Genetic Diversity, Multidrug Resistance, and Virulence of Citrobacter freundii From Diarrheal Patients and Healthy Individuals

Objectives: Citrobacter freundii is a frequent cause of nosocomial infections and a known cause of diarrheal infections, and has increasingly become multidrug resistant (MDR). In this study, we aimed to determine the genetic diversity, the antimicrobial resistance profiles and in vitro virulence properties of C. freundii from diarrheal patients and healthy individuals. Methods: 82 C. freundii isolates were obtained from human diarrheal outpatients and healthy individuals. Multilocus Sequence Typing (MLST) of seven housekeeping genes was performed. Antimicrobial susceptibility testing was carried out using the disk diffusion method according to the Clinical and Laboratory Standards Institute (CLSI) recommendations. Adhesion and cytotoxicity to HEp-2 cells were assessed. PCR and sequencing were used to identify blaCTX−M, blaSHV, blaTEM, qnrA, qnrB, qnrS, qnrC, qnrD, aac(6')-Ib-cr, and qepA genes. Results: The 82 C. freundii isolates were divided into 76 sequence types (STs) with 65 STs being novel, displaying high genetic diversity. Phylogenetic analysis divided the 82 isolates into 5 clusters. All 82 isolates were sensitive to imipenem (IPM), but resistant to one or more other 16 antibiotics tested. Twenty-six isolates (31.7%) were multidrug resistant to three or more antibiotic classes out of the 10 distinct antibiotic classes tested. Five MDR isolates, all of which were isolated from 2014, harbored one or more of the resistance genes, blaTEM−1, blaCTX−M−9, aac(6')-Ib-cr, qnrS1, qnrB9, and qnrB13. All 11 qnrB-carrying C. freundii isolates belonged to cluster 1, and one C. freundii isolate carried a new qnrB gene (qnrB92). Six isolates showed strong cytotoxicity to HEp-2 cells, one of which was multidrug resistant. Conclusions: C. freundii isolates from human diarrheal outpatients and healthy individuals were diverse with variation in sequence types, antibiotic resistance profiles and virulence properties.


INTRODUCTION
Citrobacter freundii, a member of the genus Citrobacter within the family Enterobacteriaceae, is considered a commensal resident in the intestinal tracts of both humans and animals (Bai et al., 2012). However, C. freundii can also cause diarrhea and other infections in humans (Mohanty et al., 2007;Samonis et al., 2009;Bai et al., 2012;Liu et al., 2017a). Some C. freundii isolates have acquired virulence traits and caused food poisoning or diarrhea in humans (Bai et al., 2012;Liu et al., 2017a). The main virulence factors found in diarrhea-associated C. freundii are toxins, including Shiga-like toxins, heat stable toxins and a cholera toxin B subunit homolog (Bai et al., 2012). In our previous study, we identified a cytotoxic and aggregative C. freundii strain which contained a complete type VI secretion system (T6SS) located on a genomic island (GI); we also found two strongly cytotoxic C. freundii isolates, which were multidrug resistant, with resistance to ≥3 different classes antibiotics (Liu et al., 2017a).
The qnrB genes constitute the most prevalent and diverse group within the qnr family (Ribeiro et al., 2015). Bae et al. have reported that 63.1% of the qnr positive clinical C. freundii isolates carried qnrB (Bae et al., 2010). Our previous study found that two C. freundii isolates carried an variant of the qnrB77 gene (Liu et al., 2017a).
In this study, we analyzed the genetic diversity and antimicrobial resistance profiles of 82 C. freundii isolates from diarrheal outpatients and healthy individuals in Maanshan, Anhui Province, China. We investigated the prevalence of bla CTX−M , bla SHV , bla TEM, qnrA, qnrB, qnrS, qnrC, qnrD, aac(6')-Ib-cr, and qepA genes and determined the adhesion and cytotoxicity to HEp-2 cells of the isolates.

Ethics Statement
This study was reviewed and approved by the ethics committee of National Institute for Communicable Disease Control and Prevention, the Chinese CDC. Human fecal specimens were acquired with the written informed consent of the diarrheal patients with the approval of the ethics committee of National Institute for Communicable Disease Control and Prevention, according to the medical research regulations of Ministry of Health (permit number 2007-17-3).

