Here, we present a detailed protocol for the isolation and identification of antibiotic-resistant bacteria from water and the molecular characterization of their antibiotic resistance genes (ARGs). The use of culture-based and non-culture-based (metagenomic analysis) techniques provides complete information about the total bacterial diversity and the total pool of different ARGs present in freshwaters from Mumbai, India.
The development and spread of antibiotic resistance (AR) through microbiota associated with freshwater bodies is a major global health concern. In the present study, freshwater samples were collected and analyzed with respect to the total bacterial diversity and AR genes (ARGs) using both conventional culture-based techniques and a high-throughput culture-independent metagenomic approach. This paper presents a systematic protocol for the enumeration of the total and antibiotic-resistant culturable bacteria from freshwater samples and the determination of phenotypic and genotypic resistance in the culturable isolates. Further, we report the use of whole metagenomic analysis of the total metagenomic DNA extracted from the freshwater sample for the identification of the overall bacterial diversity, including non-culturable bacteria, and the identification of the total pool of different ARGs (resistome) in the water body. Following these detailed protocols, we observed a high antibiotic-resistant bacteria load in the range of 9.6 × 105-1.2 × 109 CFU/mL. Most isolates were resistant to the multiple tested antibiotics, including cefotaxime, ampicillin, levofloxacin, chloramphenicol, ceftriaxone, gentamicin, neomycin, trimethoprim, and ciprofloxacin, with multiple antibiotic resistance (MAR) indexes of ≥0.2, indicating high levels of resistance in the isolates. The 16S rRNA sequencing identified potential human pathogens, such as Klebsiella pneumoniae, and opportunistic bacteria, such as Comamonas spp., Micrococcus spp., Arthrobacter spp., and Aeromonas spp. The molecular characterization of the isolates showed the presence of various ARGs, such as blaTEM, blaCTX-M (β-lactams), aadA, aac (6')-Ib (aminoglycosides), and dfr1 (trimethoprims), which was also confirmed by the whole metagenomic DNA analysis. A high prevalence of other ARGs encoding for antibiotic efflux pumps-mtrA, macB, mdtA, acrD, β-lactamases-SMB-1, VIM-20, ccrA, ampC, blaZ, the chloramphenicol acetyltransferase gene catB10, and the rifampicin resistance gene rphB-was also detected in the metagenomic DNA. With the help of the protocols discussed in this study, we confirmed the presence of waterborne MAR bacteria with diverse AR phenotypic and genotypic traits. Thus, whole metagenomic DNA analysis can be used as a complementary technique to conventional culture-based techniques to determine the overall AR status of a water body.
Antimicrobial resistance (AMR) has been identified as one of the most pressing global problems. The rapid evolution of AMR and its worldwide spread are one of the greatest threats to human health and the global economy in terms of the health costs associated with it1. The overuse and misuse of antibiotics have led to an increase in AR. This has been highlighted by the COVID-19 pandemic, during which the treatment of associated secondary infections, in many cases, was hugely compromised due to AMR in the affected patients2. Besides the direct use/misuse of antibiotics by humans, the overuse and misuse of antibiotics in agriculture and animal husbandry and their inappropriate discharge into the environment, including water bodies, are a major concern3. The rise of new resistance traits and multidrug resistance in bacteria urgently highlights the need for a better understanding of the factors leading to the development of AR and its dissemination. Multiple antibiotic-resistant bacteria, which often carry multiple AR genes (ARGs) on mobile genetic elements such as plasmids, can transfer these resistance genes to non-resistant microorganisms, including potential human pathogens, thus leading to the emergence of superbugs that are untreatable with even last-resort antibiotics4. These multiple antibiotic-resistant bacteria, if present in water ecosystems, can directly enter the human gut via the consumption of contaminated water-based foods such as fish, crabs, and mollusks. Previous studies have shown that the spread of AR bacteria in naturally occurring water systems can also reach other water supplies, including drinking water, and, thus, can enter the human food chain5,6,7.
The aim of the present study is to provide a comprehensive protocol using a combination of culture-based and non-culture-based (whole metagenomic analysis) techniques to obtain complete information about the total bacterial diversity and the total pool of different ARGs present in a water body in Mumbai, India. Conventionally, culture-based techniques have been used to study the bacterial diversity in water bodies. As culturable microorganisms constitute only a small percentage of the total microbiota in any niche, to have a better understanding of the overall status of bacterial diversity and the various resistant traits prevalent in any sample, various culture-based and culture-independent techniques must be used in tandem. One such robust and reliable culture-independent technique is whole metagenomic DNA analysis. This high-throughput method has been successfully utilized in various studies on bacterial diversity or the functional annotations of various ARGs8,9. This technique uses the metagenome (the total genetic material in a sample) as the starting material for various analyses and, hence, is culture-independent. The protocols in the present study can be used for whole metagenomic DNA analysis to obtain information about the total bacterial diversity and various ARGs (resistome) in water samples.
