ExPEC lineage, was identified in moderate proportion among ExPEC strains in this study. Our results reveal a moderate prevalence of carbapenamase gene carrying clinical E. coli isolates. Our results also suggest that several antibiotics such as meropenem, imipenem, amikacin and nitrofurantoin can be used to effectively treat infections in these settings. Further work is required at the genomics level to elucidate the molecular mechanisms shaping the evolution of clinical E. coli isolates with respect to acquisition of newer resistance and virulence determinants. Our data highlight the significance of longitudinal surveillance of pathogens and molecular epidemiology in different settings to understand the local epidemiological scenario and contemplate the global epidemiology on AMR.

4. Methods

4.1. Sample Collection

In this retrospective study, 128 E. coli isolates were analyzed, of which 103 were cultured from urine specimen of suspected urinary tract infected patients and 25 isolates were cultured from other body fluids (Table S1). These isolates represented 1% of all the E. coli isolates cultured at the Clinical Microbiology and Immunology Laboratory of International Centre for Diarrhoeal Disease Research, Bangladesh (icddr,b) between March 2018 to July 2019. Identification of E. coli isolates was performed by routine biochemical tests that included; Kliger’s iron agar, motility indole urease, Simmons citrate agar, oxidase and ONPG tests. Bacterial isolates were preserved at −20 °C in trypticase soy broth containing 25% glycerol.

4.2. Antimicrobial Susceptibility Testing and ESBL Detection

Antibiotic sensitivity testing was performed for all E. coli isolates by standard disc diffusion protocol using Mueller–Hinton agar as per the guidelines of Clinical Laboratory Standard Institute. The antimicrobial agents tested were ampicillin (10 µg), amoxiclav (3 µg), piperacillin–tazobactam (100/10 µg), gentamicin (10 µg), amikacin (30 µg), cotrimoxazole (25 µg), nalidixic acid (30 µg), ciprofloxacin (5 µg), nitrofurantoin (200 µg), cefuroxime (30 µg), ceftriaxone (30 µg), ceftazidime (30 µg), cefixime (5 µg), cefepime (30 µg), imipenem (10 µg) and meropenem (10 µg). E. coli ATCC 25922 strain was used for quality control. Screening of ESBL production was done using CHROMagarESBLTM (Paris, France) [29].

4.3. Molecular Characterization of Antimicrobial Resistance

Molecular determination of antimicrobial resistance was performed by PCR based amplification of genes using gene specific primers described previously. Isolates were screened for ESBL genes (CTX-M-1, -2 and -9 groups, blaCTX-M-15, blaTEM and blaOXA-1) [9], carbapenem resistance genes (blaNDM-1, blaKPC-2, blaOXA-48, blaVIM-1 and blaIMP), [30] class 1 integron gene (intl1) [4] and plasmid replicon types (FIA and FIB) [4].

4.4. Determination of Phylogroups and Major E. coli Sequence Types

All isolates were screened for phylogenetic groups A, B1, B2, C, D, E and F using one quadraplex PCR targeting chuA, yjaA, TspE4.C2 and arpA and two singleplex PCRs targeting arpAgpE and trpA on DNA template obtained by boiling lysis method [31]. Strains were assigned to the above seven phylogenetic groups based on the criteria described by Clermont and colleagues [31]. The four major E. coli sequence types (STs), namely 69, 73, 95 and 131, were determined using a rapid PCR based multiplex assay described by Doumith et al. [17].

4.5. Detection of pks-Genomic Island

All isolates were screened for the presence of pks island by using PCR primers for two representative genes of the genomic island to amplify one flanking region (clbB) and one internal region (clbA) at annealing temperature of 65 and 45 °C, respectively, using standard PCR conditions [28].