Citrobacter Isolates
Eighty-two C. freundii isolates were obtained from 62 diarrheal outpatients and 20 healthy individuals from 2014 to 2016 in Maanshan Anhui Province, China. Fifteen of the 62 diarrheal patient fecal samples harbored other known enteric bacterial or viral pathogens ( Table 1). The identity of each isolate was determined using API 20E test strips (bioMérieux, La Balme les Grottes, France) at the time of isolation, and isolates were stored as glycerol stocks at -80 • C. Bacteria were grown in Luria-Bertani (LB) broth or on LB and Mueller-Hinton agar plates (pH 7.4) at 37 • C.

In Vitro Adhesion and Cytotoxicity Assays
In vitro adhesion to host cells was performed using the human epidermoid carcinoma cell line HEp-2 (CCC0068; Beijing Union Medical College cell resource center), as previously described (Liu et al., 2017a). An adhesion index (<1; >1 and<50; >50) describing the mean number of bacteria per HEp-2 after examination of 10 visual fields was determined (Liu et al., 2017a). Infections were repeated three times in duplicate. The lactate dehydrogenase (LDH) released by the HEp-2 cells was determined using the Cytotox96 kit (Promega) according to the manufacturer's instructions. The relative amount of cytotoxicity was expressed as previously described (Liu et al., 2017a). All experiments were performed three times in duplicate.

Statistical Analysis
SPSS software version 13.0 (SPSS Inc., Chicago, IL, USA) was used to conduct all statistical comparisons. A nonparametric test (Mann-Whitney U-test) was employed to compare the different groups. Two-tailed p-value of 0.05 or less was considered to be statistically significant.

Multilocus Sequence Typing of C. freundii isolates
The 82 C. freundii isolates were divided into 76 sequence types (STs) with 65 novel STs (from ST172 to ST237), displaying high genetic diversity. No STs were predominant. Six STs each contained two isolates, of which 3 STs, ST185, ST187, and ST219, each contained two isolates with one from a diarrheal patient and one from healthy individual; two STs, ST17, and ST225 each contained two isolates from diarrheal patients; the remaining ST, ST166, had both isolates from healthy individuals.
A phylogenetic tree for the 82 isolates was constructed using the neighbor-joining algorithm based on the concatenated sequences of the seven housekeeping genes (Figure 1). Salmonella LT2 was used as an outgroup. The tree could be divided into five clusters with robust bootstrap support of the major divisions. Cluster 1 was a predominant cluster containing 26 STs. C. freundii isolates from diarrheal patients and healthy individuals were distributed among different clusters (Figure 1).
FIGURE 1 | Phylogenetic relationships as determined by MLST data. The presence of ESBLs and qnr genes, MDR (number of drugs resistant to), adhesion, LDH and antibiotic resistance phenotype among C. freundii isolates were shown on the right. The tree was constructed using neighbor joining algorithm. ST, D, H, and LDH indicate sequence types, isolates from diarrheal patients and healthy individuals, and lactate dehydrogenase respectively. Cluster divisions are marked. Numbers on or near the nodes are bootstrap values from 1,000 replicates.
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For resistance to cephalosporins, resistance to first-generation cephalosporins, such as cefazolin and second-generation cephalosporins, such as cefoxitin, were 98.8 and 74.4%, respectively; less common was resistance to ceftriaxone, ceftazidime, and cefepime with prevalence of 28.0, 29.3, and 19.5%, respectively ( Table 2).
Twenty-six isolates were multidrug resistant (MDR), with resistance to at least one antibiotic of three or more distinct classes (MDR ≥ 3). Of the 26 MDR isolates, 23 were isolated from 2014, two were from 2015 and one were from 2016 ( Table 1).
The 26 MDR isolates were distributed in 5 clusters, and mainly in cluster 1 and 3 which included 7 MDR isolates, respectively (Figure 1 and Table 1).
Mutations of quinolone resistance-determining regions (QRDRs) of gyrA and parC genes were screened by PCR sequencing in ciprofloxacin resistant strains. Four (AH2015002, AH2014032, AH2014038, and AH2014039) of the six ciprofloxacin resistant strains (AH2014008, AH2014020, AH2015002, AH2014032, AH2014038, and AH2014039) showed mutations in codons 59, 111, and/or 134 in the QRDR region of the gyrA gene: Thr59Ile in AH2015002, AH2014032, and AH2014039, and Thr59Ile, Gln111Arg, and Ile134Val in AH2014038. None of the six ciprofloxacin resistant strains had any mutations in the QRDR region of the parC gene.
One isolate (AH2014019) was found to harbor a new qnrB gene. Sequence analysis revealed that it differed from the qnrB76 gene by two nucleotide changes (GenBank accession no.KM985469.1). One, a T→G change at nt469 resulted in Ser→Ala, while the other, a C→T change at nt391 was synonymous. Hence this new qnrB allele is designated as qnrB92 (GenBank accession no. MG744557), a new variant of the qnrB gene, in accordance with the qnr nomenclature rules of Jacoby et al. (2008).
Two of the 11 qnrB isolates were MDR ≥ 3. All 11 qnrB isolates were susceptible to ciprofloxacin and levofloxacin.