1. Sample collection and processing
2. Estimation of the total bacterial load and the antibiotic-resistant bacteria count
3. Identification of culturable bacteria by 16S rRNA gene sequencing
4. Detection of antibiotic resistance in the isolates using antibiotic susceptibility testing
NOTE: This protocol describes the method for antibiotic susceptibility testing (AST) by disc diffusion. The following antibiotic discs were used: cefotaxime (5 µg), ampicillin (10 µg), levofloxacin (5 µg), chloramphenicol (30 µg), tigecycline (15 µg), ceftriaxone (30 µg), imipenem (10 µg), gentamicin (10 µg), neomycin (10 µg), trimethoprim (5 µg), and ciprofloxacin (5 µg).
5. PCR-based detection of antibiotic resistance genes in the isolates
6. Whole metagenomic DNA analysis for the identification of the total bacterial diversity and the detection of ARGs in the metagenome
Total bacterial load and antibiotic-resistant (AR) bacteria count
The enumeration of the total bacterial load was carried out by spreading 10−4 to 10−6 fold dilutions of the water samples on R2A Agar, Modified medium. For the enumeration of the AR bacteria count, 10−3 to 10−6 fold dilutions were spread on media plates containing antibiotics (Figure 3). The total and AR bacteria counts were calculated as CFU/mL, and all the plating experiments were performed in duplicate. Following the above protocols, the present study showed the total bacteria count to be 3.0 × 109 CFU/mL. The AR bacterial load was found to be high, in the range of 9.6 × 105-1.2 × 109 CFU/mL (Table 6).
Identification of culturable bacteria by 16S rRNAgene sequencing
Crude DNA from each isolate was used as a template to perform 16S rRNA gene-specific PCR. In the total of 15 AR isolates sequenced, 10 belonged to the Enterobacteriaceae family, with most being Escherichia coli and Klebsiella pneumoniae. Rare opportunistic bacteria such as Comamonas spp. belonging to the family Comamonadaceae, Micrococcus spp. and Arthrobacter spp. belonging to the family Micrococcaceae, and Aeromonas spp. belonging to the family Aeromonadaceae were also identified from the water sample (Table 7).
Detection of antibiotic resistance in the culturable bacteria using antibiotic susceptibility testing
The antibiotic resistance profile of the above identified isolates was generated by performing AST using the disc diffusion method (Figure 4). Out of the 15 isolates tested, 8 had an MAR index of ≥0.2, indicating a high degree of resistance. Moreover, many of the isolates showed co-resistance profiles (resistance to the same set of antibiotics). However, isolates such as Comamonas spp. and Arthrobacter spp. did not show resistance to any of the antibiotics tested (Table 8).
Detection and identification of antibiotic resistance genes in the culturable bacteria
A total of 10 AR isolates were screened for the presence of ARGs using PCR. The most prevalent ARG in the culturable isolates was blaTEM encoding for β-lactamase, followed by the aminoglycoside resistance gene aadA. Other amplified ARGs were blaCTX-M, dfr1, and aac(6')-Ib conferring resistance to β-lactams, trimethoprim, and aminoglycosides, respectively. The representative results of the amplification of the ARGs are shown in Figure 5. For most of the identified isolates, phenotypic resistance (AST) was confirmed at the molecular level via PCR-based genotypic AR profiling.
Identification of the total bacterial diversity in the metagenomic DNA
To check for the presence of all possible bacteria (both culturable and non-culturable) and to identify their relative abundances, a metagenomic DNA analysis for the total bacterial diversity was carried out. Using the high-throughput next-generation sequencing (HT-NGS) approach, ~96.94% of the total sequence reads were obtained, resulting in high coverage. Taxonomic annotation was carried out to classify the reads into different taxonomic groups from the phylum to the genus level (Figure 6 and Figure 7). A total of 50 phyla could be identified in the metagenome, indicating the high bacterial diversity in the water sample. Proteobacteria was the most dominant phylum, consisting of the Alphaproteobacteria, Betaproteobacteria, and Gammaproteobacteria classes. At the order level, Burkholderiales was the most prevalent order, belonging to the Betaproteobacteria class. Pseudomonas, Acinetobacter, Pedobacter, Prosthecobacter, Limnohabitans, Flavobacterium, and Comamonas were some of the abundant genera found in the water sample.