4.6. Pathotype Assignment

For analysis of virulence factors that assign isolates to different intestinal pathotypes, PCRs targeting gene encoding: shigatoxin (stx) for enterohemorrhagic E. coli (EHEC), intimin (eae) for enteropathogenic E. coli (EPEC), invasion plasmid antigen (ipaH) for enteroinvasive E. coli (EIEC), heat stable (elt) and heat labile enterotoxin (est) for enterotoxigenic E. coli (ETEC), aggregative virulence regulator (aggr), L-aspartyl-tRNA (aspU) and plasmid segment of pCVD432 for enteroaggregative E. coli (EAEC) were used [32]. The following seven ExPEC associated virulence factors were screened: afimbrial adhesion (afa), F1C fimbriae (focG), iron acquisition system (iutA), cytolytic protein toxin (hlyD), P fimbriae (papA), group 2 polysaccharide capsule (kpsMII) and S fimbriae (sfaS) [9]. Strains having three or more of these genes were classified as ExPEC according to Johnson’s criteria [33].

4.7. Statistics

All statistical analyses were performed using SPSS. Fisher’s exact test was used to compare different proportions. p-values ≤ 0.05 were considered to be significant.

Supplementary Materials

The following are available online at https://www.mdpi.com/2079-6382/9/11/796/s1, Table S1: Demographic and molecular features of 128 E. coli isolates described in this study.

Author Contributions

A.H. designed the study, performed experiments and wrote the manuscript. A.A. performed sample collection. R.M. performed microbiological work and provided inputs in quality control of PCR assays. D.A. and R.M. reviewed the manuscript. All authors have read and agreed to the published version of the manuscript.

Funding

This research received no external funding.

Acknowledgments

This research study was funded by core donors which provide unrestricted support to icddr,b for its operations and research. Current donors providing unrestricted support include: Government of the People’s Republic of Bangladesh; Global Affairs Canada (GAC); Swedish International Development Cooperation Agency (Sida); and the Department for International Development (UK Aid). We gratefully acknowledge these donors for their support and commitment to icddr,b’s research efforts. We thank Umme Saima for providing valuable technical assistance in performing experiments at different stages of this study.

Conflicts of Interest

The authors declare no conflict of interest.

