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Access Microbiol
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000818.v3
10.1099/acmi.0.000818.v3
Research Article
Antimicrobials
Clinical Microbiology
Diarrhoeal Diseases
Trends and antibiotic susceptibility patterns of diarrhoeal pathogens – experience over 14 years in southern India
Mohanty Ankita 1ankitamohanty0211@gmail.com

Lakra Nayannika 1nayanika.lakra@gmail.com

http://orcid.org/0000-0002-5945-8425
Mandal Jharna 1*drjharna@gmail.com

1 Department of Microbiology, JIPMER, Puducherry, 605006, India
The authors declare that there are no conflicts of interest.

JharnaMandal, drjharna@gmail.com
2024
23 9 2024
6 9 000818.v325 3 2024
05 9 2024
Copyright © 2024 The Authors
2024
https://creativecommons.org/licenses/by/4.0/ This is an open-access article distributed under the terms of the Creative Commons Attribution License.

Abstract

Introduction. Enteric pathogens contribute significantly to morbidity in a developing country such as India. Early and prompt diagnosis of diarrhoeal diseases can reduce the mortality rate, particularly in children. The pattern of sensitivity to antimicrobials for the common pathogens can vary from time to time. The present study was conducted to study the pathogen distribution and antimicrobial susceptibility pattern during the study period (January 2010 to December 2023).

Hypothesis/gap statement. Studying the changing trend in the antimicrobial sensitivity pattern of diarrhoeal pathogens over a decade can help to plan future treatment options.

Aim. This study was undertaken to provide insights into the changing pattern of pathogen distribution and antimicrobial susceptibility for enteric pathogens over 14 years.

Methods. A retrospective observational cohort analysis was conducted on all the stool pathogens isolated from the samples received in the microbiology department of a tertiary care hospital from 2010 to 2023. The demographic details, stool microscopy, culture reports, and antimicrobial susceptibility patterns were noted.

Results. A total of 18 336 stool specimens were received in the microbiology laboratory between January 2010 and December 2023, of which 1354 specimens had diarrhoeal pathogens grown in culture. Out of these 1354 specimens, 591 (44%) had Salmonella, 471 (35%) Shigella, 181 (13%) Vibrio cholerae, and 80 (6%) Aeromonas species. Among these pathogens, susceptibility to ceftriaxone was seen in 93% (552 isolates) of Salmonella species, 89% (420 isolates) of Shigella species, and 95% (171 isolates) of Vibrio cholerae; 91% (73 isolates) of Aeromonas species were susceptible to chloramphenicol. Some major parasites were also observed on microscopy.

Conclusion. Timely diagnosis of diarrhoeal pathogens can be life-saving for patients at the extremes of age, i.e. in children and the elderly. Pathogens can exhibit a changing susceptibility pattern to antibiotics, which should be regularly observed to plan future therapy.

antimicrobials
changing pattern
diarrhoea
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pmcData Summary

All data associated with this work are reported within the article.

Introduction

Gastroenteritis is considered to be an important health problem in India. It is a condition caused by bacteria, viruses, and parasites [1] and is a major cause of illness and death in various age groups, especially at the extremes of age groups, i.e. in children and the elderly [2]. This can be attributed to poor sanitary conditions, improper personal hygiene, and lack of proper homes. Natural calamities such as floods, cyclones, and rainstorms can worsen the situation. Nearly 90% of clinical cases of gastroenteritis are due to polluted drinking water, improper sanitation, and poor hygiene [3], associated with an ever-increasing multidrug resistance among diarrhoeal pathogens due to the indiscriminate use of antimicrobials. Ironically, amidst the rise and outbreak of resistant strains, the emergence of strains susceptible to older antibiotics has been noted [4]. Most diarrhoea cases can be managed with hydration and antibiotics are only indicated in certain situations and should be selected appropriately for the target pathogen [5]. It is important to study the distribution of enteric pathogens and their antibiotic susceptibility pattern over time in a geographical area to collect information about the common pathogens in that area. This can help formulate the antibiotic policy for empirical therapy and prevent complications by providing early treatment. Traditionally, fluoroquinolones have been used for treating diarrhoea, but due to the development of resistance, azithromycin and doxycycline have replaced them. Third-generation cephalosporins are currently considered the drug of choice for Shigella and Salmonella species, while doxycycline is the drug of choice for for Vibrio cholerae. The current study aims to study the organism profiles and antibiograms of the isolates from stool samples from cases of diarrhoea/dysentery in a tertiary care hospital. This study highlights the emerging trend in the pathogen distribution and antibiotic susceptibility of diarrhoeal isolates as well as stool parasites from 2010 to 2023.

Methods

Study design

A retrospective observational cohort analysis was conducted on all the stool pathogens isolated from the samples received from January 2010 to December 2023 with approval from the Institutional Ethics Committee (JIP/IEC/2017/0130).

Study setting

This study was conducted in a tertiary care hospital, located in the southern part of India.