Detection of ARGs from the metagenomic DNA
To understand the total pool of ARGs in the metagenome of the water sample, whole metagenomic sequencing was carried out, followed by the identification of ARGs using appropriate bioinformatics tools. The metagenomic approach ensures that the ARGs present in both culturable and non-culturable microorganisms in the sample are detected. A variety of genes conferring resistance to β-lactams (SMB-1, ampC1, VIM-20, ccrA, nmcR, ARL-1, blaZ); aminogylcosides (aac(6')-34); quinolones (qnrS6, qnrVC5); antibiotic efflux pumps-resistance-nodulation-cell division (RND) (evgA, mtrA, mdtA, acrD), ATP-binding cassette (ABC) (oleC, macB, patA, bcrA), and major facilitator superfamily (MFS) (abaQ); trimethoprim-resistant dihydrofolate reductase (dfrD, dfrA20); rifampin phosphotransferase (rphB); and chloramphenicol acetyltransferase (CAT) (catB10) were detected in the metagenome. The ARGs detected via PCR in the culturable isolates (blaTEM, blaCTX-M, aadA, aac(6')-Ib, dfr1) were also detected by whole metagenomic sequencing, thus confirming their presence in the water sample. The representative results of the ARGs identified in the metagenome using whole metagenomic DNA analysis are given in Table 9.
Figure 1: Workflow for whole metagenomic DNA analysis. The stepwise workflow for the identification of the total bacterial diversity and the detection of the ARGs from the metagenome is presented. The overall steps involve metagenomic DNA preparation, amplification, and identification. Please click here to view a larger version of this figure.
Figure 2: Flowsheet of the complete methodology. The stepwise workflow of the methodology used in the present study. A combination of both culture-based and non-culture-based techniques is used to get complete information about the bacterial diversity and the identity of the ARGs present in the water sample. Please click here to view a larger version of this figure.
Figure 3: Representative images of isolated colonies on antibiotic-containing R2A Agar, Modified plates. Water samples plated on cefotaxime (3 µg/mL)-containing R2A Agar, Modified plates. The sample was serially diluted and plated in duplicate-A1, A2: 10−4; B1, B2: 10−5; C1, C2: 10−6. After the appropriate incubation period, the isolated colonies were visible on the B1, B2, C1, and C2 plates. Please click here to view a larger version of this figure.
Figure 4: Antibiotic susceptibility test by the disc diffusion method. Representative images of AST by the disc diffusion method for an Escherichia coli isolate. AST was performed in duplicate-A1, A2: CTX, IPM, C, CIP; B1, B2: LE, TGC, AMP, GEN; C1, C2: TR, N, K, CTR. The diameters of the ZOIs were measured in millimeters (mm). To interpret if the isolate is resistant or susceptible to the antibiotic used, the ZOI was compared with the latest EUCAST tables. Abbreviations: AST = antibiotic susceptibility test; CTX = cefotaxime; IPM = imipenem; C = chloramphenicol; CIP = ciprofloxacin; LE = levofloxacin; TGC = tigecycline; AMP = ampicillin; GEN = gentamicin; TR = trimethoprim; N = neomycin; K = kanamycin; CTR = ceftriaxone; ZOI = zone of inhibition; EUCAST = European Committee on Antibiotic Susceptibility Testing. Please click here to view a larger version of this figure.
Figure 5: PCR amplification of antibiotic-resistance genes from culturable bacteria. Agarose gel electrophoresis post PCR was carried out for the visualization of amplified bands to check for the presence of ARGs in the isolates. Separated bands of PCR amplicons can be seen on the gel. The size of the individual PCR amplicons is compared with an appropriate DNA marker. Lane L1: 100 bp DNA ladder; Lanes 1-5: 1: dfr1 (425 bp); Lane 2: blaTEM (310 bp); Lane 3: blaCTX-M (500 bp); Lane 4: aac(6')-Ib (395 bp); Lane 5: aadA (624 bp). Abbreviation: ARGs = antibiotic-resistance genes. Please click here to view a larger version of this figure.
Figure 6: Taxonomical classification for the phylum and class levels. (A) Bar chart showing the phylum-level taxonomic abundance distribution of the bacterial metagenome in the water sample. A total of 50 bacterial phyla were identified by the metagenomic analysis. The first 12 dominant phyla of bacteria are shown. (B) Bar chart showing the class-level taxonomic abundance distribution of the bacterial metagenome in the water sample. A total of 50 bacterial classes were identified by the metagenomic analysis. The first 15 dominant classes of bacteria are shown. Please click here to view a larger version of this figure.
Figure 7: Taxonomical classification for the order and genus levels. (A) Bar chart showing the order-level taxonomic abundance distribution of the bacterial metagenome in the water sample. A total of 50 bacterial orders were identified by the metagenomic analysis. The first 14 dominant orders of bacteria are shown in the figure. (B) Bar chart showing the genus-level taxonomic abundance distribution of the bacterial metagenome in the water sample. A total of 50 bacterial genera were identified by the metagenomic analysis. The first 15 dominant genera of bacteria are shown are shown in the figure. Please click here to view a larger version of this figure.