References

  1. Hussain, A.; Ranjan, A.; Nandanwar, N.; Babbar, A.; Jadhav, S.; Ahmed, N. Genotypic and phenotypic profiles of Escherichia coli isolates belonging to clinical sequence type 131 (ST131), clinical non-ST131, and fecal non-ST131 lineages from India. Antimicrob. Agents Chemother. 2014, 58, 7240–7249. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  2. Ranjan, A.; Shaik, S.; Hussain, A.; Nandanwar, N.; Semmler, T.; Jadhav, S.; Wieler, L.H.; Ahmed, N. Genomic and functional portrait of a highly virulent, CTX-M-15-producing H30- Rx subclone of Escherichia coli sequence type (ST) 131. Antimicrob. Agents Chemother. 2015, 59, 6087–6095. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  3. Shaik, S.; Ranjan, A.; Tiwari, S.K.; Hussain, A.; Nandanwar, N.; Kumar, N.; Jadhav, S.; Semmler, T.; Baddam, R.; Islam, M.A.; et al. Comparative Genomic Analysis of Globally Dominant ST131 Clone with Other Epidemiologically Successful Extraintestinal Pathogenic Escherichia coli (ExPEC) Lineages. MBio 2017, 8, e01596-17. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  4. Hussain, A.; Ewers, C.; Nandanwar, N.; Guenther, S.; Jadhav, S.; Wieler, L.H.; Ahmed, N. Multiresistant Uropathogenic Escherichia coli from a Region in India Where Urinary Tract Infections Are Endemic: Genotypic and Phenotypic Characteristics of Sequence Type 131 Isolates of the CTX-M-15 Extended-Spectrum- -Lactamase-Producing Lineage. Antimicrob. Agents Chemother. 2012, 56, 6358–6365. [Google Scholar] [CrossRef] [Green Version]
  5. Jadhav, S.; Hussain, A.; Devi, S.; Kumar, A.; Parveen, S.; Gandham, N.; Wieler, L.H.; Ewers, C.; Ahmed, N. Virulence characteristics and genetic affinities of multiple drug resistant uropathogenic Escherichia coli from a semi urban locality in India. PLoS ONE 2011, 6, e18063. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  6. Doi, Y. Treatment Options for Carbapenem-resistant Gram-negative Bacterial Infections. Clin. Infect. Dis. 2019, 69, S565–S575. [Google Scholar] [CrossRef] [Green Version]
  7. D’Andrea, M.M.; Arena, F.; Pallecchi, L.; Rossolini, G.M. CTX-M-type β-lactamases: A successful story of antibiotic resistance. Int. J. Med. Microbiol. 2013, 303, 305–317. [Google Scholar] [CrossRef] [PubMed]
  8. Robins-Browne, R.M.; Holt, K.E.; Ingle, D.J.; Hocking, D.M.; Yang, J.; Tauschek, M. Are Escherichia coli Pathotypes Still Relevant in the Era of Whole-Genome Sequencing? Front. Cell. Infect. Microbiol. 2016, 6, 141. [Google Scholar] [CrossRef] [Green Version]
  9. Franz, E.; Veenman, C.; van Hoek, A.H.A.M.; Husman, A.D.R.; Blaak, H. Pathogenic Escherichia coli producing Extended-Spectrum β-Lactamases isolated from surface water and wastewater. Sci. Rep. 2015, 5, 14372. [Google Scholar] [CrossRef] [Green Version]
  10. Jee, Y.; Carlson, J.; Rafai, E.; Musonda, K.; Huong, T.T.G.; Daza, P.; Sattayawuthipong, W.; Yoon, T. Antimicrobial resistance: A threat to global health. Lancet. Infect. Dis. 2018, 18, 939–940. [Google Scholar] [CrossRef]
  11. Ayukekbong, J.A.; Ntemgwa, M.; Atabe, A.N. The threat of antimicrobial resistance in developing countries: Causes and control strategies. Antimicrob. Resist. Infect. Control 2017, 6, 47. [Google Scholar] [CrossRef] [PubMed]
  12. Riley, L.W. Pandemic lineages of extraintestinal pathogenic Escherichia coli. Clin. Microbiol. Infect. 2014, 20, 380–390. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  13. Ahmed, I.; Rabbi, M.B.; Sultana, S. Antibiotic resistance in Bangladesh: A systematic review. Int. J. Infect. Dis. 2019, 80, 54–61. [Google Scholar] [CrossRef] [Green Version]
  14. Campos, A.C.C.; Andrade, N.L.; Ferdous, M.; Chlebowicz, M.A.; Santos, C.C.; Correal, J.C.D.; Lo Ten Foe, J.R.; Rosa, A.C.P.; Damasco, P.V.; Friedrich, A.W.; et al. Comprehensive Molecular Characterization of Escherichia coli Isolates from Urine Samples of Hospitalized Patients in Rio de Janeiro, Brazil. Front. Microbiol. 2018, 9, 243. [Google Scholar] [CrossRef] [PubMed]
  15. Khairy, R.M.; Mohamed, E.S.; Ghany, H.M.A.; Abdelrahim, S.S. Phylogenic classification and virulence genes profiles of uropathogenic E. coli and diarrhegenic E. coli strains isolated from community acquired infections. PLoS ONE 2019, 14, e0222441. [Google Scholar] [CrossRef] [Green Version]