Adherence of C. freundii Isolates
We tested the 82 isolates for adhesion to HEp-2 cells and categorized the extent of adhesion using the adhesive index ( Table 1; Mange et al., 2006). Four C. freundii isolates showed the strongest adhesion, with an adhesion index greater than 50. Twenty-one isolates showed intermediate adhesion, with an adhesion index between 1 and 50. Twenty-nine isolates showed little adhesion, with an adhesion index of less than one. The remaining isolates showed ambivalent adhesion or no adhesion.
By phylogenetic clusters (Figure 1 and Table 1), the majority of the isolates (9/16) in cluster 5 showed intermediate or strong adhesion, while cluster 1 was the opposite with the majority of the isolates (25/28) showing little or no adhesion. All strongest adhesive isolates belonged to cluster 2 or 5.

Isolates
Year STs MDR Antibiotic resistance phenotype ESBLs Qnr

Cytotoxicity of C. freundii Isolates
The 82 C. freundii isolates were tested for cytotoxicity to cultured HEp-2 cells by measuring the amount of lactate dehydrogenase (LDH) released by HEp-2 cells. The released LDH levels ranged from 3.0 to 27.9% ( Table 1). C. freundii strains CF74 and CF72 were used as positive and negative controls of cytotoxicity respectively (Liu et al., 2017a). The levels of LDH released by CF74 and CF72 were 24.5 and 8.1%, respectively. Six isolates released LDH more than 24%, showing high cytotoxicity ( Table 1). Among these six isolates, two isolates showed strongest adherence while other four isolates showed intermediate adhesion (Table 1 and Figure 2). Another five isolates released LDH from 18.0 to 22.0% and are considered intermediate cytotoxic. The remaining 71 isolates showed LDH release less than 17.8% and are likely to be non-cytotoxic (Table 1). One highly cytotoxic isolate was MDR with resistance to five antibiotics (penicillins, cephalosporins, tetracyclines, phenicols, and sulfonamides) and harbored an aac(6')-Ib-cr gene. The other five highly cytotoxic isolates were resistant to fewer than 3 antibiotic classes.