Data collection

The data were collected retrospectively from the laboratory records and the laboratory information system. The demographic details, clinical history of the patients having significant microscopic findings, and pathogens in the stool samples were recorded. A standard protocol for stool processing for culture was used, employing a selective medium (xylose lysine deoxycholate agar), less selective cum differential medium (MacConkey agar), and an enrichment broth (selenite F broth); suspected colonies were screened using catalase test, oxidase test, indole detection, citrate, urea, Kligler iron agar, lysine iron agar, and mannitol motility medium. In the case of suspected cholera cases, thiosulphate citrate bile salt sucrose agar (TCBS) was also used and the specimen was inoculated into alkaline peptone water (APW). Antibiotic sensitivity testing was performed using the Kirby–Bauer technique for a panel of antibiotics (ampicillin, ceftriaxone, cotrimoxazole, cefixime, chloramphenicol, tetracycline, ciprofloxacin) and interpreted as per the CLSI M100 guidelines for Salmonella and Shigella and the CLSI M45 guidelines for Vibrio and Aeromonas for the respective years. The bacterial profile and antimicrobial susceptibility pattern of the bacteria, namely Salmonella species, Vibrio species, Shigella species, and Aeromonas species, was noted. Plesiomonas shigelloides, Edwardsiella tarda, Comamonas aquatica, and Yersinia enterocolitica were also included. Identification of Salmonella species, Vibrio species, Aeromonas species, P. shigelloides, E. tarda, and C. aquatica was simplified after the introduction of MALDI-TOF MS (bioMérieux, France) in 2019.

Serogrouping of Shigella, Salmonella and V. cholerae was performed using corresponding antisera (BD Diagnostics). Parasites detected were also noted.

Statistical analysis

The extended Mantel–Haenszel chi-square test was applied to observe the significance in the various age groups considering the absolute count of the organisms present and absent in a particular age group.

Antibiotic sensitivity patterns for the duration of the study period (14 years) are shown as linear trends in the form of line graphs.

Results

A total of 18  336 stool specimens were received in the microbiology laboratory between January 2010 to December 2023. A total of 591 Salmonella, 471 Shigella, 181 V. cholerae and 80 Aeromonas organisms were isolated. The pathogen-wise distribution is shown in Table 1 and Fig. 1.

Table 1. Year-wise distribution of the common diarrhoeal pathogens

Year	Salmonella species	Shigella species	Vibrio cholerae	Aeromonas species	
2010	14	24	75	5	
2011	9	34	36	7	
2012	12	39	28	3	
2013	15	43	4	3	
2014	38	59	1	5	
2015	24	56	0	17	
2016	27	44	3	2	
2017	41	38	4	2	
2018	77	45	4	3	
2019	100	45	4	6	
2020	31	10	13	2	
2021	22	13	2	1	
2022	90	13	1	7	
2023	91	8	6	17	
Total	591	471	181	80	

Fig. 1. Year-wise distribution of common diarrhoeal pathogens.

The age-wise distribution of pathogens is shown in Table 2 and Fig. 2. The trend over the age groups was significant for V. cholerae (P=0.0000001 by chi-square test) and Shigella species (P=0.0000001 by chi-square test) while it was insignificant for Salmonella and Aeromonas species.

Table 2. Age-wise distribution of the common diarrhoeal pathogens

Age	Salmonella species	Shigella species	Vibrio cholerae	Aeromonas species	
≤10 years	109	294	60	18	
11–20 years	53	25	15	7	
21–30 years	90	47	27	10	
31–40 years	89	34	20	11	
41–50 years	97	35	33	12	
51–60 years	92	19	15	11	
>60 years	61	17	11	11	
Total	591	471	181	80	

Fig. 2. Age-wise distribution of diarrhoeal pathogens.

Most of the Salmonella isolates were susceptible to ceftriaxone (93%), with a decreased susceptibility to nalidixic acid and furazolidone (Table 3 and Fig. 3). This was observed in the initial years (2010–2012), following which these antibiotics were abandoned because of increasing resistance.

Table 3. Antibiotic susceptibility pattern of Salmonella species*

Antibiotics	2010(n=14)	2011(n=9)	2012(n=12)	2013(n=15)	2014(n=38)	2015(n=24)	2016(n=27)	2017(n=41)	2018(n=77)	2019(n=100)	2020(n=31)	2021(n=22)	2022(n=90)	2023(n=91)	Total (n=591)	
Ampicillin	64	89	75	67	87	75	70	54	77	85	84	73	91	85	80	
Co-trimoxazole	93	100	67	87	100	88	81	85	93	99	94	95	96	89	92	
Ceftriaxone	93	100	92	87	97	96	100	95	97	96	97	82	92	86	93	
Ciprofloxacin	100	100	92	73	92	83	81	63	78	75	77	64	88	75	79	
*Percentage susceptibility values are mentioned in the table.

Fig. 3. Antibiotic susceptibility pattern of Salmonella species.

Most of the Shigella species were susceptible to ceftriaxone (92%), with a few being resistant to it (Table 4 and Fig. 4).