  16. Ramírez-Castillo, F.Y.; Moreno-Flores, A.C.; Avelar-González, F.J.; Márquez-Díaz, F.; Harel, J.; Guerrero-Barrera, A.L. An evaluation of multidrug-resistant Escherichia coli isolates in urinary tract infections from Aguascalientes, Mexico: Cross-sectional study. Ann. Clin. Microbiol. Antimicrob. 2018, 17, 34. [Google Scholar] [CrossRef]
  17. Doumith, M.; Day, M.; Ciesielczuk, H.; Hope, R.; Underwood, A.; Reynolds, R.; Wain, J.; Livermore, D.M.; Woodford, N. Rapid identification of major Escherichia coli sequence types causing urinary tract and bloodstream infections. J. Clin. Microbiol. 2015, 53, 160–166. [Google Scholar] [CrossRef] [Green Version]
  18. Manges, A.R.; Tabor, H.; Tellis, P.; Vincent, C.; Tellier, P.P. Endemic and epidemic lineages of Escherichia coli that cause urinary tract infections. Emerg. Infect. Dis. 2008, 14, 1575–1583. [Google Scholar] [CrossRef]
  19. Stephens, C.M.; Adams-Sapper, S.; Sekhon, M.; Johnson, J.R.; Riley, L.W. Genomic Analysis of Factors Associated with Low Prevalence of Antibiotic Resistance in Extraintestinal Pathogenic Escherichia coli Sequence Type 95 Strains. mSphere 2017, 2, e00390-16. [Google Scholar] [CrossRef] [Green Version]
  20. Nicolas-Chanoine, M.H.; Bertrand, X.; Madec, J.Y. Escherichia coli st131, an intriguing clonal group. Clin. Microbiol. Rev. 2014, 27, 543–574. [Google Scholar] [CrossRef] [Green Version]
  21. Hawkey, P.M. Prevalence and clonality of extended-spectrum β-lactamases in Asia. Clin. Microbiol. Infect. 2008, 14, 159–165. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  22. Kudinha, T.; Johnson, J.R.; Andrew, S.D.; Kong, F.; Anderson, P.; Gilbert, G.L. Escherichia coli sequence type 131 as a prominent cause of antibiotic resistance among urinary Escherichia coli isolates from reproductive-age women. J. Clin. Microbiol. 2013, 51, 3270–3276. [Google Scholar] [CrossRef] [Green Version]
  23. Sanchez, G.V.; Baird, A.M.G.; Karlowsky, J.A.; Master, R.N.; Bordon, J.M. Nitrofurantoin retains antimicrobial activity against multidrug-resistant urinary escherichia coli from US outpatients. J. Antimicrob. Chemother. 2014, 69, 3259–3262. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  24. Ranjan, A.; Shaik, S.; Mondal, A.; Nandanwar, N.; Hussain, A.; Semmler, T.; Kumar, N.; Tiwari, S.; Jadhav, S.; Wieler, L.H.; et al. Molecular epidemiology and genome dynamics of New Delhi metallo-beta-lactamase (NDM) producing extraintestinal pathogenic E. coli (ExPEC) strains from India. Antimicrob. Agents Chemother. 2016, 60, 6795–6805. [Google Scholar] [CrossRef] [Green Version]
  25. Malchione, M.D.; Torres, L.M.; Hartley, D.M.; Koch, M.; Goodman, J.L. Carbapenem and colistin resistance in Enterobacteriaceae in Southeast Asia: Review and mapping of emerging and overlapping challenges. Int. J. Antimicrob. Agents 2019, 54, 381–399. [Google Scholar] [CrossRef]
  26. Ding, Y.; Wang, Y.; Hsia, Y.; Sharland, M.; Heath, P.T. Systematic review of carbapenem-resistant Enterobacteriaceae causing neonatal sepsis in China. Ann. Clin. Microbiol. Antimicrob. 2019, 18, 1–8. [Google Scholar] [CrossRef] [PubMed]
  27. Sarowska, J.; Futoma-Koloch, B.; Jama-Kmiecik, A.; Frej-Madrzak, M.; Ksiazczyk, M.; Bugla-Ploskonska, G.; Choroszy-Krol, I. Virulence factors, prevalence and potential transmission of extraintestinal pathogenic Escherichia coli isolated from different sources: Recent reports. Gut Pathog. 2019, 11, 10. [Google Scholar] [CrossRef] [Green Version]
  28. Suresh, A.; Ranjan, A.; Patil, S.; Hussain, A.; Shaik, S.; Alam, M.; Baddam, R.; Lothar, W.; Ahmed, N. Molecular genetic and functional analysis of pks-harboring, extra-intestinal pathogenic Escherichia coli from India. Front. Microbiol. 2018, 9, 2631. [Google Scholar] [CrossRef]
  29. Grohs, P.; Tillecovidin, B.; Caumont-Prim, A.; Carbonnelle, E.; Day, N.; Podglajen, I.; Gutmann, L. Comparison of five media for detection of extended-spectrum Beta-lactamase by use of the wasp instrument for automated specimen processing. J. Clin. Microbiol. 2013, 51, 2713–2716. [Google Scholar] [CrossRef] [Green Version]
  30. Poirel, L.; Walsh, T.R.; Cuvillier, V.; Nordmann, P. Multiplex PCR for detection of acquired carbapenemase genes. Diagn. Microbiol. Infect. Dis. 2011, 70, 119–123. [Google Scholar] [CrossRef]