DISCUSSION
C. freundii is a recognized emerging opportunistic pathogen and has been implicated in gastroenteritis and foodborne outbreaks (Ifeadike et al., 2012;Settanni et al., 2013). A most recent foodborne outbreak reported in Germany was caused by a novel ST (Pletz et al., 2018). In this study, we examined 82 isolates of C. freundii obtained from 62 diarrheal patients from the majority of whom no other pathogens were isolated and also from 20 healthy individuals to assess the genetic diversity and antimicrobial resistance and in vitro virulence phenotypes.
The 82 isolates were separated into 76 STs and 5 phylogenetic clusters. The 76 STs from this study were compared with 171 STs from the Citrobacer MLST database, We found that 11 STs in this study shared the same sequence types with isolates from the database from other countries or regions or from different sources. Among these 11 STs, ST8 contained isolates from the urine of an acute myeloid leukemia patient from Poland (Majewski et al., 2017); ST12 contained isolates from a rectal swab; ST17 contained isolates from skin necrosis, urine and rectal swabs; ST30 contained isolates from fecal samples of diarrheal patients in our previous study (Liu et al., 2017a); ST87, ST85, and ST45 each contained isolates from food in our previous study (Liu et al., 2017a; ST116 contained isolates from blood; ST161 and ST166 contained isolates from water. Therefore strains of the same STs of C. freundii may be widely present in fecal, food, and other reservoirs. In this study, we analyzed isolates from both diarrheal patients and healthy individuals in an attempt to further understand the genetic diversity of potential diarrheagenic C. fruendii. Majority of the diarrheal cases had no other pathogens isolated with C. freundii being possibly the causal organism. However, there is no separation of isolates from clinical cases and healthy individuals. Some of the diarrheal patients also had other pathogens isolated. There was no distinction of the isolates from these different sources by STs, phylogenetic clusters or adhesion/cytotoxicity phenotypes. Among the 82 C. freundii isolates we obtained from diarrheal outpatients and healthy individuals, 25 (30.5%) of the isolates showed moderate to strong adhesion. Among these 25 adhesive isolates, 9 isolates showed moderate to strong cytotoxicity, indicating their pathogenic potential. Interestingly, adhesiveness and cytotoxicity were clustered by phylogenetic clusters. Nine (56%) and five (31%) of the 16 isolates in cluster 5 showed intermediate/strong adhesion and intermediate/high cytotoxicity, respectively. In comparison, only three (11%) and none (0%) of the 28 cluster 1 isolates were adhesive or cytotoxic respectively. All strongest adhesive and highly cytotoxic isolates belonged to cluster 2 or 5. Clearly there is a difference in virulence between clusters by the measures of in vitro virulence properties. However, both cluster 1 and cluster 5 are similarly likely to be isolated from healthy individuals with 8 of the 28 and 5 of the 16 isolates respectively. Further work is required to determine their difference in pathogenicity and disease.
C. freundii has become increasingly resistant to a range of antibiotics (Liu et al., 2017b). Liu et al. (2017b) reported that blood isolates of C. freundii from hospital in Taiwan showed FIGURE 2 | HEp-2 cell adhesion and cytotoxicity of C. freundii isolates. (A) Light micrographs show the adherence patterns displayed by six strongly cytotoxic C. freundii isolates, CF74 and CF72. Bar: 10 µm. (B) Cytotoxicity was based the LDH released from HEp-2 cells after exposure to six strongly cytotoxic C. freundii isolates at 8 h. CF72 and CF74 were control strains. a high rate of resistance (66.7-97.2%) to second-generation cephalosporin and cephamycin. Mohanty et al. (2007) reported that isolates of C. freundii isolates from patients in a tertiary care hospital of India had high degrees of resistance to ceftazidime (85%), cefotaxime (85%), piperacillin (65%), and ciprofloxacin (60%). In our study, 98.8% of the isolates were resistant to firstgeneration cephalosporins, such as cefazolin, 74.4% resistant to second-generation cephalosporins, such as cefoxitin, 28-29.3% resistant to third-generation cephalosporins and 19.5% resistant to fourth-generation cephalosporins.
C. freundii is often resistant to multiple classes of antibiotics, suggesting that both clinical and environmental strains may be a reservoir of antimicrobial resistance determinants (Pepperell et al., 2002;Gupta et al., 2003;Nada et al., 2004;Yim et al., 2013;Feng et al., 2015;Leski et al., 2016a;Sheppard et al., 2016). MDR C. freundii strains have been associated with a higher rate of in-hospital mortality compared to susceptible strains (Leski et al., 2016b). A survey of outpatients in Sierra Leone revealed that C. freundii isolates from UTIs were highly MDR with 22 isolates resistant to >7 antibiotics out of the 11 tested, and 81.8% of the isolates produced ESBLs (Leski et al., 2016b). In this study, we surveyed C. freundii from diarrheal outpatients, 30.6% isolates were resistant to ≥3 antibiotic classes out of the 10 distinct antibiotic classes tested. One MDR isolate was strongly cytotoxic. Such highly cytotoxic MDR strains may cause more severe disease and their MDR properties may limit clinical therapeutic options when they cause disease.
ESBLs in C. freundii have been widely reported (Fernandes et al., 2014;Liu et al., 2017b). In 36 blood C. freundii isolates from a Taiwanese hospital, 16.7% of the isolates carried the bla TEM−1 gene and 5.6% carried bla SHV−12 or bla CTX−M−15 (Liu et al., 2017b). In this study, we did not test for ESBL phenotype but screened by PCR for bla CTX−M , bla TEM and bla SHV genes. We found one isolate each bla CTX−M−9 and bla TEM positive, but none bla SHV positive ( Table 3).
The prevalence of qnr and aac(6')-Ib-cr genes varied (Liu et al., 2017a). In China, Yang et al. (2008) had repored that the prevalence of qnr and aac(6')-Ib-cr genes in C. freundii isolates from southern China (including Shanghai, Wuhan, Nanjing, Guangzhou, and Fuzhou) and northern China (including Beijing, Tianjin, Shenyang, and Jinan) was at 63.3 and 26.7% respectively; while Zhang et al. (2012) showed the prevalence of qnr and aac(6')-Ib-cr in C. freundii from southern China (Hangzhou) was at 72.8 and 68.9% respectively. In Korea, Park et al.  showed that 38.4% of C. freundii isolates harbored qnr determinants. In our previous study (Liu et al., 2017a), we found much lower prevalence of qnr and aac(6')-Ib-cr genes in C. freundii isolates at 23.1 and 15.4% respectively. In the present study, we also found low prevalence of qnr and aac(6')-Ib-cr genes in C. freundii isolates at 14.6 and 2.4% respectively. Our isolates for both studies were from south central region of China (Maanshan city, Anhui Province). These findings suggest regional difference in the prevalence of resistance within a country as well as between countries.
The qnrB genes constitute the most prevalent and diverse group within the qnr family, encoding proteins responsible for decreased susceptibility to fluoroquinolones (Jacoby et al., 2011;Ribeiro et al., 2015). We found a new qnrB gene, designated as qnrB92 (GenBank accession no. MG744557) in one C. freundii isolate. However, qnrB-carrying C. freundii isolates do not always show high level of quinolone resistance (Zhang et al., 2012;Liu et al., 2017a). Our results were consistent with this observation. The new qnrB92-carrying C. freundii isolate was susceptible to ciprofloxacin and levofloxacin and indeed none of the 11 qnrB isolates was resistant to ciprofloxacin and levofloxacin. However, two qnrB-carrying C. freundii isolates we previously reported had a high MIC for NAL (>128 µg/mL) (Liu et al., 2017a). C. freundii isolates carrying qnrS and aac(6')-Ib-cr have been shown to have a higher MIC for quinolones (Zhang et al., 2012). In our previous study, we found that one aac(6')-Ib-cr-carrying C. freundii and one qnrS1-carrying C. freundii isolates had high MIC of three quinolones (NAL, >128 µg/mL; CLP, >32 µg/mL; LEV, >16 µg/mL) (Liu et al., 2017a). However, in this study, two aac(6')-Ib-cr-carrying C. freundii (AH2014032 and AH2014015) and one qnrS1-carrying C. freundii (AH2014014) isolates were resistant or intermediary resistant to ciprofloxacin, but susceptible to levofloxacin. Isolate AH2014032 showed a QRDR region with the mutation of Thr59Ile of the gyrA gene and no mutation in the parC gene, while AH2014015 and AH2014014 did not carry any mutations in gyrA and parC genes.
Resistance to ciprofloxacin was lower in both our previous study and this study at 13.0% (8/62) and 7.3% (6/82) respectively. This difference may be regional. There seems to be regional difference in the prevalence of qnr and aac(6')-Ib-cr genes as discussed above. Our studies were conducted in one region of China which may differ in the prevalence of ciprofloxacin resistance from other regions in China and from other countries Yang et al., 2008;Zhang et al., 2012). It is also possible that the low prevalence was due to the source of the isolates. Isolates for our previous study and for this study were from food and from outpatients respectively, while the high rate reported in India was from isolates from hospitalized patients (Mohanty et al., 2007).

