Here comes the su­per­bug

Poul­try farms are reser­voirs of multi-drug re­sis­tant bac­te­ria and play a ma­jor role in their spread, shows the lat­est CSE study


Cen­tre for Sci­ence and En­vi­ron­ment's study shows that anti-mi­cro­bial re­sis­tance is spread­ing from poul­try farms to agri­cul­tural fields

POUL­TRY FARMS in In­dia use an­tibi­otics—not only to cure their chicken from dis­eases but also to help them gain weight and pre­vent dis­eases. The prac­tice is com­mon in the sec­tor which has been grow­ing at a steady pace of 10 per cent per year the past decade. Chand Singh, owner of a broiler poul­try farm in Haryana’s Kawi vil­lage, says he reg­u­larly gives birds a com­bi­na­tion of two an­tibi­otics—en­rocin and col­istin. Ram­chan­der, owner of an­other broiler farm in Sanpka vil­lage, some 150 km from Kawi, says he uses ciprofloxacin and en­rofloxacin an­tibi­otics.

This reck­less prac­tice could be re­spon­si­ble for the emer­gence of an­tibi­otic re­sis­tant bac­te­ria, which can sur­vive an an­tibi­otic that would nor­mally kill them or stop their growth. A re­cent study by Delhi-based non-profit Cen­tre for Sci­ence and En­vi­ron­ment (cse) high­lights the high preva­lence of an­tibi­otic re­sis­tance (abr) in the poul­try en­vi­ron­ment. Worse, the study find­ings

sug­gest that abr is also spread­ing be­yond the poul­try farms be­cause un­treated lit­ter is com­monly used as ma­nure in nearby agri­cul­tural farms.

“On the one hand, an­tibi­otic mis­use is com­mon in the poul­try sec­tor and on the other, the sec­tor is plagued with poor waste man­age­ment. The two are re­spon­si­ble for the emer­gence of abr in poul­try farms and its spread into the sur­round­ing en­vi­ron­ment. We de­cided to con­duct the study to un­der­stand the level of and spread of abr in and around broiler poul­try farms,” says Chan­dra Bhushan, deputy di­rec­tor­gen­eral, cse. Wor­ry­ingly, the study found some of the bac­te­ria to be re­sis­tant to an­tibi­otics that are nor­mally used in hospi­tals as the last re­sort to fight in­fec­tions.

The find­ings should serve as a wake-up call for the gov­ern­ment as In­dia at present does not have ad­e­quate laws to con­tain abr. Even the guide­lines of the Cen­tral Pol­lu­tion Con­trol Board (cpcb) on poul­try waste man­age­ment do not ad­e­quately ad­dress abr. This is de­spite the fact that sev­eral stud­ies over the past years have pointed to­wards mis­use of an­tibi­otics in hu­mans as well as an­i­mals, and the emer­gence of abr. In 2014, a study by cse had also found residues of mul­ti­ple an­tibi­otics, such as flu­o­ro­quinolones (en­rofloxacin and ciprofloxacin) and tetra­cy­clines (oxyte­tra­cy­cline, chlorte-tra­cy­cline, doxy­cy­cline) in chicken meat sam­ples be­cause of ram­pant use of an­tibi­otics in poul­try.

The lat­est study cov­ers broiler farms in four key poul­try meat-pro­duc­ing states— Ut­tar Pradesh, Ra­jasthan, Haryana and Pun­jab—which col­lec­tively con­trib­ute about 40 per cent of to­tal poul­try meat pro­duc­tion in In­dia. cse re­searchers col­lected a to­tal of 47 sam­ples: 35 from 12 poul­try farms and 12 con­trol soil sam­ples from ar­eas where poul­try lit­ter was not used as ma­nure. The poul­try farms were ran­domly se­lected from dif­fer­ent clus­ters (a vil­lage with at least three broiler farms) and had an op­er­a­tional size of 3,000 to 21,000 birds. An­tibi­otics were used in all the se­lected farms. cse’s pol­lu­tion mon­i­tor­ing lab col­lected three sam­ples from each farm—poul­try lit­ter from in­side the shed, soil from out­side the shed and soil from an agri­cul­tural land out­side the farm where poul­try lit­ter was used as ma­nure. Agri­cul­tural soil sam­ple could not be col­lected from Jaipur clus­ter.

The team iso­lated and iden­ti­fied three bac­te­ria—Escherichia coli (E. coli), Kleb­siella pneu­mo­niae (K. pneu­mo­niae) and Sta­phy­lo­coc­cus lentus (S. lentus). E. coli and K. pneu­mo­niae strains cause menin­gi­tis, uri­nary tract in­fec­tions and res­pi­ra­tory ill­nesses, such as pneu­mo­nia. Pa­tients in hospi­tals are also at high risk of con­tract­ing K. pneu­mo­niae in­fec­tions be­cause of their low im­mu­nity.