PCR reagents | Volume (μL) |
2x Taq Master Mix | 20 |
Forward primer (10 pico mole) | 1.5 |
Reverse primer (10 pico mole) | 1.5 |
Crude DNA template | 1.5 |
Sterile molecular biology water | 15.5 |
Total volume | 40 |
Table 1: PCR mastermix constituents. The reaction mixture composition of various PCR reagents.
Direction | Primer Sequence 5’ – 3’ | PCR conditions | No. of cycles |
Forward | GGAGGCAGCAGTAAGGAAT | 94 °C for 10 min | 1 |
Denaturation at 94 °C for 30 s | 35 | ||
Annealing at 50 °C for 30 s | |||
Extension at 72 °C for 40 s | |||
Reverse | CTACCGGGGTATCTAATCC | Final extension at 72 °C for 5 min | 1 |
Table 2: PCR cycle conditions for amplification of the 16S rRNA gene. The PCR cycle conditions required for 16S rRNA gene amplification are shown. The steps include an initial denaturation step, followed by 35 cycles of denaturation, annealing and extension, and a final extension step.
6x loading gel | |
Contents | Quantity |
Bromophenol blue | 25 mg |
85% Glycerol | 7.06 mL |
Milli-Q water | 2.94 mL |
Total volume | 10 mL |
50x Tris-acetate-EDTA (TAE) stock buffer composition | |
Contents | Quantity |
Tris base | 242 g in 700 mL of double-distilled water |
Glacial Acetic Acid (GAA) | 57.1 mL |
0.5 M (EDTA) pH 8.0 | 100 mL |
Adjust the pH to 8.5 and make up the volume to 1000 mL with double distilled water | |
For 1x TAE: 20 mL of 50x TAE buffer + 980 mL of double-distilled water |
Table 3: Composition of the 6x gel loading buffer and 50x Tris-acetate-EDTA stock buffer. The 6x gel loading buffer is mixed with the sample to be run on agarose gel electrophoresis. It contains bromophenol blue as the tracking dye. Glycerol increases the density of the sample being loaded for proper loading into the wells. The composition of the various reagents required for the preparation of the 50xTAE stock buffer is also shown. TAE buffer is one of the most common buffers used for AGE, and it maintains the pH at 8.5 and enables the migration of amplified DNA during AGE. Abbreviations: TAE = Tris-acetate-EDTA; AGE = agarose gel electrophoresis.
PCR reagents | Volume (μL) |
2x Taq Master Mix | 5 |
Forward primer (10 pico mole) | 0.5 |
Reverse primer (10 pico mole) | 0.5 |
Crude DNA template | 1.5 |
Sterile molecular biology-grade water | 2.5 |
Total volume | 10 |
Table 4: PCR mastermix composition for the identification of ARGs. The reaction mixture composition of various PCR reagents required for performing the PCR experiment.
Sr. No. | Target gene | Resistance to | Primer | Primer sequence (5’-3’) | Amplicon size (bp) | Annealing temperature (°C) | Referenzen | ||||
1 | dfrA | Trimethoprim | Forward | TGGTAGCTATATC GAAGAATGGAGT |
425 | 59 | Racewicz et al., 19 | ||||
Reverse | TATGTTAGAGGCG AAGTCTTGGGTA |
||||||||||
2 | blaTEM | β – lactams | Forward | GCACGAGTGGG TTACATCGA |
310 | 60 | Gebreyes, Thakur20 | ||||
Reverse | GGTCCTCCGAT CGTTGTCAG |
||||||||||
3 | blaCTX-M | β – lactams | Forward | CGATGGGACG ATGTCACTG |
500 | 52 | Li et al. 21 | ||||
Reverse | CGGCTTTCTG CCTTAGGTT |
||||||||||
4 | aac(6')-Ib | Aminoglycosides | Forward | TATGAGTGGC TAAATCGAT |
395 | 50 | Akers et al. 22 | ||||
Reverse | CCCGCTTTCT CGTAGCA |
||||||||||
5 | aadA | Aminoglycosides | Forward | ACCGTAAGGC TTGATGAAACA |
624 | 58 | Ciesielczuk 23 | ||||
Reverse | GCCGACTACC TTGGTGATCTC |
Table 5: Primers for the PCR of ARGs in culturable bacteria. The different ARGs used in the present study along with their respective primer sequences are shown. The expected size of the amplicon is given in base pairs. The annealing temperature of each primer set is also mentioned.