Table 4. Antibiotic susceptibility pattern of Shigella species*

Antibiotics	2010(n=24)	2011(n=34)	2012(n=39)	2013(n=43)	2014(n=59)	2015(n=56)	2016(n=44)	2017(n=38)	2018(n=45)	2019(n=45)	2020(n=10)	2021(n=13)	2022(n=13)	2023(n=8)	Total (n=471)	
Ampicillin	29	47	54	33	51	34	43	55	31	38	40	62	38	38	42	
Co-trimoxazole	8	18	21	35	12	14	14	16	9	31	0	0	54	63	19	
Ceftriaxone	96	88	97	95	80	96	98	95	98	91	90	92	69	63	92	
Cefixime	96	88	97	95	81	100	98	95	87	89	90	92	69	63	91	
Ciprofloxacin	54	47	64	63	20	41	32	21	29	22	10	8	46	13	36	
*Percentage susceptibility values are mentioned in the table.

Fig. 4. Antibiotic susceptibility pattern of Shigella species.

Among the V. cholerae isolates, the majority were susceptible to ceftriaxone (94%) (Table 5 and Fig. 5), while 91% (73/80) of the Aeromonas species were susceptible to chloramphenicol (Table 6 and Fig. 6).

Table 5. Antibiotic susceptibility pattern of Vibrio cholerae*

Antibiotics	2010(n=75)	2011(n=36)	2012(n=28)	2013(n=4)	2014(n=1)	2015(n=0)	2016(n=3)	2017(n=4)	2018(n=4)	2019(n=4)	2020(n=13)	2021(n=2)	2022(n=1)	2023(n=6)	Total (n=181)	
Ampicillin	43	83	86	75	100	0	67	50	50	25	85	0	0	17	60	
Co-trimoxazole	1	3	4	0	0	0	0	0	0	0	23	0	0	50	5	
Ceftriaxone	96	100	96	100	100	0	67	75	75	100	100	100	100	50	94	
Cefixime	96	100	96	100	100	0	67	50	75	100	100	100	100	50	94	
Ciprofloxacin	99	97	100	100	100	0	100	100	100	100	62	0	0	50	93	
Tetracycline	83	44	79	100	100	0	67	100	25	100	100	100	100	100	76	
*Percentage susceptibility values are mentioned in the table.

Fig. 5. Antibiotic susceptibility pattern of Vibrio cholerae.

Table 6. Antibiotic susceptibility pattern of Aeromonas species (n=80)*

	2010	2011	2012	2013	2014	2015	2016	2017	2018	2019	2020	2021	2022	2023	Total (%)	
Ampicillin	0	0	0	0	0	2	0	0	0	0	0	0	1	2	5 (6%)	
Co-trimoxazole	1	5	1	2	2	10	1	1	1	6	1	1	5	14	51 (64%)	
Ceftriaxone	3	3	2	2	1	10	0	0	2	5	2	1	5	15	51 (64%)	
Ciprofloxacin	2	4	3	3	1	5	1	0	1	3	1	1	2	11	38 (48%)	
Tetracycline	2	6	3	3	5	13	2	2	2	6	2	1	6	16	69 (86%)	
Chloramphenicol	5	6	3	3	3	14	2	2	3	6	2	1	7	16	73 (91%)	
*The number of susceptible isolates is mentioned in the table.

Fig. 6. Antibiotic susceptibility pattern of Aeromonas species.

In addition to the above-mentioned bacterial pathogens, other bacteria isolated were Campylobacter species (4), enteroaggregative Escherichia coli (EAEC) (1), enterohemorrhagic E. coli (EHEC) (1), Y. enterocolitica (1), E. tarda (4), P. shigelloides (8), C. aquatica (10), and Vibrio vulnificus (2).

The most commonly observed parasitic elements were cysts or trophozoites of Entamoeba spp. (n=54) followed by hookworm eggs and larvae (n=49), cysts and trophozoites of Giardia (n=37), Ascaris lumbricoides egg (n=32) and Strongyloides spp. larvae (n=29), egg of Enterobius vermicularis (n=6), Hymenolepis nana (n=1), and Trichuris trichiura (n=2).

Discussion

The present study is a retrospective analysis of the data obtained from 18  336 stool specimens received in the Department of Microbiology from 2010 to 2023. The demographic details, clinical history of the patients having significant microscopic findings, and pathogens in the stool samples were recorded. The bacterial profile and antimicrobial susceptibility pattern of the bacteria were noted. A total of 591 Salmonella, 471 Shigella, 181 Vibrio, and 80 Aeromonas species were isolated.

Salmonella, Shigella, and Vibrio were common in children <10 years of age. In a study by Anjeeta et al., the highest occurrence of diarrhoeal disease was reported among children aged 9–12 years (71.4%), while the lowest incidence was seen in the age group 5–8 years (33.3%) [6]. An increase in the incidence of diarrhoeal diseases with an increase in the age of the children was noted. This could be due to improper hand washing habits of the children as well as improper sanitary habits of caretakers after changing the napkins of the children. For most of these isolates, decreased susceptibility to nalidixic acid and furazolidone led to the discontinuation of these drugs for treatment. The trend with the different organisms is discussed subsequently.