Af­ter iso­lat­ing the bac­te­ria, they were tested in­di­vid­u­ally against 16 an­tibi­otics be­long­ing to 13 an­tibi­otic classes, which were se­lected on the ba­sis of their ex­tent of use in poul­try and im­por­tance to hu­mans. Ten of the an­tibi­otics be­long to the World Health Or­ga­ni­za­tion’s (who) crit­i­cally im­por­tant classes (CI) for hu­man medicine. The study did not test E. coli and K. pneu­mo­niae iso­lates for re­sis­tance against three of the 16 an­tibi­otics.

High on re­sis­tance

The cse study found alarm­ingly high lev­els of drug re­sis­tance not just in the bac­te­ria iso­lated from the chicken lit­ter, but also from the soil sam­ples col­lected from the poul­try farm as well as the neigh­bour­ing agri­cul­tural land (see ‘Ad­van­tage bac­te­ria’, p21). In fact, all the 62 E. coli iso­lates tested were found to be multi-drug re­sis­tant, which means re­sis­tant to at least three an­tibi­otic classes. One in ev­ery six E. coli iso­lates were re­sis­tant to 12 of the 13 tested an­tibi­otics. Two E. coli iso­lates were re­sis­tant to all the 13 tested an­tibi­otics. If th­ese E. coli iso­lates in­fect a hu­man, then hardly any medicine will work and cure them.

Sim­i­larly, 92 per cent K. pneu­mo­niae iso­lates were multi-drug re­sis­tant, 30 per cent were re­sis­tant to at least 10 an­tibi­otics and 10 per cent were re­sis­tant to all of the 13 an­tibi­otics. In the case of S. lentus, 78 per cent iso­lates were multi-drug re­sis­tant and about one-fourth iso­lates were re­sis­tant to at least eight an­tibi­otics. Over­all, high­est re­sis­tance was found in E. coli and rel­a­tively lesser re­sis­tance in K. pneu­mo­niae and S. lentus.

The study not only es­tab­lishes that poul­try farms are reser­voirs of abr, it also shows that abr is mov­ing out of the farms to neigh­bour­ing ar­eas (see ‘Spread out’, p21). It found a sim­i­lar re­sis­tance pat­tern in the E. coli iso­lates col­lected from poul­try lit­ter and agri­cul­tural soil where the un­treated lit­ter was used as ma­nure. For in­stance, 100 per cent E. coli iso­lates from both sources

were re­sis­tant to meropenem, a CI an­tibi­otic that hospi­tals use as the last re­sort to con­tain bac­te­rial in­fec­tions. E. coli iso­lates from lit­ter and agri­cul­tural soil also had sim­i­lar high (>70 per cent) re­sis­tance against an­tibi­otics of three more CI classes—peni­cillins, flu­o­ro­quinolones and 3rd and 4th gen­er­a­tion cephalosporins.

The study found a strong sta­tis­ti­cal cor­re­la­tion (p value of 0.08; Pear­son’s cor­re­la­tion co­ef­fi­cient r= 0.88) be­tween the re­sis­tance pat­tern in the iso­lates in poul­try lit­ter and agri­cul­tural soil. It also found just three E. coli iso­lates from poul­try farm soil sam­ples. The two find­ings sug­gest that the farms were di­rectly us­ing un­treated poul­try lit­ter as ma­nure.

In K. pneu­mo­niae, iso­lates from poul­try lit­ter sam­ples had high abr to CI an­tibi­otic classes, such as peni­cillins, flu­o­ro­quinolones, car­bapen­ems and 3rd and 4th gen­er­a­tion cephalosporins. abr in th­ese iso­lates from agri­cul­tural soil showed slightly lower re­sis­tance against th­ese an­tibi­otic classes. About 90 per cent of K. pneu­mo­niae iso­lates from both lit­ter and agri­cul­tural soil was re­sis­tant to amoxy­clav an­tibi­otic. How­ever, a strong sta­tis­ti­cal cor­re­la­tion be­tween the re­sis­tance pat­terns from th­ese two sources was not ob­served.

Sim­i­larly, in the case of S. lentus, all iso­lates showed high re­sis­tance to two an­tibi­otics. Over­all, the re­sis­tance pat­tern of the lit­ter iso­lates and agri­cul­tural soil iso­lates of S. lentus were not sta­tis­ti­cally com­pa­ra­ble.