Antibiotic | Concentration of antibiotic (µg/mL) | CFU/mL |
– | – | 3.0 x 109 |
CTX | 3 | 4.5 x 107 |
CIP | 0.5 | 3.2 x 108 |
K | 15 | 9.6 x 105 |
E | 20 | 1.6 x 108 |
VA | 3 | 1.2 x 109 |
Table 6: Total and antibiotic-resistant bacteria counts. Five antibiotics were used for the initial isolation of the antibiotic-resistant bacteria from the water sample. The total bacteria counts (without antibiotics) and the AR bacteria counts are presented in terms of colony-forming units per milliliter (CFU/mL). Abbreviations: AR = antibiotic resistant; CFU = colony-forming units; CTX = cefotaxime; CIP = ciprofloxacin; K = kanamycin; E = erythromycin; VA = vancomycin.
Isolate code | Microorganisms | Family |
1 | Escherichia coli | Enterobacteriaceae |
2 | Escherichia coli | Enterobacteriaceae |
3 | Escherichia coli | Enterobacteriaceae |
4 | Escherichia coli | Enterobacteriaceae |
5 | Escherichia coli | Enterobacteriaceae |
6 | Escherichia coli | Enterobacteriaceae |
7 | Klebsiella pneumoniae | Enterobacteriaceae |
8 | Klebsiella pneumoniae | Enterobacteriaceae |
9 | Klebsiella pneumoniae | Enterobacteriaceae |
10 | Klebsiella pneumoniae | Enterobacteriaceae |
11 | Comamonas spp. | Comamonadaceae |
12 | Comamonas spp. | Comamonadaceae |
13 | Micrococcus spp. | Micrococcaceae |
14 | Arthrobacter spp. | Micrococcaceae |
15 | Aeromonas spp. | Aeromonadaceae |
Table 7: Identification of antibiotic-resistant isolates by 16S rRNA gene sequencing. Colony PCR was performed for each isolate using 16S rRNA gene-specific primers. The amplicons obtained were then sequenced and identified using appropriate bioinformatics tools.
Isolate No. | Isolate | CTX | AMP | LE | C | TGC | CTR | IPM | GEN | N | TR | CIP | MAR | MAR index | ||
1 | Escherichia coli | 13R | 0R | 0R | 28S | 23S | 11R | 39S | 20S | 18S | 0R | 0R | 6 | 0.5 | ||
2 | Escherichia coli | 31S | 0R | 12R | 29S | 23S | 32S | 37S | 19S | 16S | 0R | 14R | 4 | 0.4 | ||
3 | Escherichia coli | 14R | 0R | 14R | 14R | 21S | 10R | 34S | 17S | 11R | 24S | 16R | 7 | 0.6 | ||
4 | Escherichia coli | 28S | 13R | 18R | 26S | 21S | 28S | 32S | 16R | 11R | 24S | 19R | 5 | 0.4 | ||
5 | Escherichia coli | 11R | 0R | 12R | 26S | 21S | 10R | 31S | 17S | 16S | 22S | 11R | 5 | 0.4 | ||
6 | Escherichia coli | 27S | 0R | 12R | 12R | 22S | 30S | 32S | 19S | 11R | 0R | 14R | 6 | 0.5 | ||
7 | Klebsiella pneumoniae | 28S | 0R | 17R | 27S | 22S | 30S | 32S | 18S | 22S | 0R | 16R | 4 | 0.4 | ||
8 | Klebsiella pneumoniae | 29S | 11R | 26S | 24S | 22S | 30S | 28S | 17S | 16S | 24S | 23S | 1 | 0.1 | ||
9 | Klebsiella pneumoniae | 29S | 13R | 25S | 24S | 22S | 28S | 29S | 18S | 17S | 24S | 25S | 1 | 0.1 | ||
10 | Klebsiella pneumoniae | 33S | 14S | 26S | 28S | 22S | 31S | 32S | 19S | 20S | 24S | 29S | 0 | 0 | ||
11 | Comamonas spp. | – | – | – | 23S | – | – | 37S | – | – | – | – | 0 | 0 | ||
12 | Comamonas spp. | – | – | – | 27S | – | – | 42S | – | – | – | – | 0 | 0 | ||
13 | Micrococcus spp. | 25S | 17R | 24S | 32S | 22S | 34S | 28S | 20S | – | 21S | 26S | 1 | 0.1 | ||
14 | Arthrobacter spp. | 45S | 57S | 28S | 26S | 34S | 27S | 39S | 26S | – | 28S | 28S | 0 | 0 | ||
15 | Aeromonas spp. | – | – | 20R | – | – | – | – | – | – | – | 20R | 2 | 1 |
Table 8: Antibiotic resistance phenotype of the bacterial isolates analyzed by AST. Phenotypic resistance in the isolates was analyzed using the disc diffusion method. The numbers indicate the ZOI in millimeters (mm). For the MAR index, the numbers indicate the total number of antibiotics to which an isolate is resistant. Abbreviations: AST = antibiotic susceptibility test; CTX = cefotaxime; AMP = ampicillin; LE = levofloxacin; C = chloramphenicol; TGC = tigecycline; CTR = ceftriaxone; IPM = imipenem; GEN = gentamicin; N = neomycin; TR = trimethoprim; CIP = ciprofloxacin; R = resistant; S = sensitive; MAR = multiple antibiotic resistance; ZOI = zone of inhibition.