  31. Clermont, O.; Christenson, J.K.; Denamur, E.; Gordon, D.M. The Clermont Escherichia coli phylo-typing method revisited: Improvement of specificity and detection of new phylo-groups. Environ. Microbiol. Rep. 2013, 5, 58–65. [Google Scholar] [CrossRef] [PubMed]
  32. Toma, C.; Lu, Y.; Higa, N.; Nakasone, N.; Chinen, I.; Baschkier, A.; Rivas, M.; Iwanaga, M. Multiplex PCR assay for identification of human diarrheagenic Escherichia coli. J. Clin. Microbiol. 2003, 41, 2669–2671. [Google Scholar] [CrossRef] [PubMed] [Green Version]
  33. Johnson, J.R.; Stell, A.L. Extended virulence genotypes of Escherichia coli strains from patients with urosepsis in relation to phylogeny and host compromise. J. Infect. Dis. 2000, 181, 261–272. [Google Scholar] [CrossRef] [PubMed] [Green Version]
Table
Table 1. Antimicrobial resistance trends of clinical E. coli isolates to 17 antibiotics from March 2018 to July 2019.
Table 1. Antimicrobial resistance trends of clinical E. coli isolates to 17 antibiotics from March 2018 to July 2019.
Antibiotic ClassAntibioticsNo. of Strains TestedNo. of Resistant Strains (%)No. of Sensitive Strains (%)
Aminopenicillin/β lactamAmpicillin128107 (84)21 (16)
β lactam/β lactamase inhibitorAmoxiclav12870 (55)58 (45)
Piperacillin-Tazobactam12820 (16)108 (84)
AminoglycosideGentamicin12834 (27)94 (73)
Amikacin1287 (5)121 (95)
SulfonamideCotrimoxazole12876 (59)52 (41)
Quinolone/FluoroquinoloneNalidixic Acid125104 (83)21 (17)
Ciprofloxacin12778 (61)49 (39)
NitrofuranNitrofurantoin10411 (11)93 (89)
CephalosporinCefuroxime12782 (65)45 (35)
Ceftriaxone12577 (62)48 (38)
Ceftazidime12866 (52)62 (48)
Cefixime12885 (66)43 (34)
Cefepime12759 (46)68 (54)
CarbapenemImipenem12811 (9)117 (91)
Meropenem1268 (6)118 (94)
Table
Table 2. Molecular characteristics of 128 E. coli isolates analyzed including antimicrobial resistance, virulence and phylogenetic features.
Table 2. Molecular characteristics of 128 E. coli isolates analyzed including antimicrobial resistance, virulence and phylogenetic features.
Characteristics (Overall Positives n, %)GeneNo. of Positives (%)
Antibiotic ResistanceESBL (84, 66%)blaCTX-M-1566 (52)
blaCTX-M gp166 (52)
blaCTX-M gp21 (1)
blaCTX-M gp94 (3)
blaTEM26 (20)
blaOXA-122 (17)
Carbapenem (9, 7%)blaNDM-16 (5)
blaIMP1 (1)
blaVIM-10
blaKPC-20
blaOXA-482 (2)
Phylogenetic GroupsA6 (5)
B121 (16)
B259 (46)
C9 (7)
D13 (10)
E2 (2)
F11 (9)
Unknown group7 (5)
Sequence types (48, 37%)ST-695 (4)
ST-734 (3)
ST-9511 (9)
ST-13128 (22)
PathotypesExPEC (52, 41%)afa7 (5)
hlyD31 (24)
iutA79 (62)
focG4 (3)
kpsM II75 (59)
papA50 (39)
sfaS4 (3)
EAEC (3, 2%)aggR1 (1)
CVD4323 (2)
aspU2 (2)
ETEC (11, 9%)elt10 (8)
est2 (2)
EIECipaH0
EHECstx0
EPECeae0
Class 1 integron (27, 21%)intl127 (21)
Plasmid-replicon types (70, 55%)FIA70 (55)
FIB70 (55)
pks island (11, 9%)clbA11 (9)
clbQ11 (9)
Table
Table 3. Antibiotic resistance profiles of E. coli isolates harboring carbapenem resistance genes.
Table 3. Antibiotic resistance profiles of E. coli isolates harboring carbapenem resistance genes.
PhylogroupESBL GenotypeCR b GenotypeAMR Profile cNo. of Resistant Classes
B1ND ablaNDM-1AMP-COT-NIT-CIP-CXM4
CblaCTX-M-15, TEMblaNDM-1AMP-GEN-COT-NAL-NIT-CIP-CRO-CXM-AMX-AMC-TZP5
FblaCTX-M-15, TEMblaNDM-1AMP-GEN-COT-NAL-CIP-CRO-CAZ-IPM-CXM-AMX-CFM-AMC-MEM-FEP-TZP5
DblaCTXM-15, TEM, OXA-1blaNDM-1AMP-GEN-COT-NAL-CIP-CRO-CAZ-IPM-CXM-AMX-CFM-AMC-MEM-FEP-TZP5
EblaCTXM-15, OXA-1blaNDM-1AMP-NAL-NIT-IP-CRO-CAZ-CXM-CFM-AMC-FEP3
DblaCTXM-15blaNDM-1AMP-GEN-COT-NAL-NIT-CIP-CRO-CAZ-IPM-CXM-AMX-CFM-AMC-MEM-FEP-TZP6
ND ablaCTXM-15blaIMPAMP-CRO-CXM-CFM-FEP1
AblaCTXM-15, TEM, OXA-1blaOXA-48AMP-COT-NAL-CIP-CRO-CAZ-CXM-AMX-CFM-AMC-FEP-TZP3
B1blaCTXM-15blaOXA-48AMP-GEN-COT-NAL-NIT-CIP-CRO-CAZ-IMP-CXM-AMK-CFM-AMC-MEM-FEP-TZP6
a ND, not detected; b Carbapenem resistance genotype; c AMP, ampicillin; GEN, gentamicin; COT, cotrimoxazole; NAl, nalidixic acid; NIT, nitrofurantoin; CIP, ciprofloxacin; CRO, ceftriaxone; CAZ, ceftazidime; IPM, imipenem; CXM, cefuroxime; AMK, amikacin; CFM, cefixime; AMC, amoxicillin-clavulanic acid; MEM, meropenem; FEP, cefepime.
Publisher’s Note: MDPI stays neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Share and Cite