In the con­trol soil sam­ples, no iso­lates of E. coli was found. Only a few iso­lates of K. pneu­mo­niae could be ob­tained and S. lentus was most com­mon. In both, the over­all re­sis­tance lev­els ob­served were high, but of sta­tis­ti­cally dif­fer­ent pat­tern to what was found in agri­cul­tural soil.

The re­sults of the study es­tab­lish that multi-drug re­sis­tance is mov­ing from poul­try farms to agri­cul­tural land in the case of E. coli. How­ever, more stud­ies are re­quired to un­der­stand the be­hav­iour of K. pneu­mo­niae and S. lentus in view of dif­fer­ent sources of bac­te­ria, such as other an­i­mals and use of syn­thetic fer­tiliser and pes­ti­cides in agri­cul­tural fields.

Vis­i­ble im­pacts

The cse study find­ings are al­ready vis­i­ble on the ground. A gov­ern­ment vet­eri­nary doc­tor from Jind, a dis­trict in Haryana that was cov­ered un­der the study, said they have stopped ad­min­is­ter­ing en­rofloxacin, a flu­o­ro­quinolone an­tibi­otic, be­cause it is no longer ef­fec­tive in the area. “We in­stead pre­scribe an­tibi­otics, such as neomycin, doxy­cy­cline and levofloxacin,” says the doc­tor. Re­quest­ing anonymity, he says the high an­tibi­otic mis­use in poul­try farms is re­spon­si­ble for abr in the area.

Ab­dul Gha­fur, a con­sul­tant on in­fec­tious dis­eases at the Apollo Hospi­tal, Chen­nai, says that re­sis­tant bac­te­ria from poul­try farms can di­rectly in­fect farm­ers and meat han­dlers or in­di­rectly put hu­mans at risk through agri­cul­tural pro­duce and wa­ter­bod­ies. More­over, the an­tibi­otics against which a high de­gree of re­sis­tance was ob­served in the three bac­te­ria cse tested, are los­ing ef­fec­tive­ness at a speed greater than an­tic­i­pated. “About 5-10 per cent of In­di­ans have car­bapen­em­re­sis­tant bac­te­ria in their body. This in­creases to 30-40 per cent in hospi­tals. Due to this grow­ing re­sis­tance, col­istin use is be­com­ing a reg­u­lar prac­tice. Af­ter this, there are no an­tibi­otics,” he says. High re­sis­tance ob­served in hu­mans in E. coli and K. pneu­mo­niae has prompted who to iden­tify them as “pri­or­ity pathogens” to de­velop new an­tibi­otics for them.

Sev­eral pa­pers clearly es­tab­lish the grow­ing in­ci­dence of abr and the role of an­tibi­otic mis­use in rear­ing food an­i­mals. A pol­icy pa­per, An­tibi­otics in ma­nure and soil—A grave threat to hu­man and an­i­mal health, pub­lished by the Na­tional Academy of Agri­cul­tural Sciences in 2010 recog­nises the pas­sage of an­tibi­otics into soil and food chain bea­cuse of its use in food an­i­mal pro­duc­tion.

In July 2017, En­vi­ron­men­tal Health Per­spec­tives pub­lished a study which looked at 18 poul­try farms in Pun­jab and found a link be­tween an­tibi­otic use in poul­try farms and abr. The study high­lighted high preva­lence of multi-drug re­sis­tant E. coli strains from cloa­cal swab sam­ples of birds in broiler farms. Even a who Ad­vi­sory Group on In­te­grated Surveil­lance of An­timi­cro­bial Re­sis­tance project in North In­dia (20142017) found abr in iso­lates of food-borne bac­te­ria from hu­mans and an­i­mals.

“Over­all, very high level of re­sis­tance was ob­served to­wards flu­o­ro­quinolones, tetra­cy­clines, amino­gly­co­sides, which are com­monly used in an­i­mal farms,” says Nee­lam Taneja, pro­fes­sor, De­part­ment of Med­i­cal Mi­cro­bi­ol­ogy, Post­grad­u­ate In­sti­tute of Med­i­cal Ed­u­ca­tion and Re­search, who was part of the project.

There is also grow­ing ev­i­dence that in­creased an­tibi­otic use in poul­try cre­ates reser­voirs of re­sis­tance genes that can be trans­ferred to other pathogens through a phe­nom­e­non called hor­i­zon­tal gene trans­fer. This means re­sis­tance in one bac­terium can be passed on to other kinds of bac­te­ria, even for mul­ti­ple an­tibi­otics. An Au­gust 2017 study, pub­lished in the Ap­plied and En­vi­ron­men­tal Mi­cro­bi­ol­ogy, found abr genes from bac­te­ria in soil that was ex­posed to an­tibi­otics used in hu­man medicine or food an­i­mal pro­duc­tion for about 16 years.