AMR GENE FAMILY | GENE(S) |
SMB beta-lactamase | SMB-1 |
ampC-type beta-lactamase | ampC1 |
VIM beta-lactamase | VIM-20 |
CcrA beta-lactamase | ccrA |
NmcA beta-lactamase | nmcR |
ARL Beta-lactamase | ARL-1 |
blaZ beta-lactamase | blaZ |
blaTEM beta-lactamase | blaTEM* |
blaCTX beta-lactamase | blaCTX |
AAC(6') | aac(6')-Ib, aac(6')-34 |
ANT(3'') | aadA |
quinolone resistance protein (qnr) | qnrS6, qnrVC5 |
resistance-nodulation-cell division (RND) antibiotic efflux pump | evgA, mtrA, mdtA, acrD |
ATP-binding cassette (ABC) antibiotic efflux pump | oleC, macB, patA, bcrA |
major facilitator superfamily (MFS) antibiotic efflux pump | abaQ |
trimethoprim resistant dihydrofolate reductase dfr | dfr1, dfrD, dfrA20 |
rifampin phosphotransferase | rphB |
undecaprenyl pyrophosphate related proteins | bcrC |
methicillin resistant PBP2 | mecD |
vanJ membrane protein | vanJ |
tetracycline-resistant ribosomal protection protein | tetT |
chloramphenicol acetyltransferase (CAT) | catB10 |
Erm 23S ribosomal RNA methyltransferase | erm(37) |
glycopeptide resistance gene cluster | vanRB, vanRE, vanRD |
MCR phosphoethanolamine transferase | mcr-9 |
sulfonamide resistant sul | sul3 |
*underlined genes were also detected in the culturable microorganisms |
Table 9: ARGs identified using whole metagenomic DNA analysis. The total metagenome of the water sample was used for whole metagenomic sequencing, and the obtained sequences were annotated using the appropriate ARG database. The representative results of some of the important ARGs identified in the metagenomic DNA are shown. The underlined genes were also detected in the culturable microorganisms. Abbreviation: ARG = antibiotic-resistant gene.
The sample collection and processing play a significant role and might affect the results and interpretation of the study. Hence, to rule out variability in the samples, it is important to carry out sampling at multiple locations of the freshwater body being studied. Maintaining proper aseptic environmental conditions when handling such samples can prevent contamination. Moreover, to prevent changes in the bacterial composition that may influence the quality and quantity of extracted nucleic acids, the transit conditions should be maintained at 4 °C, with a minimal time lapse from the point of sample collection to the subsequent processing. Several studies have highlighted that this interim period between sample collection and processing can give variable results during later stages of analysis if not done carefully12,13.
Using a range of dilutions for plating ensures that colonies neither clump together nor are there too few colonies to count. Performing the experiments in duplicate is necessary to account for variations in CFU/mL that might arise due to pipetting/handling errors. Moreover, control plates are maintained for every experiment to ensure that the antibiotics used are working effectively and that false-positive results are eliminated. Hence, the control plates should have no visible colony growth. This indicates the efficacy of the antibiotics used.
During AST, the inoculum culture density and the thickness of the agar plate can influence the diameter of the ZOI and, hence, the interpretation of the results. Therefore, care should be taken to keep these two factors uniform when performing the AST experiments. The most critical aspect is the number of bacterial cells present in the inoculum. Generally, 1 × 108-2 × 108 CFU/mL of cells are used as the inoculum, which is equal to the 0.5 McFarland standard14. This concentration of the inoculum must be kept constant to avoid any variation in the results. Any concentration higher or lower than the required concentration must be diluted with the help of sterile saline and used immediately for inoculation within 15 min. While spreading the inoculum on the agar plates, care must be taken to avoid an excessive amount of inoculum. Excess inoculum can be removed by pressing the swab on the sides of the bacterial suspension tube before inoculating it to the MHA plate. Any deviation from the standard AST procedure can significantly impact the data obtained from such protocols11,15. A previous study showed that an MAR index value of ≥0.2 indicates high resistance in the isolates16. Since the interpretation of the results of the AST is based on the ZOI, under-inoculation or over-inoculation of the culture should be avoided.
For the PCR, the mastermix should be prepared on an ice block to minimize the chance of degradation of the ingredients and loss of activity of the enzyme. Wearing gloves while setting up the reaction minimizes the chance of external contamination17. The voltage during the AGE should not be too high, as this may lead to a heating effect and degradation of the loaded samples. Performing the AGE at an optimum voltage ensures that the bands are well separated and are sharp without any dragging or smudging effects.