Trends in the Salmonella species

Nontyphoidal Salmonella (NTS) infections are a common cause of diarrhoeal disease and are responsible for causing 93 million enteric infections and 155 000 diarrhoeal deaths yearly [7]. Most of the NTS are usually associated with self-limiting gastroenteritis, which does not require antimicrobial treatment, but there has been evidence of invasive diseases such as bloodstream infections being caused by them in patients with underlying comorbidities [8]. This necessitates the institution of antimicrobial therapy in cases of immunocompromised individuals with co-morbidities. Chloramphenicol, ampicillin, and trimethoprim/sulphamethoxazole (cotrimoxazole) were the drugs of choice for the treatment of salmonellosis in the past [9]. In our study, resistance to conventional classes of antibiotics such as chloramphenicol, nalidixic acid, and furazolidone was observed. Interestingly, NTS that were initially resistant to cephalosporins and fluoroquinolones have shown a diminishing trend of resistance to these antibiotics in recent years [10], and a similar finding was also observed in our isolates. In a study performed by Jacob et al. in southern India, resistance to nalidixic acid (27%) was most common among the tested NTS, followed by resistance to ampicillin (19.3%), cotrimoxazole (14%), ciprofloxacin (12.4%), and chloramphenicol (4%), which is similar to the findings of our study. Ceftriaxone had the highest sensitivity [11]. The resistance to beta-lactam antibiotics such as ceftriaxone in this organism is remarkable. This is caused by extended-spectrum beta-lactamases (ESBLs), predominantly CTX-M-15 and SHV-12, being present in those strains [1213]. An ACC-1 AmpC Salmonella Typhi was identified in the blood culture of a 14-year-old girl from our setting in the past. It could have been acquired from drug-resistant bowel flora and atypical resistance was seen with it [14]. Genotypic diversity has been observed among the strains present in our region by pulsed-field gel electrophoresis, indicating the existence of many different clones of S. Typhi universally [15].

Trends in the Shigella species

Shigellosis can be life-threatening in populations at the extremes of age (young, elderly). In most communities, the incidence of shigellosis is higher in the summer months due to reduced hand hygiene habits, but a significant peak is also noted during the rainy season [16]. In our geographical region, Shigella flexneri was found to be the most common followed by Shigella sonnei, Shigella boydii, and Shigella dysenteriae [17]. Cefixime became the drug of choice for shigellosis in our centre from 2012 onwards due to the development of resistance to ciprofloxacin, co-trimoxazole, and ampicillin. Such a resistance pattern points to the ability of Shigella to survive and replicate in the human gut and incorporate externally derived genetic material, including antimicrobial resistance (AMR) genes on transposons from other Gram-negative bacteria [18]. With the ease of its availability as well as administration, ciprofloxacin was used by the majority of clinicians, which has contributed to resistance. The pattern of resistance in our study was nalidixic acid followed by cotrimoxazole, ciprofloxacin, ampicillin, and then ceftriaxone, in order of decreasing resistance. We observed a high resistance to ciprofloxacin, as reported in an earlier study from India [19].

The isolates from our centre were also found to harbour extended-spectrum β-lactamases (ESBLs). A study conducted revealed three ceftriaxone-resistant S. flexneri strains harbouring CTX-M-15, CTX-M-14, and TEM-1 genes [20]. ESBL-producing Shigella were reported from other parts of India, as well as from countries such as the Republic of Korea, Argentina, Vietnam, France, and Turkey [2126].

Virulence genes have shown diversity in all serotypes of S. flexneri. IpaH (invasion plasmid antigen H) and ial (invasion-associated locus) genes were also detected in almost all of the isolates [17].

Trends in the V. cholerae

Cholera epidemics caused by toxigenic V. cholerae pose a major threat in most developing countries [27]. Globally, epidemics of cholera have been reported in 47 countries [28]. Outbreaks were observed during the rainy season.

In Kolkata, India, during two consecutive cholera seasons (1989–1990), the Inaba serotype was prevalent, but in our study period (2010–19) the Ogawa serotype was predominant [29]. Similar genetic conversions for cholera have been reported from other parts of the world.

A comparison of contemporary reports of antibiotic sensitivity patterns for V. cholerae strains with those isolated in the past shows a vast difference in the antimicrobial resistance profile. The reversal of the antimicrobial susceptibility pattern is due to the decreased use of conventional drugs that had encountered resistance earlier [30]. In the current study, reduced susceptibility to the earlier drugs, such as co-trimoxazole, was observed. In a study performed in the same setup from 2008 to 2013, the prevalence of SXT element conserved genes (int, eex, att-prfC, and setR) was noted in all of the isolates. The spread of Haitian-like traits with a creeping MIC (0.75–2 µg m−1) for azithromycin was also noted [31]. A study performed in different parts of Odisha from 2004 to 2013 also showed decreased susceptibility to co-trimoxazole [32]. Sensitivity to ciprofloxacin was the highest, making it a drug of choice, and the sensitivity to tetracyclines showed a cyclical trend in our study, similar to a study performed in Bangladesh [33].