MDPI and ACS Style

Mazumder, R.; Abdullah, A.; Ahmed, D.; Hussain, A. High Prevalence of blaCTX-M-15 Gene among Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolates Causing Extraintestinal Infections in Bangladesh. Antibiotics 2020, 9, 796. https://doi.org/10.3390/antibiotics9110796

AMA Style

Mazumder R, Abdullah A, Ahmed D, Hussain A. High Prevalence of blaCTX-M-15 Gene among Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolates Causing Extraintestinal Infections in Bangladesh. Antibiotics. 2020; 9(11):796. https://doi.org/10.3390/antibiotics9110796

Chicago/Turabian Style

Mazumder, Razib, Ahmed Abdullah, Dilruba Ahmed, and Arif Hussain. 2020. "High Prevalence of blaCTX-M-15 Gene among Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolates Causing Extraintestinal Infections in Bangladesh" Antibiotics 9, no. 11: 796. https://doi.org/10.3390/antibiotics9110796

APA Style

Mazumder, R., Abdullah, A., Ahmed, D., & Hussain, A. (2020). High Prevalence of blaCTX-M-15 Gene among Extended-Spectrum β-Lactamase-Producing Escherichia coli Isolates Causing Extraintestinal Infections in Bangladesh. Antibiotics, 9(11), 796. https://doi.org/10.3390/antibiotics9110796

Note that from the first issue of 2016, this journal uses article numbers instead of page numbers. See further details here.

Article Metrics

Back to TopTop