Studies carried out in the past few decades have demonstrated the use of 16S rRNA gene amplicon sequencing for the identification of different microorganisms. For 16S rRNA gene sequencing, the choice of method for the extraction of the template DNA can cause biases, which, in turn, may affect the downstream analysis. Gram-positive bacteria have a thick peptidoglycan cell wall that can make it difficult to extract the nucleic acid. Therefore, the choice of the extraction method should be such that it effectively captures all the types of microbial DNA. The traditional boiling method to extract crude template DNA is one such efficient method to extract the contents of the cell, thus reducing biases in the results.
To understand the complete bacterial community of the water body, the high-throughput next-generation sequencing (HT-NGS) technique was used in this study. Whole metagenomic DNA analysis allows the study of the whole metagenome of a given sample. Culture-based techniques mainly give an aerobic count of the bacterial load, indicating the microbiological quality of a sample. However, culturable microorganisms constitute only 1% of the total microorganisms. The remaining microflora, which comprise a diverse range of species, including anaerobes, are poorly characterized and often ignored. These microorganisms might carry AR traits. Moreover, commensal microorganisms are a reservoir of AR genes that can be transmitted to pathogens via various genetic exchange events18. Many of these commensals are non-culturable and can be studied by a metagenomic approach involving HT-NGS, providing larger coverage for the identification of diverse microflora in any sample. Using metagenomic analysis, a detailed profile of the bacterial taxa was obtained, which complemented the culturable data. Moreover, such complementary approaches can provide an idea of the overall AR status of the water body under study.
In the present study, using a combination of both conventional culture-based and non-culture-based metagenomic techniques, we were able to identify the total bacterial diversity, different antibiotic-resistant bacteria, and the total pool of water-borne ARGs. The methodology described in this study can be replicated and customized for the identification of AR pathogens in any other water source-coastal water, natural water, and man-made drinking water. It can also be used for tracking the transmission of waterborne nosocomial pathogens and for monitoring hospital-associated infections in hospital and clinic settings through water sources such as sinks, toilets, bathtubs, and humidifiers. This will help in the surveillance of AMR and the identification of water-based AMR hotspots.
The authors have nothing to disclose.
This work was partially supported by financial grants from the Department of Science and Technology-Promotion of University Research and Scientific Excellence (DST-PURSE) Scheme of the University of Mumbai. Devika Ghadigaonkar worked as a Project Fellow under the scheme. The technical help provided by Harshali Shinde, Senior Research Fellow under the Department of Science and Technology-Science and Engineering Research Board (DST-SERB) Project no: CRG/2018/003624, is acknowledged.
100 bp DNA ladder | Himedia | MBT049-50LN | For estimation of size of the amplicons |
2x PCR Taq mastermix | HiMedia | MBT061-50R | For making PCR reaction mixture |
37 °C Incubator | GS-192, Gayatri Scientific | NA | For incubation of bacteria |
6x Gel Loading Buffer | HiMedia | ML015-1ML | Loading and Tracking dye which helps to weigh down the DNA sample and track the progress of electrophoresis |
Agarose powder | Himedia | MB229-50G | For resolving amplicons during Agarose Gel Electrophoresis (AGE) |
Ampicillin antibiotic disc | HiMedia | SD002 | For performing AST |
Autoclave | Equitron | NA | Required for sterilization of media, glass plates, test tubes, etc |
Bioanalyzer 2100 | Agilent Technologies | NA | To check the quality and quantity of the amplified library |
Bisafety B2 Cabinet | IMSET | IMSET BSC-Class II Type B2 | Used for microbiological work like bacterial culturing, AST etc. |
Cefotaxime antibiotic disc | HiMedia | SD295E-5VL | For performing AST |
Cefotaxime antibiotic powder | HiMedia | TC352-5G | For preparation of antibiotic stock solution required during isolation of antibiotic resistant bacteria |
Ceftriaxone antibiotic disc | HiMedia | SD065 | For performing AST |
Centrifuge Minispin | Eppendorf | Minispin Plus-5453 | Used to pellet the debris during crude DNA preparation |
Chloramphenicol antibiotic disc | HiMedia | SD006-5x50DS | For performing AST |
Ciprofloxacin antibiotic disc | HiMedia | SD060-5x50DS | For performing AST |