A meta-analysis performed by Yuan et al. showed a low resistance rate against some antibiotics, including fluoroquinolones, gentamicin, ceftriaxone, doxycycline, kanamycin, and cefotaxime, similar to our study [34]. Antibiotic resistance in V. cholerae has been reported to be due to mobile genetic elements and plasmid-mediated resistance. In our study setup, a V. cholerae Amp C producer strain due to the blaDHA gene and a carbapenemase producer due to the blaNDM-1 gene had been isolated in the past [35].

Trends in Aeromonas species

Aeromonas is an important but often neglected pathogen causing gastrointestinal diseases. It can mimic cholera. There have been several reports of increase in drug-resistant Aeromonas, especially with respect to beta-lactams, quinolones, and tetracyclines. In our study, maximum resistance was detected in Aeromonas species for ampicillin, though only a few species are known to be intrinsically resistant to it. Many of our isolates were found to be resistant to the third-generation cephalosporins, with the MIC for ceftriaxone being ≥4 µg ml−1 [36]. The presence of blaCTX-M and inducible AmpC beta-lactamase (presence of MOX gene) have been documented in 70 and 24% of the isolates. Most commonly CTX M-15 is isolated in India. Fluoroquinolones have been the drug of choice but isolates that are resistant to nalidixic acid and susceptible to ciprofloxacin are known to possess the gyrA gene and hence can develop resistance to fluoroquinolones [37]. In our study, a cyclical trend was observed for fluoroquinolones. CphA harboured in common Aeromonas species such as A. hydrophila, A. dhakensis, A. jandaei, and A. veronii is the main chromosomal MBL recognized in aeromonads [38]. Contaminated water sources can act as a medium for the transfer of antimicrobial-resistant genes.

In a study performed by Roman et al., higher susceptibility to tetracyclines was noted for Aeromonas species, similar to our study [39]. However, in some Asian studies, tetracycline resistance was also noted [4042].

In a study performed by Mohan et al. in northern India, resistance was observed to fluoroquinolones and co-trimoxazole for Aeromonas species, similar to our study [43].

Heterogeneity of the pathogens

Heterogeneity in terms of serotypes, resistotypes, or genotypes is an important factor observed in our diarrhoeal isolates of Shigella, Salmonella, and V. cholerae, as far as the survival of these pathogens is concerned. The extensive use of azithromycin led to the rise of drug-resistant strains of S. sonnei [44], a phenomenon observed in our study as well. Serotype switching among Shigella species is a well-known phenomenon and leads to the emergence of many untypable Shigella species, as documented in an earlier study [45]. Our currently circulating strains of S. flexneri are of serotype 2a, followed by 6 and 3b; though some rare types such as type 1 variant and type 4 were also seen. O antigen loss (OmpA), an observation in a few of our S. flexneri strains [17], is another factor that can affect the conventional serotyping and may lead to the failure of an effective vaccine targeted against these antigens. Genetic heterogeneity was detected by CRISPR among our S. flexneri isolates; variations were substantial, and CRISPR type 3 was the most predominant [46]. Chen et al., revealed that the presence of multiple insertion sequences in the cas genes lowered the activity of the CRISPR–Cas system, aiding the bacteria to acquire more extra genetic elements such as the AMR genes through horizontal gene transfer [47].

Salmonella, on the other hand, is known to show variations in its O and H antigens to escape immune clearance, often leading to either loss of these antigens or their masking, which can affect the conventional serotyping results. The emergence of third-generation-resistant Salmonella isolates, both typhoidal and NTS, because of the rampant use of oral cefixime has probably led to this [48].

The major driving force in the heterogenous characteristics of these pathogens is horizontal gene transfer, depending on genomic plasticity, which leads to increasing AMR and selecting out strains/species in response.

Other bacterial pathogens isolated

Campylobacter species-level identification was performed in our setup using multiplex PCR targeting 16S rRNA (genus Campylobacter), mapA (C. jejuni), ceuA (C. coli), and actB for internal control [49]. E. tarda infections may be attributed to the presence of a marine environment. P. shigelloides has been associated with ingestion of seafood, which is a common practice in coastal areas.

Bacterial and parasitic co-infections in our study

Some bacterial and parasitic co-infections were observed in our study. Shigella and Salmonella co-infection with the parasites was commonly noted. Parasites have certain mechanisms that they use to manipulate or evade the host immune response and cause infection [50]. Parasites can alter the host’s immune response and affect susceptibility to other infections. Normal gut flora affected by helminth can trigger the ability of bacteria to invade the intestine [51].