CONCLUSION
We isolated 82 C. fruendii isolates from human diarrheal outpatients and healthy individuals in Maanshan, Anhui Province, China and found a high diversity of the isolates by sequence types with 65 STs being novel. Eleven STs were found in the MLST database which contained isolates from different sources and/or geographic regions. The isolates varied in in vitro virulence phenotypes (adhesion and cytotoxicity) with most isolates in phylogenetic cluster 5 being adhesive and cytotoxic. Prevalence of MDR of three or more antibiotic classes out of the 10 distinct antibiotic classes tested was at 31.7%. Each of the bla CTX−M−9 , bla TEM−1 , qnrS1 and aac(6')-Ib-cr genes was detected in one C. freundii isolate. Six isolates that showed strong cytotoxicity to HEp-2 cells, one of which was multidrug resistant. We also found a new qnrB gene (qnrB92) in one C. freundii isolate. This study has shed more light on the genetic diversity, pathogenicity and antibiotic resistance of C. fruendii.

AUTHOR CONTRIBUTIONS
LiyL and JX: designed the project; DC: carried out the sampling work; WJ, HS, SH, and YL: carried out the experiments; LiyL, YW, and LiqL: analyzed data; LiyL and RL: drafted the manuscript. All authors have read and approved the final version of the manuscript.