Ciprofloxacin antibiotic powder | HiMedia | TC447-5G | For preparation of antibiotic stock solution required during isolation of antibiotic resistant bacteria |
Colorimeter | Quest | NA | For checking the OD of culture suspensions |
Comprehensive Antibiotic Resistance Database (CARD) database | functional annotation of ARGs; https://card.mcmaster.ca/ | ||
Cooling Shaker Incubator | BTL41 Allied Scientific | NA | For incubation of media plates for culturing bacteria |
Deep Freezer (-40 °C) | Haier | DW40L, Haier Biomedicals | For storage of glycerol stocks |
DNA Library Prep Kit | NEB Next Ultra DNA Library Prep Kit for Illumina | NA | Paired-end sequencing library preparation |
EDTA | HiMedia | GRM1195-100G | For preparation of Gel running buffer for Agarose Gel Electrophoresis (AGE) |
Electrophoresis Apparatus | TechResource | 15 cm gel casting tray | For making the agarose gel and carrying out electrophoresis |
Electrophoresis Power pack with electrodes | Genei | NA | For running the AGE |
Erythromycin antibiotic disc | HiMedia | SD222-5VL | For performing AST |
Erythromycin antibiotic powder | HiMedia | CMS528-1G | For preparation of antibiotic stock solution required during isolation of antibiotic resistant bacteria |
Erythromycin antibiotic powder | HiMedia | TC024-5G | For preparation of antibiotic stock solution required during isolation of antibiotic resistant bacteria |
Escherichia coli ATCC 25922 | HiMedia | 0335X-1 | Used as a control while performing AST |
Ethidium Bromide | HiMedia | MB071-1G | Intercalating agent and visualizaion of DNA after electrophoresis under Gel Documentation System |
Fluorometer | Qubit 2.0 | NA | For determining concentration of extracted metagenomic DNA |
Gel Documentation System | BioRad | Used for visualizing PCR amplicons after electrophoresis | |
Gentamicin antibiotic disc | HiMedia | SD170-5x50DS | For performing AST |
Glacial Acetic Acid | HiMedia | AS119-500ML | For preparation of Gel running buffer for Agarose Gel Electrophoresis (AGE) |
Glycerol | HiMedia | GRM1027-500ML | For making glycerol stocks |
Imipenem antibiotic disc | HiMedia | SD073 | For performing AST |
Kaiju Database | NA | NA | For taxonomical classification of reads; https://kaiju.binf.ku.dk/ |
Kanamycin antibiotic disc | HiMedia | SD017-5x50DS | For performing AST |
Kanamycin antibiotic powder | HiMedia | MB105-5G | For preparation of antibiotic stock solution required during isolation of antibiotic resistant bacteria |
Levofloxacin antibiotic disc | HiMedia | SD216-5VL | For performing AST |
Luria Bertani broth | Himedia | M1245-500G | For enrichment of cultures |
McFarland Standards | Himedia | R092-1No | To compare density of culture suspension |
Molecular Biology water | HiMedia | TCL018-500ML | For making PCR reaction mixture |
Mueller-Hinton Agar (MHA) | HiMedia | M173-500G | For performing Antibiotc Susceptibility Testing (AST) |
Neomycin antibiotic disc | HiMedia | SD731-5x50DS | For performing AST |
PCR Gradient Thermal Cycler | Eppendorf | Mastercycler Nexus Gradient 230V/50-60 Hz | Used for performing PCR for amplification of 16S rRNA region and various Antibiotic Resistance genes |
Primers | Xcelris | NA | For PCR amplication |
R2A Agar, Modified | HiMedia | M1743 | For preparation of media plates for isolation of total and antibiotic resistant (AR) bacterial load |
Scaffold generation | CLC Genomics Workbench 6.0 | NA | For generation of scaffolds |
Sequencer | Illumina platform (2 x 150 bp chemistry) | NA | Sequencing of amplified library |
Sodium Chloride | HiMedia | TC046-500G | For preparation of 0.85% saline for serially diluting the water sample |
Soil DNA isolation Kit | Xcelgen | NA | For extraction of whole metagenomic DNA from the filtered water sample |
Staphylococcus aureus subsp. aureus ATCC 29213 | HiMedia | 0365P | Used as a control while performing AST |
Taxonomical Classification | Kaiju ioinformatics tool | NA | For classification of reads into different taxonomic groups from phylum to genus level |
The Comprehensive Antibiotic Resistance Database (CARD) | NA | NA | For functional annotation of ARGs |
Tigecycline antibiotic disc | HiMedia | SD278 | For performing AST |
Trimethoprim antibiotic disc | HiMedia | SD039-5x50DS | For performing AST |
Tris base | HiMedia | TC072-500G | For preparation of Gel running buffer for Agarose Gel Electrophoresis (AGE) |
Vancomycin antibiotic powder | HiMedia | CMS217 | For preparation of antibiotic stock solution required during isolation of antibiotic resistant bacteria |
Weighing Balance | Mettler Toledo | ME204 Mettler Toledo | Used for weighing media powders, reagent powders etc. |
NA – Not Applicable |