Conclusion

Diarrhoeal diseases pose a major threat in developing countries. They can be caused by a lack of proper sanitary facilities and access to safe drinking water. Limited access to laboratory facilities in developing countries forces clinicians to seek a syndromic approach and empirical use of broad-spectrum antibiotics, paving the way for the increasing number of drug-resistant strains. Diarrhoeal pathogens such as Vibrio and Aeromonas are found freely in the environment and can survive in extreme conditions, hence the resistant traits can be passed on to various strains. Contaminated water can act as an agent for the transfer of antimicrobial resistance genes. Early diagnosis, targeted therapy, and proper antibiograms for diarrhoeal diseases can help in the reduction of resistant strains. Proper laboratory facilities for detecting the ESBL-producing strains and knowledge about the resistant genes prevailing in a geographical area can help to combat the spread of antimicrobial resistance among pathogens in the long run.

Abbreviations

AMR antimicrobial resistance

CRISPR clustered regularly interspaced short palindromic repeats

MALDI-TOF MS matrix-assisted laser desorption/ionization time-of-flight mass spectrometry

NTS nontyphoidal Salmonella

PCR polymerase chain reaction

Funding: This work received no specific grant from any funding agency.

Ethical statement: The study protocol was approved by the Institutional Ethics Committee (JIP/IEC/2017/0130).

Author contributions: A.M.: writing – original draft, data collection and analysis, methodology. N.L.: writing – original draft, data collection. J.M.: conceptualization, writing – review and editing. All authors read and approved the final manuscript.
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References