De­spite the wor­ry­ing trends, the sec­tor con­tin­ues to use an­tibi­otics. A re­search on the global trends in an­timi­cro­bial use in food an­i­mals pub­lished in 2015 in the Pro­ceed­ings of the Na­tional Academy of Sciences states that the use of an­timi­cro­bials, which in­cludes an­tibac­te­ri­als, in live­stock in In­dia, Brazil, Rus­sia, China and South Africa is ex­pected to in­crease by 99 per cent be­tween 2010 and 2030. In­dia’s con­tri­bu­tion in the 2030 pro­jec­tions could be sig­nif­i­cant due to grow­ing farm in­ten­si­fi­ca­tion and lim­ited reg­u­la­tory con­trol.

Slow to act

In­dia has so far fo­cused on com­bat­ing abr due to an­tibi­otic mis­use in hu­mans. The Union Min­istry of En­vi­ron­ment, For­est and Cli­mate Change (moef&cc) places poul­try and hatch­ery in the green or low pol­lu­tion po­ten­tial cat­e­gory in its pol­lut­ing in­dus­tries list. Also, cpcb guide­lines on waste from poul­try farms do not fo­cus on abr. This is de­spite the fact that In­dia is among the top pro­duc­ers of fish, poul­try and dairy, and the en­vi­ron­ment con­tri­bu­tion of abr through waste could be sig­nif­i­cant. The quan­tum of lit­ter pro­duced by about 800 mil­lion poul­try pop­u­la­tion in­di­cates to­wards the huge scale of the prob­lem. An­other chal­lenge for the coun­try is the trop­i­cal cli­mate and poor san­i­tary con­di­tions that re­sult in high in­ci­dence of in­fec­tions, which in turn, in­creases the chances of an­tibi­otic use and abr.

In April 2017, In­dia re­leased its first strate­gic Na­tional Ac­tion Plan on An­timi­cro­bial Re­sis­tance for 2017-2021. The plan was part of the coun­try’s com­mit­ment to the Global Ac­tion Plan on An­timi­cro­bial Re­sis­tance, which was en­dorsed by who, the Food and Agri­cul­ture Or­ga­ni­za­tion and the World Or­gan­i­sa­tion for An­i­mal Health in 2015.

What next

While the ac­tion plan is a step in the right di­rec­tion, In­dia needs con­crete mea­sures to be able to con­tain abr due to an­tibi­otic mis­use in rear­ing food an­i­mals. The first crit­i­cal step should be that the De­part­ment of An­i­mal Hus­bandry, Dairy­ing and Fish­eries reg­u­late to limit the non-ther­a­peu­tic use of an­tibi­otics in poul­try. The de­part­ment should also adopt al­ter­na­tives to an­tibi­otics and im­ple­ment bio-se­cu­rity mea­sures. It should also ban the use of poul­try lit­ter as feed for aqua­cul­ture.

The sec­tor re­quires abr-cen­tric en­vi­ron­men­tal reg­u­la­tions, which can hap­pen through a greater role by moef&cc and cpcb. The Union min­istry should en­sure that poul­try sec­tor waste is con­sid­ered as an im­por­tant abr con­trib­u­tor. Mean­while, cpcb, along with state pol­lu­tion con­trol boards, should pro­hibit the use of un­treated poul­try lit­ter as ma­nure and en­sure the adop­tion of waste to en­ergy mea­sures such as bio­gas gen­er­a­tion be­cause they are a less risky ma­nure man­age­ment op­tion than com­post­ing. The cse study rec­om­mends bio­gas gen­er­a­tion for big and in­te­grated play­ers and that it should be made manda­tory for ac­quir­ing poul­try farm li­cences. The study also sug­gests a na­tion­wide pro­gramme to pro­mote com­mu­nity bio­gas gen­er­a­tion plants for small poul­try farm­ers in clus­ters. It also says that farms where com­post­ing is the only op­tion, it should be done un­der su­per­vi­sion through ad­e­quate laws on process val­i­da­tion and siteap­proval. The study says that cpcb has to strengthen its ex­ist­ing guide­lines and no­tify them.

Lastly, the gov­ern­ment should in­vest in re­search to bet­ter un­der­stand the im­pact of ma­nure treat­ment on abr and re­sis­tance trans­fer mech­a­nisms.


In­dia has close to 800 mil­lion poul­try pop­u­la­tion

A worker at a poul­try farm in Haryana's Soni­pat dis­trict adds an­tibi­otics to chicken feed

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