1. Nair GB Ramamurthy T Bhattacharya MK Krishnan T Ganguly S et al Emerging trends in the etiology of enteric pathogens as evidenced from an active surveillance of hospitalized diarrhoeal patients in Kolkata, India Gut Pathog 2010 2 4 10.1186/1757-4749-2-4 20525383
2. Moharana SS Panda RK Dash M Chayani N Bokade P et al Etiology of childhood diarrhoea among under five children and molecular analysis of antibiotic resistance in isolated enteric bacterial pathogens from a tertiary care hospital, Eastern Odisha, India BMC Infect Dis 2019 19 1018 10.1186/s12879-019-4501-6 31791267
3. Ahs JW Tao W Löfgren J Forsberg BC Diarrheal diseases in low- and middle-income countries: incidence, prevention and management Open Infect Dis J 2010 4 113 124 10.2174/1874279301004010113
4. Veeraraghavan B Pragasam AK Ray P Kapil A Nagaraj S et al Evaluation of antimicrobial susceptibility profile in Salmonella typhi and Salmonella paratyphi A: presenting the current scenario in India and strategy for future management J Infect Dis 2021 224 S502 S516 10.1093/infdis/jiab144 35238369
5. Olayinka A Debate: antibiotics for diarrhoeal diseases Int J Infect Dis 2023 130 S40 10.1016/j.ijid.2023.04.094
6. Neupane A Parajuli P Bastola R Paudel A Bacterial etiology of diarrhoeal disease in children and antibiogram of the isolates Clin Microbiol 2017 06 278 10.4172/2327-5073.1000278
7. Majowicz SE Musto J Scallan E Angulo FJ Kirk M et al The global burden of nontyphoidal Salmonella gastroenteritis Clin Infect Dis 2010 50 882 889 10.1086/650733 20158401
8. Jacob JJ Solaimalai D Rachel T Pragasam AK Sugumar S et al A secular trend in invasive non-typhoidal Salmonella in South India, 2000-2020: identification challenges and antibiogram Indian J Med Microbiol 2022 40 536 540 10.1016/j.ijmmb.2022.07.015 35987666
9. McDermott PF Zhao S Tate H Antimicrobial resistance in nontyphoidal Salmonella Microbiol Spectr 2018 6 10.1128/microbiolspec.ARBA-0014-2017
10. Inbaraj S Agrawal RK Thomas P Mohan C Agarwal R K S et al Antimicrobial resistance in Indian isolates of non typhoidal Salmonella of livestock, poultry and environmental origin from 1990 to 2017 Comp Immunol Microbiol Infect Dis 2022 80 101719 10.1016/j.cimid.2021.101719 34847457
11. Jacob JJ Solaimalai D Muthuirulandi Sethuvel DP Rachel T Jeslin P et al A nineteen-year report of serotype and antimicrobial susceptibility of enteric non-typhoidal Salmonella from humans in Southern India: changing facades of taxonomy and resistance trend Gut Pathog 2020 12 49 10.1186/s13099-020-00388-z 33110449
12. Al Naiemi N Zwart B Rijnsburger MC Roosendaal R Debets-Ossenkopp YJ et al Extended-spectrum-beta-lactamase production in a Salmonella enterica serotype typhi strain from the Philippines J Clin Microbiol 2008 46 2794 2795 10.1128/JCM.00676-08 18550740
13. Rotimi VO Jamal W Pal T Sovenned A Albert MJ Emergence of CTX-M-15 type extended-spectrum beta-lactamase-producing Salmonella spp. in Kuwait and the United Arab Emirates J Med Microbiol 2008 57 881 886 10.1099/jmm.0.47509-0 18566147
14. Gokul BN Menezes GA Harish BN ACC-1 beta-Lactamase-producing Salmonella enterica Serovar typhi, India Emerg Infect Dis 2010 16 1170 1171 10.3201/eid1607.091643 20587199
15. Menezes GA Harish BN Khan MA Goessens WHF Hays JP Antimicrobial resistance trends in blood culture positive Salmonella typhi isolates from Pondicherry, India, 2005-2009 Clin Microbiol Infect 2012 18 239 245 10.1111/j.1469-0691.2011.03546.x 21714829
16. Thapa BR Ventkateswarlu K Malik AK Panigrahi D Shigellosis in children from north India: a clinicopathological study J Trop Pediatr 1995 41 303 307 10.1093/tropej/41.5.303 8531265
17. Das A Mandal J Extensive inter-strain diversity among clinical isolates of Shigella flexneri with reference to its serotype, virulence traits and plasmid incompatibility types, a study from south India over a 6-year period Gut Pathog 2019 11 33 10.1186/s13099-019-0314-9 31249630
18. Baker S Scott TA Antimicrobial-resistant Shigella: where do we go next? Nat Rev Microbiol 2023 21 409 410 10.1038/s41579-023-00906-1 37188805
19. Madhavan A Balakrishnan S Vasudevapanicker J Antibiotic susceptibility pattern of Shigella isolates in a tertiary healthcare center J Lab Physicians 2018 10 140 144 10.4103/JLP.JLP_93_17 29692577
20. Mandal J Sangeetha V Nivedithadivya D Das A Parija SC Characterization of extended-spectrum β-lactamaseproducing clinical isolates of Shigella flexneri J Health Popul Nutr 2013 31 405 408 10.3329/jhpn.v31i3.16834 24288956
21. Mandal J Mondal N Mahadevan S Parija SC Emergence of resistance to third-generation cephalosporin in Shigella--a case report J Trop Pediatr 2010 56 278 279 10.1093/tropej/fmp118 19955258
22. Varghese SR Aggarwal A Extended spectrum beta-lactamase production in Shigella isolates – a matter of concern Indian J Med Microbiol 2011 29 76 78 10.4103/0255-0857.76534 21304205
23. Bhattacharya D Bhattacharjee H Ramanathan T Sudharma SD Singhania M et al Third-generation cephalosporin resistance in clinical isolate of Shigella sonnei in Andaman & Nicobar Islands, India J Infect Dev Ctries 2011 5 674 676 10.3855/jidc.1582 21918310
24. Radice M González C Power P Vidal M del C Gutkind G Third-generation cephalosporin resistance in Shigella sonnei, Argentina Emerg Infect Dis 2001 7 442 443 10.3201/eid0703.017313 11384523
25. Nguyen NTK Ha V Tran NVT Stabler R Pham DT et al The sudden dominance of blaCTX-M harbouring plasmids in Shigella spp. circulating in southern Vietnam PLoS Negl Trop Dis 2010 4 e702 10.1371/journal.pntd.0000702 20544028
26. Acikgoz ZC Gulay Z Bicmen M Gocer S Gamberzade S CTX-M-3 extended-spectrum beta-lactamase in a Shigella sonnei clinical isolate: first report from Turkey Scand J Infect Dis 2003 35 503 505 10.1080/00365540310013270 14514153
27. Das S Saha R Kaur IR Trend of antibiotic resistance of Vibrio cholerae strains from East Delhi Indian J Med Res 2008 127 478 482 18653912
28. Legros D Partners of the Global Task Force on Cholera Control Global cholera epidemiology: opportunities to reduce the burden of cholera by 2030 J Infect Dis 2018 218 S137 S140 10.1093/infdis/jiy486 30184102
29. Ramamurthy T Pal A Bhattacharya MK Bhattacharya SK Chowdhury AS et al Serovar, biotype, phage type, toxigenicity & antibiotic susceptibility patterns of Vibrio cholerae isolated during two consecutive cholera seasons (1989-90) in Calcutta Indian J Med Res 1992 95 125 129 1506061
30. De R Mobile genetic elements of Vibrio cholerae and the evolution of its antimicrobial resistance Front Trop Dis 2021 2 691604 10.3389/fitd.2021.691604
31. Mohanraj RS Samanta P Mukhopadhyay AK Mandal J Haitian-like genetic traits with creeping MIC of Azithromycin in Vibrio cholerae O1 isolates from Puducherry, India J Med Microbiol 2020 69 372 378 10.1099/jmm.0.001131 31961790
32. Pal BB Nayak SR Khuntia HK Epidemiology and antibiogram profile of Vibrio cholerae isolates between 2004–2013 from Odisha, India Jpn J Infect Dis 2018 71 99 103 10.7883/yoken.JJID.2017.193 29279443
33. Faruque ASG Alam K Malek MA Khan MGY Ahmed S et al Emergence of multidrug-resistant strain of Vibrio cholerae O1 in Bangladesh and reversal of their susceptibility to tetracycline after two years J Health Popul Nutr 2007 25 241 243 17985827
34. Yuan X-H Li Y-M Vaziri AZ Kaviar VH Jin Y et al Global status of antimicrobial resistance among environmental isolates of Vibrio cholerae O1/O139: a systematic review and meta-analysis Antimicrob Resist Infect Control 2022 11 62 10.1186/s13756-022-01100-3 35468830
35. Mandal J Sangeetha V Ganesan V Parveen M Preethi V et al Third-generation cephalosporin-resistant Vibrio cholerae, India Emerg Infect Dis 2012 18 1326 1328 10.3201/eid1808.111686 22840562
36. Bhaskar M Dinoop KP Mandal J Characterization of ceftriaxone-resistant Aeromonas spp. isolates from stool samples of both children and adults in Southern India J Health Popul Nutr 2015 33 26 10.1186/s41043-015-0036-7 26825984
37. Pintor-Cora A Tapia O Elexpuru-Zabaleta M Ruiz de Alegría C Rodríguez-Calleja JM et al Cytotoxicity and antimicrobial resistance of Aeromonas strains isolated from fresh produce and irrigation water Antibiotics 2023 12 511 10.3390/antibiotics12030511 36978377
38. Chen P-L Tsai P-J Chen C-S Lu Y-C Chen H-M et al Aeromonas stool isolates from individuals with or without diarrhea in southern Taiwan: predominance of Aeromonas veronii J Microbiol Immunol Infect 2015 48 618 624 10.1016/j.jmii.2014.08.007 25440979
39. Aravena-Román M Inglis TJJ Henderson B Riley TV Chang BJ Antimicrobial susceptibilities of Aeromonas strains isolated from clinical and environmental sources to 26 antimicrobial agents Antimicrob Agents Chemother 2012 56 1110 1112 10.1128/AAC.05387-11 22123695
40. Chang BJ Bolton SM Plasmids and resistance to antimicrobial agents in Aeromonas sobria and Aeromonas hydrophila clinical isolates Antimicrob Agents Chemother 1987 31 1281 1282 10.1128/AAC.31.8.1281 3631947
41. Ko WC Yu KW Liu CY Huang CT Leu HS et al Increasing antibiotic resistance in clinical isolates of Aeromonas strains in Taiwan Antimicrob Agents Chemother 1996 40 1260 1262 10.1128/AAC.40.5.1260 8723478
42. McNicol LA Aziz KM Huq I Kaper JB Lockman HA et al Isolation of drug-resistant Aeromonas hydrophila from aquatic environments Antimicrob Agents Chemother 1980 17 477 483 10.1128/AAC.17.3.477 7425607
43. Mohan B Sethuraman N Verma R Taneja N Speciation, clinical profile & antibiotic resistance in Aeromonas species isolated from cholera-like illnesses in a tertiary care hospital in north India Indian J Med Res 2017 146 S53 S58 10.4103/ijmr.IJMR_378_15 29205196
44. Mason LCE Greig DR Cowley LA Partridge SR Martinez E et al The evolution and international spread of extensively drug resistant Shigella sonnei Nat Commun 1983 14 10.1038/s41467-023-37672-w
45. Juthani R Das A Doss K Mandal J Exploring the use of Congo red agar in improving the serotyping of non-serotypeable Shigella with In-silico evidence Indian J Med Microbiol 2023 44 100381 10.1016/j.ijmmb.2023.100381 37356833
46. Das A Doss K Mandal J CRISPR-cas heterogeneity and plasmid incompatibility types in relation to virulence determinants of Shigella J Med Microbiol 2022 71 10.1099/jmm.0.001607
47. Chen S Liu H Liang W Hong L Zhang B et al Insertion sequences in the CRISPR-Cas system regulate horizontal antimicrobial resistance gene transfer in Shigella strains Int J Antimicrob Agents 2019 53 109 115 10.1016/j.ijantimicag.2018.09.020 30290202
48. Biswas M Biswas S Gupta B Mascellino MT Rakshit A et al Changing paradigms in antibiotic resistance in Salmonella species with focus on fluoroquinolone resistance: a 5-year retrospective study of enteric fever in a Tertiary Care Hospital in Kolkata, India Antibiotics 2022 11 1308 10.3390/antibiotics11101308 36289966
49. Mandal J Biswal N Shanmugam L Joseph NM Study of prevalence of Campylobacter gastroenteritis among pediatric population using a multiplex PCR in a Tertiary Care Hospital in Puducherry, South India J Gastrointest Infect 2022 11 9 14 10.5005/jp-journals-10068-3050
50. Mabbott NA The influence of parasite infections on host immunity to co-infection with other pathogens Front Immunol 2018 9 2579 10.3389/fimmu.2018.02579 30467504
51. Reynolds LA Redpath SA Yurist-Doutsch S Gill N Brown EM et al Enteric helminths promote salmonella coinfection by altering the intestinal metabolome J Infect Dis 2017 215 1245 1254 10.1093/infdis/jix141 28368463
